团头鲂EST-SSR的开发及在育种中的应用
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摘要
团头鲂(Megahbrama amblycephala Yih),俗称武昌鱼,属硬骨鱼纲、鲤形目、鲤科、鲌亚科。自然分布区域狭窄,原产仅在长江中游的一些通江湖泊,如湖北省的梁子湖、淤泥湖和江西的鄱阳湖等。由于其独特的文化元素以及具有草食性、成活率高、生长较快、抗病力强、含肉率高及营养价值较高等优点,在20世纪60年代己确认为一种优良养殖鱼类。目前已经推广到全国各地饲养,成为我国池塘和网箱养殖的主要或者混养鱼类之一。由于人工繁殖的成功突破和养殖驯化水平的不断提高,在2010年团头鲂在我国的养殖产量已经达到652,215t(CAFS,2010)。然而,随着养殖驯化过程中的近亲繁殖、野生资源的过度捕捞以及生存环境的破坏,团头鲂的种质资源己经受到了严重的威胁。团头鲂的养殖群体逐渐出现了生长减缓、体型变长变薄、抗病力差和性成熟个体变小等问题。
目前团头鲂分子遗传基础薄弱、基因序列和分子标记资源匮乏、遗传育种理论尚不成熟,严重影响团头鲂遗传育种计划的开展。为了更加有效地开展团头鲂先进的育种计划,尽快培育出优良品种,本论文从团头鲂转录组高通量测序入手,开发微卫星标记,构建亲子鉴定技术平台,并在此基础上结合团头鲂F1代生长表型数据进行了全面的数量遗传学研究。在本论文结合数量遗传学、杂交育种和MAS等多方面知识,运用了家系选育、群体选择、BLUP育种和后裔测定等多种方法开展团头鲂的育种研究,为早日获得团头鲂具有生长优势的优良品种奠定了坚实的基础。总的来说主要有如下结果和结论：
1.团头鲂转录组454GS FLX高通量测序和分析
应用高通量454测序技术对团头鲂多个组织的均一化cDNA文库进行测序,一共获得了1,409,706条高质量序列,总长度为577Mbp,平均长度为411bp。经过拼接组装后获得了26,802条contigs和73,675条singletons,测序深度大约为7.6倍。Contigs的平均长度达730bp,且有74.1%的contigs序列长度超过500bp。对团头鲂拼接得到的unigenes与Nr、Swiss-prot和UniProt等公共蛋白质数据库比对,超过50%的序列获得了注释；通过GO注释对基因进行分类,获得了zinc ion bingding等41个小类别,鉴别出大量与生长、繁殖、免疫和抗逆等相关性状的候选基因。通过与斑马鱼、青鳉、绿河豚、河豚、三棘刺鱼、人、小鼠和鸡的基因组比较,发现团头鲂转录组中的基因与这些物种具有很高的比例的相似度,同时还鉴定了778条的团头鲂特有的基因。另外,在团头鲂转录组中一共检测到有4,952个SSR位点和大量的SNP位点(25,697个)和插入缺失位点(23,287个)。
2.根据团头鲂转录组EST序列,开发大量微卫星标记
EST文库筛选微卫星具有方法简便、花费较低等特点。本研究从团头鲂454转录组测序得到的大量isotigs序列中搜索SSR位点,一共随机设计了300对EST-SSR引物,经过PCR扩增和聚丙烯酰胺凝胶电泳分型,其中146个位点(48.7%)可以清晰扩增出条带,93个(31%)微卫星位点具有多态性。多态性微卫星标记应用于梁子湖野生样本的遗传多样性分析,发现有效等位基因数从2到18个,平均等位基因数为5.11个。观测杂合度(Ho)的大小在0.25到1之间,平均为0.69；期望杂合度(HE)在0.25到0.86之间,平均为0.65。此外,从所开发出的多态性微卫星标记中,筛选20个微卫星位点构建了6个多重PCR反应体系,高效地分析团头鲂淤泥湖野生群体群体的遗传多样性,发现其遗传多样性较低,并且在多个位点上显著偏离哈迪-温伯格平衡,说明了该团头鲂野生群体遭到了严重的干扰。
3.利用高质量多态性的微卫星标记构建亲子鉴定技术体系
基于微卫星的亲子鉴定技术的使用克服了传统选育过程中的种种弊端。本研究利用8个高质量多态性微卫星标记构建了团头鲂亲子鉴定平台,平均等位基因为10个,平均观测杂合度和期望杂合度分别是0.649和0.670,多态信息含量是0.655,在混养家系鉴定中准确率达到96.33%,可以实现团头鲂多个家系从出生就可以进行混养,成功地减少管理成本,增加家系数量,同时大大降低环境误差,从而为后续实验如家系生长性能评估、杂交优势和遗传参数评估等多个方面的研究更加精确地进行奠定了基础,提高选育效率,加快育种进程。
4.团头鲂子一代优良家系筛选
本研究通过收集团头鲂自然群体,然后进行群体繁育的方法,构建了团头鲂317个F1代全同胞家系。F1代从鱼苗下塘开始就一起混合饲养,直到收获(20月龄)时,利用微卫星的亲子鉴定技术进行家系鉴定。通过鉴定,708个子代(94.53%)能够准确地找到单一的父母本。结合F1代的生长性状表型值,成功筛选到了平均体重≥400g的家系的25个,其中36号、41号和1号家系生长最快,这些家系可以作为团头鲂家系育种的重要选育系。另外,根据多个生长最快的家系和生长最慢的家系的体长和体重建立关系式,分别为W=0.1059*L2.5224(R2=0.9035)和W=0.1117*L2.4608(R2=0.9106)。两关系式中a值相近,说明不同家系的生长环境较稳定,家系之间具有可比性；b<3,说明两组家系均处于异速生长阶段,符合团头鲂正常的生长规律。
5.团头鲂杂交优势和配合力分析
本研究对团头鲂梁子湖(LZ)、淤泥湖(YN)和鄱阳湖(PY)3个地理种群进行双列杂交实验,采用亲本多雌配多雄的人工繁殖方法构建团头鲂F1家系,Fl代在混合养殖的条件下,通过亲子鉴定的手段来比较各个繁殖组合20月龄的生长性状,评估了三个地理种群的配合力和杂交优势。结果表明,在总体水平上父本对于体重的一般配合力大大高于母本；不管是父本还是母本,LZ群体的一般配合力都是最大的；YN♀×PY♂的特殊配合力最大,杂交优势明显,可见种内群体间杂交是培育团头鲂优良新品系的重要方法之一。除此之外,团头鲂子一代的生长性状与亲本群体的遗传多样性指数在一定范围内存在显著性线性正相关关系,其中体重与亲本群体期望杂合度的关系。式为y=600.7x-29.472(r=0.8651, p=0.0026)。
6.团头鲂20月龄遗传参数和育种值估计
本研究采用混合家系遗传参数估计法对20月龄团头鲂F1代的生长相关性状(体重、体长、全长和体高)的遗传参数和育种值进行了估计。利用SPSS19软件的一般线性模型(GLM)计算表型变量的方差组分,估计生长相关性状的遗传力。结果显示团头鲂20月龄的生长相关性状的遗传力在0.50～0.65之间,表明在加性效应控制下,团头鲂的生长性状具有较大的遗传改良潜力；遗传相关在0.98～1之间,说明团头鲂生长相关性状紧密连锁,在选育实践中可以只针对一个性状进行选育,如体重或体长,节约操作时间和降低成本。此外,本研究采用BLUP法估计了团头鲂生长相关性状的育种值和考虑团头鲂体型因素的综合育种值。单性状(体重或体长)的育种值与综合育种值排名相比较差异不大。育种值排名靠前的亲本绝大部分来自梁子湖和鄱阳湖,说明这两个湖泊的亲本比较优秀。
7.团头鲂亲本对子代的贡献及优良亲本筛选
本研究通过利用9对微卫星亲子鉴定技术研究亲本对子代群体的贡献及筛选优良亲本。通过微卫星标记分析发现,子代生长快和生长慢群体的FST较大(0.024,P<0.0343),说明了通过表型选择会引起团头鲂子代群体间显著性的遗传差异。经过亲子鉴定分析发现,对于子代生长快群体和生长慢的群体,不是所有亲本均有贡献,在生长快和生长慢群体的有效群体数量比亲本显著降低,分别约为65和67尾。生长快和生长慢群体的近交系数分别约为0.77%和0.75%,这两个值高于亲本群体的近交系数。另外,经过亲本对生长快和生长慢群体的贡献分析,发现15个亲本(6个母本和9个父本)对生长快群体的贡献显著高于生长慢的群体,说明他们具有生产具有生长优势的后代的潜能,另外,通过对亲本体重育种值的估计,发现所选亲本的体重育种值排名均靠前,证实了通过亲本对子代的贡献筛选优秀亲本具有较高的可靠性。所筛选的亲本可用于构建团头鲂优良的家系,也可繁殖优质鱼苗直接用于生产。这些结果可以使团头鲂的选育计划更加完善,同时也为其他鱼类的选育提供了一定的借鉴。
Blunt snout bream (Megalobrama amblycephala) or Wuchang Fish, belongs to the family of Cyprinidae, which is an herbivorous freshwater fish species native to China. It was originally endemic to certain large and medium-sized lakes of middle reach of Yangtze River, such as Liangzi lake (LZ) and Yuni lake (YN) in Hubei province and Poyang lake (PY) in Jiangxi province.
Because of its special cultural elements, high resistance to diseases, high rate of meat and rich nutition, M. amblycephala has been widely favored and recognized as a main aquaculture species in the freshwater polyculture system since1960s in China. Due to its successful artificial propagation and high economic value, M. amblycephala aquaculture industry has greatly developed in the past decades and its total output had reached652,21tons in2010(CAFS,2010). As a consequence of fast domestication, over-fishing, however, germplasm resource of this fish is under threat of recession and mixture due to its artificial breeding. Nowadays, the cultured population of M. amblycephala is gradually exhibiting early sexual maturity, low growth rate and disease susceptibility. Therefore, applying genomics tools in the selection of broodstock has the potential to enhance the productivity and value of commercial production for this species.
Right now, the molecular genetic basis of M. amblycephala is very weak and genetic breeding theory is not mature, serious influencing genetic breeding program of M. amblycephala. In order to carry out advanced breeding programmes more effectively as soon as possible, and to breed better varieties, transcriptome of M. amblycephala using next genration sequencing (NGS) technique was first sequenced. And then, we developed many microsatellite markers based on these EST sequences. We used eight microsatellite markers to build a parentage assignment technology platform, and based on this technology, detailed study was conducted on quantitative genetics of M. amblycephala F1generation. In this thesis, we combined with the theoties of quantitative genetics, cross breeding and molecular-assited selection (MAS), and used the methods of family selection, mass selection, BLUP breeding and progeny testing to carry out a breeding programme of M. amblycephala. This research lays the foundation for gaining good varieties of M. amblycephal in future. Our results and conclusions are as follows:
1. De novo assembly and characterization of M. amblycephala using454pyosequencing
A total of1,409,706high quality reads (total length577Mbp) were generated from the normalized cDNA of pooled M. amblycephala individuals using454pyosequencing. These sequences were assembled into26,802contigs and73,675singletons, with7.6×sequencing depth. The average length of contigs was730bp, and more than70%of contigs were longer than500bp. After BLAST searches against the Nr and UniProt databases with an arbitrary expectation value of E-10, over40,000unigenes were functionally annotated and classified. Of which, a substantial number of candidate genes putatively involved in growth, development, reproduction and immune were identified, and were considered as an invaluable genetic resource for gene functional analysis and breeding program. A comparative genomics approach revealed a substantial proportion of genes expressed in M. amblycephala tanscriptome to be shared across the genomes of zebrafish, medaka, fugu, stickleback, tetraodon, chicken, mouse, and human, and also identified a lot of potentially novel M. amblycephala genes. A total of4,952SSRs were identified and93polymorphic loci have been characterized. A large number of SNPs (25,697) and indels (23,287) were identified based on specific filter criteria in M. amblycephala.
2. Development of SSR markers from EST sequences
It is a low cost and simple to development of SSR markers from EST sequences. In this study,300SSR loci were randomly selected for primer design, of these,146loci (48.7%) were successfully amplified and93loci (31%) were polymorphic across panels of40individuals from LZ population. Number of alleles (NA) is from2to18, with an average of5.11. The observed heterozygosity (Ho) and the expected heterozygosity (HE) ranged from0.25to1and0.25to0.86, respectively. In order to analysis population genetic diversity or genetic structure more efficient and more accurately, six multiple PCR reaction systems were constructed with20polymorphic microsatellite markers to analysis the genetic diversity of PY population. The results indicated the genetic diversity of PY population is a little low, and most loci were significantly deviated from Hardy-Weinberg equilibrium, indicating the M. amblycephal wild population suffered serious artificial interference.
3. Construction of a parentage assignment technology for M. amblycephala
In this study, we used eight highly polymorphic microsatellite markers to assign parentage to offspring under different scenarios both simulation and real. Simulations based on allele frequency data from the population of M. amblycephal demonstrated that4loci were required to assign91.3%and6loci to assign99.6%of progeny. In a real-life commercial breeding system, using8SSR loci with NA of10, the assignment success of progeny to their true parental was98%with known parental and filial information and96.33%in mixed families groups.
4. The growth performance of F1generation and rapid growth families screening
317full-sub F1families were constructed by a complete diallel crossing of three strains (Liangzi-LZ, Poyang-PY and Yuni-YN). All the F1progeny were fed in a communal pond from newborn until to when harvested. Based on microsatellite parentage assignment techniques,708(94.53%) of749offspring could be assigned directly to a single parental pair. Finally,25families with body weight (?0400g were screened, which could be as core breeding families in M. amblycephal selection program. In addition, based on these body length and weight growth fastest and growth slowest families, the body length and weight relationship was constructed with correlation coeffient R2>0.5. The a values of two equations were similar, indicating these families were in stable growth environment; The b values were both<3, implying these families were in allometric growth stage, which is in accordance with the normal growth rule of M. amblycephal.
5. Heterosis and combination ability analysis in a diallel cross of three populations of M. amblycephala
In this study, a complete diallel crossing of three strains (LZ, PY and YN) was used to evaluate the combining ability and heterosis effects of intraspecific crossbreeding on its growth performance. The offspring produced between the three strains were reared in a communal pond for20months and9microsatellites were used to pedigree. Significant differences were observed in growth among different mating combinations, indicating combining ability of body weight (BW) from each strain was significantly different. General combining ability (GCA) of BW from sire is much higher than dam. Both the GCA for dam and sire of LZ was the largest and that of YN was poorest. Special combining ability of YN(?)×PY(?) was the largest and YN(?)×PY(?) showed significantly positive heterosis effects on F1growth (P<0.05). A significant and positive linear correlation existed between the growth of progeny and the level of genetic variation in the parental generation.
6. Estimation genetic parameter and breeding value for growth traits of M. amblycephala
The genetic parameters estimates for important economic traits are needed for its selective breeding. The aim of the current study was to estimate the heritabilities for its growth-related traits and explore the genetic and phenotypic correlations among the traits using microsatellite-based pedigree approach. Offspring from a mass-spawning of92broodstocks (42sires and50dams) were reared in a communal pond and nine microsatellites were used to identify the parents of each sampled offspring. Data was analyzed by the method of restricted maximum likelihood (REML) using animal model and the results showed the heritabilities of body weight, body length, total length and body height were0.65,0.53,0.53and0.50, respectively. High genetic correlations were found among these four traits. According to these results, selection for growth seems to be feasible in M. amblycephala and the other growth traits will be heightened accordingly with the selection based on body length. In addition, breeding value for growth-related traits of20-month M. amblycephala was estimated by the BLUP method. The BLUP breeding value for single trait (body weight or body length) was similar with combined breeding value, which took full into account the body type. The results shown most of the parents with high breeding value were from Liangzi strain and Poyang strain.
7. Assessment of parental contributions to progenies in M. amblycephala and selection of parents with good traits
The parentage assignment base on microsatellite markers was used to assess the parental contributions to fast-and slow-growing progeny group.95.32%individuals could be unambiguously assigned to their putative parents. The FST value was0.024(p<0.05), implying significant genetic differences between the two progeny groups. A globally significantly unequal contribution of breeders to fast-and slow-growth progeny was found in this experiment.15breeders (6females and9males) contributed significantly more to the fast-growth progeny, while11(4females and7males) contributed significantly more to the slow-growth progeny. In addition, we estimated the BLUP breeding value for body weight of parents, and found that the breeding value of the selected parents were all much high. The result indicated it is reliable to select excellent parents by estimating parents' contribution to progeny. These excellent breeders could be used to establish good families as core selection group and could be directly used in production mass fry. The findings are helpful to perfect the selective breeding program of M. amblycephala and also gave some advices for breeding selection in other fish species.
目前团头鲂分子遗传基础薄弱、基因序列和分子标记资源匮乏、遗传育种理论尚不成熟,严重影响团头鲂遗传育种计划的开展。为了更加有效地开展团头鲂先进的育种计划,尽快培育出优良品种,本论文从团头鲂转录组高通量测序入手,开发微卫星标记,构建亲子鉴定技术平台,并在此基础上结合团头鲂F1代生长表型数据进行了全面的数量遗传学研究。在本论文结合数量遗传学、杂交育种和MAS等多方面知识,运用了家系选育、群体选择、BLUP育种和后裔测定等多种方法开展团头鲂的育种研究,为早日获得团头鲂具有生长优势的优良品种奠定了坚实的基础。总的来说主要有如下结果和结论：
1.团头鲂转录组454GS FLX高通量测序和分析
应用高通量454测序技术对团头鲂多个组织的均一化cDNA文库进行测序,一共获得了1,409,706条高质量序列,总长度为577Mbp,平均长度为411bp。经过拼接组装后获得了26,802条contigs和73,675条singletons,测序深度大约为7.6倍。Contigs的平均长度达730bp,且有74.1%的contigs序列长度超过500bp。对团头鲂拼接得到的unigenes与Nr、Swiss-prot和UniProt等公共蛋白质数据库比对,超过50%的序列获得了注释；通过GO注释对基因进行分类,获得了zinc ion bingding等41个小类别,鉴别出大量与生长、繁殖、免疫和抗逆等相关性状的候选基因。通过与斑马鱼、青鳉、绿河豚、河豚、三棘刺鱼、人、小鼠和鸡的基因组比较,发现团头鲂转录组中的基因与这些物种具有很高的比例的相似度,同时还鉴定了778条的团头鲂特有的基因。另外,在团头鲂转录组中一共检测到有4,952个SSR位点和大量的SNP位点(25,697个)和插入缺失位点(23,287个)。
2.根据团头鲂转录组EST序列,开发大量微卫星标记
EST文库筛选微卫星具有方法简便、花费较低等特点。本研究从团头鲂454转录组测序得到的大量isotigs序列中搜索SSR位点,一共随机设计了300对EST-SSR引物,经过PCR扩增和聚丙烯酰胺凝胶电泳分型,其中146个位点(48.7%)可以清晰扩增出条带,93个(31%)微卫星位点具有多态性。多态性微卫星标记应用于梁子湖野生样本的遗传多样性分析,发现有效等位基因数从2到18个,平均等位基因数为5.11个。观测杂合度(Ho)的大小在0.25到1之间,平均为0.69；期望杂合度(HE)在0.25到0.86之间,平均为0.65。此外,从所开发出的多态性微卫星标记中,筛选20个微卫星位点构建了6个多重PCR反应体系,高效地分析团头鲂淤泥湖野生群体群体的遗传多样性,发现其遗传多样性较低,并且在多个位点上显著偏离哈迪-温伯格平衡,说明了该团头鲂野生群体遭到了严重的干扰。
3.利用高质量多态性的微卫星标记构建亲子鉴定技术体系
基于微卫星的亲子鉴定技术的使用克服了传统选育过程中的种种弊端。本研究利用8个高质量多态性微卫星标记构建了团头鲂亲子鉴定平台,平均等位基因为10个,平均观测杂合度和期望杂合度分别是0.649和0.670,多态信息含量是0.655,在混养家系鉴定中准确率达到96.33%,可以实现团头鲂多个家系从出生就可以进行混养,成功地减少管理成本,增加家系数量,同时大大降低环境误差,从而为后续实验如家系生长性能评估、杂交优势和遗传参数评估等多个方面的研究更加精确地进行奠定了基础,提高选育效率,加快育种进程。
4.团头鲂子一代优良家系筛选
本研究通过收集团头鲂自然群体,然后进行群体繁育的方法,构建了团头鲂317个F1代全同胞家系。F1代从鱼苗下塘开始就一起混合饲养,直到收获(20月龄)时,利用微卫星的亲子鉴定技术进行家系鉴定。通过鉴定,708个子代(94.53%)能够准确地找到单一的父母本。结合F1代的生长性状表型值,成功筛选到了平均体重≥400g的家系的25个,其中36号、41号和1号家系生长最快,这些家系可以作为团头鲂家系育种的重要选育系。另外,根据多个生长最快的家系和生长最慢的家系的体长和体重建立关系式,分别为W=0.1059*L2.5224(R2=0.9035)和W=0.1117*L2.4608(R2=0.9106)。两关系式中a值相近,说明不同家系的生长环境较稳定,家系之间具有可比性；b<3,说明两组家系均处于异速生长阶段,符合团头鲂正常的生长规律。
5.团头鲂杂交优势和配合力分析
本研究对团头鲂梁子湖(LZ)、淤泥湖(YN)和鄱阳湖(PY)3个地理种群进行双列杂交实验,采用亲本多雌配多雄的人工繁殖方法构建团头鲂F1家系,Fl代在混合养殖的条件下,通过亲子鉴定的手段来比较各个繁殖组合20月龄的生长性状,评估了三个地理种群的配合力和杂交优势。结果表明,在总体水平上父本对于体重的一般配合力大大高于母本；不管是父本还是母本,LZ群体的一般配合力都是最大的；YN♀×PY♂的特殊配合力最大,杂交优势明显,可见种内群体间杂交是培育团头鲂优良新品系的重要方法之一。除此之外,团头鲂子一代的生长性状与亲本群体的遗传多样性指数在一定范围内存在显著性线性正相关关系,其中体重与亲本群体期望杂合度的关系。式为y=600.7x-29.472(r=0.8651, p=0.0026)。
6.团头鲂20月龄遗传参数和育种值估计
本研究采用混合家系遗传参数估计法对20月龄团头鲂F1代的生长相关性状(体重、体长、全长和体高)的遗传参数和育种值进行了估计。利用SPSS19软件的一般线性模型(GLM)计算表型变量的方差组分,估计生长相关性状的遗传力。结果显示团头鲂20月龄的生长相关性状的遗传力在0.50～0.65之间,表明在加性效应控制下,团头鲂的生长性状具有较大的遗传改良潜力；遗传相关在0.98～1之间,说明团头鲂生长相关性状紧密连锁,在选育实践中可以只针对一个性状进行选育,如体重或体长,节约操作时间和降低成本。此外,本研究采用BLUP法估计了团头鲂生长相关性状的育种值和考虑团头鲂体型因素的综合育种值。单性状(体重或体长)的育种值与综合育种值排名相比较差异不大。育种值排名靠前的亲本绝大部分来自梁子湖和鄱阳湖,说明这两个湖泊的亲本比较优秀。
7.团头鲂亲本对子代的贡献及优良亲本筛选
本研究通过利用9对微卫星亲子鉴定技术研究亲本对子代群体的贡献及筛选优良亲本。通过微卫星标记分析发现,子代生长快和生长慢群体的FST较大(0.024,P<0.0343),说明了通过表型选择会引起团头鲂子代群体间显著性的遗传差异。经过亲子鉴定分析发现,对于子代生长快群体和生长慢的群体,不是所有亲本均有贡献,在生长快和生长慢群体的有效群体数量比亲本显著降低,分别约为65和67尾。生长快和生长慢群体的近交系数分别约为0.77%和0.75%,这两个值高于亲本群体的近交系数。另外,经过亲本对生长快和生长慢群体的贡献分析,发现15个亲本(6个母本和9个父本)对生长快群体的贡献显著高于生长慢的群体,说明他们具有生产具有生长优势的后代的潜能,另外,通过对亲本体重育种值的估计,发现所选亲本的体重育种值排名均靠前,证实了通过亲本对子代的贡献筛选优秀亲本具有较高的可靠性。所筛选的亲本可用于构建团头鲂优良的家系,也可繁殖优质鱼苗直接用于生产。这些结果可以使团头鲂的选育计划更加完善,同时也为其他鱼类的选育提供了一定的借鉴。
Blunt snout bream (Megalobrama amblycephala) or Wuchang Fish, belongs to the family of Cyprinidae, which is an herbivorous freshwater fish species native to China. It was originally endemic to certain large and medium-sized lakes of middle reach of Yangtze River, such as Liangzi lake (LZ) and Yuni lake (YN) in Hubei province and Poyang lake (PY) in Jiangxi province.
Because of its special cultural elements, high resistance to diseases, high rate of meat and rich nutition, M. amblycephala has been widely favored and recognized as a main aquaculture species in the freshwater polyculture system since1960s in China. Due to its successful artificial propagation and high economic value, M. amblycephala aquaculture industry has greatly developed in the past decades and its total output had reached652,21tons in2010(CAFS,2010). As a consequence of fast domestication, over-fishing, however, germplasm resource of this fish is under threat of recession and mixture due to its artificial breeding. Nowadays, the cultured population of M. amblycephala is gradually exhibiting early sexual maturity, low growth rate and disease susceptibility. Therefore, applying genomics tools in the selection of broodstock has the potential to enhance the productivity and value of commercial production for this species.
Right now, the molecular genetic basis of M. amblycephala is very weak and genetic breeding theory is not mature, serious influencing genetic breeding program of M. amblycephala. In order to carry out advanced breeding programmes more effectively as soon as possible, and to breed better varieties, transcriptome of M. amblycephala using next genration sequencing (NGS) technique was first sequenced. And then, we developed many microsatellite markers based on these EST sequences. We used eight microsatellite markers to build a parentage assignment technology platform, and based on this technology, detailed study was conducted on quantitative genetics of M. amblycephala F1generation. In this thesis, we combined with the theoties of quantitative genetics, cross breeding and molecular-assited selection (MAS), and used the methods of family selection, mass selection, BLUP breeding and progeny testing to carry out a breeding programme of M. amblycephala. This research lays the foundation for gaining good varieties of M. amblycephal in future. Our results and conclusions are as follows:
1. De novo assembly and characterization of M. amblycephala using454pyosequencing
A total of1,409,706high quality reads (total length577Mbp) were generated from the normalized cDNA of pooled M. amblycephala individuals using454pyosequencing. These sequences were assembled into26,802contigs and73,675singletons, with7.6×sequencing depth. The average length of contigs was730bp, and more than70%of contigs were longer than500bp. After BLAST searches against the Nr and UniProt databases with an arbitrary expectation value of E-10, over40,000unigenes were functionally annotated and classified. Of which, a substantial number of candidate genes putatively involved in growth, development, reproduction and immune were identified, and were considered as an invaluable genetic resource for gene functional analysis and breeding program. A comparative genomics approach revealed a substantial proportion of genes expressed in M. amblycephala tanscriptome to be shared across the genomes of zebrafish, medaka, fugu, stickleback, tetraodon, chicken, mouse, and human, and also identified a lot of potentially novel M. amblycephala genes. A total of4,952SSRs were identified and93polymorphic loci have been characterized. A large number of SNPs (25,697) and indels (23,287) were identified based on specific filter criteria in M. amblycephala.
2. Development of SSR markers from EST sequences
It is a low cost and simple to development of SSR markers from EST sequences. In this study,300SSR loci were randomly selected for primer design, of these,146loci (48.7%) were successfully amplified and93loci (31%) were polymorphic across panels of40individuals from LZ population. Number of alleles (NA) is from2to18, with an average of5.11. The observed heterozygosity (Ho) and the expected heterozygosity (HE) ranged from0.25to1and0.25to0.86, respectively. In order to analysis population genetic diversity or genetic structure more efficient and more accurately, six multiple PCR reaction systems were constructed with20polymorphic microsatellite markers to analysis the genetic diversity of PY population. The results indicated the genetic diversity of PY population is a little low, and most loci were significantly deviated from Hardy-Weinberg equilibrium, indicating the M. amblycephal wild population suffered serious artificial interference.
3. Construction of a parentage assignment technology for M. amblycephala
In this study, we used eight highly polymorphic microsatellite markers to assign parentage to offspring under different scenarios both simulation and real. Simulations based on allele frequency data from the population of M. amblycephal demonstrated that4loci were required to assign91.3%and6loci to assign99.6%of progeny. In a real-life commercial breeding system, using8SSR loci with NA of10, the assignment success of progeny to their true parental was98%with known parental and filial information and96.33%in mixed families groups.
4. The growth performance of F1generation and rapid growth families screening
317full-sub F1families were constructed by a complete diallel crossing of three strains (Liangzi-LZ, Poyang-PY and Yuni-YN). All the F1progeny were fed in a communal pond from newborn until to when harvested. Based on microsatellite parentage assignment techniques,708(94.53%) of749offspring could be assigned directly to a single parental pair. Finally,25families with body weight (?0400g were screened, which could be as core breeding families in M. amblycephal selection program. In addition, based on these body length and weight growth fastest and growth slowest families, the body length and weight relationship was constructed with correlation coeffient R2>0.5. The a values of two equations were similar, indicating these families were in stable growth environment; The b values were both<3, implying these families were in allometric growth stage, which is in accordance with the normal growth rule of M. amblycephal.
5. Heterosis and combination ability analysis in a diallel cross of three populations of M. amblycephala
In this study, a complete diallel crossing of three strains (LZ, PY and YN) was used to evaluate the combining ability and heterosis effects of intraspecific crossbreeding on its growth performance. The offspring produced between the three strains were reared in a communal pond for20months and9microsatellites were used to pedigree. Significant differences were observed in growth among different mating combinations, indicating combining ability of body weight (BW) from each strain was significantly different. General combining ability (GCA) of BW from sire is much higher than dam. Both the GCA for dam and sire of LZ was the largest and that of YN was poorest. Special combining ability of YN(?)×PY(?) was the largest and YN(?)×PY(?) showed significantly positive heterosis effects on F1growth (P<0.05). A significant and positive linear correlation existed between the growth of progeny and the level of genetic variation in the parental generation.
6. Estimation genetic parameter and breeding value for growth traits of M. amblycephala
The genetic parameters estimates for important economic traits are needed for its selective breeding. The aim of the current study was to estimate the heritabilities for its growth-related traits and explore the genetic and phenotypic correlations among the traits using microsatellite-based pedigree approach. Offspring from a mass-spawning of92broodstocks (42sires and50dams) were reared in a communal pond and nine microsatellites were used to identify the parents of each sampled offspring. Data was analyzed by the method of restricted maximum likelihood (REML) using animal model and the results showed the heritabilities of body weight, body length, total length and body height were0.65,0.53,0.53and0.50, respectively. High genetic correlations were found among these four traits. According to these results, selection for growth seems to be feasible in M. amblycephala and the other growth traits will be heightened accordingly with the selection based on body length. In addition, breeding value for growth-related traits of20-month M. amblycephala was estimated by the BLUP method. The BLUP breeding value for single trait (body weight or body length) was similar with combined breeding value, which took full into account the body type. The results shown most of the parents with high breeding value were from Liangzi strain and Poyang strain.
7. Assessment of parental contributions to progenies in M. amblycephala and selection of parents with good traits
The parentage assignment base on microsatellite markers was used to assess the parental contributions to fast-and slow-growing progeny group.95.32%individuals could be unambiguously assigned to their putative parents. The FST value was0.024(p<0.05), implying significant genetic differences between the two progeny groups. A globally significantly unequal contribution of breeders to fast-and slow-growth progeny was found in this experiment.15breeders (6females and9males) contributed significantly more to the fast-growth progeny, while11(4females and7males) contributed significantly more to the slow-growth progeny. In addition, we estimated the BLUP breeding value for body weight of parents, and found that the breeding value of the selected parents were all much high. The result indicated it is reliable to select excellent parents by estimating parents' contribution to progeny. These excellent breeders could be used to establish good families as core selection group and could be directly used in production mass fry. The findings are helpful to perfect the selective breeding program of M. amblycephala and also gave some advices for breeding selection in other fish species.
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