四种重要养殖贝类有效繁殖群体数量研究
|
摘要
我国是海水养殖大国,海洋贝类的养殖是其中重要的组成部分。对于养殖群体来说,较低的有效群体大小(或有效繁殖群体大小)会使得群体的遗传多样性降低,增加近交和遗传漂变的比率,特别在贝类等高产卵能力的生物中,使用较少的亲本即可以获得足够的苗种,育苗所用的有效繁殖群体数量对养殖群体的遗传结构具有重要影响。本研究以分子遗传学理论为基础,在贝类中进行遗传标记的开发并检测了他们在家系鉴定中的效率。此外,应用分子家系鉴定的方法,调查了北方沿海四种具有不同生活方式的重要经济贝类:太平洋牡蛎(固着型),海湾扇贝(雌雄同体底栖型),虾夷扇贝(雌雄异体底栖型),魁蚶(埋栖型)等在常规苗种繁育过程中有效繁殖群体的大小、遗传多样性的变化以及近交程度,旨在为我国海水养殖贝类遗传多样性保护和健康苗种培育提供指导依据。主要研究结果如下:
1.海湾扇贝EST-SSR标记分离及特性分析
利用公共数据库资源,在海湾扇贝EST数据库中查找包含微卫星的序列,开发了15个EST-SSR分子标记,采用群体多态性分析结果显示,位点的等位基因数平均值为5.5,观测和期望杂合度范围分别为0.000-0.781和0.155-0.885。平均多态信息含量为0.548。进行Bonferroni校正后,发现15个位点中有8个位点显著偏离哈迪-温伯格平衡。在各位点之间未发现有连锁现象。5个多态性最高的微卫星位点在已知单亲时的累积排除概率超过99%。利用筛选出的15对引物在栉孔扇贝、虾夷扇贝和长肋日月贝中进行PCR扩增,其中9对引物在栉孔扇贝和虾夷扇贝中能扩增出产物,有5对引物扩出的微卫星标记呈多态。在长肋日月贝中有3对引物有扩增产物,有1对引物扩出的微卫星标记呈多态。
2.海湾扇贝EST-SNP标记分离及特性分析
通过对海湾扇贝EST数据库中4968条ESTs进行聚类及拼接后,共发现3905个候选SNP位点,平均密度为1/118.2bp。从中选择30个候选SNPs进行tetra-primer ARMS-PCR引物设计和优化,17组引物扩增产生与预期片段长度相符的多态性位点,多态性位点最小等位基因频率从0.016到0.484。对含有17个多态SNPs的contigs序列在GenBank中进行BLASTX比对,除一个位点所在序列外均有匹配的功能序列,其中11个已验证SNPs定位于编码区(外显子区),导致同义氨基酸替换。家系模拟鉴定结果表明,SNP标记对鉴定所用亲本的数量比微卫星标记更为敏感,因此需要更多的SNPs来抵消多态性低带来的负面效果以达到较高并且稳定性较好的鉴定成功率。通过对海湾扇贝EST数据库的分析构建了最优密码子使用表,以解释某一特定SNP不同等位基因频率上的差异,分析发现对密码子使用的选择性可能会影响编码区SNP不同等位基因的频率。这些对于海湾扇贝SNP的初步研究是对现有遗传标记的有用补充。
3.基于微卫星家系分析的海湾扇贝交配系统和繁殖成功研究
运用微卫星家系鉴定的方法对群体产卵海湾扇贝的交配系统进行了研究。对14个候选亲本和237个子代的鉴定结果表明,采用6个多态微卫星位点能够将95%的子代鉴定到亲本。根据家系鉴定结果,发现既有通过自体受精产生的子代也有通过非自体受精产生的子代,但是自体受精率在亲本个体间巨大的变异表明海湾扇贝具有混合交配模式。繁殖成功的变异造成了有效繁殖亲本数量的降低(Nb/N = 0.71)。群体的自体受精率为32.89%,近交系数为16.5%。在不考虑自交子代的情况下,半同胞和非同胞亲本在亲缘关系和繁殖成功之间没有显著的相关关系,表明可能是选择的压力而不是对近交的避免机制支持着海湾扇贝自交兼容性交配系统的进化和维持。本研究结果使我们对目前我国海湾扇贝的养殖状况有了深入了解,并且为以后对其进行繁殖技术改良提供了知识基础。
4.太平洋牡蛎EST-SSR多重PCR的开发及其在家系鉴定中的检验
我们从以往报道的太平洋牡蛎EST-SSRs中开发出了4组multiplex PCRs,并在12组单对交配家系中检验了其在家系鉴定中的效率。位点的基因丰富度和多态信息含量平均值分别为11.1和0.811,4组multiplex PCRs在家系鉴定中的累积排除能力大于99.99%。对143组分离模式的分析发现,有11个基因型分离比偏离孟德尔分离定律。通过分析位点在家系内的Mendelian分离模式,发现无效等位基因频率为4.9%。对12组单对交配家系的实际鉴定结果表明,使用2组多态信息含量最高的Multiplex PCRs,可以将97%的子代鉴定到亲本,其结果与真实的家系信息对比,错误率为4%;如果使用3组或者4组Multiplex PCRs,则可以将100%的子代鉴定到亲本,与真实的家系信息对比错误率为0。
5.太平洋牡蛎养殖群体的微卫星家系分析和有效群体大小估算
运用7个高度多态的微卫星位点对群体产卵的太平洋牡蛎进行家系分析,并比较亲本和子代的遗传多样性变化。对8个候选母本、6个候选父本和155个子代的鉴定结果与模拟鉴定一致,运用6个微卫星位点即可获得超过99%的鉴定成功率。等位基因数和观察杂合度(Ho)在亲本和子代中没有明显差异,但是,子代的期望杂合度(He)和亲本相比有显著降低。虽然所有亲本均参与子代繁殖过程,但是亲本繁殖成功的变异和不平衡的性别比例导致了Ne的降低(Ne = 11.42)。群体近交率的估算值为16.5%。这些结果表明在未来制定太平洋牡蛎群产育种方案时,需要考虑到较高的近交率和较低有效群体的因素。
6.基于微卫星家系分析的虾夷扇贝有效繁殖群体研究
运用微卫星家系鉴定的方法对群体产卵虾夷扇贝幼虫发育两个不同时期的有效繁殖群体的变化及其与亲本性状特征的相关性进行了研究。对14个候选母本、14个候选父本和1080个子代的鉴定结果表明,采用5个多态微卫星位点能够获得97%以上的鉴定成功率。亲本繁殖成功的变异是D形幼虫时期有效群体大小降低的主要原因(Ne/N = 0.87),近交率的估计为0.081。稚贝时期的有效群体大小进一步降低(Ne/N = 0. 78),近交率上升至0.090。这一变化可能与育苗过程中的幼虫分级选择有关,人为的改变了群体的遗传结构,加剧了亲本繁殖成功的变异。也可能与不同亲本组子代的存活力差异有关。回归分析表明,D形幼虫阶段母本的繁殖成功与母本壳长和壳宽存在显著正相关关系,父本的繁殖成功与父本壳高存在显著正相关关系,由此推断在群体产卵时,亲本个体大小在繁殖成功上有显著优势。然而在稚贝阶段,未检测到亲本的繁殖成功与性状特点的相关性。表明随着苗种的养成,亲本个体大小在产卵阶段的繁殖成功优势可能会逐渐消失。
7.基于微卫星同胞重建的魁蚶有效繁殖群体研究
运用5个微卫星标记,在没有亲本信息的情况下,采取同胞重建的方法研究了群体产卵魁蚶幼虫发育两个不同时期遗传多样性以及有效繁殖群体大小的变化,并对亲本的繁殖成功与交配对象数目的关系进行了相关性研究。等位基因数和观察杂合度在两个采样阶段均没有显著差异。但是对D形幼虫时期以及稚贝时期各180个个体的同胞重建结果表明,D形幼虫时期有效繁殖群体的估算值为20,稚贝时期有效繁殖群体的估算值为16,出现了明显的降低,而且稚贝时期可能的亲本数量也比D形幼虫时期降低了16.13%,?F增加了0.6%。多配繁殖在父/母本中均存在,而且在两个采样阶段,魁蚶父/母本繁殖成功与交配对象数量均存在显著正相关关系。
综上,本研究证明基于微卫星的家系分析方法具有较高的鉴定效力。运用5-6个微卫星位点即能够成功地对混合种群进行家系鉴定。在本研究的所有养殖贝类中均检测到有效繁殖群体数量(Nb,或有效种群大小Ne)的降低。交配系统,不平衡的性别比例,亲本贡献的高度变异以及家系规模的变异是导致Nb降低的主要原因。研究结果对我国海水养殖贝类遗传多样性保护和健康苗种培育具有指导作用。
The marine shellfish has served as an important component of aquaculture in China. The restricted number of effective population size (or effective number of breeders) used in culture operations can lead to a loss of genetic variability, increase the random drift in gene frequencies and inbreeding in a population. Especially, the high fecundity of some organisms in a culture environment (such as shellfish) ensure that a small number of stocks are used for production to generate sufficient offspring without concerns that genetic variability would decrease in farmed populations. In the present study, we developed different kinds of molecular markers to evaluate their utility in the parentage analysis. Furthermore, the effective population size, the difference of genetic variability and inbreeding rate were assed in four important hatchery mollusks of the northern coasts who live with different styles of life, including Crassostrea gigas (sessile), Argopecten irradians irradians (bentonic, hermaphroditic), Mizuhopecten yessoensis (bentonic, dioecious) and Scapharca broughtonii (infauna) based on microsatellite-based parentage analysis to better facilitate the protection of the genetic diversity and healthy aquaculture of seed production in these species. The main results of these studies are listed as follows:
1. A set of polymorphic expressed sequence tag–derived microsatellites from the bay scallop, Argopecten irradians irradians, and their transportability in three other scallop species
A set of 15 new EST-SSRs for Argopecten irradians irradians was developed from ESTs database. The average number of alleles was 5.5 per locus, observed heterozygosities ranged from 0.000 to 0.781, while expected heterozygosities varied from 0.155 to 0.885. The average PIC was 0.548. Significant departures from HWE were observed in 8 of the 15 single-locus (exact tests after sequential Bonferroni correction). No significant linkage disequilibrium was detected between loci. The simulated combined assignment success rate in parentage analysis for the five highest polymorphic loci was over 99% when one parent known. Cross-species amplification was examined in three other species, Chlamys farreri, Patinopecten yesoensis and Amussium pleuronectes. In both C. farreri and P. yesoensis, nine loci gave successful amplifications, although only five loci were polymorphic. In A. pleuronectes, three loci produced unambiguous PCR products, but only one was variable.
2. Characterization of expressed sequence tag-derived single nucleotide polymorphisms in the bay scallop, Argopecten irradians irradians (Lamarck 1819)
We described here the discovery of 3905 putative single-nucleotide polymorphisms (SNPs) from the alignment of 4968 sequences in a bay scallop Argopecten irradians irradians expressed sequenced tag (EST) database. The observed frequency of SNPs was estimated at one every 118.2 bp of contig sequences. Thirty of the SNPs were chosen for validation by tetra-primer amplification refractory mutation system-polymerase chain reaction procedure, and 17 of them were polymorphic with the minor allele frequency ranged from 0.016 to 0.484. BLASTX gave significant hits for all but one of the 17 genotyped SNP-containing contigs, 11 of which located in coding regions and all resulted in a synonymous substitution. Parentage simulations demonstrated that SNP markers were more sensitive to the number of parents compared with microsatellites, thus more SNPs were needed to counteract low polymorphism. A table of optimal codons was deduced from the analysis of A. i. irradians EST dataset to explain the frequency difference for a specific SNP. It seems that the selection of codon usage may be partly responsible for the frequency difference between the two alleles of the coding SNPs. These are the first SNPs developed for the bay scallop and will provide a useful complement to currently available genetic markers.
3. Mating systems and reproductive success in hermaphroditic bay scallop, Argopecten irradians irradians (Lamarck 1819) inferred by microsatellite-based parentage analysis
In this study we used microsatellite-based parentage analysis to assess the mating system of a mass spawning bay scallop, Argopecten irradians irradians. Analyses were performed on 237 offspring and 14 candidate parents. Overall, 95% of all offspring were unambiguously allocated to their putative parents based on information from six highly polymorphic loci. Offspring from both the self-fertilization and cross-fertilization style were observed, the large variation of self-fertilization rate among individuals displays a mixed mode of mating. The high variances in reproductive success resulted in a decline in effective breeding numbers (Nb/N = 0.71). The self-fertilization rate was 32.89% for this mass spawning and the coefficient of inbreeding was estimated at around 16.5% per generation. When larvae resulting from selfing were removed, the relationship between relatedness and individual reproductive success was proved insignificant between half-sibings and unrelated, which suggest that selection pressures other than avoidance of inbreeding may be responsible for the evolution and maintenance of the self-compatible mating system of A. i. irradians. These results lend insight to A. i. irradians cultivation in present China and provide a genetic basis for the development of more effective spawning techniques.
4. Development of four EST-SSR multiplex PCRs in the Pacific oyster, Crassostrea gigas and their validation in parentage assignment
We report four highly informative multiplex PCRs developed from twelve previously described EST-SSRs in Crassostrea gigas. We evaluated and validated these multiplex PCRs in twelve full-sib families. The average allelic richness and the polymorphism information content (PIC) were 11.1 and 0.811 respectively. The combined power of exclusion was greater than 99.99% using all four multiplex assays. A hundred and forty three tests of segregation ratios revealed 11 significant departures from expected Mendelian ratios. The frequency of null alleles was estimated as 4.9% of all the alleles segregating based on a within-family analysis of Mendelian segregation patterns. Parentage analysis of real offspring demonstrated that 97% of all offspring were unambiguously allocated to a pair of parents based on two multiplex PCRs with only a 4% error rate, and 100% of the offspring were correctly allocated to their parents when three multiplex PCRs were used.
5. Parentage determination and effective population size estimation in mass spawning Pacific oyster, Crassostrea gigas based on microsatellite analysis
Seven high polymorphic microsatellite loci were utilized to determine the pedigrees in a mass spawning of Pacific oyster, Crassostrea gigas and to estimate the genetic variability between broodstock and offspring. Analyses were performed on a total of 155 individuals, including 141 offspring, 8 candidate mothers and 6 candidate fathers. The assignment results of real offspring were generally in agreement with simulation with a success rate over 99% using only six of these loci. The allelic diversity and observed heterozygosity (Ho) exhibited similarity between parents and offspring populations, but the expected heterozygosity (He) had a significant decrease in offspring. Although all the males and females contributed to the next generation, the variances of reproductive success and unequal sex ratio resulted in a decline in effective population size (Ne = 11.42). The inbreeding rate of this small-scale, mass spawning population was estimated at around 16.5% per generation. This gave us an insight that when designing breeding programmes based on mass spawning for future oyster cultivation generations, the higher inbreeding and lower effective population size should be considered.
6. Effective population size in hatchery mass-spawning Japanese scallop, Mizuhopecten yessoensis based on microsatellite parentage analysis
The microsatellite-based parentage analysis was used to assess the effective population size and its relationship with parental phenotypes in two different developing times of larvae from hatchery mass-spawning Japanese scallop, Mizuhopecten yessoensis. Analyses were performed on 1080 offspring, 14 candidate mothers and 14 candidate fathers. Overall, more than 97% of all offspring were unambiguously allocated to their putative parents based on information from five highly polymorphic loci. For D-shaped larvae phase, the variances of parental reproductive success resulted in a decline in effective population size (Ne/N = 0.87), and the inbreeding rate was estimated at 0.081. The Ne decreased further for post-larval phase (Ne/N = 0. 78), and the inbreeding rate increased to 0.090, this may be a result of culling during the rearing process, which could have an impact on the population genetics, and bias the variances of reproductive success. Also, the different survival rates between families could be responsible for it. For D-shaped larvae phase, maternal shell length and shell width had a significant positive effect on reproductive success, the same was observed for paternal shell, which indicated that parental reproductive success was dependent on the magnitude of the size difference. While there was no such relationship discovered for post-larval phase, which might suggest that the effect of advantage in parental size difference would decrease along with culture process.
7. Sibship reconstruction and effective population size estimation in mass spawning ark shell, Scapharca broughtonii based on microsatellite analysis
Five high polymorphic microsatellite loci were utilized to reconstruct the sibship in a mass spawning of ark shell,Scapharca broughtonii and to estimate the genetic variability between D-shaped larvae phase and postlarvae phase. The allelic diversity, observed (Ho) and expected (He) heterozygosity exhibited similarity between the two larvae phase. But the sibship reconstruction results of 180 offspring in each larvae phase demonstrated that the effective population size (Ne) was 20 in D-shaped larvae phase and decreased to 16 in postlarvae phase, besides, the inferred number of parents decreased 16.13% and the inbreeding rate increased 0.6% in the latter. Multiple matings were detected both in males and females, and the reproductive success of both sexes in the two larvae phase was positively correlated to the number of individuals with whom it had mated.
In general, the microsatellite-based pedigree analysis has been approved to be very efficient that the pedigree of mixed populations could be determined through the use of five to six microsatellite markers. The decline of the effective number of breeders (Nb) or the effective population size (Ne) was detected in all the aquaculture mollusks in this study. The mating system, unequal sex ratios, high variance in parental contributions and family size variations were proved to be the main reasons for the decline of Nb. These results will be useful guides for the protection of the genetic diversity and healthy aquaculture of seed production in the marine shellfish.
1.海湾扇贝EST-SSR标记分离及特性分析
利用公共数据库资源,在海湾扇贝EST数据库中查找包含微卫星的序列,开发了15个EST-SSR分子标记,采用群体多态性分析结果显示,位点的等位基因数平均值为5.5,观测和期望杂合度范围分别为0.000-0.781和0.155-0.885。平均多态信息含量为0.548。进行Bonferroni校正后,发现15个位点中有8个位点显著偏离哈迪-温伯格平衡。在各位点之间未发现有连锁现象。5个多态性最高的微卫星位点在已知单亲时的累积排除概率超过99%。利用筛选出的15对引物在栉孔扇贝、虾夷扇贝和长肋日月贝中进行PCR扩增,其中9对引物在栉孔扇贝和虾夷扇贝中能扩增出产物,有5对引物扩出的微卫星标记呈多态。在长肋日月贝中有3对引物有扩增产物,有1对引物扩出的微卫星标记呈多态。
2.海湾扇贝EST-SNP标记分离及特性分析
通过对海湾扇贝EST数据库中4968条ESTs进行聚类及拼接后,共发现3905个候选SNP位点,平均密度为1/118.2bp。从中选择30个候选SNPs进行tetra-primer ARMS-PCR引物设计和优化,17组引物扩增产生与预期片段长度相符的多态性位点,多态性位点最小等位基因频率从0.016到0.484。对含有17个多态SNPs的contigs序列在GenBank中进行BLASTX比对,除一个位点所在序列外均有匹配的功能序列,其中11个已验证SNPs定位于编码区(外显子区),导致同义氨基酸替换。家系模拟鉴定结果表明,SNP标记对鉴定所用亲本的数量比微卫星标记更为敏感,因此需要更多的SNPs来抵消多态性低带来的负面效果以达到较高并且稳定性较好的鉴定成功率。通过对海湾扇贝EST数据库的分析构建了最优密码子使用表,以解释某一特定SNP不同等位基因频率上的差异,分析发现对密码子使用的选择性可能会影响编码区SNP不同等位基因的频率。这些对于海湾扇贝SNP的初步研究是对现有遗传标记的有用补充。
3.基于微卫星家系分析的海湾扇贝交配系统和繁殖成功研究
运用微卫星家系鉴定的方法对群体产卵海湾扇贝的交配系统进行了研究。对14个候选亲本和237个子代的鉴定结果表明,采用6个多态微卫星位点能够将95%的子代鉴定到亲本。根据家系鉴定结果,发现既有通过自体受精产生的子代也有通过非自体受精产生的子代,但是自体受精率在亲本个体间巨大的变异表明海湾扇贝具有混合交配模式。繁殖成功的变异造成了有效繁殖亲本数量的降低(Nb/N = 0.71)。群体的自体受精率为32.89%,近交系数为16.5%。在不考虑自交子代的情况下,半同胞和非同胞亲本在亲缘关系和繁殖成功之间没有显著的相关关系,表明可能是选择的压力而不是对近交的避免机制支持着海湾扇贝自交兼容性交配系统的进化和维持。本研究结果使我们对目前我国海湾扇贝的养殖状况有了深入了解,并且为以后对其进行繁殖技术改良提供了知识基础。
4.太平洋牡蛎EST-SSR多重PCR的开发及其在家系鉴定中的检验
我们从以往报道的太平洋牡蛎EST-SSRs中开发出了4组multiplex PCRs,并在12组单对交配家系中检验了其在家系鉴定中的效率。位点的基因丰富度和多态信息含量平均值分别为11.1和0.811,4组multiplex PCRs在家系鉴定中的累积排除能力大于99.99%。对143组分离模式的分析发现,有11个基因型分离比偏离孟德尔分离定律。通过分析位点在家系内的Mendelian分离模式,发现无效等位基因频率为4.9%。对12组单对交配家系的实际鉴定结果表明,使用2组多态信息含量最高的Multiplex PCRs,可以将97%的子代鉴定到亲本,其结果与真实的家系信息对比,错误率为4%;如果使用3组或者4组Multiplex PCRs,则可以将100%的子代鉴定到亲本,与真实的家系信息对比错误率为0。
5.太平洋牡蛎养殖群体的微卫星家系分析和有效群体大小估算
运用7个高度多态的微卫星位点对群体产卵的太平洋牡蛎进行家系分析,并比较亲本和子代的遗传多样性变化。对8个候选母本、6个候选父本和155个子代的鉴定结果与模拟鉴定一致,运用6个微卫星位点即可获得超过99%的鉴定成功率。等位基因数和观察杂合度(Ho)在亲本和子代中没有明显差异,但是,子代的期望杂合度(He)和亲本相比有显著降低。虽然所有亲本均参与子代繁殖过程,但是亲本繁殖成功的变异和不平衡的性别比例导致了Ne的降低(Ne = 11.42)。群体近交率的估算值为16.5%。这些结果表明在未来制定太平洋牡蛎群产育种方案时,需要考虑到较高的近交率和较低有效群体的因素。
6.基于微卫星家系分析的虾夷扇贝有效繁殖群体研究
运用微卫星家系鉴定的方法对群体产卵虾夷扇贝幼虫发育两个不同时期的有效繁殖群体的变化及其与亲本性状特征的相关性进行了研究。对14个候选母本、14个候选父本和1080个子代的鉴定结果表明,采用5个多态微卫星位点能够获得97%以上的鉴定成功率。亲本繁殖成功的变异是D形幼虫时期有效群体大小降低的主要原因(Ne/N = 0.87),近交率的估计为0.081。稚贝时期的有效群体大小进一步降低(Ne/N = 0. 78),近交率上升至0.090。这一变化可能与育苗过程中的幼虫分级选择有关,人为的改变了群体的遗传结构,加剧了亲本繁殖成功的变异。也可能与不同亲本组子代的存活力差异有关。回归分析表明,D形幼虫阶段母本的繁殖成功与母本壳长和壳宽存在显著正相关关系,父本的繁殖成功与父本壳高存在显著正相关关系,由此推断在群体产卵时,亲本个体大小在繁殖成功上有显著优势。然而在稚贝阶段,未检测到亲本的繁殖成功与性状特点的相关性。表明随着苗种的养成,亲本个体大小在产卵阶段的繁殖成功优势可能会逐渐消失。
7.基于微卫星同胞重建的魁蚶有效繁殖群体研究
运用5个微卫星标记,在没有亲本信息的情况下,采取同胞重建的方法研究了群体产卵魁蚶幼虫发育两个不同时期遗传多样性以及有效繁殖群体大小的变化,并对亲本的繁殖成功与交配对象数目的关系进行了相关性研究。等位基因数和观察杂合度在两个采样阶段均没有显著差异。但是对D形幼虫时期以及稚贝时期各180个个体的同胞重建结果表明,D形幼虫时期有效繁殖群体的估算值为20,稚贝时期有效繁殖群体的估算值为16,出现了明显的降低,而且稚贝时期可能的亲本数量也比D形幼虫时期降低了16.13%,?F增加了0.6%。多配繁殖在父/母本中均存在,而且在两个采样阶段,魁蚶父/母本繁殖成功与交配对象数量均存在显著正相关关系。
综上,本研究证明基于微卫星的家系分析方法具有较高的鉴定效力。运用5-6个微卫星位点即能够成功地对混合种群进行家系鉴定。在本研究的所有养殖贝类中均检测到有效繁殖群体数量(Nb,或有效种群大小Ne)的降低。交配系统,不平衡的性别比例,亲本贡献的高度变异以及家系规模的变异是导致Nb降低的主要原因。研究结果对我国海水养殖贝类遗传多样性保护和健康苗种培育具有指导作用。
The marine shellfish has served as an important component of aquaculture in China. The restricted number of effective population size (or effective number of breeders) used in culture operations can lead to a loss of genetic variability, increase the random drift in gene frequencies and inbreeding in a population. Especially, the high fecundity of some organisms in a culture environment (such as shellfish) ensure that a small number of stocks are used for production to generate sufficient offspring without concerns that genetic variability would decrease in farmed populations. In the present study, we developed different kinds of molecular markers to evaluate their utility in the parentage analysis. Furthermore, the effective population size, the difference of genetic variability and inbreeding rate were assed in four important hatchery mollusks of the northern coasts who live with different styles of life, including Crassostrea gigas (sessile), Argopecten irradians irradians (bentonic, hermaphroditic), Mizuhopecten yessoensis (bentonic, dioecious) and Scapharca broughtonii (infauna) based on microsatellite-based parentage analysis to better facilitate the protection of the genetic diversity and healthy aquaculture of seed production in these species. The main results of these studies are listed as follows:
1. A set of polymorphic expressed sequence tag–derived microsatellites from the bay scallop, Argopecten irradians irradians, and their transportability in three other scallop species
A set of 15 new EST-SSRs for Argopecten irradians irradians was developed from ESTs database. The average number of alleles was 5.5 per locus, observed heterozygosities ranged from 0.000 to 0.781, while expected heterozygosities varied from 0.155 to 0.885. The average PIC was 0.548. Significant departures from HWE were observed in 8 of the 15 single-locus (exact tests after sequential Bonferroni correction). No significant linkage disequilibrium was detected between loci. The simulated combined assignment success rate in parentage analysis for the five highest polymorphic loci was over 99% when one parent known. Cross-species amplification was examined in three other species, Chlamys farreri, Patinopecten yesoensis and Amussium pleuronectes. In both C. farreri and P. yesoensis, nine loci gave successful amplifications, although only five loci were polymorphic. In A. pleuronectes, three loci produced unambiguous PCR products, but only one was variable.
2. Characterization of expressed sequence tag-derived single nucleotide polymorphisms in the bay scallop, Argopecten irradians irradians (Lamarck 1819)
We described here the discovery of 3905 putative single-nucleotide polymorphisms (SNPs) from the alignment of 4968 sequences in a bay scallop Argopecten irradians irradians expressed sequenced tag (EST) database. The observed frequency of SNPs was estimated at one every 118.2 bp of contig sequences. Thirty of the SNPs were chosen for validation by tetra-primer amplification refractory mutation system-polymerase chain reaction procedure, and 17 of them were polymorphic with the minor allele frequency ranged from 0.016 to 0.484. BLASTX gave significant hits for all but one of the 17 genotyped SNP-containing contigs, 11 of which located in coding regions and all resulted in a synonymous substitution. Parentage simulations demonstrated that SNP markers were more sensitive to the number of parents compared with microsatellites, thus more SNPs were needed to counteract low polymorphism. A table of optimal codons was deduced from the analysis of A. i. irradians EST dataset to explain the frequency difference for a specific SNP. It seems that the selection of codon usage may be partly responsible for the frequency difference between the two alleles of the coding SNPs. These are the first SNPs developed for the bay scallop and will provide a useful complement to currently available genetic markers.
3. Mating systems and reproductive success in hermaphroditic bay scallop, Argopecten irradians irradians (Lamarck 1819) inferred by microsatellite-based parentage analysis
In this study we used microsatellite-based parentage analysis to assess the mating system of a mass spawning bay scallop, Argopecten irradians irradians. Analyses were performed on 237 offspring and 14 candidate parents. Overall, 95% of all offspring were unambiguously allocated to their putative parents based on information from six highly polymorphic loci. Offspring from both the self-fertilization and cross-fertilization style were observed, the large variation of self-fertilization rate among individuals displays a mixed mode of mating. The high variances in reproductive success resulted in a decline in effective breeding numbers (Nb/N = 0.71). The self-fertilization rate was 32.89% for this mass spawning and the coefficient of inbreeding was estimated at around 16.5% per generation. When larvae resulting from selfing were removed, the relationship between relatedness and individual reproductive success was proved insignificant between half-sibings and unrelated, which suggest that selection pressures other than avoidance of inbreeding may be responsible for the evolution and maintenance of the self-compatible mating system of A. i. irradians. These results lend insight to A. i. irradians cultivation in present China and provide a genetic basis for the development of more effective spawning techniques.
4. Development of four EST-SSR multiplex PCRs in the Pacific oyster, Crassostrea gigas and their validation in parentage assignment
We report four highly informative multiplex PCRs developed from twelve previously described EST-SSRs in Crassostrea gigas. We evaluated and validated these multiplex PCRs in twelve full-sib families. The average allelic richness and the polymorphism information content (PIC) were 11.1 and 0.811 respectively. The combined power of exclusion was greater than 99.99% using all four multiplex assays. A hundred and forty three tests of segregation ratios revealed 11 significant departures from expected Mendelian ratios. The frequency of null alleles was estimated as 4.9% of all the alleles segregating based on a within-family analysis of Mendelian segregation patterns. Parentage analysis of real offspring demonstrated that 97% of all offspring were unambiguously allocated to a pair of parents based on two multiplex PCRs with only a 4% error rate, and 100% of the offspring were correctly allocated to their parents when three multiplex PCRs were used.
5. Parentage determination and effective population size estimation in mass spawning Pacific oyster, Crassostrea gigas based on microsatellite analysis
Seven high polymorphic microsatellite loci were utilized to determine the pedigrees in a mass spawning of Pacific oyster, Crassostrea gigas and to estimate the genetic variability between broodstock and offspring. Analyses were performed on a total of 155 individuals, including 141 offspring, 8 candidate mothers and 6 candidate fathers. The assignment results of real offspring were generally in agreement with simulation with a success rate over 99% using only six of these loci. The allelic diversity and observed heterozygosity (Ho) exhibited similarity between parents and offspring populations, but the expected heterozygosity (He) had a significant decrease in offspring. Although all the males and females contributed to the next generation, the variances of reproductive success and unequal sex ratio resulted in a decline in effective population size (Ne = 11.42). The inbreeding rate of this small-scale, mass spawning population was estimated at around 16.5% per generation. This gave us an insight that when designing breeding programmes based on mass spawning for future oyster cultivation generations, the higher inbreeding and lower effective population size should be considered.
6. Effective population size in hatchery mass-spawning Japanese scallop, Mizuhopecten yessoensis based on microsatellite parentage analysis
The microsatellite-based parentage analysis was used to assess the effective population size and its relationship with parental phenotypes in two different developing times of larvae from hatchery mass-spawning Japanese scallop, Mizuhopecten yessoensis. Analyses were performed on 1080 offspring, 14 candidate mothers and 14 candidate fathers. Overall, more than 97% of all offspring were unambiguously allocated to their putative parents based on information from five highly polymorphic loci. For D-shaped larvae phase, the variances of parental reproductive success resulted in a decline in effective population size (Ne/N = 0.87), and the inbreeding rate was estimated at 0.081. The Ne decreased further for post-larval phase (Ne/N = 0. 78), and the inbreeding rate increased to 0.090, this may be a result of culling during the rearing process, which could have an impact on the population genetics, and bias the variances of reproductive success. Also, the different survival rates between families could be responsible for it. For D-shaped larvae phase, maternal shell length and shell width had a significant positive effect on reproductive success, the same was observed for paternal shell, which indicated that parental reproductive success was dependent on the magnitude of the size difference. While there was no such relationship discovered for post-larval phase, which might suggest that the effect of advantage in parental size difference would decrease along with culture process.
7. Sibship reconstruction and effective population size estimation in mass spawning ark shell, Scapharca broughtonii based on microsatellite analysis
Five high polymorphic microsatellite loci were utilized to reconstruct the sibship in a mass spawning of ark shell,Scapharca broughtonii and to estimate the genetic variability between D-shaped larvae phase and postlarvae phase. The allelic diversity, observed (Ho) and expected (He) heterozygosity exhibited similarity between the two larvae phase. But the sibship reconstruction results of 180 offspring in each larvae phase demonstrated that the effective population size (Ne) was 20 in D-shaped larvae phase and decreased to 16 in postlarvae phase, besides, the inferred number of parents decreased 16.13% and the inbreeding rate increased 0.6% in the latter. Multiple matings were detected both in males and females, and the reproductive success of both sexes in the two larvae phase was positively correlated to the number of individuals with whom it had mated.
In general, the microsatellite-based pedigree analysis has been approved to be very efficient that the pedigree of mixed populations could be determined through the use of five to six microsatellite markers. The decline of the effective number of breeders (Nb) or the effective population size (Ne) was detected in all the aquaculture mollusks in this study. The mating system, unequal sex ratios, high variance in parental contributions and family size variations were proved to be the main reasons for the decline of Nb. These results will be useful guides for the protection of the genetic diversity and healthy aquaculture of seed production in the marine shellfish.
引文
李琪.海洋贝类微卫星DNA标记的开发及其在遗传学研究中的应用.中国水产科学,2006,13 (3):502-509
宋林生,常亚青.用RAPD技术对我国栉孔扇贝野生种群与养殖群体的遗传结构及其遗传分化的研究.高技术通讯,2002,12(7):83-86.
于红.牡蛎良种选育的遗传学基础研究:[博士学位论文].青岛:中国海洋大学,2010
张振.基于微卫星和SNP标记的皱纹盘鲍遗传连锁图谱及其应用: [博士学位论文].青岛:中国科学院海洋研究所,2010
Aide TM. 1986. The influence of wind and animal pollination on variation in outcrossing rates. Evolution 40: 434-435.
Allendorf FW, Phelps SR. 1980. Loss of genetic variation in a hatchery stock of cutthroat trout. Transactions of the American Fisheries Society 109: 537-543.
Allendorf FW, Leary RF. 1986. Heterozygosity and fitness in natural populations of animals. Pages 57-76 in M. E. Soulé, editor. Conservation biology: The science of scarcity and diversity. Sinauer Associates, Sunderland, Massachusetts.
An HS, Park JY, Lee YG, Lee DS, Lee C. 2005. Ten polymorphic microsatellite loci in the giant scallop (Mizuhopecten yessoensis). Molecular Ecology Notes 5: 806-808.
An HY, PARK JY. 2005. Ten new highly polymorphic microsatellite loci in the blood clam Scapharca broughtonii. Molecular Ecology Notes 5: 896-898.
Anderson EC. 2005. An efficient Monte Carlo method for estimating Ne from temporally spaced samples using a coalescent-based likelihood method. Genetics 170: 955-967.
Anderson EC, Garza JC. 2006. The power of single nucleotide polymorphisms for large-scale parentage inference. Genetics 172:2567-2582.
Anderson EC, Williamson EG, Thompson EA. 2000. Monte Carlo evaluation of the likelihood for Ne from temporally spaced samples. Genetics 156: 2109-2118.
Andersson M. 1994. Sexual Selection. Princeton University Press, Princeton.
Araki H, Waples RS, Ardren WR, Cooper B, Blouin M.S. 2007. Effective population size of steelhead trout: influence of variance in reproductive success, hatchery programs, and genetic compensation between life-history forms. Molecular Ecology 16: 953-966.
Bardach JE, Ryther JH, McLarney WO. 1972. Aquaculture. The farming and husbandry of freshwater and marine organisms. Wiley-Interscience, New York.
Bateman AJ. 1948. Intrasexual selection in Drosophila. Heredity 2: 349-368.
Beaumont AR. 1986. Genetics aspects of hatchery rearing of the scallop Pecten maximus (L.).Aquaculture 57: 99-110.
Beaumont AR, Hoare K. 2003. Biotechnology and Genetics in Fisheries and Aquaculture. 170 pp. Blackwell Publishing, United Kingdom.
Beaumont MA. 2003. Estimation of population growth or decline in genetically monitored populations. Genetics 164:1139–1160.
Bekkevold D, Hansen MW, Loeschcke V. 2002. Male reproductive competition in spawning aggregations of cod (Gadus morhua L.). Molecular Ecology 11: 91-102.
Beninger PG., Le Pennec M. 1991. Functional anatomy of scallops. Pages 133-224 in S. E. Shumway, editor. Scallops: Biology, Ecology and Aquaculture. Elsevier, Amsterdam, The Netherlands.
Bentsen HB, Olesen I. 2002. Designing aquaculture mass selection programs to avoid high inbreeding rates. Aquaculture 204: 349–359.
Bernatchez L, Duchesne P. 2000. Individual-based genotype analysis in studies of parentage and population assignment: how many loci, how many alleles? Canadian Journal of Fisheries and Aquatic Sciences 57: 1-12.
Berthier P, Beaumont MA, Cornuet J-M, Luikart G. 2002. Likelihood-based estimation of the effective population size using temporal changes in allele frequencies: a genealogical approach. Genetics 160: 741-751.
Bijma P. 2000. Long term genetic contributions. Prediction of rates of inbreeding and genetic gain in selected populations. PhD thesis. Pages 205-206. Animal Breeding and Genetics Group, Wageningen University, The Netherlands.
Blouin MS. 2003. DNA-based methods for pedigree reconstruction and kinship analysis in natural populations. Trends in Ecology and Evolution 18: 503-511.
Blouin MS, Parsons M, Lacaille V, Lotz S. 1996. Use of microsatellite loci to classify individuals by relatedness. Molecular Ecology 5: 393-401.
Boessenkool S, Star B, Seddon PJ, Waters JM. 2010. Temporal genetic samples indicate small effective population size of the endangered yellow-eyed penguin. Conservation Genetics 11: 539-546.
Boudry P, Collet B, Cornette F, Hervouet V, Bonhomme F. 2002. High variance in reproductive success of the Pacifc oyster (Crassostrea gigas, Thunberg) revealed by microsatellite-based parentage analysis of multifactorial crosses. Aquaculture 204: 283–296.
Brawn VM. 1961. Reproductive behaviour of the cod (Gadus callarias L.). Behaviour 18: 177-197.
Brazeau DA, Gleason DF, Morgana ME. 1998. Self-fertilization in brooding hermaphroditicCaribbean corals: Evidence from molecular markers. Journal of Experimental Marine Biology and Ecology 231: 225-238.
Bretman A, Wedell N, Tregenza T. 2004. Molecular evidence of post-copulatory inbreeding avoidance in the field cricket Gryllus bimaculatus. Proceedings of the Royal Society B 271: 159-164.
Brown RC, Woolliams JA, McAndrew BJ. 2005. Factors influencing effective population size in commercial populations of gilthead seabream, Sparus aurata. Aquaculture 247: 219-225.
Caballero A. 1994. Developments in the prediction of effective population size. Heredity 73: 657-679.
Camara MD, Evans S, Langdon CJ. 2008. Parental relatedness and survival of Pacific Oysters from a naturalized population. Journal of Shellfish Research 27(2): 323–336.
Cervantes I, Pastor JM, Gutiérrez JP, Goyache F, Molina A. 2011. Computing effective population size from molecular data: The case of three rare Spanish ruminant populations. Livestock Science doi:10.1016/j.livsci.2010.12.027
ChagnéD, Gasic K, Crowhurst RN, Han Y, Bassett H, Bowatte DR, Lawrence TJ, Rikkerink EHA, Gardiner SE, Korban SS. 2008. Development of a set of SNP markers present in expressed genes of the apple. Genomics 92:353-358.
Chapuis MP, Estoup A. 2007. Microsatellite null alleles and estimation of population differentiation. Molecular Biology and Evolution 24(3): 621–631.
Charbonnel N, Rasatavonjizay R, Sellin E, Brémond P, Jarne P. 2005. The influence of genetic factors and population dynamics on the mating system of the hermaphroditic freshwater snail Biomphalaria pfeifferi. Oikos 108: 283-296.
Charlesworth D. 2006. Evolution of plant breeding systems. Current Biology 16: 726-735.
Charlesworth D, Morgan MT, Charlesworth B. 1990. Inbreeding depression, genetic load, and the evolution of outcrossing rates in a multilocus system with no linkage. Evolution 44: 1469-1489.
Chiapparino E, Lee D, Donini P. 2004. Genotyping single nucleotide polymorphisms in barley by tetra-primer ARMS-PCR. Genome 47:414-420.
Clutton-Brock TH. 1989. Mammalian mating systems. Proceedings of the Royal Society B 236: 339-372.
Cnaani A, Hallerman EM, Ron M, Weller JI, Indelman M, Kashi Y, Gall GAE, Hulata G. 2003. Detection of a chromosomal region with two quantitative trait loci, affecting cold tolerance and fish size, in an F2 tilapia hybrid. Aquaculture, 223:117-128.
Correa C, Thiel M. 2003. Mating systems in caridean shrimp (Decapoda: Caridea) and theirevolutionary consequences for sexual dimorphism and reproductive biology. Revista Chilena de Historia Natural 76: 187-203.
Cross TF, King J. 1983. Genetic effects of hatchery rearing in Atlantic salmon. Aquaculture 33: 33-40.
Crow JF, Denniston C. 1988. Inbreeding and variance effective population numbers. Evolution 42: 482-495.
Crow JF, Kimura M. 1970. An Introduction to Population Genetics Theory. 591 pp. Harper and Row, New York.
Dantec LL, ChagnéD, Pot D, Cantin O, Garnier-Ger P, Bedon F, Frigerio JM, Chaumeil P, Leger P, Garcia V, Laigret F, Daruvar A, Plomion C. 2004. Automated SNP detection in expressed sequence tags: statistical considerations and application to maritime pine sequences. Plant Molecular Biology 54: 461-470.
Danzmann RG. 1997 PROBMAX: a computer program for assigning unknown parentage in pedigree analysis from known genotypic pools of parents and progeny. Journal of Heredity 88, 333.
Danzmann RG, Ferguson MM, Allendorf FW. 1989. Genetic variability and components of fitness in hatchery strains of rainbow trout. Journal of Fish Biology 35: 313-319.
Dégremont L, Bédier E, Boudry P. 2010. Summer mortality of hatchery-produced Pacific oyster spat (Crassostrea gigas). II. Response to selection for survival and its influence on growth and yield. Aquaculture 299: 21-29.
Dégremont L, Ernande B, Bédier E, Boudry P. 2007. Summer mortality of hatchery-produced Pacific oyster spat (Crassostrea gigas). I. Estimation of genetic parameters for survival and growth. Aquaculture 262: 41–53.
Department of Fisheries, 2005. China Fisheries Statistic Yearbook 2004. China Agriculture Press, Beijing (in Chinese).
Desrosiers RR, Gerard A, Peignon JM, Naciri Y, Dufresne L, Morasse J, Ledu C, Phelipot P, Guerrier P, Dube F. 1993. A novel method to produce triploids in bivalve molluscs by the use of 6-dimethylaminopurine. Journal of Experimental Marine Biology and Ecology 170: 29–43.
DeWoody JA, Avise JC. 2001. Genetic perspectives on the natural history of fish mating systems. Journal of Heredity 92: 167-172.
Dong SR, Kong J, Zhang TS, Meng XH, Wang RC. 2006. Parentage determination of Chinese shrimp (Fenneropenaeus chinensis) based on microsatellite DNA markers. Aquaculture 258: 283-288.
Duchesne P, Castric T, Bernatchez L. 2005. PASOS (parental allocation of singles in open systems): a computer program for individual parental allocation with missing parents. Molecular Ecology Notes 5: 701–70.
Duchesne P, Godbout M-H, Bernatchez L. 2002. PAPA (package for the analysis of parental allocation): a computer program for simulated and real parental allocation. Molecular Ecology Notes 2: 191-193.
Duret L, Mouchiroud D. 1999. Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis. Proceedings of the National Academy of Sciences 6:4482-4487.
Emery AM, Wilson IJ, Craig S, Boyle PR, Noble LR. 2001. Assignment of paternity groups without access to parental genotypes: multiple mating and developmental plasticity in squid. Molecular Ecology 10: 1265–1278.
Evans BS, Knauer J, Tayler JJU, Jerry DR. 2006. Development and characterization of six new microsatellite markers for the silver- or gold-lipped pearl oyster, Pinctada maxima (Pteriidae). Molecular Ecology Notes 6: 835-837.
Evans F, Matson S, Brake J, Langdon C. 2004. The effects of inbreeding on performance traits of adult Pacific oysters (Crassostrea gigas). Aquaculture 230: 89-98.
Evans S, Langdon C. 2006. Effects of genotype×environment interactions on the selection of broadly adapted Pacific oysters (Crassostrea gigas). Aquaculture 261: 522–534.
FAO, 2010. World aquaculture production of fish, crustaceans, molluscs, etc., by principal species (ftp://ftp.fao.org/fi/STAT/summary/default. htm#aqua).
Falconer DS. 1989. Introduction to Quantitative Genetics. 3rd edn. Longman, England.
Falconer DS, Mackay TFC. 1996. Introduction to quantitative genetics, 4th edition. Prentice Hall, Harlow.
Fessehaye Y, El-bialy Z, Rezk MA, Crooijmans R, Bovenhuis H, Komen H. 2006. Mating systems and male reproductive success in Nile tilapia (Oreochromis niloticus) in breeding hapas: A microsatellite analysis. Aquaculture 256: 148-158.
Fisher RA. 1930. The genetical theory of natural selection. Clarendon Press, Oxford, United Kingdom.
Frankham R. 1995. Effective population size, adult population size ratios in wildlife—a review. Genetical Research 66: 95-107.
Gaffney PM. Scott TM. 1984. Genetic heterozygosity and production traits in natural and hatchery populations of bivalves. Aquaculture 42: 289-302.
Gaffney PM, Davis CV, Hawes RO. 1992. Assessment of drift and selection in hatcherypopulations of oysters (Crassostrea virginica). Aquaculture 105: 1-20.
Gall GAE. 1987. Inbreeding, in: Ryman, N. Utter, F. (Eds.), Population genetics and Fisheries Management. Washington Sea Grant Program, Univ. Washington Press, Seattle, USA, pp. 47-87.
Garant D, Dodson JJ, Bernatchez L. 2001. A genetic evaluation of mating system and determinants of individual reproductive success in Atlantic salmon (Salmo salar L.). Journal of Heredity 92: 137-145.
Garner TWJ, Schmidt BR. 2003. Relatedness, body size and paternity in the alpine newt, Triturus alpestris. Proceedings of the Royal Society B 270: 619-624. Gheyas AA, Woolliams JA, Taggart B, Sattar MA, Das TK, McAndrew BJ, Penman DJ. 2009.
Heritability estimation of silver carp (Hypophthalmichthys molitrix) harvest traits using microsatellite based parentage assignment. Aquaculture 294: 187-193.
Gjerde B. 1993. Breeding and selection. In: Heen, K., Monahan, R.L., Utter, F. (Eds.), Salmon Aquaculture. Fishing News Books, Cambridge USA, pp. 187-208.
Goldstein D, Schlotterer C. 1999. Microsatellites: Evolution and Applications. Oxford University Press, Oxford, UK.
Goodnight KF, Queller DC. 1999. Computer software for performing likelihood tests of pedigree relationship using genetic markers. Molecular Ecology 8: 1231–1234.
Goudet J. FSTAT, a Program to Estimate and Test Gene Diversities and Fixation Indices Version 2.9.3. 2001. http://www2.unil.ch/popgen/softwares/fstat.htm Updated from Goudet (1995).
Grantham R, Gautier C, Gouy M, Mercier R, Pave A. 1980. Codon catalog usage and the genome hypothesis. Nucleic Acids Research 8:r49-r62.
Guo X, Ford S, Zhang F. 1999. Molluscan aquaculture in China. Journal of Shellfish Research 18:19-31.
Guo X, Standish K, Allen JR. 1994. Reproductive potential and genetics of triploid Pacific oysters, Crassostrea gigas (Thunberg). The Biological Bulletin 187: 309–318.
Gupta PK, Roy JK, Prasad M. 2001 Single nucleotide polymorphisms: a new paradigm for molecular marker technology and DNA polymorphism detection with emphasis on their use in plants. Current Science 80:524-535.
Hadfield JD, Richardson DS, Burke T. 2006. Towards unbiased parentage assignment: combining genetic, behavioural and spatial data in a Bayesian framework. Molecular Ecology 15: 3715–3730.
Hara M, Sekino M. 2003. Efficient detection of parentage in a cultured Japanese flounder Paralichthys olivaceus using microsatellite DNA marker. Aquaculture 217: 107-114.
Harper FM, Hart MW. 2005. Gamete compatibility and sperm competition affect paternity and hybridization between sympatric Asterias sea stars. The Biological Bulletin 209: 113-126.
Hatanaka A, Yamada S, Sakamoto T, Mitsuboshi T. 2006. Isolation and application of microsatellite DNA markers for pedigree tracing of seedlings of red sea bream (Pagrus major). Journal of the World Aquaculture Society 37: 139-143.
Hauser L, Adcock GJ, Smith PJ, Bernal Ram?rez JH, Carvalho GR. 2002. Loss of microsatellite diversity and low effective population size in an overexploited population of New Zealand snapper (Pagrus auratus). Proceedings of the National Academy of Sciences 99: 11742-11747.
Hayes B, Laerdahl JK, Lien S, Moen T, Berg P, Hindar K., Davidson WS, Koop BF, Adzhubei A, H?yheim B. 2007. An extensive resource of single nucleotide polymorphism markers associated with Atlantic salmon (Salmo salar) expressed sequences. Aquaculture 265:82-90.
Hedgecock D. 1994. Does variance in reproductive success limit effective population sizes of marine organisms? Pages 122-134 in A. R. Beaumont, editor. Genetics and Evolution of Aquatic Organisms. Chapman and Hall, London, UK.
Hedgecock D, Launey S, Pudovkin AI, Naciri YLS, Bonhomme F. 2007. Small effective number of parents (Nb) inferred for a naturally spawned cohort of juvenile European flat oysters Ostrea edulis. Marine Biology 150: 1173-1182.
Hedgecock D, Sly F. 1990. Genetic drift and effective population sizes of hatchery-propagated stocks of the Pacific oyster, Crassostrea gigas. Aquaculture 88: 21-38.
Hedrick PW. 2000. Genetics of Populations, 2nd ed. Jones and Bartlett Publishers, London, UK.
Herbinger CM, Doyle RW, Pitman ER, Paquet D, Mesa KA, Morris DB, Wright JM, Cook D. 1995. DNA fingerprint based analysis of paternal and maternal effects on offspring growth and survival in communally reared rainbow trout. Aquaculture 137: 245-256.
Hubert S, Hedgecock D. 2004. Linkage maps of microsatellite DNA markers for the Pacific oyster Crassostrea gigas. Genetics 168:351-362.
Hutchings JA, Bishop TD, McGregor-Shaw CR. 1999. Spawning behaviour of Atlantic cod, Gadus morhua: evidence of mate competition and mate choice in a broadcast spawner. Canadian Journal of Fisheries and Aquatic Sciences 56: 97-104.
Huvet A, Boudry P, Ohresser M, Delsert C, Bonhomme F. 2000. Variable microsatellites in the Pacific Oyster Crassostrea gigas and other cupped oyster species. Animal Genetics 31: 71-72.
Huvet A, Jeffroy F, Fabioux C, Daniel JY, Quillien V, Van Wormhoudt A. 2008. Association among growth, food consumption-related traits and amylase gene polymorphism in thePacific oyster Crassostrea gigas. Animal Genetics 39: 662-665.
Ibarra AM, Cruz P, Romero BA. 1995. Effects of inbreeding on growth and survival of self-fertilized catarina scallop larvae, Argopecten circularis. Aquaculture 134: 37-47.
Jackson TR, Martin-Robichauda DJ, Reith ME. 2003. Application of DNA markers to the management of Atlantic halibut (Hippoglossus hippoglossus) broodstock. Aquaculture 220:245-259.
Jeffreys AJ, Wilson V, Thein SL. 1985. Hypervariable‘minisatellite’regions in human DNA. Nature 314: 67–73.
Jerry DR, Preston NP, Crocos PJ, Keys S, Meadows JRS, Li Y. 2004. Parentage determination of Kuruma shrimp Penaeus (Marsupenaeus) japonicus using microsatellite markers (Bate). Aquaculture 235: 237-247.
Johnson JA, Talbot SL, Sage GK, Burnham KK, Brown JW, Maechtle TL, Seegar WS, Yates MA, Anderson B, Mindell DP. 2010. The Use of Genetics for the Management of a Recovering Population: Temporal Assessment of Migratory Peregrine Falcons in North America. PLoS ONE 5: DOI: 10.1371/ journal.pone. 0014042.
Jones AG. 2001. GERUD1.0: a computer program for the reconstruction of parental genotypes from progeny arrays using multi-locus DNA data. Molecular Ecology Notes 1: 215–218.
Jones AG. 2005. GERUD2.0: a computer program for the reconstruction of parental genotypes from progeny arrays with known or unknown parents. Molecular Ecology Notes 5: 708–711.
Jones AG, Ardren WR. 2003. Methods of parentage analysis in natural populations. Molecular Ecology 12: 2511–2523.
Jones AG, Small CM, Paczolt KA, Ratterman NL. 2010. A practical guide to methods of parentage analysis. Molecular Ecology Resources 10: 6–30.
Jones OR, Wang J. 2010. COLONY: a program for parentage and sibship inference from multilocus genotype data. Molecular Ecology Resources 10: 551-555.
Jorde PE, Ryman N. 2007. Unbiased estimator for genetic drift and effective population size. Genetics 177:927-935.
Kalinowski ST, Taper ML, Marshall TC. 2007. Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Molecular Ecology 16: 1099–1106.
Kalinowski ST, Taper ML, Creel S. 2006a. Using DNA from noninvasive samples to identify individuals and census populations: an evidential approach tolerant of genotyping errors. Conservation Genetics 7: 319–329.
Kalinowski ST, Wagner AP, Taper ML. 2006b. ML-RELATE: a computer program for maximumlikelihood estimation of relatedness and relationship. Molecular Ecology Resources 6: 576-579.
Kanno Y, Vokoun JC, Letcher BH. 2010. Sibship reconstruction for inferring mating systems, dispersal and effective population size in headwater brook trout (Salvelinus fontinalis) populations. Conservation Genetics DOI: 10.1007/ s10592-010-0166-9.
Kim S, Misra A. 2007. SNP genotyping: technologies and biomedical applications. Annual Review of Biomedical Engineering 9: 289-320.
Kimura M, Crow JF. 1963. The measurement of effective population number. Evolution 17, 279-288.
Koehn RK, Diehl WJ, Scott TM. 1988. The different contribution by individual enzymes of glycolysis and protein catabolism to the relationship between heterozygosity and growth rate in the coot clam Milinia lateralis. Genetics 118: 121-130.
Koljonen ML, T?htinen J, S?is? M, Joskiniemi J. 2002. Maintenance of genetic diversity of Atlantic salmon (Salmo salar) by captive breeding programmes and the geographic distribution of microsatellite variation. Aquaculture 212: 69-92.
Konovalov DA, Manning C, Henshaw MT. 2004. KINGROUP: a program for pedigree relationship reconstruction and kin group assignment using genetic markers. Molecular Ecology Notes 4: 779–782.
Kota R, Varshney RK, Thiel T, Dehmer KJ, Graner A. 2001. Generation and comparison of EST-derived SSRs and SNPs in barley (Hordeum vulgare L.). Hereditas 135:145-151.
Krebs SL, Hancock JE. 1990. Early-acting inbreeding depression and reproductive success in the highbush blueberry, Vaccinium corymbosum L. Theoretical and Applied Genetics 79: 825-832.
Laing I, Earl NH. 1998. The lipid content, spatfall and subsequent growth of early and late settling hatchery-reared Pacific oyster, Crassostrea gigas Thunberg, larvae. Aquaculture Research 29: 19-25.
Lallias D, Taris N, Boudry P, Bonhomme F, Lapègue S. 2010. Variance in the reproductive success of flat oyster Ostrea edulis L. assessed by parentage analyses in natural and experimental conditions. Genetics Research 92:175-87.
Lande R, Barrowclough GF. 1987. Effective population size, genetic variation, and their use in population management. Pages 87-123. In: Soule, M. (Ed.), Viable Populations for Conservation. Cambridge University Press, Cambridge, UK.
Lande R, Schemske DW. 1985. The evolution of self-fertilization and inbreeding depression in plants: 1. Genetic models. Evolution 39: 24-40.
Lannan JE. 1980. Broodstock management of Crassostrea gigas: IV. Inbreeding and larval survival. Aquaculture 21: 353-356.
Lannan JE, Robinson A, Breese WP. 1980. Broodstock management of Crassostrea gigas II. Broodstock conditioning to maximize larval survival. Aquaculture 21: 337-345.
Landegren U, Nilsson M, Kwok PY. 1998. Reading bits of genetic information: methods for single-nucleotide polymorphism analysis. Genome Research 8: 769-776.
Langdon C, Evans F, Jacobson D, Blouin M. 2003. Yields of cultured Pacific oysters Crassostrea gigas Thunberg improved after one generation of selection. Aquaculture 220: 227–244.
Ledig FT. 1986. Heterozygosity, heterosis, and fitness in outbreeding plants. Pages 77-104 in M. E. Souléeditor. Conservation biology: The science of scarcity and diversity. Sinauer Associates, Sunderland, Massachusetts.
Li G, Hubert S, Bucklin K, Ribes V, Hedgecock D. 2003. Characterization of 79 microsatellite DNA markers in the Pacific oyster Crassostrea gigas. Molecular Ecology Notes 3: 228–232.
Li JJ, Li Q. 2008. Isolation and characterization of twelve novel microsatellite loci in the ark shell Scapharca broughtonii, Conservation Genetics 9: 1055-1057.
Li L, Guo X. 2004. AFLP-Based genetic linkage maps of the Pacific oyster Crassostrea gigas Thunberg. Marine Biotechnology 6: 26-36.
Li L, Guo XM, Zhang GF. 2009. Inheritance of 15 microsatellites in the Pacific oyster Crassostrea gigas: segregation and null allele identification for linkage analysis. Chinese Journal of Oceanology and Limnology 27: 74–79.
Li R, Li Q, Yu R. 2008. A set of polymorphic expressed sequence tag-derived microsatellites from the bay scallop, Argopecten irradians irradians, and their transportability in three other scallop species. Journal of the World Aquaculture Society 39: 138-141.
Li Q, Chen L, Kong L. 2009. A genetic linkage map of the sea cucumber, Apostichopus japonicus (Selenka), based on AFLP and microsatellite markers, Animal Genetics 40: 678-685.
Li Q, Kijima A. 2005. Segregation of microsatellite alleles in gynogenetic diploid Pacific abalone (Haliotis discus hannai). Marine Biotechnology 7:669–676.
Li Q, Liu SK, Kong LF. 2009. Microsatellites within genes and ESTs of the Pacific oyster Crassostrea gigas and their transferability in five other Crassostrea species. Electronic Journal of Biotechnology 12: DOI: 10.2225/vol12-issue3- fulltext-9.
Li Q, Park C, Kijima A. 2002. Isolation and characterization of microsatellite loci in the Pacific abalone, Haliotis discus hannai. Journal of Shellfish Research 21: 811-815.
Li Q, Park C, Kijima A. 2003. Allelic transmission of microsatellites and application to kinship analysis in newly hatched Pacific abalone larvae. Fisheries Science 69: 883-889.
Li Q, Park C, Kobayashi T, Kijima A. 2003. Inheritance of microsatellite DNA markers in the Pacific abalone Haliotis discus hannai. Marine Biotechnology 5:331-338.
Li Q, Xu KF, Yu RH. 2007. Genetic variation in Chinese hatchery populations of the Japanese scallop (Patinopecten yessoensis) inferred from microsatellite data, Aquaculture 269: 211-219.
Li Q, Yu H, Yu RH. 2006. Genetic variability assessed by microsatellites in cultured populations of the Pacific oyster (Crassostrea gigas) in China. Aquaculture 259: 95–102.
Li RH, Li Q, Yu RH. 2009. Parentage determination and effective population size estimation in mass spawning Pacific oyster, Crassostrea gigas, based on microsatellite analysis. Journal of the World Aquaculture Society 40: 667–677.
Li Y, Byrne K, Miggiano E, Whan V, Moore S, Keys S, Crocos P, Preston N, Lehnert S. 2003. Genetic mapping of the kuruma prawn Penaeus japonicus using AFLP markers. Aquaculture 219: 143-156.
Lind CE, Evans BS, Knauer J, Taylor JJU, Jerry DR. 2009. Decreased genetic diversity and a reduced effective population size in cultured silver-lipped pearl oysters (Pinctada maxima). Aquaculture 286: 12-19.
Liu ZJ, Tan G, Li P, Dunham RA. 1999. Transcribed dinucleotide microsatellites and their associated genes from channel catfish, Ictalurus punctatus. Biochemical and Biophysical Research Communications 259: 190–194.
Luikart G, Ryman N, Tallmon DA, Schwartz MK, Allendorf FW. 2010. Estimation of census and effective population sizes: the increasing usefulness of DNA-based approaches. Conservation Genetics 11: 355-373.
Lynch M, Ritland K. 1999. Estimation of pairwise relatedness with molecular markers. Genetics 152: 1753-1766.
Mack PD, Hammock BA, Promislow DEL. 2002. Sperm competitive ability and genetic relatedness in Drosophila melanogaster: similarity breeds contempt. Evolution 56: 1789-1795.
Magoulas A, Ghjetvaj B, Terzoglou V, Zouros E. 1998. Three polymorphic microsatellites in the Japanese oyster, Crassostrea gigas (Thunberg). Animal Genetics 29: 69-70.
Marshall TC, Slate J, Kruuk LEB, Pemberton JM. 1998. Statistical confidence for likelihood-based paternity inference in natural populations. Molecular Ecology 7: 639-655.
Martinez G, Mettifogo L, Perez MA, Callejas C. 2007. A method to eliminate self-fertilization in a simultaneous hermaphrodite scallop. 1. Effects on growth and survival of larvae and juveniles. Aquaculture 273: 459-469.
Matson SE, Camara MD, Eichert W, Banks MA. 2008. P-LOCI: a computer program for choosing the most efficient set of loci for parentage assignment. Molecular Ecology Resources 8(4): 765-768.
McGoldrick D, Hedgecock D, English LJ, Baoprasertkul P, Ward RD. 2000. The transmission of microsatellite alleles in Australian and North American stocks of the Pacific oyster (Crassostrea gigas): selection and null alleles. Journal of Shellfish Research 19:779-788.
Miggiano E, Deinnocentiis S, Ungaro A, Sola L, Crosetti D. 2005. AFLP and microsatellites as genetic tags to identify cultured gilthead seabream escapees: data from a simulated floating cage breaking event. Aquaculture International 13: 137-146.
M?ller L.M, Beheregaray LB, Harcourt RG, Krützen M. 2001. Alliance membership and kinship in wild male bottlenose dolphins (Tursiops aduncus) of southeastern Australia. Proceedings of the Royal Society B 268: 1941-1947.
Mori K. 1979. Effects of artificial eutrophication on the metabolism of the Japanese oyster Crassostrea gigas. Marine Biology 53: 361–369.
Morin PA, Luikart G, Wayne RK, the SNP workshop Group. 2004. SNPs in ecology, evolution and conservation. Trends in Ecology & Evolution 19:208-216.
Moriyama EN. 2003. Codon usage, Encyclopedia of the human genome. Macmillan Publishers, Nature Publishing Group. http://www.ehgonline.net4.
Musto H, Cruveiller S, D’Onofrio G, Romero H, Bernardi G. 2001. Translational selection on codon usage in Xenopus laevis. Molecular Biology and Evolution 18:1703-1707.
Neff BD, Pitcher TE. 2005. Genetic quality and sexual selection: an integrated framework for good genes and compatible genes. Molecular Ecology 14: 19-38.
Nichols KM, Young WP, Danzmann RG, Robison BD, Rexroad C, Noakes M, Phillips RB, Bentzen P, Spies I, Knudsen K, Allendorf FW, Cunningham BM, Brunelli J, Zhang H, Ristow S, Drew R, Brown KH, Wheeler PA, Thorgaard GH. 2003. A consolidated linkage map for rainbow trout (Oncorhynchus mykiss). Animal Genetics 34(2):102-15.
Norris AT, Bradley DG, Cunningham EP. 2000. Parentage and relatedness determination in farmed Atlantic salmon (Salmo salar) using microsatellite markers. Aquaculture 182: 73-83.
Nunney L. 1993. The influence of mating systems and overlapping generations on effective population size. Evolution 47: 1329-1341.
Nunney L, Elam DR. 1994. Estimating the effective population size of conserved populations. Conservation Biology 8:175-184.
Olsson M, Shine R, Madsen T, Gullberg A, Tegelstrom H. 1996. Sperm selection by females. Nature 383: 585.
O’Reilly PT, Herbinger CM, Wright JM. 1998. Analysis of parentage determination in Atlantic salmon (Salmo salar) using microsatellites. Animal Genetics 29: 363-370.
Ortega-Villaizan Romo M, Suzuki S, Nakajima M, Taniguchi N. 2006. Genetic evaluation of interindividual relatedness for broodstock management of the rare species barfin flounder Verasper moseri using microsatellite DNA markers. Fisheries Science 72: 33-39.
Palm S, Laikre L, Jorde PE, Ryman N. 2003. Effective population size and temporal genetic change in stream resident brown trout (Salmo trutta, L.). Conservation Genetics 4: 249–264.
Park C, Li Q, Kobayashi T, Kijima A. 2006. Inbreeding depression traits in Pacific abalone Haliotis discus hannai by factorial mating experiments. Fisheries Science 72: 774-780.
Pashley CH, Ellis JR, Mccauley DE, Burke JM. 2006. EST Databases as a Source for Molecular Markers: Lessons from Helianthus. Journal of Heredity 97:381-388.
Peel D, Ovenden JR, Peel SL. 2004. Neestimator: software for estimating effective population size, Queensland Government, Department of Primary Industries and Fisheries, Brisbane, Australia, version 12.
Perdue J, Erickson G. 1984. A comparison of the gametogenetic cycle between the Pacific oyster Crassostrea gigas and the suminoe oyster Crassostrea rivularis in Washington state, Aquaculture 37: 231–237.
Perez-Enriquez R, Takagi M, Taniguchi N. 1999. Genetic variability and pedigree tracing of a hatchery-reared stock of red sea bream (Pagrus major) used for stock enhancement, based on microsatellite DNA markers. Aquaculture 173: 413-423.
Picoult-Newberg L, Ideker TE, Pohl MG, Taylor SL, Donaldson MA, Nickerson DA, Boyce-Jacino M. 1999. Mining SNPs from EST databases. Genome Research 9:167-174.
Porta J, Porta JM, Martinez-Rotriguez G, Alvarez MDC. 2006. Development of a microsatellite multiplex PCR for Senegalese sole (Solea senegalensis) and its application to broodstock management. Aquaculture 56: 159–166.
Prudence M, Moal J, Boudry P, Daniel JY, QuéréC, Jeffroy F. 2006. An amylase gene polymorphism is associated with growth differences in the Pacific cupped oyster Crassostrea gigas. Animal Genetics 37:348-351.
Qin YJ, Liu X, Zhang HB, Zhang GF, Guo XM. 2007a. Genetic mapping of size-related quantitative trait loci (QTL) in the bay scallop (Argopecten irradians) using AFLP and microsatellite markers. Aquaculture 272: 281-290.
Qin YJ, Liu X, Zhang HB, Zhang GF, Guo XM. 2007b. Identification and Mapping of Amplified Fragment Length Polymorphism Markers Linked to Shell Color in Bay Scallop, Argopecten irradians irradians (Lamarck, 1819). Marine Biotechnology 9, 66-73.
Qin YJ, Liu X, Zhang HB, Zhang GF. 2007c. Effect of parental stock size on F1 genetic structure in the bay scallop, Argopecten irradians (Lamarck, 1819). Aquaculture Research 38: 174-181.
Queller DC, Goodnight KF. 1989. Estimating relatedness using genetic markers. Evolution 43:258-275.
Park C, Li Q, Kobayashi T, Kijima A. 2006. Inbreeding depression traits in Pacific abalone Haliotis discus hannai by factorial mating experiments. Fisheries Science 72: 774-780.
Perez-Enriquez R, Takagi M, Taniguchi N. 1999. Genetic variability and pedigree tracing of a hatchery-reared stock of red sea bream (Pagrus major) used for stock enhancement, based on microsatellite DNA markers. Aquaculture 173: 413-423.
Pollak E. 1977. Effective population numbers and their interrelations. Proceedings of the Washington State University Conference on Biomathematics and Biostatistics, pp. 115-144.
Department of Pure and Applied Mathematics, Washington State University, Spokane, WA. Primack RB. 1998. The problems of small populations. Essentials of Conservation Biology. Pages 253-276. Sinauer Associates, Sunderland, MA.
Rafalski JA. 2002. Application of single nucleotide polymorphisms in crop genetics. Current Opinion in Plant Biology 5:94-100.
Rakitin A, Ferguson MM, Trippel EA. 1999. Sperm competition and fertilization success in Atlantic cod (Gadus morhua): effect of sire size and condition factor on gamete quality. Canadian Journal of Fisheries and Aquatic Sciences 56: 2315-2323.
Raymond M, Rousset F. 1995. Population genetics software for exact tests and ecumenicism. Journal of Heredity 86: 248-249.
Rice RW. 1989. Analyzing tables of statistical tests. Evolution 43: 223-225.
Roberts S, Romano C, Gerlach G. 2005. Characterization of EST derived SSRs from the bay scallop, Argopecten irradians. Molecular Ecology Notes 5:567-568.
Robison BD, Wheeler PA, Sundin K, Sikka P, Thorgaard GH. 2001. Composite interval mapping reveals a major locus influencing embryonic development rate in rainbow trout (Oncorhynchus mykiss). Journal of Heredity 92: 16–22.
Ryman N, Stahl G. 1980. Genetic changes in hatchery stocks of brown trout (Salmo trutta). Canadian Journal of Fisheries and Aquatic Sciences 37: 82-87.
Sachidanandam R, Weissman D, Schmidt SC, Kakol JM, Stein LD, Marth G, Sherry S, Mullikin JC, Mortimore BJ, Willey DL, Hunt SE, Cole CG, Coggill PC, Rice CM, Ning Z, Rogers J, Bentley DR, Kwok PY, Mardis ER, Yeh RT, Schultz B, Cook L, Davenport R, Dante M, Fulton L, Hillier L, Waterston RH, McPherson JD, Gilman B, Schaffner S,. Van EWJ, ReichD, Higgins J, Daly MJ, Blumenstiel B, Baldwin J, Stange-Thomann N, Zody MC, Linton L, Lander ES, Altshuler D. 2001. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409:928-933.
Sakamotoa T, Danzmanna RG, Okamotob N, Fergusona MM, Ihssen1 PE. 1999 Linkage analysis of quantitative trait loci associated with spawning time in rainbow trout (Oncorhynchus mykiss). Aquaculture 173: 33–43.
Samain JF, McCombie H. 2008. Summer mortality of Pacific Oyster Crassostrea gigas. Versailles, France.
Sato M, Kawamata K, Zaslavskaya N, Nakamura A, Ohta T, Nishikiori T, Brykov V, Nagashima K. 2005. Development of microsatellite markers for Japanese scallop (Mizuhopecten yessoensis) and their application to a population genetic study. Marine Biotechnology 7: 713-728.
Sauvage C, Bierne N, Lapègue S, Boudry P. 2007. Single Nucleotide polymorphisms and their relationship to codon usage bias in the Pacific oyster Crassostrea gigas. Gene 406:13-22.
Sauvage C, Boudry P, De Koning DJ, Haley CS, Heurtebise S, Lapègue S. 2010. Quantitative Trait Loci for resistance to summer mortality and OsHV1 load in the Pacific oyster (Crassostrea gigas). Animal Genetics 41: 390–399.
Sauvage C, Boudry P, Lapègue S. 2009. Identification and characterization of 18 novel polymorphic microsatellite makers derived from expressed sequence tags in the Pacific oyster Crassostrea gigas. Molecular Ecology Resources 9: 853–855.
Sekino M, Saitoh K, Yamada T, Kumagai A, Hara M, Yamashita Y. 2003. Microsatellite-based pedigree tracing in a Japanese flounder Paralichthys olivaceus hatchery strain: implications for hatchery management related to stock enhancement program. Aquaculture 221: 255-263.
Sellos D, Moal J, Degremont L, Huvet A, Daniel JY, Nicoulaud S, Boudry P, Samain JF, Wormhoudt AV. 2003. Structure of amylase genes in populations of Pacific cupped oyster (Crassostrea gigas): tissue expression and allelic polymorphism. Marine Biotechnology 5: 360-72.
Shields DC, Sharp PM, Higgins DG, Wright F. 1988.‘Silent’sites in Drosophila genes are not neutral: evidence of selection among synonymous codons. Molecular Biology and Evolution 5:704-716.
Signorovitch J, Nielsen R. 2002. PATRI– paternity inference using genetic data. Bioinformatics 18: 341–342.
Smith BR, Herbinger CM, Merry HR. 2001. Accurate partition of individuals into full-sib families from genetic data without parental information. Genetics 158: 1329-1338.
Song L, Xu W, Li C, Li H, Wu L, Xiang J, Guo X. 2006. Development of Expressed Sequence Tags from the Bay Scallop, Argopecten irradians irradians. Marine Biotechnology 8:161-169.
Stenico MA, Lloyd T, Sharp PM. 1994. Codon usage in Caenorhabditis elegans: delineation of translational selection and mutational biases. Nucleic Acids Research 22: 2437-2446.
Stockley P, Gage MJG, Parker GA, M?ller AP. 1997. Sperm competition in fishes: the evolution of testis size and ejaculate characteristics. American Naturalist 149: 933-954.
Sugama K, Taniguchi N, Umeda S. 1988. An experimental study on genetic drift in hatchery population of red sea bream. Nippon Suisan Gakkaishi 54: 739-744.
Sun B, Liu X, Zhang G, Zheng H, Guo X. 2006. Molecular verification of fertilization between bay scallop individuals. Journal of Fisheries of China 30: 713-719.
Syvanen AC. 2001. Accessing genetic variation: genotyping single nucleotide polymorphisms. Nature Reviews Genetics 2:930-942.
Taggart JB. 2007. FAP: an exclusion-based parental assignment program with enhanced predictive functions. Molecular Ecology Notes 7: 412-415.
Tallmon DA, Koyuk A, Luikart G, Beaumont MA. 2008. ONeSAMP: a program to estimate effective population size using approximate Bayesian computation. Molecular Ecology Resources 8: 299-301.
Tanguy A, Bierne N, Saavedra C, Pina B, Bachère E, Kube M, Bazin E, Bonhomme F, Boudry P, Boulo V, Boutet I, Cancela L, Dossat C, Favrel P, Huvet A, Jarque S, Jollivet D, Klages S, Lapègue S, Leite R, Moal J, Moraga D, Reinhardt R, Samain JF, Zouros E, Canario A. 2008.
Increasing genomic information in bivalves through new EST collections in four species: Development of new genetic markers for environmental studies and genome evolution. Gene 408: 27-36.
Taniguchi N, Sumantadinata K, Iyama S. 1983. Genetic change in the first and second generations of hatchery stock of black sea bream. Aquaculture 35: 309-320.
Taris N, Baron S, Sharbel TF, Sauvage C, Boudry P. 2005. A combined microsatellite multiplexing and boiling DNA extraction method for high throughput parentage analyses in the Pacific Oyster (Crassostrea gigas). Aquaculture Research 36: 516-518.
Taris N, Ernande B, McCombie H, Boudry P. 2006. Phenotypic and genetic consequences of size selection at the larval stage in the Pacific oyster (Crassostrea gigas). Journal of Experimental Marine Biology and Ecology 333: 147-158.
Tautz D. 1989. Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Research 17: 6463-6471.
Tave D. 1993. Genetics for Fish Hatchery Managers, 2nd edition. Kluwer Academic Publishers, Boston.
Toro JE, Montoya MP, Martínez V, Gutiérrez D, Vergara AM. 2010. Consequences of self-fertilization on the growth rate and survival of Argopecten purpuratus. Archivos de Medicina Veterinaria 42: 63-70.
Tregenza T, Wedell N. 2002. Polyandrous females avoid costs of inbreeding. Nature 415: 71-73.
Umashankar V, Arunkumar V, Dorairaj S. 2007. ACUA: A software tool for automated codon usage analysis. Bioinformation 2: 62-63.
Useche FJ, Gao G, Harafey M, Rafalski A. 2001. High-throughput identification, database storage and analysis of SNPs in EST sequences. Genome Informatics 12: 194-203.
Varshney RK, Graner A, Sorrells ME. 2005. Genic microsatellite markers in plants: features and applications. Trends in Biotechnology 23:48-55.
Vignal A, Milan D, SanCristobal M, Eggen A. 2002. A review on SNP and other types of molecular markers and their use in animal genetics. Genetics Selection Evolution 34: 275-305.
Waldbieser GY, Wolters WR. 1999. Application of polymorphic microsatellite loci in a channel catfish Zctalurus punctatus breeding program. Journal of the World Aquaculture Society 30: 256-262.
Wang J. 2001. A pseudo-likelihood method for estimating effective population size from temporally spaced samples. Genetical Research 78: 243-257.
Wang J. 2004. Sibship reconstruction from genetic data with typing errors. Genetics 166: 1963.
Wang J. 2005. Estimation of effective population sizes from data on genetic markers. Philosophical Transactions of the Royal Society B 360: 1395-1409.
Wang J. 2009. A new method for estimating effective population size from a single sample of multilocus genotypes. Molecular Ecology 18: 2148-2164.
Wang J, Whitlock MC. 2003. Estimating effective population size and migration rates from genetic samples over space and time. Genetics 163: 429-446.
Wang JL. 2004. Sibship reconstruction from genetic data with typing errors. Genetics 166: 1963–1979.
Wang LL, Song LS, Xu W, Zhang H. 2006. Screening microsatellite markers from EST sequences of bay scallop Argopecten irradians. High Technology Letters 12: 97-102.
Wang L, Song L, Zhang H, Gao Q, Guo X. 2007. Genetic linkage map of bay scallop, Argopecten irradians irradians (Lamarck 1819). Aquaculture Research 38: 409-419.
Wang Y, Guo X. 2008. Mapping disease-resistance genes in the eastern oyster (Crassostreavirginica). Journal of Shellfish Research 27:1061-1062.
Waples RS, Do C. 2008. LdNe: a program for estimating effective population size from data on linkage disequilibrium. Molecular Ecology Resources 8: 753-756.
Williams RN, DeWoody JA. 2009. Reproductive Success and Sexual Selection in Wild Eastern Tiger Salamanders (Ambystoma t. tigrinum). Evolutionary Biology 36: 201-213.
Wilson K, Li Y, Whan V, Lehnert S, Byrne K, Moore S, Pongsomboon S, Tassanakajon A, Rosenberg G, Ballment E, Fayazi Z, Swan J, Kenway M, Benzie J. 2002. Genetic mapping of the black tiger shrimp Penaeus monodon with amplified fragment length polymorphism. Aquaculture 204: 297-309.
Wright S. 1931. Evolution in Mendelian populations. Genetics 16: 97-159.
Winkler FM, Estévez B F. 2003. Effects of self-fertilization on growth and survival of larvae and juveniles of the scallop Argopecten purpuratus L. Journal of Experimental Marine Biology and Ecology 292: 93-102.
Wray NR, Thompson R. 1990. Prediction of rates of inbreeding in selected populations. Genetical Research 55: 41-54.
Wright S. 1922. Coefficients of inbreeding and relationship. The American Naturalist 56: 330-338.
Xu Z, Primavera JP, Pena LD, Pettit P, Belak J, Alcivar-warren, A. 2001. Genetic diversity of wild and cultured Black Tiger Shrimp (Penaeus monodon) in the Philippines using microsatellites. Aquaculture 199: 13-40.
Ye S, Dhillon S, Ke X, Collins AR, Day IN. 2001. An efficient procedure for genotyping single nucleotide polymorphisms. Nucleic Acids Research 29: e88.
You FM, Huo N, Gu YQ, Luo M, Ma Y, Hane D, Lazo GR, Dvorak J, Anderson OD. 2008.
BatchPrimer3: A high throughput web application for PCR and sequencing primer design. BMC Bioinformatics 9:253.
Young WP, Wheeler PA, Coryell VH, Keim P, Thorgaard GH. 1998. A detailed linkage map of rainbow trout produced using doubled haploids. Genetics 148: 1-13.
Yu H, Li Q. 2007a. EST-SSR markers from the Pacific oyster, Crassostrea gigas. Molecular Ecology Notes 7: 860-862.
Yu H, Li Q. 2007b. Genetic variation of wild and hatchery populations of the Pacific oyster Crassostrea gigas assessed by microsatellite markers. Journal of Genetics and Genomics 34:1114-1122.
Yu H, Li Q. 2008. Exploiting EST Databases for the Development and Characterization of EST–SSRs in the Pacific Oyster (Crassostrea gigas). Journal of Heredity 99(2): 208-214.
Yu Z, Guo X. 2003. Genetic linkage map of the eastern oyster Crassostrea virginica Gmelin. The Biological Bulletin 204: 327-338.
Yu Z, Guo X. 2006. Identification and mapping of disease-resistance QTLs in the eastern oyster, Crassostrea virginica Gmelin. Aquaculture. 254: 160-170.
Zabeau M, Vos P. 1993. Selective restriction fragment amplification: a general method for DNA fingerprinting. European Patent Application number: 92402629.
Zar JH. 1999. Paired-sample hypotheses, In: Zar, J.H. (Ed.), Biostatistical Analysis. Pages 161-176. 4th ed. Prentice Hall, New Jersey.
Zhan AB, Bao ZM, Wang XL, Hu JJ. 2005. Microsatellite markers derived from bay scallop Argopecten irradians expressed sequence tags. Fisheries Science 71: 1341-1346.
Zhan A, Hu J, Hu X, Hui M, Wang M, Peng W, Huang X, Wang S, Lu W, Sun C, Bao Z. 2009.
Construction of microsatellite-based linkage maps and identification of size-related quantitative trait loci for Zhikong scallop (Chlamys farreri). Animal Genetics 40: 821-831.
Zhang FS. 2003. China aquaculture industry development in modern times and contemporary age: status and prospects. World Sci-Tech R & D 25: 5-13 (in Chinese).
Zhang FS, He Y, Liu X, Ma J, Li S. 1986. A report on the introduction, spat-rearing and experimental culture of bay scallop, Argopecten irradians Lamarck. Oceanologia et Limnologia Sinica 17: 367-374 (in Chinese).
Zhang GF, Liu SX, and X. Liu. 2003. Self-fertilization family establishment in bay scallop Argopecten irradians. Journal of Fisheries Sciences of China10: 441-445 (in Chinese).
Zhang L, Guo X, Bushek D, Ford S. 2008. Mapping quantitative trait loci conferring dermo resistance in the eastern oyster Crassostrea virginica. Journal of Shellfish Research 27: 1067-1067.
Zhdanova OL, Pudovkin AI. 2008. Nb_HetEx: a program to estimate the effective number of breeders. Journal of Heredity 99:694-695.
Zheng H, Zhang G, Guo X, Liu X. 2008. Inbreeding depression for various traits in two cultured populations of the American bay scallop, Argopecten irradians irradians Lamarck (1819) introduced into China. Journal of Experimental Marine Biology and Ecology 364: 42-47.
宋林生,常亚青.用RAPD技术对我国栉孔扇贝野生种群与养殖群体的遗传结构及其遗传分化的研究.高技术通讯,2002,12(7):83-86.
于红.牡蛎良种选育的遗传学基础研究:[博士学位论文].青岛:中国海洋大学,2010
张振.基于微卫星和SNP标记的皱纹盘鲍遗传连锁图谱及其应用: [博士学位论文].青岛:中国科学院海洋研究所,2010
Aide TM. 1986. The influence of wind and animal pollination on variation in outcrossing rates. Evolution 40: 434-435.
Allendorf FW, Phelps SR. 1980. Loss of genetic variation in a hatchery stock of cutthroat trout. Transactions of the American Fisheries Society 109: 537-543.
Allendorf FW, Leary RF. 1986. Heterozygosity and fitness in natural populations of animals. Pages 57-76 in M. E. Soulé, editor. Conservation biology: The science of scarcity and diversity. Sinauer Associates, Sunderland, Massachusetts.
An HS, Park JY, Lee YG, Lee DS, Lee C. 2005. Ten polymorphic microsatellite loci in the giant scallop (Mizuhopecten yessoensis). Molecular Ecology Notes 5: 806-808.
An HY, PARK JY. 2005. Ten new highly polymorphic microsatellite loci in the blood clam Scapharca broughtonii. Molecular Ecology Notes 5: 896-898.
Anderson EC. 2005. An efficient Monte Carlo method for estimating Ne from temporally spaced samples using a coalescent-based likelihood method. Genetics 170: 955-967.
Anderson EC, Garza JC. 2006. The power of single nucleotide polymorphisms for large-scale parentage inference. Genetics 172:2567-2582.
Anderson EC, Williamson EG, Thompson EA. 2000. Monte Carlo evaluation of the likelihood for Ne from temporally spaced samples. Genetics 156: 2109-2118.
Andersson M. 1994. Sexual Selection. Princeton University Press, Princeton.
Araki H, Waples RS, Ardren WR, Cooper B, Blouin M.S. 2007. Effective population size of steelhead trout: influence of variance in reproductive success, hatchery programs, and genetic compensation between life-history forms. Molecular Ecology 16: 953-966.
Bardach JE, Ryther JH, McLarney WO. 1972. Aquaculture. The farming and husbandry of freshwater and marine organisms. Wiley-Interscience, New York.
Bateman AJ. 1948. Intrasexual selection in Drosophila. Heredity 2: 349-368.
Beaumont AR. 1986. Genetics aspects of hatchery rearing of the scallop Pecten maximus (L.).Aquaculture 57: 99-110.
Beaumont AR, Hoare K. 2003. Biotechnology and Genetics in Fisheries and Aquaculture. 170 pp. Blackwell Publishing, United Kingdom.
Beaumont MA. 2003. Estimation of population growth or decline in genetically monitored populations. Genetics 164:1139–1160.
Bekkevold D, Hansen MW, Loeschcke V. 2002. Male reproductive competition in spawning aggregations of cod (Gadus morhua L.). Molecular Ecology 11: 91-102.
Beninger PG., Le Pennec M. 1991. Functional anatomy of scallops. Pages 133-224 in S. E. Shumway, editor. Scallops: Biology, Ecology and Aquaculture. Elsevier, Amsterdam, The Netherlands.
Bentsen HB, Olesen I. 2002. Designing aquaculture mass selection programs to avoid high inbreeding rates. Aquaculture 204: 349–359.
Bernatchez L, Duchesne P. 2000. Individual-based genotype analysis in studies of parentage and population assignment: how many loci, how many alleles? Canadian Journal of Fisheries and Aquatic Sciences 57: 1-12.
Berthier P, Beaumont MA, Cornuet J-M, Luikart G. 2002. Likelihood-based estimation of the effective population size using temporal changes in allele frequencies: a genealogical approach. Genetics 160: 741-751.
Bijma P. 2000. Long term genetic contributions. Prediction of rates of inbreeding and genetic gain in selected populations. PhD thesis. Pages 205-206. Animal Breeding and Genetics Group, Wageningen University, The Netherlands.
Blouin MS. 2003. DNA-based methods for pedigree reconstruction and kinship analysis in natural populations. Trends in Ecology and Evolution 18: 503-511.
Blouin MS, Parsons M, Lacaille V, Lotz S. 1996. Use of microsatellite loci to classify individuals by relatedness. Molecular Ecology 5: 393-401.
Boessenkool S, Star B, Seddon PJ, Waters JM. 2010. Temporal genetic samples indicate small effective population size of the endangered yellow-eyed penguin. Conservation Genetics 11: 539-546.
Boudry P, Collet B, Cornette F, Hervouet V, Bonhomme F. 2002. High variance in reproductive success of the Pacifc oyster (Crassostrea gigas, Thunberg) revealed by microsatellite-based parentage analysis of multifactorial crosses. Aquaculture 204: 283–296.
Brawn VM. 1961. Reproductive behaviour of the cod (Gadus callarias L.). Behaviour 18: 177-197.
Brazeau DA, Gleason DF, Morgana ME. 1998. Self-fertilization in brooding hermaphroditicCaribbean corals: Evidence from molecular markers. Journal of Experimental Marine Biology and Ecology 231: 225-238.
Bretman A, Wedell N, Tregenza T. 2004. Molecular evidence of post-copulatory inbreeding avoidance in the field cricket Gryllus bimaculatus. Proceedings of the Royal Society B 271: 159-164.
Brown RC, Woolliams JA, McAndrew BJ. 2005. Factors influencing effective population size in commercial populations of gilthead seabream, Sparus aurata. Aquaculture 247: 219-225.
Caballero A. 1994. Developments in the prediction of effective population size. Heredity 73: 657-679.
Camara MD, Evans S, Langdon CJ. 2008. Parental relatedness and survival of Pacific Oysters from a naturalized population. Journal of Shellfish Research 27(2): 323–336.
Cervantes I, Pastor JM, Gutiérrez JP, Goyache F, Molina A. 2011. Computing effective population size from molecular data: The case of three rare Spanish ruminant populations. Livestock Science doi:10.1016/j.livsci.2010.12.027
ChagnéD, Gasic K, Crowhurst RN, Han Y, Bassett H, Bowatte DR, Lawrence TJ, Rikkerink EHA, Gardiner SE, Korban SS. 2008. Development of a set of SNP markers present in expressed genes of the apple. Genomics 92:353-358.
Chapuis MP, Estoup A. 2007. Microsatellite null alleles and estimation of population differentiation. Molecular Biology and Evolution 24(3): 621–631.
Charbonnel N, Rasatavonjizay R, Sellin E, Brémond P, Jarne P. 2005. The influence of genetic factors and population dynamics on the mating system of the hermaphroditic freshwater snail Biomphalaria pfeifferi. Oikos 108: 283-296.
Charlesworth D. 2006. Evolution of plant breeding systems. Current Biology 16: 726-735.
Charlesworth D, Morgan MT, Charlesworth B. 1990. Inbreeding depression, genetic load, and the evolution of outcrossing rates in a multilocus system with no linkage. Evolution 44: 1469-1489.
Chiapparino E, Lee D, Donini P. 2004. Genotyping single nucleotide polymorphisms in barley by tetra-primer ARMS-PCR. Genome 47:414-420.
Clutton-Brock TH. 1989. Mammalian mating systems. Proceedings of the Royal Society B 236: 339-372.
Cnaani A, Hallerman EM, Ron M, Weller JI, Indelman M, Kashi Y, Gall GAE, Hulata G. 2003. Detection of a chromosomal region with two quantitative trait loci, affecting cold tolerance and fish size, in an F2 tilapia hybrid. Aquaculture, 223:117-128.
Correa C, Thiel M. 2003. Mating systems in caridean shrimp (Decapoda: Caridea) and theirevolutionary consequences for sexual dimorphism and reproductive biology. Revista Chilena de Historia Natural 76: 187-203.
Cross TF, King J. 1983. Genetic effects of hatchery rearing in Atlantic salmon. Aquaculture 33: 33-40.
Crow JF, Denniston C. 1988. Inbreeding and variance effective population numbers. Evolution 42: 482-495.
Crow JF, Kimura M. 1970. An Introduction to Population Genetics Theory. 591 pp. Harper and Row, New York.
Dantec LL, ChagnéD, Pot D, Cantin O, Garnier-Ger P, Bedon F, Frigerio JM, Chaumeil P, Leger P, Garcia V, Laigret F, Daruvar A, Plomion C. 2004. Automated SNP detection in expressed sequence tags: statistical considerations and application to maritime pine sequences. Plant Molecular Biology 54: 461-470.
Danzmann RG. 1997 PROBMAX: a computer program for assigning unknown parentage in pedigree analysis from known genotypic pools of parents and progeny. Journal of Heredity 88, 333.
Danzmann RG, Ferguson MM, Allendorf FW. 1989. Genetic variability and components of fitness in hatchery strains of rainbow trout. Journal of Fish Biology 35: 313-319.
Dégremont L, Bédier E, Boudry P. 2010. Summer mortality of hatchery-produced Pacific oyster spat (Crassostrea gigas). II. Response to selection for survival and its influence on growth and yield. Aquaculture 299: 21-29.
Dégremont L, Ernande B, Bédier E, Boudry P. 2007. Summer mortality of hatchery-produced Pacific oyster spat (Crassostrea gigas). I. Estimation of genetic parameters for survival and growth. Aquaculture 262: 41–53.
Department of Fisheries, 2005. China Fisheries Statistic Yearbook 2004. China Agriculture Press, Beijing (in Chinese).
Desrosiers RR, Gerard A, Peignon JM, Naciri Y, Dufresne L, Morasse J, Ledu C, Phelipot P, Guerrier P, Dube F. 1993. A novel method to produce triploids in bivalve molluscs by the use of 6-dimethylaminopurine. Journal of Experimental Marine Biology and Ecology 170: 29–43.
DeWoody JA, Avise JC. 2001. Genetic perspectives on the natural history of fish mating systems. Journal of Heredity 92: 167-172.
Dong SR, Kong J, Zhang TS, Meng XH, Wang RC. 2006. Parentage determination of Chinese shrimp (Fenneropenaeus chinensis) based on microsatellite DNA markers. Aquaculture 258: 283-288.
Duchesne P, Castric T, Bernatchez L. 2005. PASOS (parental allocation of singles in open systems): a computer program for individual parental allocation with missing parents. Molecular Ecology Notes 5: 701–70.
Duchesne P, Godbout M-H, Bernatchez L. 2002. PAPA (package for the analysis of parental allocation): a computer program for simulated and real parental allocation. Molecular Ecology Notes 2: 191-193.
Duret L, Mouchiroud D. 1999. Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis. Proceedings of the National Academy of Sciences 6:4482-4487.
Emery AM, Wilson IJ, Craig S, Boyle PR, Noble LR. 2001. Assignment of paternity groups without access to parental genotypes: multiple mating and developmental plasticity in squid. Molecular Ecology 10: 1265–1278.
Evans BS, Knauer J, Tayler JJU, Jerry DR. 2006. Development and characterization of six new microsatellite markers for the silver- or gold-lipped pearl oyster, Pinctada maxima (Pteriidae). Molecular Ecology Notes 6: 835-837.
Evans F, Matson S, Brake J, Langdon C. 2004. The effects of inbreeding on performance traits of adult Pacific oysters (Crassostrea gigas). Aquaculture 230: 89-98.
Evans S, Langdon C. 2006. Effects of genotype×environment interactions on the selection of broadly adapted Pacific oysters (Crassostrea gigas). Aquaculture 261: 522–534.
FAO, 2010. World aquaculture production of fish, crustaceans, molluscs, etc., by principal species (ftp://ftp.fao.org/fi/STAT/summary/default. htm#aqua).
Falconer DS. 1989. Introduction to Quantitative Genetics. 3rd edn. Longman, England.
Falconer DS, Mackay TFC. 1996. Introduction to quantitative genetics, 4th edition. Prentice Hall, Harlow.
Fessehaye Y, El-bialy Z, Rezk MA, Crooijmans R, Bovenhuis H, Komen H. 2006. Mating systems and male reproductive success in Nile tilapia (Oreochromis niloticus) in breeding hapas: A microsatellite analysis. Aquaculture 256: 148-158.
Fisher RA. 1930. The genetical theory of natural selection. Clarendon Press, Oxford, United Kingdom.
Frankham R. 1995. Effective population size, adult population size ratios in wildlife—a review. Genetical Research 66: 95-107.
Gaffney PM. Scott TM. 1984. Genetic heterozygosity and production traits in natural and hatchery populations of bivalves. Aquaculture 42: 289-302.
Gaffney PM, Davis CV, Hawes RO. 1992. Assessment of drift and selection in hatcherypopulations of oysters (Crassostrea virginica). Aquaculture 105: 1-20.
Gall GAE. 1987. Inbreeding, in: Ryman, N. Utter, F. (Eds.), Population genetics and Fisheries Management. Washington Sea Grant Program, Univ. Washington Press, Seattle, USA, pp. 47-87.
Garant D, Dodson JJ, Bernatchez L. 2001. A genetic evaluation of mating system and determinants of individual reproductive success in Atlantic salmon (Salmo salar L.). Journal of Heredity 92: 137-145.
Garner TWJ, Schmidt BR. 2003. Relatedness, body size and paternity in the alpine newt, Triturus alpestris. Proceedings of the Royal Society B 270: 619-624. Gheyas AA, Woolliams JA, Taggart B, Sattar MA, Das TK, McAndrew BJ, Penman DJ. 2009.
Heritability estimation of silver carp (Hypophthalmichthys molitrix) harvest traits using microsatellite based parentage assignment. Aquaculture 294: 187-193.
Gjerde B. 1993. Breeding and selection. In: Heen, K., Monahan, R.L., Utter, F. (Eds.), Salmon Aquaculture. Fishing News Books, Cambridge USA, pp. 187-208.
Goldstein D, Schlotterer C. 1999. Microsatellites: Evolution and Applications. Oxford University Press, Oxford, UK.
Goodnight KF, Queller DC. 1999. Computer software for performing likelihood tests of pedigree relationship using genetic markers. Molecular Ecology 8: 1231–1234.
Goudet J. FSTAT, a Program to Estimate and Test Gene Diversities and Fixation Indices Version 2.9.3. 2001. http://www2.unil.ch/popgen/softwares/fstat.htm Updated from Goudet (1995).
Grantham R, Gautier C, Gouy M, Mercier R, Pave A. 1980. Codon catalog usage and the genome hypothesis. Nucleic Acids Research 8:r49-r62.
Guo X, Ford S, Zhang F. 1999. Molluscan aquaculture in China. Journal of Shellfish Research 18:19-31.
Guo X, Standish K, Allen JR. 1994. Reproductive potential and genetics of triploid Pacific oysters, Crassostrea gigas (Thunberg). The Biological Bulletin 187: 309–318.
Gupta PK, Roy JK, Prasad M. 2001 Single nucleotide polymorphisms: a new paradigm for molecular marker technology and DNA polymorphism detection with emphasis on their use in plants. Current Science 80:524-535.
Hadfield JD, Richardson DS, Burke T. 2006. Towards unbiased parentage assignment: combining genetic, behavioural and spatial data in a Bayesian framework. Molecular Ecology 15: 3715–3730.
Hara M, Sekino M. 2003. Efficient detection of parentage in a cultured Japanese flounder Paralichthys olivaceus using microsatellite DNA marker. Aquaculture 217: 107-114.
Harper FM, Hart MW. 2005. Gamete compatibility and sperm competition affect paternity and hybridization between sympatric Asterias sea stars. The Biological Bulletin 209: 113-126.
Hatanaka A, Yamada S, Sakamoto T, Mitsuboshi T. 2006. Isolation and application of microsatellite DNA markers for pedigree tracing of seedlings of red sea bream (Pagrus major). Journal of the World Aquaculture Society 37: 139-143.
Hauser L, Adcock GJ, Smith PJ, Bernal Ram?rez JH, Carvalho GR. 2002. Loss of microsatellite diversity and low effective population size in an overexploited population of New Zealand snapper (Pagrus auratus). Proceedings of the National Academy of Sciences 99: 11742-11747.
Hayes B, Laerdahl JK, Lien S, Moen T, Berg P, Hindar K., Davidson WS, Koop BF, Adzhubei A, H?yheim B. 2007. An extensive resource of single nucleotide polymorphism markers associated with Atlantic salmon (Salmo salar) expressed sequences. Aquaculture 265:82-90.
Hedgecock D. 1994. Does variance in reproductive success limit effective population sizes of marine organisms? Pages 122-134 in A. R. Beaumont, editor. Genetics and Evolution of Aquatic Organisms. Chapman and Hall, London, UK.
Hedgecock D, Launey S, Pudovkin AI, Naciri YLS, Bonhomme F. 2007. Small effective number of parents (Nb) inferred for a naturally spawned cohort of juvenile European flat oysters Ostrea edulis. Marine Biology 150: 1173-1182.
Hedgecock D, Sly F. 1990. Genetic drift and effective population sizes of hatchery-propagated stocks of the Pacific oyster, Crassostrea gigas. Aquaculture 88: 21-38.
Hedrick PW. 2000. Genetics of Populations, 2nd ed. Jones and Bartlett Publishers, London, UK.
Herbinger CM, Doyle RW, Pitman ER, Paquet D, Mesa KA, Morris DB, Wright JM, Cook D. 1995. DNA fingerprint based analysis of paternal and maternal effects on offspring growth and survival in communally reared rainbow trout. Aquaculture 137: 245-256.
Hubert S, Hedgecock D. 2004. Linkage maps of microsatellite DNA markers for the Pacific oyster Crassostrea gigas. Genetics 168:351-362.
Hutchings JA, Bishop TD, McGregor-Shaw CR. 1999. Spawning behaviour of Atlantic cod, Gadus morhua: evidence of mate competition and mate choice in a broadcast spawner. Canadian Journal of Fisheries and Aquatic Sciences 56: 97-104.
Huvet A, Boudry P, Ohresser M, Delsert C, Bonhomme F. 2000. Variable microsatellites in the Pacific Oyster Crassostrea gigas and other cupped oyster species. Animal Genetics 31: 71-72.
Huvet A, Jeffroy F, Fabioux C, Daniel JY, Quillien V, Van Wormhoudt A. 2008. Association among growth, food consumption-related traits and amylase gene polymorphism in thePacific oyster Crassostrea gigas. Animal Genetics 39: 662-665.
Ibarra AM, Cruz P, Romero BA. 1995. Effects of inbreeding on growth and survival of self-fertilized catarina scallop larvae, Argopecten circularis. Aquaculture 134: 37-47.
Jackson TR, Martin-Robichauda DJ, Reith ME. 2003. Application of DNA markers to the management of Atlantic halibut (Hippoglossus hippoglossus) broodstock. Aquaculture 220:245-259.
Jeffreys AJ, Wilson V, Thein SL. 1985. Hypervariable‘minisatellite’regions in human DNA. Nature 314: 67–73.
Jerry DR, Preston NP, Crocos PJ, Keys S, Meadows JRS, Li Y. 2004. Parentage determination of Kuruma shrimp Penaeus (Marsupenaeus) japonicus using microsatellite markers (Bate). Aquaculture 235: 237-247.
Johnson JA, Talbot SL, Sage GK, Burnham KK, Brown JW, Maechtle TL, Seegar WS, Yates MA, Anderson B, Mindell DP. 2010. The Use of Genetics for the Management of a Recovering Population: Temporal Assessment of Migratory Peregrine Falcons in North America. PLoS ONE 5: DOI: 10.1371/ journal.pone. 0014042.
Jones AG. 2001. GERUD1.0: a computer program for the reconstruction of parental genotypes from progeny arrays using multi-locus DNA data. Molecular Ecology Notes 1: 215–218.
Jones AG. 2005. GERUD2.0: a computer program for the reconstruction of parental genotypes from progeny arrays with known or unknown parents. Molecular Ecology Notes 5: 708–711.
Jones AG, Ardren WR. 2003. Methods of parentage analysis in natural populations. Molecular Ecology 12: 2511–2523.
Jones AG, Small CM, Paczolt KA, Ratterman NL. 2010. A practical guide to methods of parentage analysis. Molecular Ecology Resources 10: 6–30.
Jones OR, Wang J. 2010. COLONY: a program for parentage and sibship inference from multilocus genotype data. Molecular Ecology Resources 10: 551-555.
Jorde PE, Ryman N. 2007. Unbiased estimator for genetic drift and effective population size. Genetics 177:927-935.
Kalinowski ST, Taper ML, Marshall TC. 2007. Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Molecular Ecology 16: 1099–1106.
Kalinowski ST, Taper ML, Creel S. 2006a. Using DNA from noninvasive samples to identify individuals and census populations: an evidential approach tolerant of genotyping errors. Conservation Genetics 7: 319–329.
Kalinowski ST, Wagner AP, Taper ML. 2006b. ML-RELATE: a computer program for maximumlikelihood estimation of relatedness and relationship. Molecular Ecology Resources 6: 576-579.
Kanno Y, Vokoun JC, Letcher BH. 2010. Sibship reconstruction for inferring mating systems, dispersal and effective population size in headwater brook trout (Salvelinus fontinalis) populations. Conservation Genetics DOI: 10.1007/ s10592-010-0166-9.
Kim S, Misra A. 2007. SNP genotyping: technologies and biomedical applications. Annual Review of Biomedical Engineering 9: 289-320.
Kimura M, Crow JF. 1963. The measurement of effective population number. Evolution 17, 279-288.
Koehn RK, Diehl WJ, Scott TM. 1988. The different contribution by individual enzymes of glycolysis and protein catabolism to the relationship between heterozygosity and growth rate in the coot clam Milinia lateralis. Genetics 118: 121-130.
Koljonen ML, T?htinen J, S?is? M, Joskiniemi J. 2002. Maintenance of genetic diversity of Atlantic salmon (Salmo salar) by captive breeding programmes and the geographic distribution of microsatellite variation. Aquaculture 212: 69-92.
Konovalov DA, Manning C, Henshaw MT. 2004. KINGROUP: a program for pedigree relationship reconstruction and kin group assignment using genetic markers. Molecular Ecology Notes 4: 779–782.
Kota R, Varshney RK, Thiel T, Dehmer KJ, Graner A. 2001. Generation and comparison of EST-derived SSRs and SNPs in barley (Hordeum vulgare L.). Hereditas 135:145-151.
Krebs SL, Hancock JE. 1990. Early-acting inbreeding depression and reproductive success in the highbush blueberry, Vaccinium corymbosum L. Theoretical and Applied Genetics 79: 825-832.
Laing I, Earl NH. 1998. The lipid content, spatfall and subsequent growth of early and late settling hatchery-reared Pacific oyster, Crassostrea gigas Thunberg, larvae. Aquaculture Research 29: 19-25.
Lallias D, Taris N, Boudry P, Bonhomme F, Lapègue S. 2010. Variance in the reproductive success of flat oyster Ostrea edulis L. assessed by parentage analyses in natural and experimental conditions. Genetics Research 92:175-87.
Lande R, Barrowclough GF. 1987. Effective population size, genetic variation, and their use in population management. Pages 87-123. In: Soule, M. (Ed.), Viable Populations for Conservation. Cambridge University Press, Cambridge, UK.
Lande R, Schemske DW. 1985. The evolution of self-fertilization and inbreeding depression in plants: 1. Genetic models. Evolution 39: 24-40.
Lannan JE. 1980. Broodstock management of Crassostrea gigas: IV. Inbreeding and larval survival. Aquaculture 21: 353-356.
Lannan JE, Robinson A, Breese WP. 1980. Broodstock management of Crassostrea gigas II. Broodstock conditioning to maximize larval survival. Aquaculture 21: 337-345.
Landegren U, Nilsson M, Kwok PY. 1998. Reading bits of genetic information: methods for single-nucleotide polymorphism analysis. Genome Research 8: 769-776.
Langdon C, Evans F, Jacobson D, Blouin M. 2003. Yields of cultured Pacific oysters Crassostrea gigas Thunberg improved after one generation of selection. Aquaculture 220: 227–244.
Ledig FT. 1986. Heterozygosity, heterosis, and fitness in outbreeding plants. Pages 77-104 in M. E. Souléeditor. Conservation biology: The science of scarcity and diversity. Sinauer Associates, Sunderland, Massachusetts.
Li G, Hubert S, Bucklin K, Ribes V, Hedgecock D. 2003. Characterization of 79 microsatellite DNA markers in the Pacific oyster Crassostrea gigas. Molecular Ecology Notes 3: 228–232.
Li JJ, Li Q. 2008. Isolation and characterization of twelve novel microsatellite loci in the ark shell Scapharca broughtonii, Conservation Genetics 9: 1055-1057.
Li L, Guo X. 2004. AFLP-Based genetic linkage maps of the Pacific oyster Crassostrea gigas Thunberg. Marine Biotechnology 6: 26-36.
Li L, Guo XM, Zhang GF. 2009. Inheritance of 15 microsatellites in the Pacific oyster Crassostrea gigas: segregation and null allele identification for linkage analysis. Chinese Journal of Oceanology and Limnology 27: 74–79.
Li R, Li Q, Yu R. 2008. A set of polymorphic expressed sequence tag-derived microsatellites from the bay scallop, Argopecten irradians irradians, and their transportability in three other scallop species. Journal of the World Aquaculture Society 39: 138-141.
Li Q, Chen L, Kong L. 2009. A genetic linkage map of the sea cucumber, Apostichopus japonicus (Selenka), based on AFLP and microsatellite markers, Animal Genetics 40: 678-685.
Li Q, Kijima A. 2005. Segregation of microsatellite alleles in gynogenetic diploid Pacific abalone (Haliotis discus hannai). Marine Biotechnology 7:669–676.
Li Q, Liu SK, Kong LF. 2009. Microsatellites within genes and ESTs of the Pacific oyster Crassostrea gigas and their transferability in five other Crassostrea species. Electronic Journal of Biotechnology 12: DOI: 10.2225/vol12-issue3- fulltext-9.
Li Q, Park C, Kijima A. 2002. Isolation and characterization of microsatellite loci in the Pacific abalone, Haliotis discus hannai. Journal of Shellfish Research 21: 811-815.
Li Q, Park C, Kijima A. 2003. Allelic transmission of microsatellites and application to kinship analysis in newly hatched Pacific abalone larvae. Fisheries Science 69: 883-889.
Li Q, Park C, Kobayashi T, Kijima A. 2003. Inheritance of microsatellite DNA markers in the Pacific abalone Haliotis discus hannai. Marine Biotechnology 5:331-338.
Li Q, Xu KF, Yu RH. 2007. Genetic variation in Chinese hatchery populations of the Japanese scallop (Patinopecten yessoensis) inferred from microsatellite data, Aquaculture 269: 211-219.
Li Q, Yu H, Yu RH. 2006. Genetic variability assessed by microsatellites in cultured populations of the Pacific oyster (Crassostrea gigas) in China. Aquaculture 259: 95–102.
Li RH, Li Q, Yu RH. 2009. Parentage determination and effective population size estimation in mass spawning Pacific oyster, Crassostrea gigas, based on microsatellite analysis. Journal of the World Aquaculture Society 40: 667–677.
Li Y, Byrne K, Miggiano E, Whan V, Moore S, Keys S, Crocos P, Preston N, Lehnert S. 2003. Genetic mapping of the kuruma prawn Penaeus japonicus using AFLP markers. Aquaculture 219: 143-156.
Lind CE, Evans BS, Knauer J, Taylor JJU, Jerry DR. 2009. Decreased genetic diversity and a reduced effective population size in cultured silver-lipped pearl oysters (Pinctada maxima). Aquaculture 286: 12-19.
Liu ZJ, Tan G, Li P, Dunham RA. 1999. Transcribed dinucleotide microsatellites and their associated genes from channel catfish, Ictalurus punctatus. Biochemical and Biophysical Research Communications 259: 190–194.
Luikart G, Ryman N, Tallmon DA, Schwartz MK, Allendorf FW. 2010. Estimation of census and effective population sizes: the increasing usefulness of DNA-based approaches. Conservation Genetics 11: 355-373.
Lynch M, Ritland K. 1999. Estimation of pairwise relatedness with molecular markers. Genetics 152: 1753-1766.
Mack PD, Hammock BA, Promislow DEL. 2002. Sperm competitive ability and genetic relatedness in Drosophila melanogaster: similarity breeds contempt. Evolution 56: 1789-1795.
Magoulas A, Ghjetvaj B, Terzoglou V, Zouros E. 1998. Three polymorphic microsatellites in the Japanese oyster, Crassostrea gigas (Thunberg). Animal Genetics 29: 69-70.
Marshall TC, Slate J, Kruuk LEB, Pemberton JM. 1998. Statistical confidence for likelihood-based paternity inference in natural populations. Molecular Ecology 7: 639-655.
Martinez G, Mettifogo L, Perez MA, Callejas C. 2007. A method to eliminate self-fertilization in a simultaneous hermaphrodite scallop. 1. Effects on growth and survival of larvae and juveniles. Aquaculture 273: 459-469.
Matson SE, Camara MD, Eichert W, Banks MA. 2008. P-LOCI: a computer program for choosing the most efficient set of loci for parentage assignment. Molecular Ecology Resources 8(4): 765-768.
McGoldrick D, Hedgecock D, English LJ, Baoprasertkul P, Ward RD. 2000. The transmission of microsatellite alleles in Australian and North American stocks of the Pacific oyster (Crassostrea gigas): selection and null alleles. Journal of Shellfish Research 19:779-788.
Miggiano E, Deinnocentiis S, Ungaro A, Sola L, Crosetti D. 2005. AFLP and microsatellites as genetic tags to identify cultured gilthead seabream escapees: data from a simulated floating cage breaking event. Aquaculture International 13: 137-146.
M?ller L.M, Beheregaray LB, Harcourt RG, Krützen M. 2001. Alliance membership and kinship in wild male bottlenose dolphins (Tursiops aduncus) of southeastern Australia. Proceedings of the Royal Society B 268: 1941-1947.
Mori K. 1979. Effects of artificial eutrophication on the metabolism of the Japanese oyster Crassostrea gigas. Marine Biology 53: 361–369.
Morin PA, Luikart G, Wayne RK, the SNP workshop Group. 2004. SNPs in ecology, evolution and conservation. Trends in Ecology & Evolution 19:208-216.
Moriyama EN. 2003. Codon usage, Encyclopedia of the human genome. Macmillan Publishers, Nature Publishing Group. http://www.ehgonline.net4.
Musto H, Cruveiller S, D’Onofrio G, Romero H, Bernardi G. 2001. Translational selection on codon usage in Xenopus laevis. Molecular Biology and Evolution 18:1703-1707.
Neff BD, Pitcher TE. 2005. Genetic quality and sexual selection: an integrated framework for good genes and compatible genes. Molecular Ecology 14: 19-38.
Nichols KM, Young WP, Danzmann RG, Robison BD, Rexroad C, Noakes M, Phillips RB, Bentzen P, Spies I, Knudsen K, Allendorf FW, Cunningham BM, Brunelli J, Zhang H, Ristow S, Drew R, Brown KH, Wheeler PA, Thorgaard GH. 2003. A consolidated linkage map for rainbow trout (Oncorhynchus mykiss). Animal Genetics 34(2):102-15.
Norris AT, Bradley DG, Cunningham EP. 2000. Parentage and relatedness determination in farmed Atlantic salmon (Salmo salar) using microsatellite markers. Aquaculture 182: 73-83.
Nunney L. 1993. The influence of mating systems and overlapping generations on effective population size. Evolution 47: 1329-1341.
Nunney L, Elam DR. 1994. Estimating the effective population size of conserved populations. Conservation Biology 8:175-184.
Olsson M, Shine R, Madsen T, Gullberg A, Tegelstrom H. 1996. Sperm selection by females. Nature 383: 585.
O’Reilly PT, Herbinger CM, Wright JM. 1998. Analysis of parentage determination in Atlantic salmon (Salmo salar) using microsatellites. Animal Genetics 29: 363-370.
Ortega-Villaizan Romo M, Suzuki S, Nakajima M, Taniguchi N. 2006. Genetic evaluation of interindividual relatedness for broodstock management of the rare species barfin flounder Verasper moseri using microsatellite DNA markers. Fisheries Science 72: 33-39.
Palm S, Laikre L, Jorde PE, Ryman N. 2003. Effective population size and temporal genetic change in stream resident brown trout (Salmo trutta, L.). Conservation Genetics 4: 249–264.
Park C, Li Q, Kobayashi T, Kijima A. 2006. Inbreeding depression traits in Pacific abalone Haliotis discus hannai by factorial mating experiments. Fisheries Science 72: 774-780.
Pashley CH, Ellis JR, Mccauley DE, Burke JM. 2006. EST Databases as a Source for Molecular Markers: Lessons from Helianthus. Journal of Heredity 97:381-388.
Peel D, Ovenden JR, Peel SL. 2004. Neestimator: software for estimating effective population size, Queensland Government, Department of Primary Industries and Fisheries, Brisbane, Australia, version 12.
Perdue J, Erickson G. 1984. A comparison of the gametogenetic cycle between the Pacific oyster Crassostrea gigas and the suminoe oyster Crassostrea rivularis in Washington state, Aquaculture 37: 231–237.
Perez-Enriquez R, Takagi M, Taniguchi N. 1999. Genetic variability and pedigree tracing of a hatchery-reared stock of red sea bream (Pagrus major) used for stock enhancement, based on microsatellite DNA markers. Aquaculture 173: 413-423.
Picoult-Newberg L, Ideker TE, Pohl MG, Taylor SL, Donaldson MA, Nickerson DA, Boyce-Jacino M. 1999. Mining SNPs from EST databases. Genome Research 9:167-174.
Porta J, Porta JM, Martinez-Rotriguez G, Alvarez MDC. 2006. Development of a microsatellite multiplex PCR for Senegalese sole (Solea senegalensis) and its application to broodstock management. Aquaculture 56: 159–166.
Prudence M, Moal J, Boudry P, Daniel JY, QuéréC, Jeffroy F. 2006. An amylase gene polymorphism is associated with growth differences in the Pacific cupped oyster Crassostrea gigas. Animal Genetics 37:348-351.
Qin YJ, Liu X, Zhang HB, Zhang GF, Guo XM. 2007a. Genetic mapping of size-related quantitative trait loci (QTL) in the bay scallop (Argopecten irradians) using AFLP and microsatellite markers. Aquaculture 272: 281-290.
Qin YJ, Liu X, Zhang HB, Zhang GF, Guo XM. 2007b. Identification and Mapping of Amplified Fragment Length Polymorphism Markers Linked to Shell Color in Bay Scallop, Argopecten irradians irradians (Lamarck, 1819). Marine Biotechnology 9, 66-73.
Qin YJ, Liu X, Zhang HB, Zhang GF. 2007c. Effect of parental stock size on F1 genetic structure in the bay scallop, Argopecten irradians (Lamarck, 1819). Aquaculture Research 38: 174-181.
Queller DC, Goodnight KF. 1989. Estimating relatedness using genetic markers. Evolution 43:258-275.
Park C, Li Q, Kobayashi T, Kijima A. 2006. Inbreeding depression traits in Pacific abalone Haliotis discus hannai by factorial mating experiments. Fisheries Science 72: 774-780.
Perez-Enriquez R, Takagi M, Taniguchi N. 1999. Genetic variability and pedigree tracing of a hatchery-reared stock of red sea bream (Pagrus major) used for stock enhancement, based on microsatellite DNA markers. Aquaculture 173: 413-423.
Pollak E. 1977. Effective population numbers and their interrelations. Proceedings of the Washington State University Conference on Biomathematics and Biostatistics, pp. 115-144.
Department of Pure and Applied Mathematics, Washington State University, Spokane, WA. Primack RB. 1998. The problems of small populations. Essentials of Conservation Biology. Pages 253-276. Sinauer Associates, Sunderland, MA.
Rafalski JA. 2002. Application of single nucleotide polymorphisms in crop genetics. Current Opinion in Plant Biology 5:94-100.
Rakitin A, Ferguson MM, Trippel EA. 1999. Sperm competition and fertilization success in Atlantic cod (Gadus morhua): effect of sire size and condition factor on gamete quality. Canadian Journal of Fisheries and Aquatic Sciences 56: 2315-2323.
Raymond M, Rousset F. 1995. Population genetics software for exact tests and ecumenicism. Journal of Heredity 86: 248-249.
Rice RW. 1989. Analyzing tables of statistical tests. Evolution 43: 223-225.
Roberts S, Romano C, Gerlach G. 2005. Characterization of EST derived SSRs from the bay scallop, Argopecten irradians. Molecular Ecology Notes 5:567-568.
Robison BD, Wheeler PA, Sundin K, Sikka P, Thorgaard GH. 2001. Composite interval mapping reveals a major locus influencing embryonic development rate in rainbow trout (Oncorhynchus mykiss). Journal of Heredity 92: 16–22.
Ryman N, Stahl G. 1980. Genetic changes in hatchery stocks of brown trout (Salmo trutta). Canadian Journal of Fisheries and Aquatic Sciences 37: 82-87.
Sachidanandam R, Weissman D, Schmidt SC, Kakol JM, Stein LD, Marth G, Sherry S, Mullikin JC, Mortimore BJ, Willey DL, Hunt SE, Cole CG, Coggill PC, Rice CM, Ning Z, Rogers J, Bentley DR, Kwok PY, Mardis ER, Yeh RT, Schultz B, Cook L, Davenport R, Dante M, Fulton L, Hillier L, Waterston RH, McPherson JD, Gilman B, Schaffner S,. Van EWJ, ReichD, Higgins J, Daly MJ, Blumenstiel B, Baldwin J, Stange-Thomann N, Zody MC, Linton L, Lander ES, Altshuler D. 2001. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409:928-933.
Sakamotoa T, Danzmanna RG, Okamotob N, Fergusona MM, Ihssen1 PE. 1999 Linkage analysis of quantitative trait loci associated with spawning time in rainbow trout (Oncorhynchus mykiss). Aquaculture 173: 33–43.
Samain JF, McCombie H. 2008. Summer mortality of Pacific Oyster Crassostrea gigas. Versailles, France.
Sato M, Kawamata K, Zaslavskaya N, Nakamura A, Ohta T, Nishikiori T, Brykov V, Nagashima K. 2005. Development of microsatellite markers for Japanese scallop (Mizuhopecten yessoensis) and their application to a population genetic study. Marine Biotechnology 7: 713-728.
Sauvage C, Bierne N, Lapègue S, Boudry P. 2007. Single Nucleotide polymorphisms and their relationship to codon usage bias in the Pacific oyster Crassostrea gigas. Gene 406:13-22.
Sauvage C, Boudry P, De Koning DJ, Haley CS, Heurtebise S, Lapègue S. 2010. Quantitative Trait Loci for resistance to summer mortality and OsHV1 load in the Pacific oyster (Crassostrea gigas). Animal Genetics 41: 390–399.
Sauvage C, Boudry P, Lapègue S. 2009. Identification and characterization of 18 novel polymorphic microsatellite makers derived from expressed sequence tags in the Pacific oyster Crassostrea gigas. Molecular Ecology Resources 9: 853–855.
Sekino M, Saitoh K, Yamada T, Kumagai A, Hara M, Yamashita Y. 2003. Microsatellite-based pedigree tracing in a Japanese flounder Paralichthys olivaceus hatchery strain: implications for hatchery management related to stock enhancement program. Aquaculture 221: 255-263.
Sellos D, Moal J, Degremont L, Huvet A, Daniel JY, Nicoulaud S, Boudry P, Samain JF, Wormhoudt AV. 2003. Structure of amylase genes in populations of Pacific cupped oyster (Crassostrea gigas): tissue expression and allelic polymorphism. Marine Biotechnology 5: 360-72.
Shields DC, Sharp PM, Higgins DG, Wright F. 1988.‘Silent’sites in Drosophila genes are not neutral: evidence of selection among synonymous codons. Molecular Biology and Evolution 5:704-716.
Signorovitch J, Nielsen R. 2002. PATRI– paternity inference using genetic data. Bioinformatics 18: 341–342.
Smith BR, Herbinger CM, Merry HR. 2001. Accurate partition of individuals into full-sib families from genetic data without parental information. Genetics 158: 1329-1338.
Song L, Xu W, Li C, Li H, Wu L, Xiang J, Guo X. 2006. Development of Expressed Sequence Tags from the Bay Scallop, Argopecten irradians irradians. Marine Biotechnology 8:161-169.
Stenico MA, Lloyd T, Sharp PM. 1994. Codon usage in Caenorhabditis elegans: delineation of translational selection and mutational biases. Nucleic Acids Research 22: 2437-2446.
Stockley P, Gage MJG, Parker GA, M?ller AP. 1997. Sperm competition in fishes: the evolution of testis size and ejaculate characteristics. American Naturalist 149: 933-954.
Sugama K, Taniguchi N, Umeda S. 1988. An experimental study on genetic drift in hatchery population of red sea bream. Nippon Suisan Gakkaishi 54: 739-744.
Sun B, Liu X, Zhang G, Zheng H, Guo X. 2006. Molecular verification of fertilization between bay scallop individuals. Journal of Fisheries of China 30: 713-719.
Syvanen AC. 2001. Accessing genetic variation: genotyping single nucleotide polymorphisms. Nature Reviews Genetics 2:930-942.
Taggart JB. 2007. FAP: an exclusion-based parental assignment program with enhanced predictive functions. Molecular Ecology Notes 7: 412-415.
Tallmon DA, Koyuk A, Luikart G, Beaumont MA. 2008. ONeSAMP: a program to estimate effective population size using approximate Bayesian computation. Molecular Ecology Resources 8: 299-301.
Tanguy A, Bierne N, Saavedra C, Pina B, Bachère E, Kube M, Bazin E, Bonhomme F, Boudry P, Boulo V, Boutet I, Cancela L, Dossat C, Favrel P, Huvet A, Jarque S, Jollivet D, Klages S, Lapègue S, Leite R, Moal J, Moraga D, Reinhardt R, Samain JF, Zouros E, Canario A. 2008.
Increasing genomic information in bivalves through new EST collections in four species: Development of new genetic markers for environmental studies and genome evolution. Gene 408: 27-36.
Taniguchi N, Sumantadinata K, Iyama S. 1983. Genetic change in the first and second generations of hatchery stock of black sea bream. Aquaculture 35: 309-320.
Taris N, Baron S, Sharbel TF, Sauvage C, Boudry P. 2005. A combined microsatellite multiplexing and boiling DNA extraction method for high throughput parentage analyses in the Pacific Oyster (Crassostrea gigas). Aquaculture Research 36: 516-518.
Taris N, Ernande B, McCombie H, Boudry P. 2006. Phenotypic and genetic consequences of size selection at the larval stage in the Pacific oyster (Crassostrea gigas). Journal of Experimental Marine Biology and Ecology 333: 147-158.
Tautz D. 1989. Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Research 17: 6463-6471.
Tave D. 1993. Genetics for Fish Hatchery Managers, 2nd edition. Kluwer Academic Publishers, Boston.
Toro JE, Montoya MP, Martínez V, Gutiérrez D, Vergara AM. 2010. Consequences of self-fertilization on the growth rate and survival of Argopecten purpuratus. Archivos de Medicina Veterinaria 42: 63-70.
Tregenza T, Wedell N. 2002. Polyandrous females avoid costs of inbreeding. Nature 415: 71-73.
Umashankar V, Arunkumar V, Dorairaj S. 2007. ACUA: A software tool for automated codon usage analysis. Bioinformation 2: 62-63.
Useche FJ, Gao G, Harafey M, Rafalski A. 2001. High-throughput identification, database storage and analysis of SNPs in EST sequences. Genome Informatics 12: 194-203.
Varshney RK, Graner A, Sorrells ME. 2005. Genic microsatellite markers in plants: features and applications. Trends in Biotechnology 23:48-55.
Vignal A, Milan D, SanCristobal M, Eggen A. 2002. A review on SNP and other types of molecular markers and their use in animal genetics. Genetics Selection Evolution 34: 275-305.
Waldbieser GY, Wolters WR. 1999. Application of polymorphic microsatellite loci in a channel catfish Zctalurus punctatus breeding program. Journal of the World Aquaculture Society 30: 256-262.
Wang J. 2001. A pseudo-likelihood method for estimating effective population size from temporally spaced samples. Genetical Research 78: 243-257.
Wang J. 2004. Sibship reconstruction from genetic data with typing errors. Genetics 166: 1963.
Wang J. 2005. Estimation of effective population sizes from data on genetic markers. Philosophical Transactions of the Royal Society B 360: 1395-1409.
Wang J. 2009. A new method for estimating effective population size from a single sample of multilocus genotypes. Molecular Ecology 18: 2148-2164.
Wang J, Whitlock MC. 2003. Estimating effective population size and migration rates from genetic samples over space and time. Genetics 163: 429-446.
Wang JL. 2004. Sibship reconstruction from genetic data with typing errors. Genetics 166: 1963–1979.
Wang LL, Song LS, Xu W, Zhang H. 2006. Screening microsatellite markers from EST sequences of bay scallop Argopecten irradians. High Technology Letters 12: 97-102.
Wang L, Song L, Zhang H, Gao Q, Guo X. 2007. Genetic linkage map of bay scallop, Argopecten irradians irradians (Lamarck 1819). Aquaculture Research 38: 409-419.
Wang Y, Guo X. 2008. Mapping disease-resistance genes in the eastern oyster (Crassostreavirginica). Journal of Shellfish Research 27:1061-1062.
Waples RS, Do C. 2008. LdNe: a program for estimating effective population size from data on linkage disequilibrium. Molecular Ecology Resources 8: 753-756.
Williams RN, DeWoody JA. 2009. Reproductive Success and Sexual Selection in Wild Eastern Tiger Salamanders (Ambystoma t. tigrinum). Evolutionary Biology 36: 201-213.
Wilson K, Li Y, Whan V, Lehnert S, Byrne K, Moore S, Pongsomboon S, Tassanakajon A, Rosenberg G, Ballment E, Fayazi Z, Swan J, Kenway M, Benzie J. 2002. Genetic mapping of the black tiger shrimp Penaeus monodon with amplified fragment length polymorphism. Aquaculture 204: 297-309.
Wright S. 1931. Evolution in Mendelian populations. Genetics 16: 97-159.
Winkler FM, Estévez B F. 2003. Effects of self-fertilization on growth and survival of larvae and juveniles of the scallop Argopecten purpuratus L. Journal of Experimental Marine Biology and Ecology 292: 93-102.
Wray NR, Thompson R. 1990. Prediction of rates of inbreeding in selected populations. Genetical Research 55: 41-54.
Wright S. 1922. Coefficients of inbreeding and relationship. The American Naturalist 56: 330-338.
Xu Z, Primavera JP, Pena LD, Pettit P, Belak J, Alcivar-warren, A. 2001. Genetic diversity of wild and cultured Black Tiger Shrimp (Penaeus monodon) in the Philippines using microsatellites. Aquaculture 199: 13-40.
Ye S, Dhillon S, Ke X, Collins AR, Day IN. 2001. An efficient procedure for genotyping single nucleotide polymorphisms. Nucleic Acids Research 29: e88.
You FM, Huo N, Gu YQ, Luo M, Ma Y, Hane D, Lazo GR, Dvorak J, Anderson OD. 2008.
BatchPrimer3: A high throughput web application for PCR and sequencing primer design. BMC Bioinformatics 9:253.
Young WP, Wheeler PA, Coryell VH, Keim P, Thorgaard GH. 1998. A detailed linkage map of rainbow trout produced using doubled haploids. Genetics 148: 1-13.
Yu H, Li Q. 2007a. EST-SSR markers from the Pacific oyster, Crassostrea gigas. Molecular Ecology Notes 7: 860-862.
Yu H, Li Q. 2007b. Genetic variation of wild and hatchery populations of the Pacific oyster Crassostrea gigas assessed by microsatellite markers. Journal of Genetics and Genomics 34:1114-1122.
Yu H, Li Q. 2008. Exploiting EST Databases for the Development and Characterization of EST–SSRs in the Pacific Oyster (Crassostrea gigas). Journal of Heredity 99(2): 208-214.
Yu Z, Guo X. 2003. Genetic linkage map of the eastern oyster Crassostrea virginica Gmelin. The Biological Bulletin 204: 327-338.
Yu Z, Guo X. 2006. Identification and mapping of disease-resistance QTLs in the eastern oyster, Crassostrea virginica Gmelin. Aquaculture. 254: 160-170.
Zabeau M, Vos P. 1993. Selective restriction fragment amplification: a general method for DNA fingerprinting. European Patent Application number: 92402629.
Zar JH. 1999. Paired-sample hypotheses, In: Zar, J.H. (Ed.), Biostatistical Analysis. Pages 161-176. 4th ed. Prentice Hall, New Jersey.
Zhan AB, Bao ZM, Wang XL, Hu JJ. 2005. Microsatellite markers derived from bay scallop Argopecten irradians expressed sequence tags. Fisheries Science 71: 1341-1346.
Zhan A, Hu J, Hu X, Hui M, Wang M, Peng W, Huang X, Wang S, Lu W, Sun C, Bao Z. 2009.
Construction of microsatellite-based linkage maps and identification of size-related quantitative trait loci for Zhikong scallop (Chlamys farreri). Animal Genetics 40: 821-831.
Zhang FS. 2003. China aquaculture industry development in modern times and contemporary age: status and prospects. World Sci-Tech R & D 25: 5-13 (in Chinese).
Zhang FS, He Y, Liu X, Ma J, Li S. 1986. A report on the introduction, spat-rearing and experimental culture of bay scallop, Argopecten irradians Lamarck. Oceanologia et Limnologia Sinica 17: 367-374 (in Chinese).
Zhang GF, Liu SX, and X. Liu. 2003. Self-fertilization family establishment in bay scallop Argopecten irradians. Journal of Fisheries Sciences of China10: 441-445 (in Chinese).
Zhang L, Guo X, Bushek D, Ford S. 2008. Mapping quantitative trait loci conferring dermo resistance in the eastern oyster Crassostrea virginica. Journal of Shellfish Research 27: 1067-1067.
Zhdanova OL, Pudovkin AI. 2008. Nb_HetEx: a program to estimate the effective number of breeders. Journal of Heredity 99:694-695.
Zheng H, Zhang G, Guo X, Liu X. 2008. Inbreeding depression for various traits in two cultured populations of the American bay scallop, Argopecten irradians irradians Lamarck (1819) introduced into China. Journal of Experimental Marine Biology and Ecology 364: 42-47.
© 2004-2018 中国地质图书馆版权所有 京ICP备05064691号 京公网安备11010802017129号 地址：北京市海淀区学院路29号 邮编：100083 电话：办公室：(+86 10)66554848；文献借阅、咨询服务、科技查新：66554700 |