中国地方品种杏花鸡的群体全基因组选择印记分析  

Analysis on Selective Signatures of Chinese Indigenous Xinghua Breed

作　　者：孔少芬 罗威 郑茗[1,2] 聂庆华 KONG Shaofen;LUO Wei;ZHENG Ming;NIE Qinghua(College of Animal Science,South China Agricultural University,Guangzhou,Guangdong 510642;Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding,and Key Laboratory of Chicken Genetics,Breeding and Reproduction,Ministry of Agriculture,Guangzhou and Rural Affairs,Guangzhou,Guangdong 510642;State Key Laboratory of Livestock and Poultry Breeding,Guangdong Key Laboratory of Animal Breeding and Nutrition,Institute of Animal Science,Guangdong Academy of Agricultural Sciences,Guangzhou,Guangdong 510640)

机构地区：[1]华南农业大学动物科学学院,广东广州510642 [2]广东省农业动物基因组学和分子育种重点实验室,农业农村部鸡遗传育种与繁殖重点实验室,广东广州510642 [3]广东省农业科学院动物科学研究所,畜禽育种国家重点实验室,广东省畜禽育种与营养研究重点实验室,广东广州510640

出　　处：《中国家禽》2023年第3期30-37,共8页China Poultry

基　　金：2018年广东省乡村振兴战略专项;广州市科技计划项目(202103000084);广东省现代农业产业技术体系创新团队项目(2021KJ128)。

摘　　要：试验旨在挖掘杏花鸡品种的群体特征性选择印记,筛选杏花鸡特征性基因和核心基因。研究基于已报道的来源于22个群体的157只鸡的全基因组数据,通过窗口内群体间遗传分化系数(ZFst)及群体内杂合度(ZHp),对其中的杏花鸡群体(n=9)进行全基因组选择印记分析,挖掘杏花鸡群体特征性选择印记,对候选基因进行GO功能分析和KEGG通路富集分析,蛋白相互作用网络分析和核心基因的筛选。结果显示:通过ZFst与ZHp,分别鉴定到172个杏花鸡群体基因组潜在受选择基因,其中包含29个共同受选择基因,包括COL3A1、LMO3、TBC1D14、COL22A1、EP300、TMTC3、KCNE5、PAICS、SGK1、DERA、GPR20、LHFPL6、PREX1、PIK3C2G、HEPACAM2、KITLG、KIAA0232、SMAD1、RIMKLB、SLIT2、LONRF1、NXT2、LDB2、TSNARE1、ABLIM2、VPS50、TCF12、ACSL4与FOXJ2;两种方法共鉴定到的受选择基因进行GO分析,分别富集到68条、82条和16条通路,主要涉及磷和含磷化合物代谢、细胞分化的调节、连接酶活性、转录因子复合体等;杏花鸡特征性核心相关基因为EP300和SMAD1,EP300和SMAD1均参与杏花鸡的肌肉和脂肪的发育和代谢过程。研究表明筛选出的群体特征性基因和核心基因可能通过调节磷代谢和细胞分化等途径影响杏花鸡的形态、肉质和风味。The purpose of this study was to excavate the selective signatures of population of Xinghua chicken, and to screen characteristic genes and Hub genes of Xinghua chicken. Based on the reported whole genome data of 157 chickens from 22 populations, we conducted genome-wide selection imprinting analysis on the Xinghua chicken population(n=9) by using the coefficient of genetic differentiation(ZFst) and heterozygosity(ZHp) within a window to explore the characteristic selection imprinting of Xinghua chicken population. GO function analysis, KEGG pathway enrichment analysis, protein interaction network analysis and core gene screening were performed for candidate genes. The results showed that by ZFst and ZHp, 172 potential selected genes were identified, including 29 common selected genes, including COL3A1, LMO3, TBC1D14, COL22A1, EP300, TMTC3,KCNE5, PAICS, SGK1, DERA, GPR20, LHFPL6, PREX1, PIK3C2G, HEPACAM2, KITLG, KIAA0232, SMAD1, RIMKLB, SLIT2,LONRF1, NXT2, LDB2, TSNARE1, ABLIM2, VPS50, TCF12, ACSL4 and FOXJ2. GO analysis of the selected genes identified by the two methods showed that 68, 82 and 16 pathways were enriched respectively, which were mainly involved in phosphorus and phosphorus-containing compounds metabolism, cell differentiation regulation, ligase activity, transcription factor complex, etc.EP300 and SMAD1 were the characteristic core related genes of Xinghua chickens. EP300 and SMAD1 were involved in the development and metabolism of muscle and fat. The results indicated that the population characteristic genes and core genes may affect the morphology, meat quality and flavor of Xinghua chickens by regulating phosphorus metabolism and cell differentiation.

关 键 词：杏花鸡 遗传多样性 基因组选择印记 核心基因 

分 类 号：S831.2[农业科学—畜牧学]