Table_1_Genome-Wide Association Study-Based Identification of SNPs and Haplotypes Associated With Goose Reproductive Performance and Egg Quality.xlsx

Geese are one of the most economically important waterfowl. However, the low reproductive performance and egg quality of geese hinder the development of the goose industry. The identification and application of genetic markers may improve the accuracy of beneficial trait selection. To identify the genetic markers associated with goose reproductive performance and egg quality traits, we performed a genome-wide association study (GWAS) for body weight at birth (BBW), the number of eggs at 48 weeks of age (EN48), the number of eggs at 60 weeks of age (EN60) and egg yolk color (EYC). The GWAS acquired 2.896 Tb of raw sequencing data with an average depth of 12.44× and identified 9,279,339 SNPs. The results of GWAS showed that 26 SNPs were significantly associated with BBW, EN48, EN60, and EYC. Moreover, five of these SNPs significantly associated with EN48 and EN60 were in a haplotype block on chromosome 35 from 4,512,855 to 4,541,709 bp, oriented to TMEM161A and another five SNPs significantly correlated to EYC were constructed in haplotype block on chromosome 5 from 21,069,009 to 21,363,580, which annotated by TMEM161A, CALCR, TFPI2, and GLP1R. Those genes were enriched in epidermal growth factor-activated receptor activity, regulation of epidermal growth factor receptor signaling pathway. The SNPs, haplotype markers, and candidate genes identified in this study can be used to improve the accuracy of marker-assisted selection for the reproductive performance and egg quality traits of geese. In addition, the candidate genes significantly associated with these traits may provide a foundation for better understanding the mechanisms underlying reproduction and egg quality in geese.

鹅是经济价值最为重要的水禽之一。然而，鹅的繁殖性能偏低、蛋品质不佳，制约了鹅产业的发展。遗传标记（genetic markers）的鉴定与应用，可提升有益性状选择的精准度。为鉴定与鹅繁殖性能及蛋品质性状相关的遗传标记，本研究针对鹅初生体重（BBW）、48周龄产蛋数（EN48）、60周龄产蛋数（EN60）及蛋黄颜色（EYC），开展了全基因组关联分析（genome-wide association study, GWAS）。本次GWAS共获取2.896 Tb原始测序数据，平均测序深度为12.44×，并鉴定得到9,279,339个单核苷酸多态性位点（single nucleotide polymorphisms, SNPs）。GWAS分析结果显示，共有26个SNPs与BBW、EN48、EN60及EYC性状显著相关。此外，其中与EN48和EN60显著相关的5个SNPs，位于35号染色体4,512,855至4,541,709 bp区间的单倍型块（haplotype block）内，定位于TMEM161A基因；另有5个与EYC显著相关的SNPs，构成了5号染色体21,069,009至21,363,580 bp区间的单倍型块，其注释基因为TMEM161A、CALCR、TFPI2及GLP1R。上述富集基因涉及表皮生长因子激活受体活性、表皮生长因子受体信号通路调控等生物学过程。本研究鉴定得到的SNPs、单倍型标记及候选基因，可用于提升鹅繁殖性能与蛋品质性状的标记辅助选择（marker-assisted selection）精准度。此外，与上述性状显著相关的候选基因，可为深入解析鹅繁殖与蛋品质形成的分子机制提供理论基础。