Whole-genome resequencing revealed genetic structure and specific breed identification loci of Ningxia Jingyuan chicken breed (Gallus gallus)

Jingyuan (JY) chicken breed is one of the Chinese regional livestock and poultry genetic resources protection breeds raised in Ningxia, China. The phenotypic characteristics of JY chickens, such as feather color, skin color, and meat quality, exhibit distinct local traits, but the genetic foundation remains unclear. This study utilized whole-genome resequencing to analyze the genetic structure, genome diversity, selection signals, and genes associated with meat quality, growth and development of the Ningxia JY chicken breed. The results showed that JY chicken exhibited a relatively independent genetic structure compared to other local chicken breeds in China. Selective sweep analysis identified several genes and biological processes/pathways such as the FGF family, ANKRD family, PPARα, and HSP family, which are related to growth and metabolism. Through machine learning analysis, 7 breed specific loci were identified in the genome of JY chickens. JY chickens exhibit relatively low genetic diversity and have distinct genetic backgrounds compared to other chicken breeds studied. These results help us understand the traits and utilization potential of JY chicken germplasm resources.