数字农科院2.0

Identification of SNPs and INDELS associated with duck egg quality traits through a genome-wide association analysis

文献类型： 外文期刊

作者： Min Zhang;Lizhi Lu;Yan Li;Qiong Wu;Yanhui Liu;Hongfei Liu;Hehe Tang;Rulong Lin;Hongping Chen;Tao Zeng;Yong Tian;Yuting Yan;Yanning Wei;Chenyu Ren;Wenfu Li;Min Liu;Jie Yu;Jiawen Liu;Xin Lin;Guanghua Zeng;Chunmei Cheng;Xiaobing Jiang;Yanfa Sun

作者机构：

关键词： Egg quality trait;GWAS;Indel;Longyan Shan-ma duck;SNP

期刊名称： Poultry Science

ISSN： 0032-5791

年卷期： 2024 年 103 卷 12 期

页码：

收录情况： SCIE（2024版）

摘要： Egg quality traits are economically important in the poultry industry. To explore the genetic architecture and identify potential candidate genes, a genome-wide association study (GWAS) was performed for 13 egg quality traits using data from whole-genome sequencing of 299 Longyan Shan-ma female ducks, including 12 quantitative traits and one qualitative trait, eggshell color (ESC; white, light green, green). From estimation of pedigree genetic parameters, heritability (h2) ranged from 0.022 to 0.996 for the 12 quantitative traits, with the highest h2 (0.996) for eggshell color a* value (ESCA) and the lowest h2 (0.022) for egg yolk percentage relative to EW. A total of 8,874 single nucleotide polymorphism (SNP)-based significant associations (1.0 × 10−6) and 247 insertion-deletion (indel)-based significant associations (1.00 × 10−5) were identified, including 5,980 SNPs and 159 indel markers. From 5,924 SNPs and 143 indels associated with ESC traits, 181 potential candidate genes were identified, and most significant SNPs and indels (P < 1.0 × 10−20) were located at 1.86 Mb (44.29−46.15 Mb) on chromosome 4. The top SNP (chr4:45325309:C>A; P = 7.97 × 10−43) and the top indel (chr4:45299595:delTTCCACTCCAC; P = 4.20 × 10−36) for the ESC a* value were within two known ESC candidate genes; ATP-binding cassette subfamily G member 2 (ABCG2) and protein kinase cGMP-dependent 2 (PRKG2). Of 56 SNPs and 16 indels associated with other egg quality traits, 46 potential candidate genes were identified including synapse differentiation-inducing 1-like (SYNDIG1L) for EW, and core histone macro-H2A.1 (LOC101795967) and neurogenin 1 (NEUROG1) for egg shape index; and four genes including collagen type VI alpha 3 chain (COL6A3), lysine demethylase 7A (KDM7A), LOC101802169, and sperm-associated antigen 16 (SPAG16) for egg yolk weight and the percentage of yolk to total egg weight. Of the 46 genes, the molecular functions of 22 are related to protein binding, indicating important roles in the formation of egg quality traits. Our findings provide new insight into the genetic basis of egg quality traits in ducks.

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