| Pork quality is an economically important trait and improving pork quality is an important goal in modern pig breeding programs.However,it is difficult to improve pork quality by traditional breeding methods due to its complexity and low heritability,in addition to the difficulty of phenotypes.Therefore,understanding the genetic mechanisms that underlie meat quality traits is essential to achieve the goal.This study involved 610 pigs from a [Duroc×?Landrace×Yorkshire?]?DLY?three-way crossed population with record of pH,RG,drip loss,a* value,b* value,L* value,meat color,marbling and moisture content measured at postmortem 36 h.GWAS for these traits have been conducted using the Illumina PorcineSNP60 K Beadchip.The GWAS results showed that a total of 17 chromosome-wide significant SNPs were identified for these traits,of which,3 SNPs reached genome-wide significance level.We also identified two distinct QTLS?QTL1 and QTL2?at 121 Mb and 134 Mb on SSC15 with pleiotropic effects on RG,drip loss and meat color.In the QTL1 region?129135 Mb?,we identified a significant SNP SS478944394 at 129.80 Mb associated with RG(P < 10-11)and another SNP SS107833468 at 134.40 Mb associated with drip loss and meat color(P < 10-5).The PRKAG3?133.80 Mb?gene nearby the two SNPs regarded as strong candidate for the QTL.To verify it,15 SNPs around PRKAG3 gene were genotyped and included in the association analysis.The result showed that SNP rs42?133.80 Mb?in the coding region of PRKAG3 was significantly associated with multiple meat quality traits,including RG(P = 1.08×10-49),drip loss(P = 1.95×10-12),pH(P = 3.19×10-6),L* value?P = 1.54×10-9?,a* value(P = 9.36×10-8)and b* value(P = 2.55×10-4).This locus explained 40.6% and 8.6% of phenotypic variance in RG and drip loss,respectively.In the QTL2 region?120.78122.78 Mb?,SNP SS478943559?121.78 Mb?showed consistent association with RG(P = 4.89×10-10),drip loss(P = 2.39×10-5)and b* value(P = 2.55×10-4).Two nearby genes,FASTKD2 and MDH1 B were considered as candidate genes because of their functional relevance to glucose metabolism.To refine the QTL location,45 additional SNPs within the QTL region were analyzed.The results showed the SNP SS478943559 was still the most significant SNP and it lied in a 23 Kb haplotype block.Two missense mutations were individually detected in FASTKD2 and MDH1 B through cDNA sequencing.The minor allele frequency of g.6742G>A in FASTKD2 gene was 40%.This SNP was significantly associated with RG(P = 4.47×10-4)and drip loss(P = 5.37×10-4),thus it can be used for marker assisted selection?MAS?.No significant association was obtained between g.3597A>G in MDH1 B gene and RG?P = 0.93?and drip loss?P = 0.40?,so it can be excluded as causal mutation underlying the QTL.This study provides insights into the molecular basis of DLY pigs,and benefits the development of molecular markers for MAS and further identification of causative genes or causative mutations for RG,drip loss and other related meat quality traits. |
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