Genome-Wide Association Study Identifies Loci for Body Composition and Structural Soundness Traits in Pigs

Abstract

BackgroundThe recent completion of the swine genome sequencing project and development of a high density porcine SNP array has made genome-wide association (GWA) studies feasible in pigs.Methodology/Principal FindingsUsing Illumina's PorcineSNP60 BeadChip, we performed a pilot GWA study in 820 commercial female pigs phenotyped for backfat, loin muscle area, body conformation in addition to feet and leg (FL) structural soundness traits. A total of 51,385 SNPs were jointly fitted using Bayesian techniques as random effects in a mixture model that assumed a known large proportion (99.5%) of SNPs had zero effect. SNP annotations were implemented through the Sus scrofa Build 9 available from pig Ensembl. We discovered a number of candidate chromosomal regions, and some of them corresponded to QTL regions previously reported. We not only have identified some well-known candidate genes for the traits of interest, such as MC4R (for backfat) and IGF2 (for loin muscle area), but also obtained novel promising genes, including CHCHD3 (for backfat), BMP2 (for loin muscle area, body size and several FL structure traits), and some HOXA family genes (for overall leg action). The candidate regions responsible for body conformation and FL structure soundness did not overlap greatly which implied that these traits were controlled by different genes. Functional clustering analyses classified the genes into categories related to bone and cartilage development, muscle growth and development or the insulin pathway suggesting the traits are regulated by common pathways or gene networks that exert roles at different spatial and temporal stages.Conclusions/SignificanceThis study is one of the earliest GWA reports on important quantitative traits in pigs, and the findings will contribute to the further biological function analysis of the identified candidate genes and potential utilization of them in marker assisted selection.

Genome-wide association study of the backfat thickness trait in two pig populations

“…Among the 25 mapped SNPs, the largest number were on SSC1 (9), and the rest were distributed on SSC6 (6), SSC7 (3), SSC9 (2), SSC12 (2), SSC16 (2) and SSCX (1). The location of the SNPs on SSC1 and SSC7 were consistent previous reports [7,13], and the SNPs on SSC1 showed the greatest association with the trait. The top four significant SNPs were located on SSC1 (ALGA0006623, ALGA0006599, INRA0004898 and DRGA0001605).…”

“…Also, CCBE1 (collagen and calcium binding EGF domains 1) gene (within gene, ASGA0005017) on SSC1, has been related to fat metabolism through DAVID (http://david.abcc.ncifcrf. gov/) functional annotation [7]. Two SNPs (H3GA00 20700 and MARC0069646) corresponded to a fat QTL region between TNFB (58 cM) and S0102 (70.1 cM) on SSC7 [13].…”

“…Phenotype assessments of the tenth rib backfat thickness were recorded as previously described [4,7], when individual pigs reached a bodyweight of about 130 kg.…”

“…A number of economically important traits in pigs have been investigated in genome-wide association (GWA) studies [6,7]. However, in most of the GWA studies only one experimental population was used, and the results have not been verified in independent populations.…”

Genome association study through nonlinear mixed models revealed new candidate genes for pig growth curves

“…Regarding the MYL9 (Myosin Regulatory Light Chain) gene, Fan et al (2011) reported an important role of this gene in pathways involving bone and cartilage development, muscle growth, and development while considering different spatial and temporal stages. In this same region, Onteru et al (2013) reported significant QTL for ADG when considering Yorkshire derived lines.…”