【作者】 张璐；

【导师】 包振民；

【作者基本信息】 中国海洋大学 ， 海洋生物学， 2015， 博士

【摘要】 栉孔扇贝(Chlamys farreri)是我国重要的海洋水产贝类,具有较高的营养价值和经济价值。本研究构建了栉孔扇贝连续三代选择群体,借助二代测序平台,采用2b-RAD技术获得了大量SNP位点,对三个世代进行了系统的群体遗传学研究。同时采用全基因组选择和全基因组关联分析技术针对栉孔扇贝进行全基因组育种值估计,QTL精细定位等。本研究将为水产养殖尤其是贝类育种方面提供宝贵的经验。1栉孔扇贝连续选择群体的构建本章节着重介绍了构建栉孔扇贝三个世代连续选择群体。在一个容量为2000只扇贝的群体中采用截头法以壳高为目的性状上选前5%进行选择,两年性成熟后继续以壳高为候选性状采用截头法进行选择,待第三世代长成一年后,测量其体尺性状,挑取鳃丝以备DNA提取。在选择的过程中,子代在24月龄的体尺性状遗传增量不明显。2栉孔扇贝三个连续选择世代群体遗传学分析采用2b-RAD技术构建了栉孔扇贝三个世代群体共计539个扇贝的测序文库,测序数据通过分型可拿到18450个SNP标记。对三个世代进行群体遗传学研究发现,随着世代的递进,群体偏离哈迪-温伯格平衡的标记比例为10.34%、12.64%、23.11%,香农多样性指数为0.0999±0.0404、0.0921±0.0388、0.0733±0.0308,近交系数为0.0256、0.0323、0.0468。通过构建分子亲缘关系矩阵发现无明显块状聚集,Fst检验无明显群体分化,全基因组范围内的连锁不平衡检测发现随着世代的选择,LD出现了衰减现象。这说明连续选择对栉孔扇贝“蓬莱红”品种养殖群体的群体遗传结构产生了影响,但是群体遗传多样性仍维持在较高水平,可以继续进行群体选育。3全基因组选择与全基因组关联分析在栉孔扇贝中的应用采用GBLUP, Bayes lasso, Bayes A, Bayes B四种全基因组选择的方法对539只扇贝分别进行了个体全基因组育种值估计及各标记效应的估计。结果表明四种方法估计的标记效应分布大致相同,可统一的估计出育种值最高的个体,标记效应估计、育种估计结果相对统一。以壳高为目的性状进行全基因组关联分析,在两个世代分别发现20、10个特异性位点。完善了全基因组选择育种系统,架构平台为LAMP(Linux+Apache+MySQL+PHP),实现了估计育种值的快速计算,更适合应用于实际生产。更多还原

【Abstract】 Zhikong Scallop (Chlamys farreri) is an important marine shellfish aquaculture, has a high nutritional value and economic value. In this study the scallop select group of three successive generations.A large number of SNP loci are developed in three populatinos with the second-generation sequencing platform and 2b-RAD techniques.Population genetic analysis,Genome selection and Genome-wide association study are commenced in scallop to estimate breeding value, QTL fine positioning. This study will provide valuable aquaculture, especially shellfish breeding experience.1 Construction of the continuous selective populationThis chapter focuses on the construction of three generations of continuous scallop select groups. Using a truncated method with a capacity of 2000 scallop population to shell height for the top 5% on selected traits to choose, after two years of sexual maturity continued to shell height as a candidate trait selection method using a truncated until the third generation after a year long, measuring their body size traits, picked cheek wire to prepare for DNA extraction. In the selection process, the progeny of genetic traits in 24 months body size is not obvious.2 Population genetic analysis in three continuous selective populationUsing 2b-RAD sequencing technology to build a library of scallop populations in three generations of a total of 539 scallops, return data received 18,840 SNP markers. Three generations of population genetics studies found that as generations of progressive, groups marked deviation from HW equilibrium ratio of 10.34%,12.64%、 23.11%, Shannon diversity index was 0.3034 ± 0.2075,0.2963 ± 0.2138,0.2968 ± 0.1997, inbreeding coefficient for 0.0256,0.0323,0.0468. By constructing molecular phylogenetic relationship matrix found no obvious massive gathering, Fst test no significant population differentiation, linkage disequilibrium in the genome-wide detection of discovery with generations of selection choice, LD decay occurred. This shows that the continuous selection of population genetic structure Penglai red scallop species breeding population had an impact, but the genetic diversity remained at a high level, can continue breeding populations.3 Application of Genome selection an Genome-wide association analysis in scallop.Four genome selection method,GBLUP, Bayes lasso, Bayes A and Bayes B,are carried out to calculate estimate breeding value of 539 scallop individual and estimated marker effect. The results showed that four kinds of methods to estimate the distribution of marks roughly the same effect can be unified highest estimated breeding values of individuals, marking effect estimated breeding estimation results relatively uniform. With shell height for the purpose of traits Genome-wide association study, were found in two generations 20,10 a specific site. Improve the whole genome selection breeding system architecture platform for LAMP (Linux+Apache+MySQL+PHP), to achieve a rapid calculation of the estimated breeding value, more suitable for actual production.更多还原