全基因组关联分析筛选文昌鸡体尺性状相关分子标记  

Identification of Molecular Markers Associated with Body Size Traits Through Genome-Wide Association Analysis in Wenchang Chickens

作　　者：骆娜 安炳星 魏立民[1,2] 文杰[3] 赵桂苹 LUO Na;AN BingXing;WEI LiMin;WEN Jie;ZHAO GuiPing(Sanya Research Institute,Hainan Academy of Agricultural Sciences,Sanya 572025,Hainan;Institute of Animal Husbandry and Veterinary Medicine,Hainan Academy of Agricultural Sciences,Haikou 571100;State Key Laboratory of Animal Nutrition/Institute of Animal Sciences of Chinese Academy of Agricultural Sciences,Beijing 100193)

机构地区：[1]海南省农业科学院三亚研究院(海南省实验动物研究中心),海南三亚572025 [2]海南省农业科学院畜牧兽医研究所,海口571100 [3]中国农业科学院北京畜牧兽医研究所/动物营养学国家重点实验室,北京100193

出　　处：《中国农业科学》2024年第10期2046-2060,共15页Scientia Agricultura Sinica

基　　金：文昌鸡优势特色产业集群项目(WCSCICP20211106);海南省三亚崖州湾科技项目(SKJC-2022-PTDX-002);现代农业产业技术体系建设专项资金(CARS-41)。

摘　　要：【目的】体尺是评价禽类生长特性的主要指标,通过筛选与文昌鸡体尺性状相关的分子标记及候选基因,为解析体尺性状的遗传机制及分子育种提供理论支撑。【方法】利用海南省文昌鸡品系3个世代(n=2024)群体作为研究对象,测定每只鸡在上市日龄的胫长、胫围、体斜长、龙骨长及胸宽等5个体尺性状。采集血液进行鸡“京芯一号”55 K芯片测序及基因分型,使用GEMMA软件与PLINK软件进行全基因组关联分析,鉴定与体尺性状相关的SNP位点和候选基因,通过LD分析鉴定与体尺性状显著相关的单倍型。【结果】表型结果显示,113日龄文昌鸡公鸡平均胫长8.64 cm,胫围0.46 cm,体斜长19.73 cm,龙骨长12.32 cm,胸宽6.81 cm;母鸡平均胫长6.98 cm,胫围0.40 cm,体斜长17.79 cm,龙骨长10.45 cm,胸宽6.24 cm。经过质控后,共保留42206个SNPs和2024个个体用于后续研究。使用Plink软件进行PCA主成分分析,结果发现3个世代群体存在一定的分散情况,因此在GWAS关联分析中加入了前3个主成分作为协变量,以校正群体结构对关联分析的影响。GWAS结果研究共鉴定出19个SNPs位点与胫长性状显著或建议性显著相关(P值分别为2.17789E-06和4.35578E-05),23个SNPs位点与胫围性状显著或建议性显著相关,7个SNPs位点与体斜长性状显著或建议性显著相关,2个SNPs位点与龙骨长性状显著或建议性显著相关,未鉴定出与胸宽性状或建议性显著相关的SNPs位点。通过对显著性位点进行注释,结果共鉴定到16个体尺性状相关的候选基因,包括羧基末端LIM结构域结合蛋白2(LIM domain binding 2,LDB2)、染色体缩合蛋白G(non-SMC condensin I complex subunit G,NCAPG)、序列相似家族184成员B基因(family with sequence similarity 184 member B,FAM184B)、A型钾离子通道调节蛋白4(potassium voltage-gated channel interacting protein 4,KCNIP4)等。通过LD单倍型分析结果显示,GGA4存在3个显著关联的单倍�【Objective】Body size traits are the primary indicators for evaluating avian growth characteristics.By selecting molecular markers and candidate genes related to body size traits in Wenchang chickens,this study could provide the theoretical support for deciphering the genetic mechanisms and molecular breeding of body size traits.【Method】Three generations of Wenchang chicken lines in Hainan Province(n=2024)were used in this study.Five body size traits were measured on each chicken at market age,including shank length,shank girth,body slope length,keel length,and chest width.Blood samples were collected for DNA extraction,followed by sequencing and genotyping using the"Jingxin No.1"55 K chip.Genome-wide association analysis was conducted using GEMMA and PLINK software to identify SNP loci and important candidate genes associated with body size traits.LD analysis was performed to identify haplotypes significantly associated with body size traits.【Result】Phenotypic data showed that,at 113 days of age,Wenchang cockerels had average shank length of 8.64 cm,shank girth of 0.46 cm,body slope length of 19.73 cm,keel length of 12.32 cm,and chest width of 6.81 cm.Wenchang hens had average shank length of 6.98 cm,shank girth of 0.40 cm,body slope length of 17.79 cm,keel length of 10.45 cm,and chest width of 6.24 cm.After quality control,42206 SNPs and 2024 individuals were retained for further analysis.PCA analysis using PLINK software revealed some dispersion among the three generations,prompting the inclusion of the top three principal components as covariates in the GWAS analysis to correct for population structure effects.The GWAS results identified 19 SNPs significantly or suggestively associated with shank length(P value=2.17789E-06/4.35578E-05),23 SNPs associated with shank girth,7 SNPs associated with body slope length,and 2 SNPs associated with keel length.No SNPs significantly associated with chest width were identified.Annotation of significant loci identified 16 candidate genes related to body size tra

关 键 词：全基因组关联分析 鸡 体尺性状 胫长 胫围 

分 类 号：S831.2[农业科学—畜牧学]