A genome-wide association study identified candidate genes associated with egg quality traits in Muscovy duck

Egg quality directly determines embryo development in meat-type poultry. However, it is difficult to directly select the egg quality of Muscovy duck. The genes and SNPs associated with egg quality screened by GWAS can be used for molecular breeding and accelerate the progress of selection in Muscovy duck.

295 Muscovy ducks were used for whole genome sequencing, and a total of 6,131,623 SNPs were obtained for further analysis. The heritability of egg quality ranged from 0.01 to 0.41, in which egg weight (EW) was 0.19, albumen weight (AW) was 0.16 and the yolk weight (YW) was 0.27. The genetic correlation of EW and AW, EW and YW, and eggshell thickness (EST) and eggshell strength (ESS) were 0.65, 0.51, and 0.74, respectively. Phenotypic correlations between egg quality ranged from - 0.13 to 0.17. A total of 68 SNPs significantly associated with EW were located within the genes PSMG4, SLC22A23, DNAH5, FABP6, ADAMST17, IGF1R, NTRK3, and SCAI. The linkage disequilibrium (LD) analysis identified 2_75684453_C > G, 2_76305509_A > G, 2_76350118_T > A, 11_3834664_C > T, 11_4339778_C > T, and 11_8079686_C > T as tagSNPs to represent the significant SNPs. Fifty SNPs significantly associated with YW were located within the genes XKR6, DNAJC24, SNCB, UNC5A, MAD1L1, NOTCH1, and WDR7. The SNPs 14_9186714_C > T, 14_9199818_A > G, 15_5452098_C > T, and 18_9038052_C > T were selected as tagSNPs. Fifty-four SNPs significantly associated with albumen height were located within the genes LIN9 and NID1. The SNP 3_17718980_A > G was selected as the tagSNP. The significant SNPs associated with eggshell strength were located within the genes CLPX, EPHA5, ZBTB44, NOL6, and UBAP1. The SNPs 25_1996726_A > C and 25_2078328_A > G were selected as tagSNPs. Genes associated with egg quality were significantly enriched in the positive regulation of the BMP signaling pathway in the GO enrichment analysis of biological processes. The KEGG enrichment analysis suggested that the SNPs located genes were significantly enriched in Axon guidance, Endocrine resistance, and Progesterone-mediated oocyte maturation.

Some tagSNPs were identified that may be useful for molecular breeding of egg quality. RNF423, RNF220, IGF1R, SLC22A23, WDR7, and NTRK3 may be candidate genes for egg quality traits in Muscovy duck.