Integrative Genomic Analyses Identify and Prioritize Candidate Loci for Metatarsal Length and Circumference in...

The objective of this study was to characterize the genetic basis of metatarsal length (MeL) and circumference (MeC), identify candidate loci and genes associated with these traits, and evaluate the predictive utility of integrated candidate-marker sets for broiler leg traits. A total of 330 male broilers phenotyped at 49 days of age and subjected to whole-genome resequencing were used for the analyses. Genomic heritability estimates were 0.266 for MeL and 0.516 for MeC. Single-trait GWAS identified 102 and 165 suggestive SNPs for MeL and MeC, respectively, while bivariate analysis identified 263 SNPs, including 159 not detected by either single-trait analysis. Integration with genetic differentiation and nucleotide diversity prioritized 55 candidate SNPs for MeL and 62 for MeC, with three loci shared between the two traits. Linkage disequilibrium refinement and functional annotation identified 120 candidate variants and 64 candidate genes, including APP, LDB3, ADH6, MTTP, and a missense variant in ANKRD50. Across six models, mean heritability-adjusted prediction estimates ranged from 0.197 to 0.230 for MeL and 0.273 to 0.322 for MeC. Exploratory within-population analyses indicated that the candidate-marker sets were enriched for trait-relevant predictive information. These results provide insights into the genetic architecture of broiler leg traits and provide candidate markers for further validation and evaluation in genomic prediction.