全基因组关联分析筛选鹅蛋品质相关分子标记  

Identification of Molecular Markers Associated with Goose Egg Quality Through Genome-Wide Association Analysis

作　　者：高广亮[1,2] 张克山 赵献芝[1,2] 许国洋 谢友慧[1,2] 周莉 张昌莲 王启贵[1,2] GAO GuangLiang;ZHANG KeShan;ZHAO XianZhi;XU GuoYang;XIE YouHui;ZHOU Li;ZHANG ChangLian;WANG QiGui(Chongqing Academy of Animal Science,Chongqing 402460;Chongqing Engineering Research Center of Goose Genetic Improvement,Chongqing 402460;Chongqing Qijiang Animal Disease Control Center,Chongqing 401420)

机构地区：[1]重庆市畜牧科学院,重庆402460 [2]重庆市肉鹅遗传改良工程技术研究中心,重庆402460 [3]重庆綦江区动物疫病预防控制中心,重庆401420

出　　处：《中国农业科学》2023年第19期3894-3904,共11页Scientia Agricultura Sinica

基　　金：重庆市科研机构绩效激励引导专项项目(cstc2022jxjl80007);重庆市科研院所绩效激励引导专项项目(22527J);财政部和农业部:国家现代农业产业技术体系(CARS-42-51);重庆市技术创新与应用发展专项重点项目(cstc2019jscx-gksbX0097)。

摘　　要：【目的】通过筛选与鹅蛋品质性状相关的分子标记和候选基因,为解析蛋品质性状的遗传机制及分子标记辅助选择提供理论支撑。【方法】采用同批次健康四川白鹅群体(209只)作为研究对象。收集了每只鹅在产蛋高峰期连续生产的5枚蛋,并测定了蛋重、蛋形指数、蛋壳强度、蛋壳厚度、蛋壳重和蛋黄重量等6个蛋品质性状。基于前期209只四川白鹅(母鹅)2.896 Tb全基因组重测序数据(12.44×/个体),采用全基因组关联分析的方法,筛选与蛋品质性状相关的SNP位点和重要候选基因,并通过核酸飞行时间质谱方法检测了这些SNP位点的基因型频率。【结果】经过筛选过滤,共有9279339个SNPs和209个个体用于后续研究。GWAS研究发现,48个SNP位点与6个鹅蛋品质性状显著或建议性显著相关(阈值分别为5.43×10-9和1.09×10-7),并注释出27个蛋品质性状相关的候选基因,包括妊娠相关血浆蛋白A(pappalysin1,PAPPA)、蛋白丝氨酸/苏氨酸磷酸酶调节亚基2基因(serine/threonine-protein phosphatase 4 regulatory subunit 2,PP4R2)、乙醇胺磷酸转移酶1(ethanolamine phosphotransferase 1,EPT1)和离子型谷氨酸受体K2(glutamate receptor ionotropic,kainate 2,GRIK2)等,其中候选基因PAPPA参与蛋白质代谢,促进生长因子IGF生成,在PP4R2的11bp范围内存在5个SNPs与蛋壳厚度显著相关,另外在GRIK2上有6个SNPs与蛋黄重量显著相关,GRIK2和PP4R2分别与机体血钙维持功能以及胆固醇代谢相关。功能富集研究发现,候选基因主要参与了response to growth factor(GO:0070848)、intracellular chemical homeostasis(GO:0055082)、response to hormone(GO:0009725)和regulation of the monoatomic ion transport(GO:43269)等代谢通路。【结论】经GWAS方法筛选出PAPPA、GRIK2、ASCC3和EPT1分别作为蛋重、蛋黄重、蛋壳强度等蛋品质性状潜在功能基因,为鹅蛋品质性状的改良提供了分子遗传标记的理论参考。【Objective】The objective of this study was to screen molecular markers and candidate genes related to goose egg quality traits,to provide a theoretical support for the analysis of the genetic mechanism of egg quality traits and marker-assisted selection.【Method】In this study,a batch of healthy Sichuan White Geese(209 individuals)was selected as the research subjects.Five eggs from each goose during the peak egg production period were collected,and then six egg quality traits were measured,including egg weight,egg shape index,eggshell strength,eggshell thickness,eggshell weight,and egg yolk weight.Based on the whole-genome resequencing data(2.896 Tb,12.44×/individual)of 209 Sichuan White Geese(female geese),a genome-wide association analysis was conducted to identify SNP loci and important candidate genes associated with egg quality traits.The genotype frequencies of the SNP loci were determined using the nucleic acid flight time mass spectrometry method.【Result】After filtering,a total of 9279339 SNPs and 209 individuals were included for further analysis.The GWAS analysis identified 48 SNP loci significantly or suggestively associated with six egg quality traits(thresholds:5.43×10-9 and 1.09×10-7).These loci were annotated to 27 candidate genes related to egg quality traits,including Pregnancy-associated plasma protein A(PAPPA),Serine/threonine-protein phosphatase 4 regulatory subunit 2(PP4R2),Ethanolamine phosphotransferase 1(EPT1),and Glutamate receptor ionotropic,kainate 2(GRIK2).Among them,the candidate gene PAPPA was involved in protein metabolism and promotes the generation of insulin-like growth factor.Five SNPs within the 11 bp range of PP4R2 were significantly associated with eggshell thickness.Additionally,six SNPs on the GRIK2 gene were significantly associated with yolk weight.GRIK2 and PP4R2 were respectively associated with blood calcium homeostasis and cholesterol metabolism in organisms.Functional enrichment analysis revealed that the candidate genes were mainly annotated to“respo

关 键 词：全基因组关联分析 分子标记辅助选择 鹅 蛋品质性状 

分 类 号：S835[农业科学—畜牧学]