Swine

GWAS on imputed wgsSNP reveals novel SNP affecting feed efficiency and body composition in a crossbred swine population

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Abstract

Improving feed efficiency traits, such as feed conversion ratio (FCR), alongside optimizing body composition traits like backfat thickness and lean muscle mass is essential for enhancing economic viability, sustainability, and meat quality in swine production. Given the polygenic and environmentally influenced nature of feed efficiency and body composition traits, conventional selection approaches have limited ability to pinpoint causal genetic factors driving variation. While traditional genome-wide association studies (GWAS) using single nucleotide polymorphism (SNP) arrays have identified key loci influencing traits like FCR, residual feed intake (RFI), and backfat thickness, these arrays are limited in marker density and allele diversity, potentially missing causal or low-frequency variants. Whole-genome sequence (WGS) data, when imputed from commercial SNP array using reference panels, offers a cost-effective way to capture millions of variants, including rare and functional alleles. In this study, we performed a single-step genome-wide association study (ssGWAS), with imputed WGS data, for feed efficiency and body composition traits using a multi-generational crossbred swine population. Overall, the three-generation pedigree consisted of 14,242 pigs, of which 9,336 pigs were phenotyped and 7,339 were genotyped. WGS variants were clustered into 775,353 haplotype blocks, ranging from 0.001 to 9981.80 kb in size. Traits analyzed included average daily gain, average daily feed intake, FCR, backfat thickness, loin eye area, lean muscle mass, and lean mass percentage. A total of 133 haplotype blocks were significantly associated with the studied traits, several with potentially large pleiotropic effects. A total of 453 candidate genes were identified in the genomic regions of significant haplotype blocks. Novel functional variants in three candidate genes (SIRT2, RYR1, and LEPR) were associated with backfat and lean muscle traits. SNPs identified in this study provide new potential targets for genetic selection, offering opportunities to more precisely improve feed efficiency and body composition in swine. USDA is an equal opportunity provider and employer.

Keywords: 2026

How to Cite:

Keel, B., Bradford, H., Oliver, W., Lindholm-Perry, A. & Rohrer, G., (2026) “GWAS on imputed wgsSNP reveals novel SNP affecting feed efficiency and body composition in a crossbred swine population”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2294314. doi: https://doi.org/10.31274/wcgalp.24318

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