金定鸭产蛋数性状的全基因组关联研究

doi:10.3864/j.issn.0578-1752.2025.15.015

摘要/Abstract

摘要：

【目的】基于全基因组关联研究（genome-wide association study，GWAS）技术筛选和鉴定金定鸭产蛋数性状相关的单核苷酸多态性（single nucleotide polymorphisms，SNPs）位点及候选基因，为金定鸭产蛋性状的分子育种提供参考信息。【方法】采用441只同批次健康金定鸭（母鸭）群体作为研究对象，分别收集每只个体从产第一枚蛋开始至43周龄、55周龄和72周龄的产蛋数（分别为W43、W55和W72）共3个产蛋数性状。所有441只个体翅静脉采血后进行全基因组重测序，下机数据与鸭参考基因组（ZJU1.0）比对得到全基因组范围内的SNPs位点，利用plink软件质控后获取高质量SNPs位点，使用ASReml-R 4.2软件多性状动物模型估计43周龄、55周龄、72周龄产蛋数性状的遗传力，以及两两性状间的遗传相关、表型相关。利用gemma软件分别对3个产蛋数性状进行全基因组关联分析，鉴定3个产蛋数性状共享的关联标记位点，利用bedtools软件对这些位点进行注释，挖掘标记位点附近的候选基因。【结果】金定鸭W43、W55和W72遗传力均较低，遗传力范围在0.17—0.30之间，并随着周龄的增加，遗传力逐渐降低。不同周龄产蛋数间均具有较高的遗传正相关，相邻时间点间的遗传相关系数高于间隔时间点之间的遗传相关系数，其中W43与W55的遗传相关系数为0.75，W55与W72遗传相关系数为0.89。GWAS研究结果表明，W43筛选到174个潜在显著SNPs位点（P<9.43×10^-7），分布于3、13、21号染色体上；W55筛选到297个潜在显著SNPs位点（P<9.43×10^-7），分布于3、13号染色体上；W72筛选到36个潜在显著SNPs位点（P<9.43×10^-7），均位于3号染色体上。3个产蛋数性状共享20个重叠的潜在显著SNPs位点（P<9.43×10^-7），且均位于3号染色体上。这些位点形成了两个较大的单倍型块，并涉及5个候选基因，包括参与钙离子作用的VSNL1基因、参与中胚层形成的MSGN1基因、具有钾离子通道作用的KCNS3基因，参与DNA修复的SMC6和GEN1基因。【结论】估计了金定鸭43周龄、55周龄和72周龄产蛋数性状的遗传参数，通过产蛋数性状的GWAS研究鉴定了同时影响3个周龄产蛋数性状的20个潜在显著的SNPs位点、5个候选基因，这些结果为金定鸭产蛋数性状分子育种提供了参考信息。

关键词: 金定鸭, 产蛋性状, 遗传参数, 单核苷酸多态性, 全基因组关联研究

Abstract:

【Objective】 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. 【Method】 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. 【Result】 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.【Conclusion】 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.

Key words: Jinding duck, egg production, genetic parameter, SNPs, GWAS

刘宏祥, 张雪萍, 王逸飞, 王志成, 顾昊天, 宋卫涛, 陶志云, 徐文娟, 章双杰, 卢立志, 李慧芳, 朱春红. 金定鸭产蛋数性状的全基因组关联研究[J]. 中国农业科学, 2025, 58(15): 3145-3158.

LIU HongXiang, ZHANG XuePing, WANG YiFei, WANG ZhiCheng, GU HaoTian, SONG WeiTao, TAO ZhiYun, XU WenJuan, ZHANG ShuangJie, LU LiZhi, LI HuiFang, ZHU ChunHong. Genome-Wide Association Study of Egg Production Traits in Jinding Duck[J]. Scientia Agricultura Sinica, 2025, 58(15): 3145-3158.

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链接本文: https://www.chinaagrisci.com/CN/10.3864/j.issn.0578-1752.2025.15.015

https://www.chinaagrisci.com/CN/Y2025/V58/I15/3145

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产蛋数性状关联的重叠显著SNP位点"

染色体 Chr	SNP编号 SNP NO.	物理位置 Position	基因型 Genotype	P值 P value	相对基因位置 Location relative to gene	基因注释 Gene symbol	NCBI基因ID号 Entrez gene ID	基因区间 Gene range
3	SNP01	107735478	G/A	5.15E-07	下游D 67.424	VSNL1	101800936	107799901:107888236
					下游D 30.808	SMC6	101800359	107924852:107889694
					上游U 9.105	MSGN1	101799965	107957897:107959553
	SNP02	107761347	T/C	3.93E-07	上游U 38.554	VSNL1	101800936	107799901:107888236
	SNP03	107762776	G/A	1.58E-07	上游U 37.125	VSNL1	101800936	107799901:107888236
	SNP04	107763098	A/G	3.47E-07	上游U 36.803	VSNL1	101800936	107799901:107888236
	SNP05	107771354	T/C	3.33E-07	上游U 28.547	VSNL1	101800936	107799901:107888236
	SNP06	107775833	A/C	4.84E-07	上游U 24.068	VSNL1	101800936	107799901:107888236
	SNP07	107782079	C/T	3.98E-07	上游U 17.822	VSNL1	101800936	107799901:107888236
	SNP08	107783298	G/A	2.61E-07	上游U 16.603	VSNL1	101800936	107799901:107888236
	SNP09	108004296	T/A	4.56E-08	下游D 79.444	SMC6	101800359	107924852:107889694
					下游D 44.743	MSGN1	101799965	107957897:107959553
					下游D 61.142	GEN1	101800161	107924858:107943154
	SNP10	108024959	T/C	6.92E-08	下游D 65.406	MSGN1	101799965	107957897:107959553
	SNP10	108024959	T/C	6.92E-08	下游D 81.805	GEN1	101800161	107924858:107943154
	SNP11	108032737	A/G	9.54E-08	下游D 73.184	MSGN1	101799965	107957897:107959553
	SNP11	108032737	A/G	9.54E-08	下游D 89.583	GEN1	101800161	107924858:107943154
	SNP12	108040405	G/A	1.54E-08	下游D 80.852	MSGN1	101799965	107957897:107959553
	SNP12	108040405	G/A	1.54E-08	下游D 97.251	GEN1	101800161	107924858:107943154
	SNP13	108046603	A/G	1.07E-07	下游D 87.050	MSGN1	101799965	107957897:107959553
	SNP14	108047441	A/G	1.12E-07	下游D 87.888	MSGN1	101799965	107957897:107959553
	SNP15	108049654	T/C	3.13E-07	下游D 90.101	MSGN1	101799965	107957897:107959553
	SNP16	108050428	C/A	7.59E-08	下游D 90.875	MSGN1	101799965	107957897:107959553
	SNP17	108062144	T/C	7.39E-08	下游D 24.603	KCNS3	101799545	107994943:108037541
	SNP18	108065681	T/G	7.01E-08	下游D 28.140	KCNS3	101799545	107994943:108037541
	SNP19	108068212	G/A	1.13E-07	下游D 30.671	KCNS3	101799545	107994943:108037541
	SNP20	108070236	A/G	3.00E-07	下游D 89.657	KCNS3	101799545	107994943:108037541

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性状 Trait	数量 N	最大值 Max	最小值 Min	平均值 Mean	标准差 SD	变异系数 CV (%)
43周龄产蛋数 Egg count of week 43	396	195	105	160.91	14.39	8.93
55周龄产蛋数 Egg count of week 55	363	279	187	239.93	17.39	7.25
72周龄产蛋数 Egg count of week 72	355	384	253	340.54	29.57	8.68

	43周龄 W43	55周龄 W55	72周龄 W72
43周龄W43	0.30±0.12	0.75±0.18	0.69±0.17
55周龄W55	0.72±0.19	0.22±0.09	0.89±0.19
72周龄W72	0.63±0.21	0.84±0.19	0.17±0.08