中国农业大学学报2025，Vol.30Issue(8)：96-106,11.DOI:10.11841/j.issn.1007-4333.2025.08.09
"太行云牛"群体遗传结构与基因组选择信号分析
Population genetic structure and genomic selection signals analysis in"Taihang Yun"cattle
摘要
Abstract
The purpose of this paper is to explore the genetic structure of"Taihang Yun"cattle,and to select important genomic selection signals and candidate genes related with economic traits in"Taihang Yun"cattle.This study utilized the"YuXin-1"bovine 200 K liquid phase SNP chip to conduct SNP genotyping,population genetic structure analysis,and linkage disequilibrium decay analysis in 113"Taihang Yun"cattle and 26 Jinnan cattle;FST and θπ methods were applied combinedly to select the genomic signal areas,also the potential candidate genes were explored through GO and KEGG annotations.The results showed that:1)After quality control of the chip data,a total of 187 988 SNPs loci were obtained.Principal component analysis and NJ tree analysis both clearly divided"Taihang Yun"cattle and Jinnan cattle into two clades,which both exhibited a gradual decay of linkage disequilibrium with increasing distance.The degree of linkage disequilibrium in"Taihang Yun"cattle was higher than that in Jinnan cattle.2)ADMIXTURE was used for ancestral component analysis,and when K=3,the result was closest to the real ancestral content,with the lowest cross validation value.3)Two analysis methods detected 618 selected sites in"Taihang Yun"cattle,including 257 genes,which contained 2 genes related with coat color(KIT,MITF),2 genes related with fat deposition and meat tenderness(SOAT2,CYP2R1),4 genes related with reproduction(EIF4B,MAP3K1,IFNAR2,TGFβ2),4 genes related with disease resistance and stress(PDGFRA,FGF6,KDR,RPS6KA6).In conclusion,FST and θπ method were applied in both populations and detected 618 selected regions and 257 genes,which involved biological processes as coat color,fat metabolism,reproduction,disease resistance and growth and development.The results provided essential genetic information to molecular mechanisms of excellent traits in"Taihang Yun"cattle,the sites and candidate genes identified also provided data bases for molecular breeding and selection.关键词
"太行云牛"/基因芯片/遗传结构/选择信号/候选基因Key words
"Taihang Yun"cattle/DNA chip/genetic structure/selection signal/candidate genes分类
畜牧业引用本文复制引用
王坤,张元庆,陈卓,刘彦杰,王泽昭,李博,程景,牛晓艳.."太行云牛"群体遗传结构与基因组选择信号分析[J].中国农业大学学报,2025,30(8):96-106,11.基金项目
山西省关键核心技术攻关子项目(NYGG22-02) （NYGG22-02）
和顺县现代肉牛产业发展研究院项目(XDHZHSY2024-03) （XDHZHSY2024-03）
山西省科技重大专项计划"揭榜挂帅"项目(202201140601026) （202201140601026）
