广益黑猪繁殖性状的全基因组关联分析

Genome-wide association study of reproductive traits in Guangyi black pigs

选取441头广益黑猪经产母猪为研究对象,利用猪50KSNP芯片对猪耳组织DNA进行基因型分型,PLINK 1.9质控后,采用GMAT中的重复力模型进行猪繁殖性状相关的全基因组关联分析,确定显著位点。结果表明:441头经产广益黑猪母猪的耳组织DNA基因分型共获得50898个SNPs,经质控剩余46165个SNPs位点用于关联分析;平均亲缘关系系数为-0.0022,平均亲缘关系较远,不存在明显的群体分层;总产仔数性状有1个SNP在全基因组范围内达到显著相关,4个SNPs达到潜在显著关联,候选基因包括PIK3C3、ENSSSCG00000003753、MAP3K3、DCAF7;产活仔数性状有6个SNPs潜在显著关联,候选基因包括ZNF585A、ENSSSCG00000022411、ZNF784、ENSSSCG00000029007、PigE-108A11.5、PigE-108A11.3、ENSSSCG00000023343;弱仔性状有1个SNP达潜在显著关联,候选基因包括KRTAP7-1和TIAM1;经基因功能分析推测,PIK3C3、MAP3K3可能是影响猪总产仔数的候选基因。

This experiment involved the collection of ear tissue samples from 441 multiparous sows of Guangyi black pigs.DNA was extracted and genotyped using a porcine 50K SNP beadchip.Quality control(QC) was performed using PLINK 1.9 software.Genome-wide association analysis of porcine reproductive traits was conducted based on QC results using the mixed linear model of GMAT.Results revealed that among 414 Guangyi black sows,a total of 50 898 SNPs were obtained,but after quality control,46 165 SNPs remained suitable for GWAS.The population's kinship coefficient was -0.002 2,indicating a relatively low average genetic relationship and negligible population stratification.One SNP exhibited significant correlation,and four SNPs showed potential significant correlation with total number born at a genome-wide level.The associated candidate genes included PIK3C3,ENSSSCG00000003753,MAP3K3 and DCAF7.Additionally,six SNPs potentially displayed significant correlation with the number born alive,involving associated candidate genes such as ZNF585A,ENSSSCG00000022411,ZNF784,ENSSSCG00000029007,PigE-108A11.5,PigE-108A11.3 and ENSSSCG00000023343.Furthermore,one SNP showed potential significant correlation with the number born weak,and the associated candidate genes were KRTAP7-1 and TIAM1.Gene functional analysis suggested that PIK3C3 and MAP3K3 might be candidate genes influencing the total number born in Guangyi black pigs.