Abstract
In past decades, meat quality traits have been shaped by human-driven selection in the process of genetic improvement programs. Exploring the potential genetic basis of artificial selection and mapping functional candidate genes for economic traits are of great significance in genetic improvement of pigs. In this study, we focus on investigating the genetic basis of five meat quality traits, including intramuscular fat content (IMF), drip loss, water binding capacity, pH at 45 min (pH45min), and ultimate pH (pH24h). Through making phenotypic gradient differential population pairs, Wright’s fixation index (FST) and the cross-population extended haplotype homozogysity (XPEHH) were applied to detect selection signatures for these five traits. Finally, a total of 427 and 307 trait-specific selection signatures were revealed by FST and XPEHH, respectively. Further bioinformatics analysis indicates that some genes, such as USF1, NDUFS2, PIGM, IGSF8, CASQ1, and ACBD6, overlapping with the trait-specific selection signatures are responsible for the phenotypes including fat metabolism and muscle development. Among them, a series of promising trait-specific selection signatures that were detected in the high IMF subpopulation are located in the region of 93544042-95179724bp on SSC4, and the genes harboring in this region are all related to lipids and muscle development. Overall, these candidate genes of meat quality traits identified in this analysis may provide some fundamental information for further exploring the genetic basis of this complex trait.
Highlights
The most important purpose of pig breeding is the genetic improvement of important economic traits (Price 1999; Zhang et al, 2020)
The extreme individuals were chosen to construct three phenotypic gradient differential population pairs based on the ranking of phenotype values
Based on the pigQTLdb, we found that 10 quantitative trait loci (QTL) related to meat quality and fat metabolism are harbored in this genomic region (Supplementary Table S4)
Summary
The most important purpose of pig breeding is the genetic improvement of important economic traits (Price 1999; Zhang et al, 2020). The aim of genetic improvement of pig breeding has mainly focused on improving meat production through growth rate and feed efficiency, lean percentage, and decreasing backfat thickness. Human-driven selection has indirectly shaped the meat quality traits, such as intramuscular fat content (IMF), pH values, drip loss (DL), and meat color (Herault et al, 2018). From the perspective of population genetics, the effect of human-driven selection as well as natural selection would leave detectable signatures in the genome. Detecting the selection signatures of these important economic traits can provide an insight into molecular mechanisms by which genomic fragments shape phenotypic diversity (Qanbari and Simianer 2014)
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