Yang Wanli, Yu Shiqi, Song Danyu, Lin Weihuang, Xu Hanqi, Lang Xuqiao, Zhang Cheng, Guo Liping, Chen Xingyong
College of Animal Science and Technology, Anhui Agricultural University, No. 130 Changjiang West Road, Hefei, 230036, P. R. China.
Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Biobreeding, Anhui Agricultural University, No. 130 Changjiang West Road, Hefei, 230036, P. R. China.
BMC Genomics. 2025 Apr 29;26(1):422. doi: 10.1186/s12864-025-11503-2.
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.
蛋品质直接决定肉用型家禽的胚胎发育。然而，番鸭的蛋品质难以直接进行选择。通过全基因组关联研究（GWAS）筛选出的与蛋品质相关的基因和单核苷酸多态性（SNP）可用于分子育种，加快番鸭的选择进程。
使用295只番鸭进行全基因组测序，共获得6,131,623个SNP用于进一步分析。蛋品质的遗传力范围为0.01至0.41，其中蛋重（EW）为0.19，蛋白重（AW）为0.16，蛋黄重（YW）为0.27。EW与AW、EW与YW以及蛋壳厚度（EST）与蛋壳强度（ESS）的遗传相关性分别为0.65、0.51和0.74。蛋品质之间的表型相关性范围为-0.13至0.17。共有68个与EW显著相关的SNP位于PSMG4、SLC22A23、DNAH5、FABP6、ADAMST17、IGF1R、NTRK3和SCAI基因内。连锁不平衡（LD）分析确定2_75684453_C＞G、2_76305509_A＞G、2_76350118_T＞A、11_3834664_C＞T、11_4339778_C＞T和11_8079686_C＞T作为标签SNP来代表显著的SNP。50个与YW显著相关的SNP位于XKR6、DNAJC24、SNCB、UNC5A、MAD1L1、NOTCH1和WDR7基因内。选择14_9186714_C＞T、14_9199818_A＞G、15_5452098_C＞T和18_9038052_C＞T作为标签SNP。54个与蛋白高度显著相关的SNP位于LIN9和NID1基因内。选择3_17718980_A＞G作为标签SNP。与蛋壳强度相关的显著SNP位于CLPX、EPHA5、ZBTB44、NOL6和UBAP1基因内。选择25_1996726_A＞C和25_2078328_A＞G作为标签SNP。在生物过程的GO富集分析中，与蛋品质相关的基因在BMP信号通路的正调控中显著富集。KEGG富集分析表明，定位到SNP的基因在轴突导向、内分泌抵抗和孕酮介导的卵母细胞成熟中显著富集。
鉴定出一些可能对蛋品质分子育种有用的标签SNP。RNF423、RNF220、IGF1R、SLC22A23、WDR7和NTRK3可能是番鸭蛋品质性状的候选基因。
