Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China.
Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China..
Genomics. 2018 May;110(3):171-179. doi: 10.1016/j.ygeno.2017.09.009. Epub 2017 Sep 21.
In this study, data genotyping by sequence (GBS) was used to perform single step GWAS (ssGWAS) to identify SNPs associated with the litter traits in domestic pigs and search for candidate genes in the region of significant SNPs. After quality control, 167,355 high-quality SNPs from 532 pigs were obtained. Phenotypic traits on 2112 gilt litters from 532 pigs were recorded including total number born (TNB), number born alive (NBA), and litter weight born alive (LWB). A single-step genomic BLUP approach (ssGBLUP) was used to implement the genome-wide association analysis at a 5% genome-wide significance level. A total of 8, 23 and 20 significant SNPs were associated with TNB, NBA, and LWB, respectively, and these significant SNPs accounted for 62.78%, 79.75%, and 58.79% of genetic variance. Furthermore, 1 (SSC14: 16314857), 4 (SSC1: 81986236, SSC1: 66599775, SSC1: 161999013, and SSC1: 267883107), and 5 (SSC9: 29030061, SSC2: 32368561, SSC5: 110375350, SSC13: 45619882 and SSC13: 45647829) significant SNPs for TNB, NBA, and LWB were inferred to be novel loci. At SSC1, the AIM1 and FOXO3 genes were found to be associated with NBA; these genes increase ovarian reproductive capacity and follicle number and decrease gonadotropin levels. The genes SLC36A4 and INTU are involved in cell growth, cytogenesis and development were found to be associated with LWB. These significant SNPs can be used as an indication for regions in the Sus scrofa genome for variability in litter traits, but further studies are expected to confirm causative mutations.
在这项研究中，我们使用基于序列的数据基因分型（GBS）来进行单步 GWAS（ssGWAS），以鉴定与家猪产仔性状相关的 SNP，并在显著 SNP 区域搜索候选基因。经过质量控制，从 532 头猪中获得了 167355 个高质量 SNP。记录了 532 头母猪的 2112 窝母猪的表型性状，包括总产仔数（TNB）、活产仔数（NBA）和产活仔窝重（LWB）。采用单步基因组 BLUP 方法（ssGBLUP），在全基因组显著水平 5%处进行全基因组关联分析。共鉴定到与 TNB、NBA 和 LWB 显著相关的 SNP 分别为 8、23 和 20 个，这些显著 SNP 分别解释了遗传变异的 62.78%、79.75%和 58.79%。此外，在 SSC14:16314857 处鉴定到 1 个（SSC14:16314857）、在 SSC1:81986236、SSC1:66599775、SSC1:161999013 和 SSC1:267883107 处鉴定到 4 个、在 SSC9:29030061、SSC2:32368561、SSC5:110375350、SSC13:45619882 和 SSC13:45647829 处鉴定到 5 个与 TNB、NBA 和 LWB 显著相关的 SNP，推测为新的位点。在 SSC1 上，发现 AIM1 和 FOXO3 基因与 NBA 相关；这些基因增加卵巢生殖能力和卵泡数量，降低促性腺激素水平。与 LWB 相关的基因 SLC36A4 和 INTU 参与细胞生长、细胞发生和发育。这些显著的 SNP 可以作为 Sus scrofa 基因组中与产仔性状变异相关的区域的指标，但需要进一步的研究来确认因果突变。
