Genome-wide association analysis reveals genetic loci and candidate genes for meat quality traits in Chinese Laiwu pigs

Abstract

Meat quality traits have economically significant impacts on the pig industry, and can be improved using molecular approaches in pig breeding. Since 1994 when the first genome-wide scan for quantitative trait loci (QTLs) in pig was reported, over the past two decades, numerous QTLs have been identified for meat quality traits by family based linkage analyses. However, little is known about the genetic variants for meat quality traits in Chinese purebred or outbred populations. To unveil it, we performed a genome-wide association study for 10 meat quality traits in Chinese purebred Laiwu pigs. In total, 75 significant SNPs (P < 1.01 × 10(-6)) and 33 suggestive SNPs (P < 2.03 × 10(-5)) were identified. On SSC12, a region between 56.22 and 61.49 Mb harbored a cluster of SNPs that were associated with meat color parameters (L*, lightness; a*, redness; b*, yellowness) and moisture content of longissimus muscle (LM) and semimembranosus muscle at the genome-wide significance level. A region on SSC4 also has pleiotropic effects on moisture content and drip loss of LM. In addition, this study revealed at least five novel QTLs and several candidate genes including 4-linked MYH genes (MYH1, MYH2, MYH3, and MYH13), MAL2, LPAR1, and PRKAG3 at four significant loci. Except for the SSC12 QTL, other QTLs are likely tissue-specific. These results provide new insights into the genetic basis of meat quality traits in Chinese Laiwu pigs and some significant SNPs reported here could be incorporated into the selection programs involving this breed.

Competitive endogenous RNA network reveals that miR-1343 play key regulatory roles in longissimus dorsi muscle between Saba and Yorkshire pigs

“…Pork quality is an important economic trait in pig industry, and many studies have demonstrated that the pork formation has significant differences between Chinese indigenous pig breeds and Western mainly commercial pig breeds [3,13,41]. Despite some advances in molecular genetic mechanism [3,9,12,13,42], the regulatory mechanism of pork quality formation remains unclear. Uncovering the regulatory mechanism involved in pork formation contributes to better utilizing Chinese and Western pig resources and producing crossbred pig breed with better performances such as higher pork quality and faster growth.…”

“…For example, Liu et al conducted GWAS for pork quality traits using Western DLY (Duroc×(Landrace×Yorkshire)) commercial population and Chinese Erhualian population, and totally identified 37 SNPs on 14 chromosomes associated with drip loss, pH and pork color [3]. Again, Xiong et al performed GWAS for pork quality traits for 316 Chinese Laiwu pigs, and 75 SNPs were identified to associate with pork quality [13]. These studies contribute to uncovering the genetic mechanism involved in pork quality, and provide help for pork quality improvement in pig industry.…”

Genome-wide association study identifies loci and candidate genes for internal organ weights in Simmental beef cattle

“…Some SNPs passed the multiple threshold for SW and KW, while for the remaining traits, such was the stringency that only one SNP passed the multiple threshold. Here, we adopted a Bonferroni-corrected genome-wide significance of 0.01/N (1/ 671,192 ϭ 1.49 ϫ 10 Ϫ6 ) for heart weight (HW), liver weight (LIW), and lung weight (LUW) (39,55,62,64). Meanwhile, the linkage disequilibrium blocks were constructed by Haploview4.2 under the default parameters (2).…”

Genome-wide association analysis reveals genetic loci and candidate genes associated with intramuscular fat in Duroc pigs

“…The shaded region shows a 95% confidence interval based on a beta distribution. An overall deviation above the diagonal identity line is generally suggestive of severe population stratification [19] . Deviations from the diagonal line suggest that either the assumed distribution is incorrect or that the sample contains values arising in some other manner, as by a true association [20] .…”