Zhang Min, Lu Lizhi, Li Yan, Wu Qiong, Liu Yanhui, Liu Hongfei, Tang Hehe, Lin Rulong, Chen Hongping, Zeng Tao, Tian Yong, Yan Yuting, Wei Yanning, Ren Chenyu, Li Wenfu, Liu Min, Yu Jie, Liu Jiawen, Lin Xin, Zeng Guanghua, Cheng Chunmei, Jiang Xiaobing, Sun Yanfa
College of Life Science, Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Provincial Universities Key Laboratory of Preventive Veterinary Medicine and Biotechnology (Longyan University), Longyan University, Longyan, Fujian, 364012, PR China.
Institute of Animal Science and Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, PR China.
Poult Sci. 2024 Dec;103(12):104459. doi: 10.1016/j.psj.2024.104459. Epub 2024 Oct 29.
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 (h) ranged from 0.022 to 0.996 for the 12 quantitative traits, with the highest h (0.996) for eggshell color a* value (ESCA) and the lowest h (0.022) for egg yolk percentage relative to EW. A total of 8,874 single nucleotide polymorphism (SNP)-based significant associations (1.0 × 10) and 247 insertion-deletion (indel)-based significant associations (1.00 × 10) 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) 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) and the top indel (chr4:45299595:delTTCCACTCCAC; P = 4.20 × 10) 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.
蛋品质性状在养禽业中具有重要经济意义。为探究其遗传结构并鉴定潜在候选基因，利用299只龙岩山麻鸭母鸭的全基因组测序数据，对13个蛋品质性状进行了全基因组关联研究（GWAS），其中包括12个数量性状和1个质量性状——蛋壳颜色（ESC；白色、浅绿、绿色）。通过系谱遗传参数估计，12个数量性状的遗传力（h）范围为0.022至0.996，蛋壳颜色a*值（ESCA）的h最高（0.996），蛋黄占蛋重百分比的h最低（0.022）。共鉴定出8874个基于单核苷酸多态性（SNP）的显著关联（1.0×10）和247个基于插入缺失（indel）的显著关联（1.00×10），包括5980个SNP和159个indel标记。从与ESC性状相关的5924个SNP和143个indel中，鉴定出181个潜在候选基因，最显著的SNP和indel（P<1.0×10）位于4号染色体上1.86 Mb（44.29 - 46.15 Mb）处。ESC a*值的顶级SNP（chr4:45325309:C>A；P = 7.97×10）和顶级indel（chr4:45299595:delTTCCACTCCAC；P = 4.20×10）位于两个已知的ESC候选基因内；ATP结合盒亚家族G成员2（ABCG2）和蛋白激酶cGMP依赖性2（PRKG2）。在与其他蛋品质性状相关的56个SNP和16个indel中，鉴定出46个潜在候选基因，包括与蛋重相关的突触分化诱导样蛋白1（SYNDIG1L），与蛋形指数相关的核心组蛋白macro - H2A.1（LOC101795967）和神经生成素1（NEUROG1）；以及与蛋黄重和蛋黄占总蛋重百分比相关的四个基因，包括VI型胶原蛋白α3链（COL6A3）、赖氨酸去甲基化酶7A（KDM7A）、LOC101802169和精子相关抗原16（SPAG16）。在这46个基因中，22个基因的分子功能与蛋白质结合有关，表明它们在蛋品质性状形成中具有重要作用。我们的研究结果为鸭蛋品质性状的遗传基础提供了新的见解。
