Thuy Thi-Ngoc Dinh

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 F_ST 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.

Copy number variants (CNVs) are large-scale genomic alterations that contribute substantially to genetic diversity and may influence phenotypic variation in livestock. This study investigated the genome-wide CNV landscape of three Vietnamese indigenous chicken breeds. Whole-genome sequencing on the Illumina platform (3–5× coverage) was performed on 24 individuals from Dong Tao (DT), Cay Cum (CC), and Ri (RI) breeds. A total of 1743 CNVs were detected, clustering into 315 copy number variation regions (CNVRs). Most CNVRs were rare, with 31.7% present in only one animal among breeds. Across the genome, 122 unique CNVRs were distributed over 28 chromosomes, predominantly the first five. Losses were the most frequent type (45.9%), followed by gains (39.3%), and mixed events (14.8%). Within these CNVRs, 3633 genes were identified. In DT and RI, CNVR-embedded genes included several candidates, potentially related to adaptability, development, and phenotypic diversification. Notably, DT harbored genes such as EGLN1, OASL, GPX1, DUOX1/DUOXA2 (adaptation, stress/immune response) and LRP4, ZIC1, ZIC4, JARID2, KMT2C, OGN, OMD, and PLOD2 (developmental and skeletal traits), whereas in RI they included genes such as CACNA1S, CALCR, CAPN3, and MAPK13/MAPK14, which may contribute to muscle, bone, and physiological regulation. Functional enrichment analysis revealed numerous genes and Quantitative Trait Loci (QTLs) associated with metabolic, developmental, and immune-related pathways. This study provides the first comprehensive genome-wide CNV profile of Vietnamese indigenous chickens and offers a valuable genomic resource for investigating the genetic basis of breed-specific and adaptive phenotypes.

Bang Troi chicken (GBT) is a local chicken that is free-gardening raised in Quang Ninh province. A 1,268 bp of mitochondrial DNA (mtDNA) D-loop of 17 Bang Troi chicken individuals was sequenced and analyzed. Comparative multiple sequence alignment revealed 17 base substitutions within 17 Bang Troi chicken individuals. Bang Troi chicken had a relatively high level of genetic diversity, expressed in the number of 13 haplotypes, haplotype diversity of 0.949. The Tajima’s test indicated that the analysed population in balancing selection with a D-value of 2.39. A phylogenetic tree based on 455 bp of hypervariable mtD-loop sequence classified 17 Bang Troi chicken individuals into three clades A, B, and E, which are common groups of Vietnamese and Asia indigenous chickens. This result provides the first genetic information and maternal lineages of Bang Troi chickens and it can support for registration of local chicken breeds.