Investigation of the genetic determinism of amino acid digestibility traits in Duroc×Landrace×Yorkshire crossbred pigs

Objective: The objective of this study was to delineate the genetic architecture of ileal amino acid digestibility in Duroc×(Landrace×Yorkshire) hybrid (DLY) pigs through genome-wide association study (GWAS). The goal was to identify associated single nucleotide polymorphisms (SNPs) and candidate genes to inform precision breeding strategies for enhanced nutrient utilization and environmental sustainability. Methods: We conducted a GWAS on 600 DLY pigs to identify genetic markers associated with ileal amino acid digestibility, employing the GGP Porcine 50K SNP Chip and analyzing fifteen amino acid digestibility traits. GLM and FarmCPU-based GWAS approaches were utilized to detect SNP associations, followed by gene annotation to identify candidate genes near significant SNP loci. Results: We identified two SNPs, chr3:33019982 and Chr17:34715741, significantly associated with the digestibility of multiple amino acids. SNP chr3:33019982 was linked to threonine, leucine, histidine, proline, and arginine digestibility, while Chr17:34715741 was associated with arginine. Gene annotation revealed Trans-Golgi network vesicle protein 23 homolog A (TVP23A) and Synapse differentiation-induced gene I (SynDIG1) as potential candidates for amino acid metabolism in the terminal ileum. Conclusion: Our study identified key SNPs and genes linked to amino acid digestibility in DLY pigs, specifically highlighting the pleiotropic effects of the SNP WU_10.2_3_33019982 and the potential roles of TVP23A and SynDIG1 genes. These findings contribute to the molecular breeding of DLY pigs for improved amino acid utilization and provide insights into the genetic control of this trait.