Estimation of genetic parameters for hatching performance and genome-wide association analysis in Baicheng-You chickens

The Baicheng-You chicken is a precious local chicken breed unique to Xinjiang, renowned for its strong stress resistance and excellent meat quality. However, its reproductive performance, particularly low hatching efficiency, severely restricts the industrial development of this breed. This study aims to systematically elucidate the genetic basis of the hatching performance of Baicheng-You chickens to provide a theoretical foundation for molecular breeding. A total of 844 44-week-old Baicheng-You chickens were studied, and key hatching traits such as the viable egg rate (VER), fertilization rate (FR), hatchability of eggs set (HES), hatchability of fertilized eggs (HFE), and chick hatching weight (CHW) were measured. High-density variation maps were constructed using whole-genome resequencing technology, genetic parameters were estimated using a mixed linear model, and genome-wide association studies (GWAS) were conducted to screen for significantly associated SNPs and candidate genes. Genetic parameter estimates revealed that the viable egg rate (VER, h 2 = 0.27) and chick hatching weight (CHW, h 2 = 0.40) exhibited moderate to high heritability, while the fertilization rate (FR, h 2 = 0.07) and hatchability (HES, h 2 = 0.02; HFE, h 2 = 0.01) showed low heritability. GWAS identified 44 genome-wide significant SNPs ( p < 4.36 × 10 −8 ) and 130 suggestive significant SNPs ( p < 8.71 × 10 −7 ). Gene annotation identified 1,146 candidate genes significantly associated with the traits, including the AvBD family genes, ATP5G3 , JAM2 , APP , and ABCE1 . Functional enrichment analysis indicated that these genes were significantly enriched in pathways closely related to embryonic immunity and developmental regulation, such as “defense response to bacterium,” “positive chemotaxis,” “cell cycle,” “ubiquitin-mediated proteolysis,” and the “apelin signaling pathway.” This study is the first to systematically reveal the genetic architecture of hatching performance in Baicheng-You chickens at the whole-genome level. The identified key genes and signaling pathways provide new insights into the molecular regulatory mechanisms of embryonic development and hatching efficiency. The findings not only offer important candidate targets for molecular marker-assisted selection in Baicheng-You chickens but also provide valuable genetic information and scientific support for the conservation and sustainable utilization of this unique local genetic resource.