Abstract
Intramuscular fat (IMF) is an important quantitative trait of meat, which affects the associated sensory properties and nutritional value of pork. To gain a better understanding of the genetic determinants of IMF, we used a composite strategy, including single-locus and multi-locus association analyses to perform genome-wide association studies (GWAS) for IMF in 1,490 Duroc boars. We estimated the genomic heritability of IMF to be 0.23 ± 0.04. A total of 30 single nucleotide polymorphisms (SNPs) were found to be significantly associated with IMF. The single-locus mixed linear model (MLM) and multiple-locus methods multi-locus random-SNP-effect mixed linear model (mrMLM), fast multi-locus random-SNP-effect efficient mixed model association (FASTmrEMMA), and integrative sure independence screening expectation maximization Bayesian least absolute shrinkage and selection operator model (ISIS EM-BLASSO) analyses identified 5, 9, 8, and 21 significant SNPs, respectively. Interestingly, a novel quantitative trait locus (QTL) on SSC 7 was found to affect IMF. In addition, 10 candidate genes (BDKRB2, GTF2IRD1, UTRN, TMEM138, DPYD, CASQ2, ZNF518B, S1PR1, GPC6, and GLI1) were found to be associated with IMF based on their potential functional roles in IMF. GO analysis showed that most of the genes were involved in muscle and organ development. A significantly enriched KEGG pathway, the sphingolipid signaling pathway, was reported to be associated with fat deposition and obesity. Identification of novel variants and functional genes will advance our understanding of the genetic mechanisms of IMF and provide specific opportunities for marker-assisted or genomic selection in pigs. In general, such a composite single-locus and multi-locus strategy for GWAS may be useful for understanding the genetic architecture of economic traits in livestock.
Highlights
In the past few decades, increasing lean meat content and reducing backfat thickness have been the main targets of pig breeding programs (Dong et al, 2014)
As one of the largest genome-wide association studies (GWAS) for Intramuscular fat (IMF), we identified 30 single nucleotide polymorphisms (SNPs) that were significantly associated with IMF by combining single-locus and multi-locus GWAS
Among the 30 significant SNPs, the phenotypic variance explained (PVE) of eight of them is greater than 2% in at least one GWAS method, and the PVE of rs80946633 and rs329147631 was even greater than 5%
Summary
In the past few decades, increasing lean meat content and reducing backfat thickness have been the main targets of pig breeding programs (Dong et al, 2014). Due to insufficient attention to the quality of pork and negative correlation with selected traits, such as backfat thickness (Sellier et al, 2010), it has been challenging to satisfy consumer demand for meat quality GWAS for IMF in Pigs et al, 2013). Intramuscular fat (IMF) is an important trait directly related to flavor and consumer acceptance (Sato et al, 2017; Won et al, 2018). Many studies have suggested that IMF influences pork tenderness, hydraulics, shearing force, and juicy flavor (Hocquette et al, 2010; Cho et al, 2015; Gong et al, 2018). Muscles with sufficient IMF content are suitable for conversion to dry products (Bosi and Russo, 2004)
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