摘要
旨在明确苏山猪群体和巴克夏猪群体的遗传变异位点和多态信息,本研究首先对43个苏山猪样本和21个巴克夏猪样本进行DNA提取,然后利用“中芯一号”50K SNP芯片对DNA的SNP位点进行检测;使用Plink软件对SNP位点进行主成分分析;使用DetectRUNS软件包对样本进行全基因组ROH检测;选用3种方法(ROH、CLR和iHS)对选择信号进行分析。本研究总共鉴定到苏山猪42282个SNPs位点和巴克夏猪27718个SNPs位点。其中,苏山猪和巴克夏猪均被划分为3个家系。本研究在苏山猪中共检测到2071个ROH片段,F_(ROH)平均值为0.096。巴克夏猪中共检测到1853个ROH片段,F_(ROH)平均值为0.199。在苏山猪和巴克夏猪群体中分别检测到4个和40个高频ROH区域,分别注释到8个和103个基因,通过富集分析鉴定了50个显著的候选基因。另外,通过ROH、CLR和iHS共3种选择信号分析方法,对苏山猪和巴克夏猪的选择信号区域进行了鉴定,发现有42个基因可能受到选择。本研究初步揭示了苏山猪和巴克夏猪的基因组SNP图谱,并通过高频ROH分析和选择信号检测鉴定到一些可能影响猪的生长发育、肉质、营养和一般抗病力的基因,为苏山猪和巴克夏猪的选育利用提供了理论基础。
In order to clarify the genetic variation sites and polymorphic information of the Sushan pig population and the Berkshire pig population,the DNA samples from 43 Sushan pigs and 21 Berkshire pigs were extracted and SNP sites were detected by 50K SNP beadchip in this study.Plink software was used for principal component analysis of the SNP sites;The DetectRUNS software package was used for whole-genome ROH detection of the samples;Three methods(ROH,CLR,and iHS)were used to analyze the selection signals.A total of 42282 SNPs were identified in Sushan pigs and 27718 SNPs in Berkshire pigs.Both breeds were divided into 3 families.There were 2071 ROH segments were detected in Sushan pigs with an average F_(ROH)value of 0.096,and 1853 ROH segments were detected in Berkshire pigs with an average F_(ROH)value of 0.199.Four and 40 high-frequency ROH regions were detected in the Sushan pig and Berkshire pig populations,respectively,which were annotated to 8 and 103 genes.There were 50 significant candidate genes were identified through enrichment analysis.Additionally,three selection signal analysis methods(ROH,CLR and iHS)were used to identify selection signal regions in Sushan pigs and Berkshire pigs,which illustrated that 42 genes could be under selection.This study preliminarily revealed the genomic SNP pattern of Sushan pigs and Berkshire pigs and excavated some genes that may affect pig growth and development,meat quality,nutrition,and general disease resistance by high-frequency ROH analysis and selection signal detection,which provided a theoretical basis for the breeding and utilization of Sushan pigs and Berkshire pigs.
作者
戴超辉
崔乐康
李辉
赵为民
付言峰
李碧侠
王学敏
廖超
陈彦羽
包文斌
程金花
DAI Chaohui;CUI Lekang;LI Hui;ZHAO Weimin;FU Yanfeng;LI Bixia;WANG Xuemin;LIAO Chao;CHEN Yanyu;BAO Wenbin;CHENG Jinhua(Institute of Animal Science,Jiangsu Academy of Agricultural Sciences,Key Laboratory of Crop and Livestock Integration of Ministry of Agriculture and Rural Affairs,Jiangsu Germplasm Resources Protection and Utilization Platform,Nanjing 210014,China;College of Animal Science and Technology,Yangzhou University,Yangzhou 225009,China;ProNet Biotech Co.,Ltd.,Nanjing 210033,China)
出处
《畜牧兽医学报》
CAS
CSCD
北大核心
2024年第12期5452-5463,共12页
ACTA VETERINARIA ET ZOOTECHNICA SINICA
基金
江苏省种业振兴揭榜挂帅项目(JBGS[2021]099)
江苏省青年基金项目(BK20230753)
国家生猪产业技术体系(CARS-PIG-35)。
