丹系大白母猪背膘厚性状的全基因组关联分析

A genome-wide association study of backfat thickness traits in Denmark Large White pigs

背膘厚影响生猪育肥效果、脂肪沉积能力及母猪繁殖性能,是大白猪选育的重要指标之一。为寻找与丹系大白母猪背膘厚性状相关的分子标记,利用55K SNP芯片对695头大白母猪群体进行基因分型,并对背膘厚性状进行全基因组关联分析(GWAS),筛选显著影响背膘厚性状的单核苷酸多态性(SNP)位点及候选基因。结果表明:丹系大白母猪平均背膘厚为9.33 mm,经质控后共获得64812个SNP位点,GWAS分析筛选出2个与背膘厚显著相关的SNPs(rs332580652、rs336799903);群体遗传多样性分析显示,仅rs336799903多态性分布处于Hardy-Weinberg平衡,且该位点在丹系大白猪群体中呈中度多态;对关联显著的SNPs上下游200 kb内编码基因进行筛查,共发现4个候选基因(ENSSSCG00000021336、THEG、ENSSSCG00000020950、ENSSSCG00000026639);对关联显著的SNPs与染色质修饰关系进行注释,发现rs332580652仅仅在肝脏组织中存在H3K27me3修饰,而rs336799903在猪的不同组织中存在H3K27me3和ATAC修饰。综上,利用GWAS筛选出丹系大白母猪背膘厚相关SNPs及候选基因,为后续通过分子育种手段降低丹系大白母猪背膘厚进而改善猪肉品质,为生猪绿色健康养殖提供一定的理论依据和借鉴。

Backfat thickness(BFT)could affect the fattening effect,fat deposition ability and reproductive performance of sows,which acts as an important index for breeding in Large White pigs.In order to identify the molecular markers related to backfat thickness of Large White pigs,695 samples with backfat thickness records were genotyped by porcine 55K SNP beadchip.Then,we screened out significant SNPs and candidate genes related to backfat thickness by genome-wide association analysis(GWAS).Results showed that the average of backfat thickness in Denmark Large White pigs was 9.33 mm.After quality control,a total of 64812 SNPs were obtained and 2 significant SNPs(rs332580652,rs336799903)related to backfat thickness were screened by GWAS analysis.Population genetic diversity analysis indicated that only the polymorphism of rs336799903 mutation was in Hardy-Weinberg equilibrium,and this locus showed a moderately polymorphic in Denmark Large White pigs.Based on the screening of coding genes in the region between 200 kb upstream and downstream of the associated significant SNP loci,we identified 4 candidate genes(ENSSSCG00000021336,THEG,ENSSSCG00000020950,ENSSSCG00000026639)related to backfat thickness.Based on the annotation of the relationship between significant SNPs and chromatin state,we found that the mutation of rs332580652 affected H3K27me3 modification in the liver tissue,but rs336799903 could affect H3K27me3 and ATAC modification in different tissues.Thus,our findings that screened out important SNPs and candidate genes will provide a theoretical basis and reference for the molecular breeding of backfat thickness to improve pork quality and healthy breeding of pigs.