摘要鸡(Gallus gallus)脚重性状为鸡产业中的重要经济性状。为了揭示鸡脚重性状的遗传基础，寻找可用于鸡脚改良的分子标记，本研究以核心群京海黄鸡为实验动物，测定其脚重，利用简化基因组测序技术在整个基因组范围内检测与脚重相关的SNPs。共检测到16个与脚重相关的SNPs位点，其中13个集中分布在4号染色体上72.8~77.9 Mb区域；2个SNP位点rs475641139和rs475548810达到5% Bonferroni全基因组显著水平(P＜5.5E-07)，其余位点达到全基因组潜在显著水平(P＜1.1E-05)。筛选每个SNP周围1 Mb区域内的基因，共找到9个可能的候选基因，并使用基因本体论(Gene Ontology, GO)数据库对9个候选基因的细胞组分、分子功能和参与的生物学进程进行了分析。结果表明二氢蝶啶还原酶(dihydropteridine deductase, QDPR)基因、LIM域结合蛋白2(LIM domain-binding protein 2, LDB2)基因、类184B家族(family with sequence similarity 184 member B, FAM184B)基因、复合信号免疫球蛋白J结合蛋白(recombination signal binding protein for immunoglobulin kappa J region, RBPJ)基因、纤维母细胞生长因子结合蛋白2(fibroblast growth factor-binding protein 2, FGFBP2)基因、富亮氨酸重复蛋白5(F-box and leucine-rich repeat protein 5, FBXL5)基因、胆囊收缩素受体A(cholecystokinin receptor type A, CCK1R)基因、肌动蛋白互作蛋白1(WD repeat containing protein 1, WDR1)基因和类桶状蛋白4(tubby like protein 4, TULP4) 9个基因和4号染色体72.8~77.9 Mb区域可能为影响鸡脚重性状的重要候选基因和潜在功能区域。本研究为鸡脚重性状的标记辅助选择提供了理论依据。
Abstract：The feet weight trait of chicken (Gallus gallus) is one of the most important economic traits in the chicken industry. In order to reveal the genetic basis of feet weight trait and scan molecular markers which can be used to improve the feet weight trait, the feet weight trait was measured after Jinghai yellow chicken in core group being slaughtered. Genome-wide association study was carried to detect SNPs that was associated with feet weight trait by using specific-locus amplified fragment sequencing technology. Chicken reference genome was analyzed using the prediction software based on the gene characteristics to choose the appropriate restriction enzyme. Then a series of procedures were put into effect to create database to do the sequencing by IlluminaHiSeq2000. A total of 103 680 specific-locus amplified fragment sequencing technology (SLAFs) were found with an average read depth of 5.46 in the research population. Of these, 88 135 were found to be polymorphic (85%). The distribution of the SLAFs was even throughout the whole genome. After SNPs were detected among the defined SLAF fragments, 90 929 SNPs were identified after quality control measures. Then the SNPs that associated with chicken's feet weight trait were used to do enome level SNP classification and analysis method (GWAS) analysis, 16 SNPs that were related to feet weight were detected. 2 SNPs of rs475641139 and rs475548810 reached 5% Bonferroni genome-wide significance (P＜5.5E-07) and the rest of 14 SNPs reached "suggestive" genome-wide significance (P＜1.1E-05). At last, 9 potential functional genes were got after screening every important SNPs' ambient 1 Mb window areas (SNP location right and left 0.5 Mb). The cellular component, molecular function and biological process were analyzed by using Gene Ontology (GO) database. Furthermore, all 13 SNPs were distributed in the region of 72.8~77.9 Mb on chromosome 4. Nine genes of dihydropteridine deductase gene (QDPR), LIM domain-binding protein 2 gene (LDB2), family with sequence similarity 184 member B gene (FAM184B), recombination signal binding protein for immunoglobulin kappa J region gene (RBPJ), fibroblast growth factor-binding protein 2 gene (FGFBP2), F-box and leucine-rich repeat protein 5 gene (FBXL5), cholecystokinin receptor type A gene (CCK1R), WD repeat containing protein 1 gene (WDR1) and tubby like protein 4 gene (TULP4) and 72.8~77.9 Mb region on chromosome 4 were important candidate genes and region affecting feet weight trait in Jinghai yellow chcken. This study can provide the theory basis for the feet weight trait's marker assisted selection.
