Effects of STAT5B and BMPR-1B genes on growth and production traits in Red Jungle Fowl, Fayoumi, Hilly chickens, and their crossbreeds

Abstract

This study explored the genome sequence, genetic diversity, and single nucleotide polymorphisms (SNPs) within the STAT5B and BMPR-1B genes, and their association across Red Jungle Fowl (RJF), Fayoumi (Fay), and Hilly chickens, as well as in Hilly Reddish Brown (RB) × Fay crossbreed chickens. A cohort comprising 40 cocks and 320 hens of each chicken genotype (except for RJF, where 4 cocks and 12 hens were utilized), was raised from day-old to 1-y of age. Genotyping of 30 chickens of each population except RJF for SNPs was performed using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method, with genotype frequencies compared using the chi-square test. Marker-trait association analyses were carried out using estimated breeding values. Genetic flow among breeds and diversity was assessed using molecular co-ancestry and polymorphic information criteria. The AG genotype predominated over GG and AA genotypes in the STAT5B gene, whereas heterozygote genotype frequency exceeded homozygote genotype frequency in the BMPR-IB gene. Recessive gene frequencies surpassed dominant gene frequencies. Chi-square tests confirmed Hardy–Weinberg equilibrium for all genotypes. Mutations were detected in Hilly genotypes, with polymorphic information criteria values of 0.27–0.37 for STAT5B and 0.34–0.39 for BMPR-1B. The SNP marker of BMPR-1B was associated with mature live weight but not egg production. Phylogenetic trees of both genes indicated that the genetic distance among the genotypes was close. These findings suggest a shared ancestry among the studied chickens, with the STAT5B SNP emerging as a potential genetic marker for enhancing productive traits.