Genome-wide association study and candidate gene analysis of reproductive traits in Yili geese

Reproductive traits are important economic traits in goose production, and geese's reproductive ability directly affects goose farms' economic benefits. In this study, we selected 240 Yili females goose in the egg-laying stage to construct a test population and measured the individual egg-laying performance and hatching performance of Yili females goose. Based on the above phenotypic data, we conducted genome-wide linkage analysis for five indicators of reproductive traits of Yili geese (egg-laying capacity, fertilization rate, hatching rate, egg weight, and egg shape) to screen candidate genes. Genome-wide association analysis of reproductive traits in Yili geese was performed by resequencing, and a total of 1 single nucleotide polymorphism (SNP) were screened for significant association with hatchability, 34 SNPs were screened for potential association with egg production, egg weight, egg shape, and fertilisation rate, and 35 candidate genes were screened for association with egg production, egg weight, egg shape and fertilization rate in the vicinity of these loci across the whole genome. 35 candidate genes were screened near these loci. Through bioinformatics analysis, genes such as carbonic anhydrase 2 (CA2), very low density lipoprotein receptor (VLDLR), HMG-box transcription factor 1 (HBP1), and transient receptor potential cation channel subfamily M member 5 (TRPM5) were obtained to be closely related to calcium deposition, follicular development, embryonic development, and estrogen secretion level. These genes can be used as candidate genes affecting the reproductive performance of Yili geese. This study provides a reference basis for further analysis of the molecular regulation mechanism of goose reproductive performance and enriches the theory of genetic regulation of goose reproductive performance.