EGI OpenIR  > 研究系统  > 荒漠环境研究室
基于高密度 SNP 芯片的绵羊肉用性状全基因组关联分析
张志峰
学位类型博士
导师田长彦 ; 刘明军
2017-12-01
学位授予单位中国科学院大学
学位授予地点新疆乌鲁木齐
学位专业理学博士
关键词全基因组关联分析 绵羊 肉用性状 单核苷酸多态性 高密度 Snp芯片
摘要随着羊肉需求数量的增加,绵羊肉用性状的选育工作越来越受到重视。利用标记或基因辅助选择(MAS)是快速提高绵羊肉用性能、培育优良肉羊品种的最佳途径,而标记或基因辅助选择的前提条件是肉用性状功能基因的准确定位。全基因组关联分析(GWAS)是目前畜禽功能基因快速、准确定位的主要策略和手段。本研究以特克塞尔羊(Texel)为父本、阿勒泰羊(Altay Sheep)为母本,组建了由 303 只个体组成的 F2 代资源群体。对所有个体的生长发育性状(出生重、断奶重、宰前活重、断奶前日增重和断奶后日增重)、胴体体尺(胴体长、后腿长、臀宽、胸宽、肩宽、胸深和踝骨宽)、胴体分块重(胴体重、屠宰率、脖子重、前腱重、胸腹肉重、方切肩重、脊排重、腰椎肉重、带臀腿重)、胴体脂肪(背部脂肪厚、GR 值、肠系膜脂肪重、肾周脂肪重和尾脂重)和胴体肌肉(眼肌面积、背最长肌重、大里脊重、小里脊重、针扒重、膝圆重、烩扒重、尾龙扒重和后腱重)等肉用性能共计36个性状进行测定,利用Illumina绵羊高密度(600K)SNP 芯片对分布于基因组范围内的 606006 个 SNP 位点进行基因分型。通过TASSEL 软件构建的混合线性模型,利用质控后分布于常染色体上的 530354 个SNPs 对上述 36 个肉用性状进行全基因组关联分析,筛选与目的性状显著相关的SNPs。依据绵羊基因组(Ovis_aries_v3.1)对 GWAS 中发现的显著相关 SNPs 进行基因注释,并结合功能基因组学确定候选基因。结果如下:(1)与断奶重、宰前活重(8 月龄)和胴体重在基因组水平上显著相关的 SNPs 有 3 个,初步确定KCNC2 基因是断奶重的候选基因,RAB3C 基因和 PLK2 基因是影响宰前活重和胴体重的候选基因,没有发现与出生重和日增重显著相关的 SNP。(2)与胴体长、胸深和后腿长显著相关的 SNPs 有 12 个,初步确定 MC4R 基因是影响绵羊胴体长的候选基因,NPNT 基因和 Smad5 基因是影响胸深的候选基因,TMED2 基因和 CALCRL 是影响后腿长的候选基因。没有发现与肩宽、胸宽、臀宽和踝骨宽显著相关的 SNP。(3)与背部脂肪厚、GR 值、肠系膜脂肪重、肾周脂肪重和尾脂重显著相关的 SNPs 共有 21 个,初步确定 FFAR2 基因和 SERPINA6 是影响背部脂肪厚的候选基因,CENPF 基因是影响绵羊 GR 值的候选基因,SLC6A15 基因是影响肠系膜脂肪重量和尾脂重的候选基因,PPARα和 CELSR1 基因为影响肾周脂肪重的候选基因。(4)与带臀腿重显著相关的 SNP 有 24 个,其中有 19个 SNPs 集中分布在 2 号染色体上 10 Mb(120.72Mb-130.64 Mb)的区域内,初步确定 DNAJC10、TMED2、CALCRL 和 EGF 影响带臀腿重的候选基因。没有发现与脖子重、前腱重等其它胴体切块重显著相关的 SNP。(5)与带臀腿肌肉总重及其肌肉块重显著相关的 SNPs 有 61 个,主要集中分布在 2 号染色体 13.8Mb(110.8Mb-122.2Mb)的区域内,MSTN、BIN1 和 TMED2 是影响带臀腿肌肉总重的主要候选基因。与眼肌面积显著相关的 SNP 有 5 个,MSTN 基因和 IGFBP3基因是影响眼肌面积的候选基因,没有发现与小里脊重和背最长肌重显著相关SNP。为了筛选和确定影响背部脂肪厚的数量性状核苷酸(QTN),本研究选择FFAR2 基因为研究对象,采用 PCR 扩增、Sanger 测序方法进行突变碱基的检测,利用单标记回归方法筛选与背部脂肪厚显著相关的 SNPs,并采用荧光定量 PCR方法分析 SNP 与 FFAR2 基因表达量之间的关系。结果显示,在 FFAR2 基因上共发现 23 个 SNPs,其中位于 FFAR2 基因 3’UTR 的 SNP2709(A->G)位点与背部脂肪厚显著相关。荧光定量 PCR 分析发现,SNP2709 基因型与 FFAR2 基因在背部脂肪中的相对表达水平呈正相关关系。由此推测,SNP2709 可能是影响背部脂肪厚的候选 QTN。本项研究从全基因组水平分析了与 36 个绵羊肉用性状相关的 SNP 位点和候选基因,共检测到 129 个与带臀腿肌肉总重、眼肌面积、背部脂肪厚、尾脂重等性状显著相关的 SNPs,定位到 2 号染色体的 MSTN、BIN1、CALCRL 和 TMED2基因,3 号染色体上 SLC6A15、PPARα、CELSR1、PEX5 和 GFBP3 基因及 14号染色体上 FFAR2 基因,其中与重要影响胴体品质的背部脂肪厚性状相关的基因被确定为 14 染色体的 FFAR2 基因,通过 QTN 分析、群体验证和表达水平分析初步确定了该基因的功能。
其他摘要With the consumption increase for lamb, carcass and meat production traits have been highlighted in the world. MAS (marker-assisted selection) as an effective method to speed animal breeding and improve meat production can’t be harnessed until the position of particular functional genes on the chromosome to be determined accurately. Many studies show that the genome-wide association studies (GWAS) is a very important method to locate functional genes.In this study, F2 population generated by intercross-bred of Texel sheep with Altay sheep, includes 303 lambs slaughtered at the age around 8 month. A total of 36 carcass traits, including growth traits (birth weight, weaning weight, pre-weaning gain,post-weaning gain and body weight), carcass size (carcass length, leg length, chest width, shoulder width, chest depth, and ankle width), carcass cut weight (carcass weight, slaughter rate, neck weight, fore shank weight, chump weight, square cut shoulder weight, rack weight, breast and flap weight, leg-chump on weight), carcass fat chatacters (back fat thickness, GR value, tail fat weight, perirenal fat weight,mesenteric fat weight) and carcass muscle traits (eye muscle area, longissimus dorsi muscle weight, tenderloin weight, pork tenderloin weight, topside weight, knuckle weight, silverside weight, rump weight, hind shank weight, total leg-chump muscle weight). All the 303 lambs were genotyped by high-density Illumina OvineSNP600K BeadChip. Among the 606,006 single nucleotide polymorphisms (SNPs) on the chip,530,354 SNPs were used to perform GWAS to identify SNPs associated with 36 traits above by use of the TASSEL program with a mixed linear model (MLM). The genes nearby SNPs were annotated based on the Ovis_aries_v3.1 genome. The results obtained were as follows:1. Three SNPs that reached genome-wide significance level for weaning weight,body weight and carcass weight were positioned near KCNC2, RAB3C and PLK2 gene, which were thought to be the candidate genes for weaning weight, body weight and carcass weight, respectively. SNPs that were associated with birth weight and daily gain significantly at genome-wide level were not detected.2. Twelve significant SNPs were associated with carcass length, chest depth and leg length at genome-wide level. GWAS data showed that MC4R was a candidate gene for carcass length, NPNT and Smad5 were candidate genes for chest depth, TMED2 and CALCRL was candidate genes for leg length. SNPs which were associated with shoulder width, chest depth and ankle width significantly at genome-wide level were not detected.3. For carcass fat traits, 21 SNPs reached genome-wide significant level for back fat thickness, GR value, perirenal fat weight, mesenteric fat weight and tail fat weight were identified. The data strongly suggested that FFAR2 and SERPINA6 were candidate genes for back fat thickness, CENPF for GR value, SLC6A15 for mesenteric fat weight and tail fat weight, and PPARα and CELSR1 for perirenal fat weight traits.4. Among 24 SNPs that were associated with leg-chump weight significantly at genome-wide level, 19 SNPs were distributed in 10 Mb region (120.72 Mb-130.64 Mb). DNAJC10, TMED2, CALCRL and EGF were in the region and thought to be the important candidate genes for leg-chump weight. The SNPs, which were significantly associated with the other carcass cut weight traits at genome-wide level, were not detected.5. A total of 61 SNPs which were associated with total leg-chump muscle weight significantly at genome-wide level were almost distributed in 13.8 Mb region (110.8Mb-122.2Mb). MSTN, TMED2 and BIN1 were in the region and thought to be the important candidate genes for leg-chump muscle weight. Five SNPs that were associated with eye-muscle area significantly at genome-wide level were detected near two well-known genes of MSTN and IGFBP3, which suggested to be candidate genes for eye-muscle area. The SNPs, which ware associated with longissimus dorsi muscle weight, pork tenderloin weight significantly at genome-wide level were not detected.In order to detect quantitative trait nucleotides (QTN) influencing back fat thickness, all the mutations of FFAR2 gene were detected by PCR and Sanger sequencing. The association between mutations and back fat thickness was analyzed using single marker regression method. 23 SNPs were found and SNP2709 (A->G) was significantly associated with back fat thickness. Moreover, the relative expression of FFAR2 mRNA in the back fat in three genotypes of SNP2709 was measured by qPCR. The expression level of FFAR2 was positively with back fat thickness and consistent with the GWAS results. It was inferred that SNP2709 most possibly was the candidate QTN that influenced sheep back fat thickness.By the association between 36 carcass traits and SNPs and candidate genes in genome-wide region, 129 significant SNPs were identified and were located within MSTN, FFAR2, BIN1, TMED2, SLC6A15, PPARα, CELSR1, PEX5, CALCRL and IGFBP3 genes. FFAR2 on OAR 14 was thought be important candidate gene for back fat thickness trait which had an impact on carcass meat quality. Furthermore, the function of FFAR2 which played important roly on fat deposition were elucidated for the first time by QTN screening, population test and gene expression analysis.
学科领域生态学
语种中文
文献类型学位论文
条目标识符http://ir.xjlas.org/handle/365004/14770
专题研究系统_荒漠环境研究室
作者单位1.中国科学院新疆生态与地理研究所
2.新疆畜牧科学院生物技术研究所
推荐引用方式
GB/T 7714
张志峰. 基于高密度 SNP 芯片的绵羊肉用性状全基因组关联分析[D]. 新疆乌鲁木齐. 中国科学院大学,2017.
条目包含的文件
文件名称/大小 文献类型 版本类型 开放类型 使用许可
基于高密度 SNP 芯片的绵羊肉用性状全(6276KB)学位论文 开放获取CC BY-NC-SA请求全文
个性服务
推荐该条目
保存到收藏夹
查看访问统计
导出为Endnote文件
谷歌学术
谷歌学术中相似的文章
[张志峰]的文章
百度学术
百度学术中相似的文章
[张志峰]的文章
必应学术
必应学术中相似的文章
[张志峰]的文章
相关权益政策
暂无数据
收藏/分享
所有评论 (0)
暂无评论
 

除非特别说明,本系统中所有内容都受版权保护,并保留所有权利。