Genomic Insights into the Giant Shank Phenotype of Dong Tao Chickens Reveal Candidate Loci Involved in Skeletal Growth and Development

Background: The Dong Tao (DT) chicken is a traditional Vietnamese breed characterized by extremely enlarged shanks, representing one of the most distinctive morphological traits observed in domestic chickens. Despite its economic and cultural importance, the genetic basis underlying this phenotype remains poorly understood. Therefore, this study aimed to identify genomic regions and candidate genes associated with the giant shank phenotype in DT chickens. Methods: A total of 87 chickens were analyzed, including 30 DT individuals displaying the giant shank phenotype and 57 control animals from the Ac, Choi, and Ho Vietnamese breeds. Genotype data were obtained from high-density 600K single-nucleotide polymorphism arrays and low-coverage whole-genome sequencing datasets. Genome-wide association study (GWAS) was performed using a linear mixed model, while genetic differentiation between DT and control populations was evaluated through FST estimates. Candidate regions were further investigated through linkage disequilibrium analyses, gene annotation, and comparison with previously reported chicken quantitative trait loci (QTLs). Results: Four significant genomic regions were identified on chromosomes 2, 4, 5, and 7. These regions harbored several biologically relevant candidate genes, including IGFBP1, IGFBP3, MYLK, CD44, and KALRN, which are involved in growth regulation, skeletal development, tissue organization, and cellular signaling. The strongest evidence was observed for the chromosome 2 locus containing IGFBP1 and IGFBP3, which exhibited the highest level of genetic differentiation between DT and control populations (maximum FST = 0.47) and overlapped a body weight QTL. Additional overlaps with shank length and feed conversion ratio QTLs were identified in other associated regions. Conclusions: These findings provide novel insights into the genetic architecture underlying the giant shank phenotype in domestic chickens and establish a foundation for future studies aimed at identifying the causal variants and molecular mechanisms involved in giant shank development.