Identification Of Major QTLs Affecting Intramuscular Fat Traits In Pigs Using Single Marker And Multipliable Mixed Linear Models

Pork is one of the major meat sources for human beings and the output of pork accounts for more than 48%of the world's total meat production.High quality pork can increase the acceptability of consumers,and also bring great profits to farmers and meat processing industry.Therefore,the quality of pork has always been the focus of genetic improvement.Intramuscular Fat?IMF?,specifically,refers to the fat deposited between the muscle fibers and the perimysial fibers.The amount of IMF directly affects the tenderness,flavor,juiciness,and apparent acceptance of the meat.Therefore,it is an important indicator of meat quality.The IMF content of pork is affected by many factors such as heredity,nutrition,and environment,among which heredity is the main cause.According to the statistics of pig QTL database,213 Quantitative Trait Loci?QTL?related to the pig IMF have been identified.However,there has been no substantial breakthrough in the identification of major genes.It is noteworthy that the IMF content of local pig breeds in China?>3%?is much higher than that of Western lean-type pig breeds?about 1.6%?,while more than half of China's commercial pigs?>70%?are sourced from Western pig breeds.So,it is of great significance to improve the quality of pork by purposefully increasing the IMF content of the existing lean-type pig breeds.This study collected data on the intramuscular fat of 1491 Duroc boars and collected DNA from these pig ear tissues.Then we used different kinds of linear mixed models to perform a genome-wide association analysis of the IMF content of Duroc pigs in order to find the key molecular markers that significantly influence the IMF so that can provide reference for the genetic improvement of lean-type pork quality.The research results of this paper mainly include the following points:1.According to the herd pedigree records,the heritability of the IMF was estimated using the constrained maximum likelihood method in the DMU software.The heritability of IMF was found to be 0.26,which is a medium heritability trait.2.Genome-wide association analysis based on univariate linear mixed model was performed using GEMMA software,and a total of 5 genome-level SNPs were detected(P<3.11×10^-5).Among them,WU₁0.2₂₂6432683 is located at 379675bp upstream of chromosome 2 gene C11orf74,WU₁0.2₃₁1233043 is located at 9430bp upstream of chromosome 3 gene GTF2IRD1,and the remaining 3 SNPs are located at a region of approximately 0.023Mb?117.427Mb-117.44Mb?on chromosome 7.Internally,the gene BDKRB2 partially overlaps with the above region.At the same time QTL on chromosome 7was reported for the first time.3.Genome-wide association analysis was performed using three kinds of multivariate linear mixed models in the R language's MrMLM software package.LOD value?3 was used as the test of significance.Multivariate linear mixed models identified a total of 28SNPs that were significantly associated with IMF traits.Of the SNPs,12 SNPs were located within the gene?ROS1,TMEM138,AMH,GET4,RNF115,CASQ2,KIAA1644,FAF1,BDKRB2,and TIAM1?.4.Gene ontology analysis of the above candidate genes revealed that these genes were significantly enriched in eight regulatory pathways including multicellular organism development,tissue development,and development regulation(GO:0007275,P=3.77×10^-2;GO:2000026,P=1.02×10^-2;GO:0050793,P=2.22×10^-2,etc).In this study,a large number of SNPs that affected the IMF content of pigs were further enriched,which further deepened the understanding that pigs'IMF content is a complex quantitative trait,and the identified molecular markers can be directly applied to Duroc and its synthetic lines.The genetic improvement of meat quality traits will lay the foundation for the cultivation of high-quality lean-type breeding pigs.