This study aimed to screen and identify single nucleotide polymorphisms (SNPs) and candidate genes associated with egg production traits in Jinding ducks using genome-wide association study (GWAS) technology, providing the reference information for molecular breeding of Jinding ducks.

A group of 441 healthy female Jinding ducks from the same batch was used as the research subjects, and the number of eggs laid by each duck from the first egg until 43, 55, and 72 weeks of age (referred to W43, W55 and W72, respectively) was collected. Blood samples were collected from the wing veins of all 441 individuals for whole-genome resequencing. The sequencing data was aligned with the duck reference genome (ZJU1.0) to identify SNPs across the genome. After quality control using plink software to obtain high-quality SNPs, the heritability of egg production at 43, 55 and 72 weeks of age as well as the genetic and phenotypic correlations between each pair of traits were estimated using multi-trait animal model of the ASReml-R 4.2 software. Gemma software was used to separately conduct genome-wide association analyses for the three egg production traits, identifying the associated marker loci shared by them. Then, Bedtools software was employed to annotate these loci and mine for candidate genes near the markers.

The heritability of egg production at 43, 55, and 72 weeks of age in Jinding ducks was relatively low, ranging from 0.17 to 0.30, and decreased gradually with increasing age. There was a high genetic positive correlation between egg production at different ages, with higher genetic correlation coefficients between adjacent time points than between non-adjacent time points. The genetic correlation coefficient between 43 and 55 weeks of age was 0.75, and between 55 and 72 weeks of age was 0.89. The GWAS results showed that 174 suggestively significant SNPs (P<9.43×10^-7) were identified for the egg production trait at 43 weeks of age, distributed on chromosomes 3, 13, and 21; 297 suggestively significant SNPs (P<9.43×10^-7) were identified for the egg production trait at 55 weeks of age, distributed on chromosomes 3 and 13; 36 suggestively significant SNPs (P<9.43×10^-7) were identified for the egg production trait at 72 weeks of age, all located on chromosome 3.20 overlapping suggestively significant SNPs (P<9.43×10^-7) were shared among the three egg production traits, all located on chromosome 3. These loci formed two large haplotype blocks and involved 5 candidate genes, including the VSNL1 gene involved in calcium ion action, the MSGN1 gene involved in mesoderm formation, the KCNS3 gene with potassium ion channel function, and the SMC6 and GEN1 genes involved in DNA repair.

The genetic parameters of egg production traits at 43, 55 and 72 weeks of age in Jinding ducks were estimated, and 20 suggestively significant SNPs and 5 candidate genes affecting egg production traits at 3 different ages were identified through GWAS, providing the reference information for molecular breeding of egg production traits in Jinding ducks.