Identify Key Gene Resources Of Carcass And Meat Quality Traits Of Qingyu Pig Based On Resuquencing Data

Qingyu pig is an important local breed resource and belongs to a group of mountain pigs around the basin in the southwest type.Qingyu pig has strong fat deposituon ability,developed leg and hip muscles,rich intramuscular fat,rich flavor and excellent meat quality,but the slaughter rate and lean meat rate are low.Detect the key QTL and candidate genes of carcass and meat quality traits of Qingyu pigs can improve the carcass performance of Qingyu by molecular breeding,while retaining the the advantages of Qingyu pigs in meat quality traits.Genome-wide association study(GWAS)is the most direct method for detecting genetic resources of traits.At present,there is no GWAS study specifically for carcass and meat quality traits of Qingyu pigs.It is urgent to use GWAS to find mutation sites and candidate gene resources that are significantly associated with carcass and meat quality traits of Qingyu pigs.In this study,30 purebred Qingyu pigs were sequenced using re-sequencing technology to obtain 18 436 759 high-quality SNPs throughtout the genome.Carcass traits(carcass weight,carcass length,backfat thickness at 6-7 ribs,average backfat thickness,loin muscle area,leaf fat weight,leg and hip weight)and meat quality traits(drip loss,pressure loss,cooking loss,pH for longissmus dorsi,pH for semimembranosus,loin muscle color,semimembranosus color,loin muscle tenderness,loin muscle firmness)for GWAS by single-mark mixed linear model,and the bonferroni method was used to correct the association analysis results.The main results are as follows:1.Based on the single-mark linear mixed model,this study identified 18 SNP loci that were significantly associated with 9 carcass traits that reached genome-wide or chromosomal significance.These SNP loci were mainly located at 1,3,6,7,9,11,13,15,18 and X chromosomes.Through candidate gene analysis,12 candidate genes were found in the 40 kb region near the significant site,including: UNC80,RPE,RUBCNL,DST,OPA1,DNER,HEYL,NT5C1 A,CDKAL1,UBTFL1,LOC100737633 and PHACTR1.2.Aiming at the meat color and pH phenotype values at three different time nodes (45min,24 h and 48 h after slaughter)of Qingyu pigs after slaughter,the time-specific genes affecting pork color and pH at different time nodes were tapped.Through GWAS of loin muscle pH and color: 11 and 69 SNPs were significantly associated with loin muscle pH and color,respectively.Through candidate genes search,4candidate genes for pH and 26 candidate genes for color were founcd respectively.The GWAS of psoas muscle pH and color was found that 32 SNPs were significantly associated with the psoas muscle pH,and 29 SNPs were significantly correlated with psoas muscle color,and 6 and 14 candidate genes were found,respectively.Comparing the GWAS results of different time nodos,a total of 16 SNP loci were found to overlap in at least two traits.There are three candidate genes TIAM2,MYCT1 and UQCRFS1 near these overlapping loci.In summary,based on whole-genome resequencing data,this study identified the SNPs and candidate genes related to carcass and meat quality traits of Qingyu pigs using single-marker regression analysis,and through literature search and functional analysis,finally determined 8 important Candidate genes related to carcass and meat quality traits(UNC80,TIAM2,UQCRFS1,ATP4 A,PHGDH,HMGCS2,BNIP3,RYR3).This study initially explored the genetic resources that affected the carcass and meat quality traits of Qingyu pigs,and provide an important theoretical basis for the conservation and genetic improvement of carcass and meat quality traits of Qingyu pigs.