Abstract
Intramuscular fat (IMF) content and fatty acid composition affect the organoleptic quality and nutritional value of pork. A genome-wide association study was performed on 138 Duroc pigs genotyped with a 60k SNP chip to detect biologically relevant genomic variants influencing fat content and composition. Despite the limited sample size, the genome-wide association study was powerful enough to detect the association between fatty acid composition and a known haplotypic variant in SCD (SSC14) and to reveal an association of IMF and fatty acid composition in the LEPR region (SSC6). The association of LEPR was later validated with an independent set of 853 pigs using a candidate quantitative trait nucleotide. The SCD gene is responsible for the biosynthesis of oleic acid (C18:1) from stearic acid. This locus affected the stearic to oleic desaturation index (C18:1/C18:0), C18:1, and saturated (SFA) and monounsaturated (MUFA) fatty acids content. These effects were consistently detected in gluteus medius, longissimus dorsi, and subcutaneous fat. The association of LEPR with fatty acid composition was detected only in muscle and was, at least in part, a consequence of its effect on IMF content, with increased IMF resulting in more SFA, less polyunsaturated fatty acids (PUFA), and greater SFA/PUFA ratio. Marker substitution effects estimated with a subset of 65 animals were used to predict the genomic estimated breeding values of 70 animals born 7 years later. Although predictions with the whole SNP chip information were in relatively high correlation with observed SFA, MUFA, and C18:1/C18:0 (0.48–0.60), IMF content and composition were in general better predicted by using only SNPs at the SCD and LEPR loci, in which case the correlation between predicted and observed values was in the range of 0.36 to 0.54 for all traits. Results indicate that markers in the SCD and LEPR genes can be useful to select for optimum fatty acid profiles of pork.
Highlights
Intramuscular fat (IMF) content and fatty acid (FA) composition affect both organoleptic quality and nutritional value of pork and, there is increasing interest in including these traits in the selection objectives of pigs bred for quality pork markets
An exception is the quantitative trait loci (QTL) in the Sus scrofa chromosome (SSC) 14 affecting SFA and monounsaturated FA (MUFA) in purebred Duroc [10,11], which has been matched to a haplotype of three single nucleotide polymorphisms (SNPs) in the promoter region of the stearoyl-CoA desaturase (SCD) gene [12]
The BF of individual markers for BT and IMF content and composition of GM are shown in Fig 1, and those of LD and SF are in Figs 2 and 3, respectively
Summary
Intramuscular fat (IMF) content and fatty acid (FA) composition affect both organoleptic quality and nutritional value of pork and, there is increasing interest in including these traits in the selection objectives of pigs bred for quality pork markets. Oleic acid (C18:1) is the most abundant FA in pork and it can be regarded as a good target for the simultaneous improvement of organoleptic, technological, and nutritional attributes of pork Both IMF and FA contents display substantial genetic variation, even within purebred lines [3,4]. A lot of efforts have been put into the detection of quantitative trait loci (QTL) affecting IMF content and FA composition using low-density microsatellite linkage maps [5,6,7,8]. Most of these QTL were detected in experimental crosses and, to our knowledge, they have not been used in commercial breeding programs [9]. An exception is the QTL in the Sus scrofa chromosome (SSC) 14 affecting SFA and MUFA in purebred Duroc [10,11], which has been matched to a haplotype of three single nucleotide polymorphisms (SNPs) in the promoter region of the stearoyl-CoA desaturase (SCD) gene [12]
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