A genome-wide association study of growth and fatness traits in two pig populations with different genetic backgrounds

Abstract

Improvement in growth and fatness traits are the main objectives in pig all breeding programs. Tenth rib backfat thickness (10RIBBFT) and days to 100 kg (D100), which are good predictors of carcass lean content and growth rate, respectively, are economically important traits and also main breeding target traits in pigs. To investigate the genetic mechanisms of 10RIBBFT and D100 of pigs, we sampled 1,137 and 888 pigs from 2 Yorkshire populations of American and British origin, respectively, and conducted genome-wide association study (GWAS) through combined analysis and meta-analysis, to identify SNPs associated with 10RIBBFT and D100. A total of 11 and 7 significant SNPs were identified by combined analysis for 10RIBBFT and D100, respectively. And in meta-analysis, 8 and 7 significant SNPs were identified for 10RIBBFT and D100, respectively. Among them, 6 and 5 common significant SNPs in two analysis results were, respectively, identified associated with 10RIBBFT and D100, and correspondingly explained 2.09% and 0.52% of the additive genetic variance of 10RIBBFT and D100. Further bioinformatics analysis revealed 10 genes harboring or close to these common significant SNPs, 5 for 10RIBBFT and 5 for D100. In particular, Gene Ontology analysis highlighted 6 genes, PCK1, ANGPTL3, EEF1A2, TNFAIP8L3, PITX2, and PLA2G12, as promising candidate genes relevant with backfat thickness and growth. PCK1, ANGPTL3, EEF1A2, and TNFAIP8L3 could influence backfat thickness through phospholipid transport, regulation of lipid metabolic process through the glycerophospholipid biosynthesis and metabolism pathway, the metabolism of lipids and lipoproteins pathway. PITX2 has a crucial role in skeletal muscle tissue development and animal organ morphogenesis, and PLA2G12A plays a role in the lipid catabolic and phospholipid catabolic processes, which both are involved in the body weight pathway. All these candidate genes could directly or indirectly influence fat production and growth in Yorkshire pigs. Our findings provide novel insights into the genetic basis of growth and fatness traits in pigs. The candidate genes for D100 and 10RIBBFT are worthy of further investigation.

Identifying Selection Signatures for Backfat Thickness in Yorkshire Pigs Highlights New Regions Affecting Fat Metabolism

“…In theory, the backfat thickness traits of pig are a quantitative trait, and their genetic mechanism is complex and controlled by many genes with small effects. This quantitative genetics view is supported by most of the recent gene mapping researches, including genome-wide association studies [3,4,5]. Although these loci are associated with complex traits but are less effect and are not easily detected by genome-wide association analysis, they may be accurately mapped by sweep analysis because they have always been subjected to high-intensity artificial selection.…”

“…Backfat thickness is an important breeding objective trait, because it indirectly affects carcass lean percentage, fat deposition, meat quality, and consumers’ acceptance of pork [2]. Although many genome wide association (GWA) studies have been conducted in the past decades with the development of molecular marker technology, the genetic mechanism affecting backfat thickness still appears to be confusing [2,3,4,5]. From the view of population genetics, the effect of artificial selection affecting backfat thickness would leave detectable selection signatures within the pig genome [6,7,8].…”

Identification and Functional Prediction of Long Intergenic Non-coding RNAs Related to Subcutaneous Adipose Development in Pigs

“…According to GO and pathway analysis, we found that the adjacent genes of lincRNAs (<100 kb) were involved in glycosaminoglycan biosynthetic process, glycerophospholipid metabolism, and glycosaminoglycan catabolic process. Among them, glycerophospholipid metabolism is closely related to fat deposition (Ecker and Liebisch, 2014; Jiang et al, 2018). Thus, we speculate that lincRNAs may have a regulatory role in subcutaneous fat development.…”

“…With the improvement of human living standards, the demand for lean meat rate of pigs is also increasing. The 10th rib BFT and days to 100 kg are the economically important traits in pigs and are commonly used to predict carcass lean meat content and growth rate in pig breeding programs, respectively (Guo et al, 2017; Jiang et al, 2018). Furthermore, a previous study indicated that a low amount of subcutaneous fat or backfat deposition means good growth performance (Zambonelli et al, 2016).…”

Expression Analysis of the PITX2 Gene and Associations between Its Polymorphisms and Body Size and Carcass Traits in Chickens

“…Recently, polymorphism studies of the PITX2 gene were carried out on humans and mainly focused on its associations with diseases [22][23][24]. In livestock, polymorphisms of the PITX2 gene have been reported to be related to the milk traits of dairy goats and the meat quality and growth of pigs [25][26][27]. However, the expression profile and polymorphisms of PITX2 remain unclear in poultry.…”