基于全基因组关联分析的牡蛎生长与营养品质性状的遗传解析

China ranks the first for the oyster production in the world. The total production of China accounts for more than 80% of the global production, but the export quantity only accounts for 3% in the international market and the unit price is about 1/3 of that in other countries. One reason leading to this embarrassing situation is the low quality of oyster production. Genetic improvement for the growth and the nutritional composition is one of the key approaches to resolve the high-production with low-efficiency problem in the oyster mariculture. The research team has finished the oyster genome sequencing, the world wide germplasm collection and the common garden experiment of 486 families with different females and a single male. This provide the basis for this study as follows: 1) The growth parameters (the shell size, total weight, wet meat weight, dry meat weight, condition index) and the nutritional composition ( the amount of the amino acids, fatty acid, glycogen, taurine, EPA, DHA as well as the Zn, Fe and Se) will be measured at multiple growth stages and in different seasons. The descriptive statistics and the correlation analysis among different traits will be conducted. 2) The SNP will be genotyped using reduced-representation sequencing of several families, and the quantitative trait loci of the growth and the nutritional composition will be mapped by the QTL analysis to obtain major quantitative loci. 3) The 486 females and the one male were used for resequencing to screen and genotype the SNPs, and the fine mapping of the growth and nutritional composition will be conducted by the genome-wide association analysis to identify the associated genes and variations. 4) The genes obtained by the QTL and GWAS together with those obtained by the transcriptome sequencing of the individuals with extreme phenotype will be designed as the key genes underlying the phenotypic variations. The expression of the key genes will be assayed in the families used for the QTL and GWAS analysis to get the cis-regulated loci and the trans-regulated genes. Combined with the co-expression mapping, the gene network related to the growth and nutritional composition will be constructed. This study will dissect the genetic architecture of the growth and the nutritional content in oyster and obtain the associated SNP markers potentially used for the molecular breeding for Pacific oyster to produce the oysters with fast growth and high quality.

改良生长和营养品质性状是解决我国牡蛎产业高产低效现状的重要途径，基于全基因组信息的分子育种使批量育成高品质新品种以提高牡蛎产业效益成为可能。项目组率先构建了牡蛎全基因组序列精细图谱，完成了全球长牡蛎种质资源的收集, 构建了486个关联家系并进行同质化驯养。在此基础上，对不同季节和生长阶段的体尺规格和营养物质（氨基酸、糖原、牛磺酸、微量元素等）的含量及组成进行定期检测；对典型家系进行精简基因组测序，以定位生长和营养品质性状主效QTL；利用重测序方法对SNP进行筛查与分型，通过GWAS实现对目标性状的精细定位；以关键基因的表达量为性状进行关联和连锁分析，结合表型极端个体的基因表达研究，构建生长与营养品质性状遗传调控网络。本研究旨在解析牡蛎生长与营养品质性状的遗传机制，获得目标性状的主效位点和关键基因，构建目标性状调控网络，批量筛查用于育种的SNP标记，为育成生长快、品质优的牡蛎新品种奠定基础。

长牡蛎是我国黄渤海域养殖产量最高的双壳贝类，但其高端产品匮乏，对品质性状进行遗传改良是亟待解决的问题。本文通过连锁和关联分析对品质性状进行精细定位，主要结论如下: (1) 牡蛎品质性状遗传力评估：糖原，蛋白质，脂肪的狭义遗传力估计值分别为0.29±0.02,0.38±0.02和0.58±0.08。且糖原和蛋白质(-0.95±0.004)以及脂肪和蛋白质(-0.59±0.05)间存在强的负遗传相关，脂肪和糖原间存在正相关 (0.16±0.06). (2) 牡蛎生长品质性状QTL定位：精简基因组测序对5024 个单倍型标记构建遗传连锁图谱，均匀分布于10 条连锁群，图谱总长1982.07cM，独特位点平均间距 0.68 cM，是目前牡蛎中上图标记最多、密度最大图谱。品质性状QTL 定位表明，生长，脂肪酸，氨基酸，糖原等17 个性状定位到41 个区间，且区间基因参与其代谢调控和转运。(3) 牡蛎生长品质性状全基因组关联分析：通过构建427 个半同胞家系，对 19个生长和品质性状关联分析找到 33 个基因组模块，通过对连锁不平衡区间的基因解读，鉴定出700余个性状相关基因，具极大分子育种价值。此外构建遗传调控模块，鉴定出影响糖原和氨基酸的基因组区域3个。(4) 全基因组单倍型关联分析：由于上述单分子标记 GWAS 分析并未得到显著的成簇 SNP，我们通过 190K 芯片分型数据构建全基因组单倍型块，并进 一步进行单倍型关联分析，最终得到 2916 个单倍型块，其中 25 个单倍型与目标显著相关。其中 5 个单倍型中包含单标记全基因组关联分析中得到的显著 SNP，这些单倍型将作为优秀单倍型进行进一步验证应用。 (5)构建品质性状代谢调控网络: 锁定糖原和脂肪酸代谢的关键基因生糖蛋白、糖原合成磷酸化酶PPP1R3B, 调控糖异生基因CYP17A1, 游离脂肪酸受体FFAR4进行功能验证。结果表明生糖蛋白和PP1R3R均通过调控糖原合成，影响胞内糖原含量。而CYP17A1通过调控糖原异生，调控糖原含量。综上所述，该研究为牡蛎遗传改良提供大量候选标记与关键基因，结合基因功能研究手段，候选基因影响性状的遗传机制进一步坐实。这将作为生长和品质等重要经济性状的分子育种提供重要靶标，加速分子育种进程。