栉孔扇贝（Chlamys farreri）EST-SNP的开发及其应用
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摘要
栉孔扇贝（Chlamys farreri）是我国重要经济海水养殖贝类之一，近年来养殖过程中出现了病害频发、大规模死亡、个体小型化等问题，为此，进行品质优良、高产、生长迅速、抗病、抗逆新品种的选育成为其养殖产业健康可持续发展的基础。分子标记辅助育种技术和基于分子标记的功能基因研究为优良品种的培育提供了理论基础和有效途径。为此，本研究以栉孔扇贝为主要研究材料，探讨了栉孔扇贝EST-SNP标记的有效筛选条件及其在栉孔扇贝遗传育种中的应用。
1.栉孔扇贝EST-SNP分型技术的建立及标记的筛查和评价
本研究针对HRM非标记探针技术进行改进，利用3’端非配对碱基进行探针的末端封闭，并对利用HRM非标记探针技术进行EST-SNP筛查的流程进行优化，建立了一套高灵敏度、低成本筛查EST-SNP的技术体系。利用该技术体系，首次进行了大规模EST-SNP标记的开发，从栉孔扇贝5630个候选SNP位点中，成功筛选出1696个多态性SNP标记，并利用青岛群体对其进行了评价，次要等位基因频率在0.010-0.500之间，观测杂合度和期望杂合度分别介于0.000-0.942和0.020-0.507，所有的位点均处于连锁平衡状态，102个位点偏离哈代-温伯格平衡。这些位点将为栉孔扇贝的遗传连锁图谱构建、功能基因分析、QTL定位等奠定坚实的基础。
同时以本研究结果为依据，提出了进行EST-SNP筛选时，为提高多态性位点的筛选比例，应优先选择含4条以上EST序列的contig大小、次要等位基因频数在2以上并且次要等位基因频率高于25%的位点作为候选位点进行验证实验。
2. EST-SNP的种间通用性研究
本研究进行了扇贝中EST-SNP的通用性研究，利用在栉孔扇贝中筛选得到的34个多态性EST-SNP标记，在五个近源种扇贝（华贵栉孔扇贝Chlamysnobilis、海湾扇贝Argopectens irradias、日月贝Amusium pleuronectes、虾夷扇贝Patinopecten yessoensis、紫扇贝Argopecten purpuratus）中进行了通用性验证。结果显示有19个位点可以在至少一种近源扇贝中表现出多态性，其中2个位点在4种扇贝中保持多态性。研究结果表明，EST来源的SNP标记具有较好的通用性，并且统计显示通用性较好的SNP位点多位同义突变，而非同义突变则在种间较难通用。
3.栉孔扇贝任意BSA群体选择性基因分型
为了进行与表型相关基因的发掘，为分子标记辅助提供理论基础和参考数据，本研究在栉孔扇贝两个自然群体中选择壳高极大和极小的个体组成任意BSA群体，利用1696个EST-SNP标记，进行了选择性基因分型，扫描与壳高相关的基因。研究发现，有12个位点在壳高极大和壳高极小群体间存在基因频率和（或）基因型频率差异，其中6个位点存在基因频率的差异，6个位点基因频率差异不显著但基因型频率差异显著。扫描结果对于进行栉孔扇贝壳高决定基因的研究、以壳高性状为目标的选种选育奠定了基础。
4.栉孔扇贝EST-SNP雄性遗传连锁图谱的构建
利用具有共父关系的三个全同胞家系、一个父系半同胞家系和285个EST-SNP标记成功进行了栉孔扇贝雄性遗传连锁图谱的构建。所构建的图谱图谱总长度为2025.4cM，图谱覆盖度约为87.1%。标记间最大间隔为25.8cM，最小间隔为0.0cM，平均间隔为7.70cM；最长连锁群234.5cM，连锁群最短22.3cM，平均长度为106.6cM；连锁群上的分子标记数目最多为44个，最少为3个，每个连锁群平均定位标记数目为15.0个。并初步进行了栉孔扇贝主要生长性状的QTL定位，共定位到16个影响栉孔扇贝壳高、壳长、壳宽、总重和肉柱重的QTL，这些QTL成簇分布于6个连锁群上，单个QTL可以解释的表型变异方差界于4.2%-17.9%。这是栉孔扇贝第一张SNP遗传连锁图谱，该图谱的建立将极大的便利栉孔扇贝QTL定位、图位克隆及功能基因定位研究。
Zhikong scallop (Chlamys farreri) is one of the most economic mariculturespecies in China. Cultivating strains with good quality, high yield, fast-growth,resistance to diseases and stress are the basis for sustainable development ofaquaculture of this species, since various problems have risen recent years, such asfrequenct brokeout of disease, mass mortalities, individual miniaturization andso on. Marker-assist selection (MAS) and molecular marker based functionalresearch provided theories and effective approaches for the development ofnew strains. Here in this study, we validated and characterized a panel ofEST-SNPs and studied their applications in genetic breeding of C. farreri.
1. Establishment of EST-SNP genotyping technology, validation andcharacterization of EST-SNPs in C. farreri
In this study, using two mistaches at the3’ end to block the probe, we modifiedHRM unlabelled probe technology, optimizated the screeing process, and establisheda high sensitivity, low-cost genotyping sestem for EST-SNP validation. With thissystem, the first massive EST-SNP development of C. farreri wrer conducted.5,630candidate loci were chosen for validation, of which1,696proved to bepolymorphism. Evaluated with48individuals from Qingdao population, all thepolymorphic loci had two alleles with the minor allele frequency ranged between0.010and0.500. The expected and observed heterozygosities ranged from0.0625to0.7447and from0.0998to0.5046, respectively. No significant linkage disequilibriawere detected and102loci exhibited significant departures from Hardy-Weinbergequilibrium. These novel polymorphic loci presented here will facilitatethe followingresearches, such as linkage map construction, functional genetic analysis and QTL mapping. And based on the results here, contig size of≥4sequences with the minorsequence allele at least twice and minor allele frequency above20%, were highlyrecommended as candidate sites for validation test when similar researches wereconducted.
2. Inter-species transferibility of EST-SNP
In this study, the first transferability test of SNP between scallops was reported.Thirty-four EST-SNPs developed from C. farreri were chosen to test theirtransferability in in other five bivalve scallops in China: Noble Scallop (Chlamysnobilis), bay scallop (Argopectens irradias), moon scallop (Amusium pleuronectes),yesso scallop (Patinopecten yessoensis) and purple scallop (Argopecten purpuratus).And19maintained polymorphism in at least one relative species, of which two lociexihibited good transferability in four of the five scallops tested. The results heresuggested the good transferability of EST-SNPs, especially those synonymoussubstitutions, while the nonsynonymous substitutions were kind of species-specific.
3. Scanning of shell height related genes in C. farreri
In order to search out phenotype-determing genes and provide theoretical basisand pratical experieces, we selected the individuals from two wild populations withmaximum or minimum shell height, and genotyped with1,696EST-SNPs. Allelefrequencies of six loci were different between the two extreme phenotype groups.Allele frequencies of another six loci did not significantly differ but the genotypefrequencies were significantly different between the two extreme phenotype groups.The scan results laid the foundation for research of shell height-determining genes andshell height-oriented breeding scheme.
4. Construciton of EST-SNP linkage map of a male C. farreri
A linkage map of a male C. farreri was constructed with three full-sib families, aparental half-sib family and285EST-SNP markers. The total length of the map was 2,025.4cM and the genome coverage was about87.1%. The maximum intervalbetween markers was25.8cM, while the minimum interval was0.0cM, with anaverage interval of7.70cM. The linkage group length was between22.3cM and234.5cM with an average of106.6cM. The number of mapped markers ranged from3to44with an average of15.0. Preliminary QTL mapping were conducted for thegrowth traits of C. farreri, and a total of16QTLs affecting shell height, shell length,shell width, weight and weight of adductor muscle were located. These QTL were on5linkage groups explaining4.0%–22.2%of the trait variation. This is the first SNPgenetic linkage map of C. farreri, and it will greatly facilitate QTL mapping,positional cloning and gene mapping research.
1.栉孔扇贝EST-SNP分型技术的建立及标记的筛查和评价
本研究针对HRM非标记探针技术进行改进，利用3’端非配对碱基进行探针的末端封闭，并对利用HRM非标记探针技术进行EST-SNP筛查的流程进行优化，建立了一套高灵敏度、低成本筛查EST-SNP的技术体系。利用该技术体系，首次进行了大规模EST-SNP标记的开发，从栉孔扇贝5630个候选SNP位点中，成功筛选出1696个多态性SNP标记，并利用青岛群体对其进行了评价，次要等位基因频率在0.010-0.500之间，观测杂合度和期望杂合度分别介于0.000-0.942和0.020-0.507，所有的位点均处于连锁平衡状态，102个位点偏离哈代-温伯格平衡。这些位点将为栉孔扇贝的遗传连锁图谱构建、功能基因分析、QTL定位等奠定坚实的基础。
同时以本研究结果为依据，提出了进行EST-SNP筛选时，为提高多态性位点的筛选比例，应优先选择含4条以上EST序列的contig大小、次要等位基因频数在2以上并且次要等位基因频率高于25%的位点作为候选位点进行验证实验。
2. EST-SNP的种间通用性研究
本研究进行了扇贝中EST-SNP的通用性研究，利用在栉孔扇贝中筛选得到的34个多态性EST-SNP标记，在五个近源种扇贝（华贵栉孔扇贝Chlamysnobilis、海湾扇贝Argopectens irradias、日月贝Amusium pleuronectes、虾夷扇贝Patinopecten yessoensis、紫扇贝Argopecten purpuratus）中进行了通用性验证。结果显示有19个位点可以在至少一种近源扇贝中表现出多态性，其中2个位点在4种扇贝中保持多态性。研究结果表明，EST来源的SNP标记具有较好的通用性，并且统计显示通用性较好的SNP位点多位同义突变，而非同义突变则在种间较难通用。
3.栉孔扇贝任意BSA群体选择性基因分型
为了进行与表型相关基因的发掘，为分子标记辅助提供理论基础和参考数据，本研究在栉孔扇贝两个自然群体中选择壳高极大和极小的个体组成任意BSA群体，利用1696个EST-SNP标记，进行了选择性基因分型，扫描与壳高相关的基因。研究发现，有12个位点在壳高极大和壳高极小群体间存在基因频率和（或）基因型频率差异，其中6个位点存在基因频率的差异，6个位点基因频率差异不显著但基因型频率差异显著。扫描结果对于进行栉孔扇贝壳高决定基因的研究、以壳高性状为目标的选种选育奠定了基础。
4.栉孔扇贝EST-SNP雄性遗传连锁图谱的构建
利用具有共父关系的三个全同胞家系、一个父系半同胞家系和285个EST-SNP标记成功进行了栉孔扇贝雄性遗传连锁图谱的构建。所构建的图谱图谱总长度为2025.4cM，图谱覆盖度约为87.1%。标记间最大间隔为25.8cM，最小间隔为0.0cM，平均间隔为7.70cM；最长连锁群234.5cM，连锁群最短22.3cM，平均长度为106.6cM；连锁群上的分子标记数目最多为44个，最少为3个，每个连锁群平均定位标记数目为15.0个。并初步进行了栉孔扇贝主要生长性状的QTL定位，共定位到16个影响栉孔扇贝壳高、壳长、壳宽、总重和肉柱重的QTL，这些QTL成簇分布于6个连锁群上，单个QTL可以解释的表型变异方差界于4.2%-17.9%。这是栉孔扇贝第一张SNP遗传连锁图谱，该图谱的建立将极大的便利栉孔扇贝QTL定位、图位克隆及功能基因定位研究。
Zhikong scallop (Chlamys farreri) is one of the most economic mariculturespecies in China. Cultivating strains with good quality, high yield, fast-growth,resistance to diseases and stress are the basis for sustainable development ofaquaculture of this species, since various problems have risen recent years, such asfrequenct brokeout of disease, mass mortalities, individual miniaturization andso on. Marker-assist selection (MAS) and molecular marker based functionalresearch provided theories and effective approaches for the development ofnew strains. Here in this study, we validated and characterized a panel ofEST-SNPs and studied their applications in genetic breeding of C. farreri.
1. Establishment of EST-SNP genotyping technology, validation andcharacterization of EST-SNPs in C. farreri
In this study, using two mistaches at the3’ end to block the probe, we modifiedHRM unlabelled probe technology, optimizated the screeing process, and establisheda high sensitivity, low-cost genotyping sestem for EST-SNP validation. With thissystem, the first massive EST-SNP development of C. farreri wrer conducted.5,630candidate loci were chosen for validation, of which1,696proved to bepolymorphism. Evaluated with48individuals from Qingdao population, all thepolymorphic loci had two alleles with the minor allele frequency ranged between0.010and0.500. The expected and observed heterozygosities ranged from0.0625to0.7447and from0.0998to0.5046, respectively. No significant linkage disequilibriawere detected and102loci exhibited significant departures from Hardy-Weinbergequilibrium. These novel polymorphic loci presented here will facilitatethe followingresearches, such as linkage map construction, functional genetic analysis and QTL mapping. And based on the results here, contig size of≥4sequences with the minorsequence allele at least twice and minor allele frequency above20%, were highlyrecommended as candidate sites for validation test when similar researches wereconducted.
2. Inter-species transferibility of EST-SNP
In this study, the first transferability test of SNP between scallops was reported.Thirty-four EST-SNPs developed from C. farreri were chosen to test theirtransferability in in other five bivalve scallops in China: Noble Scallop (Chlamysnobilis), bay scallop (Argopectens irradias), moon scallop (Amusium pleuronectes),yesso scallop (Patinopecten yessoensis) and purple scallop (Argopecten purpuratus).And19maintained polymorphism in at least one relative species, of which two lociexihibited good transferability in four of the five scallops tested. The results heresuggested the good transferability of EST-SNPs, especially those synonymoussubstitutions, while the nonsynonymous substitutions were kind of species-specific.
3. Scanning of shell height related genes in C. farreri
In order to search out phenotype-determing genes and provide theoretical basisand pratical experieces, we selected the individuals from two wild populations withmaximum or minimum shell height, and genotyped with1,696EST-SNPs. Allelefrequencies of six loci were different between the two extreme phenotype groups.Allele frequencies of another six loci did not significantly differ but the genotypefrequencies were significantly different between the two extreme phenotype groups.The scan results laid the foundation for research of shell height-determining genes andshell height-oriented breeding scheme.
4. Construciton of EST-SNP linkage map of a male C. farreri
A linkage map of a male C. farreri was constructed with three full-sib families, aparental half-sib family and285EST-SNP markers. The total length of the map was 2,025.4cM and the genome coverage was about87.1%. The maximum intervalbetween markers was25.8cM, while the minimum interval was0.0cM, with anaverage interval of7.70cM. The linkage group length was between22.3cM and234.5cM with an average of106.6cM. The number of mapped markers ranged from3to44with an average of15.0. Preliminary QTL mapping were conducted for thegrowth traits of C. farreri, and a total of16QTLs affecting shell height, shell length,shell width, weight and weight of adductor muscle were located. These QTL were on5linkage groups explaining4.0%–22.2%of the trait variation. This is the first SNPgenetic linkage map of C. farreri, and it will greatly facilitate QTL mapping,positional cloning and gene mapping research.
引文
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