College of Animal Science and Technology, Sichuan Agricultural University , Chengdu, Sichuan , China.
College of Life Science, Sichuan Agricultural University, Yaan, Sichuan , China.
Physiol Genomics. 2018 Dec 1;50(12):1026-1035. doi: 10.1152/physiolgenomics.00071.2018. Epub 2018 Oct 5.
Total number born (TNB), number born alive (NBA), and litter weight born alive (LWB) are critically important traits in pig production. The sow's parity is one of the major factors influencing litter traits. Because of monogenic or polygenic contributions and the presence of temporal gene effects in different sows' parities, it is difficult to clarify the biological and genetic background. To systematically explore the genetic mechanism of litter traits, we conducted 18 GWASs using single-step GWAS (ssGWAS) based on two breeds (908 Landrace and 1,130 Large White sow litter records) for each litter trait in different parities. A total of 300 Landrace and 300 Large White sows were genotyped by sequencing (GBS). ssGWAS was performed separately for each breed and each parity due to population stratification and temporal gene effect. In summary, we identified 80 (15 for Landrace and 65 for Large White), 227 (52 for Landrace, 175 for Large White), and 187 (34 for Landrace, 153 for Large White) single nucleotide polymorphisms (SNPs) affecting TNB, NBA, and LWB, respectively. Of them, we suggest that a total of 22 loci (SSC1: 125098202, SSC1: 117560058, SSC14: 147794697, SSC8: 84823302, SSC9: 143554876, and SSC9: 138766097 for Landrace; SSC1: 4023577, SSC1: 3859573, SSC1: 4891063, SSC16: 5197665, SSC10: 32050819, SSC13: 13552924, SSC13: 92819, SSC17: 3579607, SSC13: 196698221, SSC7: 30918403, SSC16: 46221484, SSC16: 46169204, SSC2: 41988642, SSC2: 44475457, SSC2: 42521875, and SSC7: 58411951 for Large White) are shared by TNB, NBA, and LWB. These results indicate the existence of gene temporal effect in each parity. Furthermore, our findings suggest four interesting candidate genes (FBXL7, ALDH1A2, LEPR, and DDX1) associated with litter traits in different parities that have a major effect on embryonic development progression. In conclusion, 22 crucial SNPs and four interesting candidate genes were identified for three litter traits across six parities. These findings advance our understanding of the genetic architecture of litter traits and confirm the presence of temporal gene effects in different parities. Importantly, functional validation studies for findings of particular interest are recommended in litter traits.
总产仔数（TNB）、产活仔数（NBA）和产活仔窝重（LWB）是猪生产中非常重要的性状。母猪胎次是影响窝产仔数的主要因素之一。由于单基因或多基因的贡献以及不同胎次母猪中存在的时间基因效应，很难阐明其生物学和遗传背景。为了系统地探索窝产仔数的遗传机制，我们基于两个品种（908 头长白母猪和 1130 头大白母猪的窝产仔记录），针对不同胎次的每个窝产仔数进行了 18 项单步 GWAS（ssGWAS）。共有 300 头长白母猪和 300 头大白母猪通过测序（GBS）进行了基因分型。由于群体分层和时间基因效应，每个品种和每个胎次都分别进行了 ssGWAS。总的来说，我们鉴定出了分别影响 TNB、NBA 和 LWB 的 80 个（长白母猪 15 个，大白母猪 65 个）、227 个（长白母猪 52 个，大白母猪 175 个）和 187 个（长白母猪 34 个，大白母猪 153 个）单核苷酸多态性（SNP）。其中，我们建议共有 22 个位点（SSC1：125098202、SSC1：117560058、SSC14：147794697、SSC8：84823302、SSC9：143554876 和 SSC9：138766097 对长白母猪；SSC1：4023577、SSC1：3859573、SSC1：4891063、SSC16：5197665、SSC10：32050819、SSC13：13552924、SSC13：92819、SSC17：3579607、SSC13：196698221、SSC7：30918403、SSC16：46221484、SSC16：46169204、SSC2：41988642、SSC2：44475457、SSC2：42521875 和 SSC7：58411951 对长白母猪）同时影响 TNB、NBA 和 LWB。这些结果表明每个胎次都存在基因时间效应。此外，我们的研究结果还提示了四个有趣的候选基因（FBXL7、ALDH1A2、LEPR 和 DDX1）与不同胎次的窝产仔数有关，这些基因对胚胎发育进程有重要影响。总之，我们在六个胎次中鉴定了 22 个关键 SNP 和四个有趣的候选基因，用于三个窝产仔数性状。这些发现增进了我们对窝产仔数遗传结构的理解，并证实了不同胎次中存在时间基因效应。重要的是，建议对窝产仔数性状的特定感兴趣的发现进行功能验证研究。
