Genome-wide Association Study For Meat Trait In Swine

Pork quality is an economically important trait and the key index for pig breeding at present. Thecontinuous appearance of high density SNP chips and the sustainable development of genotypingtechnique make it possible to implement the Genome-wide Association Study(GWAS) in pigs.455pigsof F2generation from a porcine Large White×Minzhu intercross resource population were used as theexperimental animals. The Illumina PorcineSNP60BeadChip(including62,163SNPs)technology, theGenome-wide Rapid Association using the Mixed Model and Regression-GenomicControl(GRAMMAR-GC) method, DMU software and GenABEL software package under the Rstatistical environment were used to carry out the GWAS analysis on the intramuscular fat content(IMF), meat color(MC), tenderness, acidity, moisture, water loss rate, lean meat percentage, lean meatyield, ham lean weight such as a total of16indexes of9traits in longissimus muscle in order to searchfor the genetic variation related to the pork quality traits. The results showed that:1.455pigs were slaughtered and cutted and16indexes related to pork quality were measured andrecorded. The descriptive statistics indicated that the distribution of phenotype values of all traits werein accordance with the character of resource family segregating population. The relationship betweenKF and NF, among WLR24, WLR48, WLR72, between IMF and MS, MC, between L*and MS weresignificant(P <0.01).2. The significant SNPs related to IMF, marbling score, moisture content, meat color score, a*value, ham lean weight were detected using GWAS analysis. The number of significant SNPs at genomelevel were40,37,6,6,4,25and5, respectively. The number of very significant SNPs among themwere27,27,5,1,3,12and2, respectively. The SNPs related to meat color, L*value, b*value, pH24,tenderness, water loss rate and lean meat weight were not detected.3. According to the sequence information of SNP chip, the significant SNPs related to meatquality traits were annotated using Sus scrofa Build9genome database and NCBI database. The resultsindicated that, for IMF, MS, MC, CS and a*value, a total of45SNPs showed significant associationwith one or multiple traits of them. Of the45SNPs,36were located on SSC12. A tatal of24SNPsshowed significant association with one or two traits for ham lean weight and lean meat percentage,19of them located on SSC2.4. According the database information from NCBI, Ensembl, KEGG, Uniprot, and GeneCards, thefunction of genes in the vicinity of the significant SNPs were annotated using bioinformatics andcomparative genomics. The results showed that the gene functions mainly involved in DNA repair,transcriptional regulation and translational control, cytoskeleton and matrix components, adjusting thebody's metabolism of nutrients and balance, cell proliferation, regeneration and apoptosis, kinaseactivity, participating in cellular signal transduction and ion channels constitute, and so on.5. The HAPLOVIEW V3.1program was used to detect the haplotype blocks in this work. Theresults showed that two haplotype blocks associated with pork quality traits were identified on SSC12,and block1was ASGA0100525-ASGA0055225-ALGA0067099-MARC0004712-DIAS0000861for325kb and block2was ASGA0085522-H3GA0056170for0.99kb. For block1, the AGAAG (47.7%and positive effect) and CAGGA (37.0%and negative effect) haplotypes were significantly associated (P <0.001) with IMF, marbling, color a*and color score. Narrowed the scope of the study, MYH1,MYH2, MYH3and MYH4genes contained in haplotype block1were preliminary screened as theimportant candidate genes for meat quality traits.6. In summary, MYH, SLC and GAS gene family were preliminary identified as the key candidategenes and candidate family for meat quality traits in the study.