三个鲤选育种遗传优势的群体基因组学研究

The common carp selective breeding is long-lasting with clear history. Some traits are significantly improved. Many bred strains have been authenticated as new and recommended varieties. However, studies on genetic patterns, genetic diversity and domestication genes in elite common carp are lacking. In addition, the density and sensitivity of traditional molecular markers including microsatellites are low, hindering the downstream functional study and the application into breeding. Developing tag SNPs to represent the major genetic variants will provide more efficient markers for future association studies and breeding. In this study, we intend to study the genetic basis of selectively bred traits and develop the first haplotype map of common carp. We will select three recommended varieties (Songpu mirror carp, Yuxuan Yellow River carp, and Jinxin Carp) and their parent strains for study. We will perform whole genome re-sequencing to comprehensively investigate genetic diversity in six common carp strains. Firstly, population genetic analysis will be performed to investigate the genetic diversity difference between bred strains and corresponding parent strains. Phylogenetic tree will reveal the distance and relationship across different strains to demonstrate the selective breeding history. Secondly, we will perform selective sweep analysis to trace the genome imprints of breeding and identify the domestication genes and biological processes. Thirdly, genome-wide association study will be applied into the identification of loci significantly associated with improved traits and then the domestication genes will be classified into different traits. Finally, we will measure linkage disequilibrium, partition the genomic regions into segments of strong LD and select tag SNPs to represent the segments. On the basis of these segments and corresponding tag SNPs, we will select the tag SNPs significantly associated with improved traits. In sum, our study will explore the genetic basis of selectively bred traits. The method is valuable for studying the genetic basis of breeding in other species. The developed tag SNPs have practical value for association study of other traits.

鲤选育历时长，历史清晰，性状改良显著。部分选育种已被审定为新品种，并被列为主导种。但选育过程如何改变品种遗传多样性，哪些基因和过程参与到性状改良，这些问题尚未明了。包括微卫星在内的传统分子标记在性状定位上密度低且灵敏度差。有必要开发精简的标签SNP，以代表大部分基因组遗传信息，为性状关联分析提供更有效标记。本研究选择三个鲤主导选育种（松浦镜鲤、豫选黄河鲤、津新鲤）及其亲本种为研究对象，开展群体基因组测序，明确选育种和亲本种间遗传多态性差异；利用选择清除分析确定选育基因及生物过程，总结选育种的遗传变异规律；利用全基因组关联分析定位与改良性状紧密相关位点，将选育区域归类到各改良性状，解释改良性状的遗传优势；构建鲤单体型图谱，定位改良性状相关的标签SNP。本研究探明鲤选育种优势性状的遗传机制，对研究其他水产物种选育机制有重要指导意义；开发精简标签SNP，对开展其他性状关联研究有重要应用意义。

鲤选育历时长，性状改良显著。部分选育种已被审定为新品种，并被列为主导种。但选育品种是否有特异性的优势性状，哪些基因和过程参与到性状改良，这些问题尚未明了。本研究开展如下研究。第一，比较多个鲤主导选育种的生长和品质性状，发现品种间包括高不饱和脂肪酸含量在内的多个性状差异显著，进一步在三个品种更大群体（269尾个体）中检测高不饱和脂肪酸含量，发现高不饱和脂肪酸优势品种。第二，为比较群体间的遗传多样性，开发2个基因组结构解析算法，结合三代测序技术，组装获得高质量鲤基因组图谱，相比之前已发表图谱的质量有显著提升。第三，开展三个选育种(福瑞鲤、黄河鲤和建鲤)93个个体的群体基因组测序，获得各个品种的多态性位点，计算每个品种的遗传多样性，构建物种间的系统进化树，显示三个品种已独立成簇，具有显著的遗传差异。但是福瑞鲤和黄河鲤两个群体在聚类中更接近，说明这两个群体遗传差异性较接近。开展群体结构分析，发现鲤不同品种至少有2个祖先亚种，福瑞鲤的祖先成分较单一，遗传多样性较低。通过选择清除分析定位福瑞鲤1057个受选择位点和黄河鲤737个受选择位点。GO富集分析发现，福瑞鲤受选择基因参与细胞内催化正向调控、热休克蛋白结合、翻译调控，代谢相关过程和激素分泌等功能上。黄河鲤受选择基因富集在离子通道相关活性、过氧化酶活性和泛素蛋白转移酶活性。连锁不平衡分析分别构建福瑞鲤连锁不平衡区块和黄河鲤连锁不平衡区块。第四，对269尾个体开展高不饱和脂肪酸关联分析，定位3个与高不饱和脂肪酸含量水平显著关联的SNP标记。通过基因编辑方法将调控高不饱和脂肪酸合成的3个鲤基因敲入到斑马鱼后，发现均能显著上调高不饱和脂肪酸含量，证明这些基因的调控作用。本研究通过群体基因组分析，阐明鲤品种改良的分子机制，定位候选基因和通路，为后续开展更加精细的功能研究提供目标基因；获得与高不饱和脂肪酸相关的SNP，对开展筛选和培育高品质鲤有重要应用价值。

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