Genome-Wide Association Analysis Reveals Genetic Loci and Candidate Genes for Chest, Abdominal, and Waist Circumferences in Two Duroc Pig Populations

Abstract

Chest circumference (CC), abdominal circumference (AC), and waist circumference (WC) are regarded as important indicators for improving economic traits because they can reflect the growth and physiological status in pigs. However, the genetic architecture of CC, AC, and WC is still elusive. Here, we performed single-trait and multi-trait genome-wide association studies (GWASs) for CC, AC, and WC in 2,206 American origin Duroc (AOD) and 2,082 Canadian origin Duroc (COD) pigs. As a result, one novel quantitative trait locus (QTL) on Sus scrofa chromosome (SSC) one was associated with CC and AC in COD pigs, which spans 6.92 Mb (from 170.06 to 176.98 Mb). Moreover, multi-trait GWAS identified 21 significant SNPs associated with the three conformation traits, indicating the multi-trait GWAS is a powerful statistical approach that uncovers pleiotropic locus. Finally, the three candidate genes (ITGA11, TLE3, and GALC) were selected that may play a role in the conformation traits. Further bioinformatics analysis indicated that the candidate genes for the three conformation traits mainly participated in sphingolipid metabolism and lysosome pathways. For all we know, this study was the first GWAS for WC in pigs. In general, our findings further reveal the genetic architecture of CC, AC, and WC, which may offer a useful reference for improving the conformation traits in pigs.

Association between Head-to-Chest Circumference Ratio and Intrauterine Growth-Retardation Related Outcomes during Preweaning and Postweaning

“…Current evidence suggests that the morphology of body parts and organ weights are associated with performance and survival, which are potentially related to IUGR. For instance, separate measurements of head and chest circumferences have been proposed as relevant indicators of economic traits in pigs because they can estimate growth and physiological status [ 19 ]. Additionally, greater abdominal circumference has been associated with greater ADG during the postweaning period [ 29 ].…”

“…In response to this issue, morphometrics and facial features have been associated with IUGR and lower performance. For instance, a positive genetic correlation between chest circumference and backfat thickness, as well as body weight, has been observed in Duroc pigs [ 19 ]. Moreover, the organ weights of piglets suffering IUGR are significantly lower compared with normal piglets [ 1 ].…”

Genome-Wide Association Study of Body Conformation Traits in a Three-Way Crossbred Commercial Pig Population

“…After reaching a fattening weight, 1518 pigs born between 2018 and 2019 were processed for phenotype recording with an average body weight of 115 kg in 13 batches. All the pigs were measured on the following traits: BH (body height) was measured from shoulder to ground; BL (body length) was measured from the midpoint of the ear to the tail [4]; the CC (chest circumference), AC (abdominal circumference), and WC (waist circumference) were measured by circling the trailing edge of the scapula, the largest part of the abdomen, and the front edge region of the hind leg in the pigs [11], respectively. All five body conformation trait measurements were performed on the same flat surface and the pig was kept in a natural standing posture during the measurement.…”

“…In this study, we used Pearson's correlation coefficient to calculate the phenotypic correlation (r p ) between the traits [11]. Moreover, we estimated the genetic correlation and heritability using GCTA in bivariate mode.…”

“…For example, Li et al identified 714 significantly associated SNPs located at 39 regions for body traits and seven functionally related candidate genes [10]. Zhou et al showed that ITGA11, TLE3, and GALC might play a role in the body conformation traits based on single and multi-trait GWASs in two Duroc pig populations [11]. Hong et al reported that a highly significant SNP (S17_15781294) located on Sus scrofa chromosome 7 (SSC7) explained 9.09% of the genetic variance for body length and 9.57% of the genetic variance for body height in Large White pigs [4].…”