Phenotype Measurement And Genetic Deciphering For Pork Color Traits

Meat color is one of the most direct sensory indicators of pork quality determining consumers’purchasing behavior.With the intensive breeding of growth traits and lean rate,many commercial pig breeds have defects of generating inferior meat color,which prompts the breeding circle to pay great attention to the breeding of pork color.However,the determination of meat color requires slaughtering,and the detection of its phenotype is mainly based on the physical determination of optical instruments.Few studies based on the detection of specific biological substances for meat color.Therefore,the interpretation of genetic mechanism for meat color and the establishment of efficient breeding technology has been slow.Aimed at the genetic mechanism of meat color formation,we carried out accurate phenotypic detection for muscle myoglobin（Mb）content in a large scale of 7^thgeneration of heterogeneous population（N=624）from aspect of chemical methods.And based on physical methods,we used Minolta instrument to measure 9 meat color indicators at 45minutes and 24 hours after slaughter in longissimus muscle（LT）.Results show that,in the same individual,muscle Mb content is significantly positive correlated with phenotypic values of color score,Minolta a*for redness and Minolta b*for yellowness,while was negatively correlated with Minolta L*for lightness.Thus,myoglobin is the major ingredients for meat color.When we make breeding strategies for muscle Mb content to improve meat color,it is necessary to systematically evaluate the phenotypic and genetic correlation between muscle Mb content and other meat quality traits such as marbling score,firmness,loin eye area,and overall liking.And the phenotypic and genetic correlation between muscle Mb content other traits including growth,carcass,fat deposition traits,blood physiological parameters are also needed.In this study,phenotypic and genetic correlations were conducted between muscle Mb content and 93 other traits including the above classification of traits.The results showed that muscle Mb content was positively correlated with marbling score,oliliness,shearforce and overall likeing,but negatively correlated with moisture content,firmness,tremble score and loin eye area.The results suggested that the genetic improvement for muscle Mb content will not affect growth,carcass,and blood physiological parameters.This will provide an important experimental basis and weight reference for the application of myoglobin content in breeding practice.In addition to accurate phenotyping,we performed the whole genome sequence at the average genome coverage of 7～8×in the 624 F₇individuals.After quality control,a total of3,022 miliion variants were used to performed genome-wide association analysis（GWAS）on 9 meat color indicators including Mb content.Results showed that a total of 12,564significant variants(P<5×10^-8)were detected,99.8%（12,542 loci）of which were distributed on SSC 12,and 19 were located on SSC 11,2 were located on SSC 15;and1was located on SSC 16.All significant loci can be summarized into six QTL regions.Except for significant loci for a*detected at 45min after slaughter in LT muscle,QTLs for the other eight meat color-related traits were located in a 5.05 Mbp region of 53.41～58.46Mbp on SSC 12.We use the criterion of the 2 LOD-drop and r²≥0.8 to determine the confidence intervals（CI）of QTL for each color trait and found that the confidence intervals of the QTLs affecting muscle Mb content,color score detected at 24h after slaughter,a*for redness detected at 45min and 24h after slaughter,and b*for yellowness detected at45min after slaughter in LT muscle were highly overlaped.By combining the overlapping regions of the CI described above,we finally fine-mapped the QTL interval affecting meat color to a 290Kb region（55.06～55.35 Mbp）on SSC12,in which MYH13,MYH8,MYH4,MYH1,MYH2 and MYH3 located.To further explore the causal genes affecting meat color,we obtain expression data for longissimus thoracis samples from whole transcriptome RNA sequencing on about 300 F₇individual having accurate phenotype.After quality control,284 high quality transcriptome data were obtained.QTT analysis was performed and found that the expression levels of MYH13,MYH8,MYH1 and MYH2 in CI region were significantly correlated with at least one trait mentioned above,which further indicated that they were important candidate causal genes for color traits.Furthermore,using the whole genome SNP and indel mutations,e QTL mapping analysis of whole transcriptome individuals mentioned above discovered.significant e QTLs of MYH8 and MYH13.But the most significant SNP located on MYH1 and MYH2,indicating that mutual regulations exist among these MYH family genes.The top signal of Jxlab＿color＿1 for muscle Mb content,color score detected at 24h after slaughter,a*for redness detected at 45min and 24h after slaughter,and b*for yellowness detected at 45min after slaughter in LT muscle is located on MYH13 gene,which can explain the phenotypic variation ranging from 14.25 to 27.8%.It was also significantly correlated with other meat quality traits,such as marbling score,with the P value ranging from 2.43×10^-5to 4.26×10^-32.In summary,this study systematically investageted the phenotypical and genetic correlations between muscle Mb content and other traits including meat quality and identify the candidate genes and mutations significantly associated with muscle Mb content,color score,a*for redness,b*for yellowness.The results provided the theoretical basis and efficient breeding technology for the selection of high-quality pork.