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。
【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.
作者
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
LIU HongXiang;ZHANG XuePing;WANG YiFei;WANG ZhiCheng;GU HaoTian;SONG WeiTao;TAO ZhiYun;XU WenJuan;ZHANG ShuangJie;LU LiZhi;LI HuiFang;ZHU ChunHong(Jiangsu Institute of Poultry Sciences,Yangzhou 225125,Jiangsu;Institute of Animal Husbandry and Veterinary Science,Zhejiang Academy of Agricultural Science,Hangzhou 310021)
出处
《中国农业科学》
北大核心
2025年第15期3145-3158,共14页
Scientia Agricultura Sinica
基金
国家重点研发计划(2022YFD1300100)
扬州市现代农业(YZ2024054)
江苏省“种业振兴”揭榜挂帅项目(JBGS[2021]030,JBGS[2021]111)。
