Genome-wide association study of body weight and body size traits in Langya hens

Langya chicken is a Chinese indigenous chicken breed with high genetic diversity. To systematically analyse the genetic basis of body size traits, eight traits (including BW, comb shape, and body size) of 2 952 Langya hens were measured at 130 days of age and at first egg of age. A total of 9 708 856 high-quality single-nucleotide polymorphisms (SNPs) were obtained through whole-genome resequencing and used for subsequent genetic parameter estimation and genome-wide association study (GWAS). The results of genetic parameter analysis revealed significant differences in the SNP heritability of different body size traits, with an overall range of 0.13-0.64. In particular, BW, comb length, comb height, and tibia length exhibited moderate-to-high heritability (0.34-0.64) during both developmental stages. GWAS revealed significantly associated SNP loci distributed across multiple chromosomal regions, indicating that body size traits have a complex multilocus genetic regulatory structure and that some chromosomal regions recur for different body size traits and during different developmental stages, showing potential pleiotropic effects or shared genomic regions. Notably, multiple stable body size trait-associated regions were identified on Gallus gallus autosome (GGA) 1, 4, and 27, including genomic regions on GGA1 (167.56-178.18 Mb), GGA4 (68.24-81.17 Mb), and GGA27 (5.22-6.73 Mb), in which significantly associated signals were repeatedly detected for multiple body size traits, such as BW and tibia length. The significant SNPs in the above regions were characterised by strong linkage disequilibrium and were associated with multiple body size traits, indicating that these SNPs may serve as important genetic hotspots for the regulation of chicken body shape and structure. Candidate genes annotated in these core regions include NCAPG, KPNA3, LDB2, PPARGC1A, FNDC3A, SOST, RB1, STON2, and TARP; the functions of these genes are involved mainly in the regulation of cell proliferation, energy metabolism, bone development, and tissue growth. NCAPG was consistently associated with multiple traits at both developmental stages. Functional enrichment analysis further revealed that these candidate genes were significantly enriched in the phosphatidylinositol, GnRH, energy metabolism, skeletal development and protein biosynthesis signalling pathways. The genetic characteristics of Langya chicken body size traits during the growth stage at the genome-wide level and the underlying molecular mechanisms were systematically revealed in this study. The findings provide important candidate gene resources and a theoretical basis for the screening of molecular markers for body size traits and the genomic breeding of regional chicken breeds.