Abstract
BackgroundNatural and artificial selection following domestication has led to the existence of more than a hundred pig breeds, as well as incredible variation in phenotypic traits. Berkshire pigs are regarded as having superior meat quality compared to other breeds. As the meat production industry seeks selective breeding approaches to improve profitable traits such as meat quality, information about genetic determinants of these traits is in high demand. However, most of the studies have been performed using trained sensory panel analysis without investigating the underlying genetic factors. Here we investigate the relationship between genomic composition and this phenotypic trait by scanning for signatures of positive selection in whole-genome sequencing data.ResultsWe generated genomes of 10 Berkshire pigs at a total of 100.6 coverage depth, using the Illumina Hiseq2000 platform. Along with the genomes of 11 Landrace and 13 Yorkshire pigs, we identified genomic variants of 18.9 million SNVs and 3.4 million Indels in the mapped regions. We identified several associated genes related to lipid metabolism, intramuscular fatty acid deposition, and muscle fiber type which attribute to pork quality (TG, FABP1, AKIRIN2, GLP2R, TGFBR3, JPH3, ICAM2, and ERN1) by applying between population statistical tests (XP-EHH and XP-CLR). A statistical enrichment test was also conducted to detect breed specific genetic variation. In addition, de novo short sequence read assembly strategy identified several candidate genes (SLC25A14, IGF1, PI4KA, CACNA1A) as also contributing to lipid metabolism.ConclusionsResults revealed several candidate genes involved in Berkshire meat quality; most of these genes are involved in lipid metabolism and intramuscular fat deposition. These results can provide a basis for future research on the genomic characteristics of Berkshire pigs.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-015-0265-1) contains supplementary material, which is available to authorized users.
Highlights
Natural and artificial selection following domestication has led to the existence of more than a hundred pig breeds, as well as incredible variation in phenotypic traits
Berkshire pigs have been renowned for their superior meat quality since their meat contains a great proportion of neutral lipid fatty acids and marbling fat [3] which is important for palatability characteristics such as tenderness and juiciness
To explore deep into the phenotypic traits of Berkshire breed, we further investigated the 114 genes (Additional file 1: Table S4) observed using The cross-population composite likelihood ratio test (XP-CLR) (Fig. 1(b)). 13 genes intersected with the results from The cross-population extended haplotype homozygosity test (XP-EHH) selection candidate genes (Additional file 1: Table S4)
Summary
Natural and artificial selection following domestication has led to the existence of more than a hundred pig breeds, as well as incredible variation in phenotypic traits. Berkshire pigs have been renowned for their superior meat quality since their meat contains a great proportion of neutral lipid fatty acids and marbling fat [3] which is important for palatability characteristics such as tenderness and juiciness. This breed has been intensively selected for meat quality in recent centuries, especially in East Asia where it is marketed as black pork at a premium price. While several studies have investigated genetic factors relating to meat quality in Berkshire pigs [4,5,6,7], most of the research is performed in the traditional way using trained sensory panel analysis without investigating underlying genetic factors
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