Genome-Wide Association Study of Meat Quality Traits in a White Duroc×Erhualian F2 Intercross and Chinese Sutai Pigs

Abstract

Thousands of QTLs for meat quality traits have been identified by linkage mapping studies, but most of them lack precise position or replication between populations, which hinder their application in pig breeding programs. To localize QTLs for meat quality traits to precise genomic regions, we performed a genome-wide association (GWA) study using the Illumina PorcineSNP60K Beadchip in two swine populations: 434 Sutai pigs and 933 F2 pigs from a White Duroc×Erhualian intercross. Meat quality traits, including pH, color, drip loss, moisture content, protein content and intramuscular fat content (IMF), marbling and firmness scores in the M. longissimus (LM) and M. semimembranosus (SM) muscles, were recorded on the two populations. In total, 127 chromosome-wide significant SNPs for these traits were identified. Among them, 11 SNPs reached genome-wise significance level, including 1 on SSC3 for pH, 1 on SSC3 and 3 on SSC15 for drip loss, 3 (unmapped) for color a*, and 2 for IMF each on SSC9 and SSCX. Except for 11 unmapped SNPs, 116 significant SNPs fell into 28 genomic regions of approximately 10 Mb or less. Most of these regions corresponded to previously reported QTL regions and spanned smaller intervals than before. The loci on SSC3 and SSC7 appeared to have pleiotropic effects on several related traits. Besides them, a few QTL signals were replicated between the two populations. Further, we identified thirteen new candidate genes for IMF, marbling and firmness, on the basis of their positions, functional annotations and reported expression patterns. The findings will contribute to further identification of the causal mutation underlying these QTLs and future marker-assisted selection in pigs.

Intermuscular and intramuscular adipose tissues: Bad vs. good adipose tissues

“…Indeed, both IM fat and collagen accumulation is lower while muscle mass is higher in the largest compared with the smallest littermates of pigs, indicating the shifting of myogenesis to fibro/adipogenesis in the smallest piglets. 92,93 Consistently, previous studies demonstrated both IM accumulation and fibrosis in fetal and offspring sheep due to maternal over-nutrition, which correlates with downregulated myogenesis [94][95][96] and suggests that IM adipogenesis and fibrogenesis are correlated due to a common cell lineage. Predictably, in genetically high marbling Wagyu cattle, both IM adipogenesis and collagen accumulation are higher than in relatively low marbling Angus cattle.…”

Joint QTL mapping and gene expression analysis identify positional candidate genes influencing pork quality traits

“…For instance, when we compared our a*, b* and pH 24 data with those described in six additional GWAS studies4629303132 we only found one positional coincidence between the SSC10 (70.6 Mb) genomic region associated with LD a* in the Lipgen population (Table 3) and the SSC10 (72.8 Mb) region identified by Ma et al 4. as associated with the same trait in the semimembranosus muscle of White Duroc × Erhualian F 2 pigs.…”

“…The genetic determinism of electrical conductivity, acidity and color, which have been often used as predictors of meat quality, has been explored by performing genome-wide association studies (GWAS) in F 2 populations234 as well as in purebred pigs56. An important limitation of using F 2 intercrosses in GWAS studies is that they are not representative of the purebred populations that constitute the selection nuclei of breeding companies.…”

The optimal number of partial least squares components in genomic selection for pork pH

“…Other studies have reported the relevance of this same chromosomal region. Among these, STRATZ et al (2012) andMA et al (2013) stands out, who also used F2 populations involving commercial lines and identified QTL for pH 45 at positions of 79.5 and 88.26Mbp, respectively, and PONSUKSILI et al (2010), which reported QTL for pH u at 82Mbps using different populations derived from the Duroc breed.…”