Genome-wide association study identifies significant SNP and related genes associated with body size in Yorkshire pigs using latent variable modelling

Abstract This study aimed to quantify a latent variable for body size (BS) in pigs by using five linear body measurements including body length (BL), body height (BH), chest width (CW), chest girth (CG) and tube girth (TG), and also to identify the most associated single nucleotide polymorphisms (SNP) and related genes with BS by using the genomic best linear unbiased prediction (GBLUP) based genome-wide association study (GWAS) or GBLUP-GWAS methodology. To perform a GWAS on the BS latent trait, we used a mixed linear model and identified a total of 53 significant SNPs. Additionally, we found that nine genes, including Rho GTPase activating protein 12 ( ARHGAP12 ), transmembrane protein 108 ( TMEM108 ), T-cell lymphoma invasion and metastasis inducing factor 1 ( TIAM1 ), ras homologue gene family member B ( RHOB ), POU class 4 homeobox 1 ( POU4F1 ), follistatin-related protein 4 ( FSTL4 ), cellular communication network factor 2 ( CCN2 ), beaded filament structural protein 2 ( BFSP2 ) and attractin-like protein 1 ( ATRNL1 ) were associated with the BS trait in pigs. These genes are involved in several biological processes, including the regulation of anatomical structure, morphogenesis, the regulation of cell size and growth. The results suggest that the identified SNP and related genes may play important roles in regulating the growth and development of pigs. The results imply that these genes could be promising candidates for further exploration of the underlying mechanisms of body size variation. Furthermore, the findings have significant practical implications for enhancing the efficiency and profitability of pig farming through genetic selection.