【作者】 张莉；

【导师】 郑友民； 杜立新；

【作者基本信息】 中国农业科学院 ， 动物遗传育种与繁殖， 2013， 博士

【摘要】 随着世界养羊业格局的变化，肉羊生产比重不断增加，绵羊肉用性状的选择越来越受到遗传学家和育种学家的关注，肉用性状的功能基因定位已成为肉羊分子育种研究热点。为了在全基因组范围内寻找和挖掘影响绵羊肉用性状的重要功能基因，本研究对苏尼特羊、德国肉用美利奴羊和杜泊羊共计329只绵羊的11个影响其肉用性状的数量性状开展全基因组关联分析。采用Illumina公司开发的OvineSNP50BeadChip中密度商业化羊芯片，通过SNP分型技术和高通量测序技术，对研究群体的11个肉用性状（初生重、断奶重、六月龄重、眼肌面积、背膘厚度、断奶前日增重、断奶后日增重、日增重、体高、胸围和管围）进行全基因组关联分析。对研究个体和基因型分别进行质量控制后，最后共有319个个体和48198个SNPs用于关联分析。统计分析基于TASSLE软件和混合线性模型（mixed linear model，MLM）进行计算，同时考虑试验群体中的群体分层和个体间亲缘关系。分析结果表明，在全基因组范围内共检测到36个单核苷酸多态位点（single nucleotide polymorphisms，SNPs）与7个肉用性状（断奶重、六月龄重、断奶前日增重、断奶后日增重、日增重、胸围和管围）显著相关，其中10个SNPs位点达到全基因组显著水平，并全部与断奶后日增重相关。显著位点的基因注释依据最新绵羊基因组Ovis_aries_v3.1和其他物种（人、牛、小鼠和大鼠）的基因组信息。在检测到的显著的SNPs位点中，有14个落在已知的羊注释基因内，另一些分布在羊注释基因附近，距离范围在878bp至398165bp之间。本研究最重要的发现是检测并推断影响断奶后日增重的5个关键候选基因：s58995.1位于MEF2B和RFXANK基因内； OAR3₈4073899.1、 OAR3₁15712045.1和OAR9₉1721507.1三个位点分别位于CAMKMT、TRHDE和RIPK2基因内。此外，GRM1、POL、MBD5、UBR2、RPL7和SMC2也被认为是影响断奶后日增重的重要候选基因。其余达到染色体显著水平的SNPs位点有25个，分别与断奶重、六月龄重、断奶前日增重、日增重、胸围和管围6个性状相关。通过基因注释，获得25个可能与绵羊肉用性状相关的潜在候选基因，分别是NLGN1、EPB41L3、C1ORF87、CHMP5、LRPPRC、TGIF1、STT3A、ADAMTS2、TRPS1、SRP68、HYDIN、LSM3、MYO10、CCDC15、MSL1、NTN1、ZWINT、PLA2G6、PFKFB4、TRDN、OXSM、RARB、LRRC2、ADK和SHISA9。在本研究中，没有在基因组水平或染色体水平上检测到与初生重、体高、背膘厚度和眼肌面积显著相关的SNPs位点。本研究是首次在绵羊肉用性状中开展的全基因组关联研究，同时也是关注较多肉用性状指标并利用最新绵羊基因组Ovis_aries_v3.1序列信息和GWAS方法进行的绵羊肉用性状主效基因的鉴定研究。研究结果对定位绵羊肉用性状数量性状座位（quantitative trait locus，QTL）和候选基因有重要的意义。同时也为探索绵羊肉用性状功能基因提供了重要的理论依据和参考，为后续功能基因的网络分析、功能验证及解释性状变异的分子遗传机制奠定了基础。更多还原

【Abstract】 Growth and meat production are significant economic traits in sheep, but a few investigations areemployed to identify genes associated with growth and meat production at genome level. Motivated bymining major candidate genes across ovine genome, the present study is to perform genome-wideassociation studies （GWAS） to detect genes associated with growth and meat production traits.Using Illumina OvineSNP50BeadChip, we performed a GWA study in329purebred sheepphenotyped for11growth and meat production traits （birth weight, weaning weight,6-month weight,eye muscle area, fat thickness, pre-weaning gain, post-weaning gain, daily weight gain, height atwithers, chest girth, and shin circumference）. A total of319sheep and48,198single nucleotidepolymorphisms （SNPs） were fitted using the TASSEL program with a mixed linear model，meanwhile,we considered population stratification assessment and relationship between any two individuals in thepopulation.36chromosome-wise significant SNPs were identified for7traits, and10of themconsistently reached genome-wise significance level for post-weaning gain. Gene annotation wasimplemented based on the latest Ovis_aries_v3.1genome sequence （released October2012）, and, in themeantime,we referenced genomic information of human, bovine, mouse and rat. More than one-thirdSNPs （14out of36） were located within ovine genes, some others were located close to ovine genes（878bp-398165bp apart）. The strongest new finding is5genes were thought to be the most crucialcandidate genes associated with post-weaning gain: s58995.1was located within the ovine genesMEF2B and RFXANK, OAR3₈4073899.1, OAR3₁15712045.1and OAR9₉1721507.1were locatedwithin CAMKMT, TRHDE, and RIPK2respectively. GRM1, POL, MBD5, UBR2, RPL7and SMC2werethought to be the important candidate genes influencing post-weaning gain too. Additionally,25genes（NLGN1,EPB41L3,C1ORF87,CHMP5,LRPPRC,TGIF1,STT3A,ADAMTS2,TRPS1,SRP68,HYDIN,LSM3,MYO10,CCDC15,MSL1,NTN1,ZWINT,PLA2G6,PFKFB4,TRDN,OXSM,RARB,LRRC2,ADK,andSHISA9）at the chromosome-wise significance level were also forecasted to be the promising genes thatinfluencing the sheep growth and meat production traits. In this study, we did not detected anysingnificant SNPs at genome-wise or chromosome-wise level that associated with birth weight,height atwithers,fat thickness and eye muscle area.This study is one of the earliest GWA reports which simultaneously related so many growth andmeat production traits based on the latest Ovis_aries_v3.1genome sequence. The results will contributeto identify quantitative trait locus（QTL）and candidate genes for growth and meat production traits. Ourfindings also provide an insight into the additional novel functions of genes that is previouslyconsidered having no relationship with growth and meat production traits. It will facilitate the potentialutilization of genes involved in growth and meat production traits in sheep in future.更多还原