利用简化基因组测序筛选安格斯牛生长相关的受选择基因

doi:10.11843/j.issn.0366-6964.2020.04.007

畜牧兽医学报 ›› 2020, Vol. 51 ›› Issue (4): 713-721.doi: 10.11843/j.issn.0366-6964.2020.04.007

利用简化基因组测序筛选安格斯牛生长相关的受选择基因

吕世杰^1,2, 陈付英^1,2, 金磊^1,2, 张子敬^1,2, 朱肖亭^1,2, 施巧婷^1,2, 辛晓玲^1,2, 楚秋霞^1,2, 柏中林³, 王二耀^1,2*, 徐照学^1,2*

1. 河南省农业科学院畜牧兽医研究所, 郑州 450002;
2. 河南省畜禽繁育与营养调控重点实验室, 郑州 450002;
3. 泌阳县动物疫病预防控制中心, 驻马店 463700

收稿日期:2019-10-29 出版日期:2020-04-25 发布日期:2020-04-21
通讯作者: 徐照学,主要从事动物胚胎工程方面的研究,E-mail:xuzhaoxue11@163.com;王二耀,主要从事动物发育及胚胎工程方面的研究,E-mail:wangeryao666@qq.com
作者简介:吕世杰(1989-),男,河南三门峡人,助理研究员,博士,主要从事动物遗传育种与繁殖方面的研究,E-mail:sjlyu@outlook.com;陈付英(1973-),女,河南南阳人,副研究员,博士,主要从事黄牛分子育种方面的研究,E-mail:fychen2004@sina.com
基金资助:
国家重点研发计划（2018YFD0501700）；河南省肉牛产业技术体系项目（S2013-08）；国家肉牛牦牛产业技术体系项目（CARS-37）；科研发展专项资金项目（2019CY08）；河南省农业科学院科技创新创意项目（2020CX09）

Identification of Growth-Related Genes under Selection in Angus Cattle Using SLAF-seq

Lü Shijie^1,2, CHEN Fuying^1,2, JIN Lei^1,2, ZHANG Zijing^1,2, ZHU Xiaoting^1,2, SHI Qiaoting^1,2, XIN Xiaoling^1,2, CHU Qiuxia^1,2, BAI Zhonglin³, WANG Eryao^1,2*, XU Zhaoxue^1,2*

1. Institute of Animal Science and Veterinary Medicine, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China;
2. Henan Key Laboratory of Livestock and Poultry Breeding and Nutrition Regulation, Zhengzhou 450002, China;
3. Center of Animal Disease Prevention and Control of Biyang, Zhumadian 463700, China

Received:2019-10-29 Online:2020-04-25 Published:2020-04-21

摘要/Abstract

摘要： 旨在探究安格斯牛生长相关的受选择基因，为肉牛生长相关主效基因的鉴定提供参考。本试验共采集72头南阳牛母牛和14头黑安格斯牛母牛血样并提取基因组DNA。利用SLAF-seq（specific-locus amplified fragment sequencing）技术获得全基因组SNP标记并对试验个体基因型进行分型。通过计算各SNP位点的遗传分化系数（Fst值）和核苷酸多态性（π ratio）筛选两品种间的差异基因组区域，并与动物QTL数据库中牛生长性状QTLs进行比对，重合区域作为候选区域。随后对候选区域内基因进行功能注释以筛选候选基因，并根据"Expression Atlas"数据库对候选基因的组织表达情况进行分析。经筛选后，本试验共得到69 762个SNPs，以Fst值和π ratio值的99%分位数为阈值筛选得到33个两品种间高度差异的基因组区域，其中16个基因组区域与生长性状相关QTLs重合。这些区域共包含27个基因，其中4个基因（FXR1、ADAR、IGF1和MNF1）与骨生长、肌肉发育和生长调控有关。FXR1和MNF1均在骨骼肌组织中高表达，ADAR和IGF1分别在脑组织和肝脏中表达最高。结果提示，IGF1基因可作为影响肉牛生长的关键候选基因，FXR1、ADAR、MNF1基因可优先进行进一步验证研究。

关键词: 南阳牛, 生长性状, 候选基因, 选择性清除, 遗传分化系数

Abstract: The aims of this study were to investigate the growth-related genes under selection in Angus cattle and provide a reference for identification of major genes for beef cattle growth. Blood samples of 72 Nanyang cows and 14 Black Angus cows were collected and used to isolate genomic DNA. The genome-wide SNP markers and genotypes of individuals were obtained by using SLAF-seq technology. Fst and π ratio values of each SNP were calculated for selecting the different genomic regions between the two breeds. Afterward, these identified regions were compared with the cattle growth QTLs in animal QTLdb. The overlapping regions were considered as candidate regions for further analysis. Genes within the overlapping regions were screened as candidate genes based on the gene annotation. Tissue expression status of candidate genes were checked in the "Expression Atlas" database. After filtering, 69 762 SNPs were remained for the further analysis. Using the 99% quantiles of Fst and π ratio values as thresholds, 33 genomic regions with high differences between the two breeds were screened. Among them, there were 16 genomic regions overlapped with the cattle growth QTLs. Within the 16 regions, 27 genes were located, among them, 4 genes (FXR1, ADAR, IGF1, MNF1) were related to bone/muscle development and growth regulation. FXR1 and MNF1 genes were highly expressed in the skeletal muscle. ADAR and IGF1 genes were highly expressed in the brain and liver, respectively. IGF1 gene can be considered as a major candidate gene for beef cattle growth, FXR1, ADAR and MNF1 genes are prioritized as potential candidate genes for further verification.

Key words: Nanyang cattle, growth trait, candidate gene, selective sweep, Fst

中图分类号:

S823.2

吕世杰, 陈付英, 金磊, 张子敬, 朱肖亭, 施巧婷, 辛晓玲, 楚秋霞, 柏中林, 王二耀, 徐照学. 利用简化基因组测序筛选安格斯牛生长相关的受选择基因[J]. 畜牧兽医学报, 2020, 51(4): 713-721.

Lü Shijie, CHEN Fuying, JIN Lei, ZHANG Zijing, ZHU Xiaoting, SHI Qiaoting, XIN Xiaoling, CHU Qiuxia, BAI Zhonglin, WANG Eryao, XU Zhaoxue. Identification of Growth-Related Genes under Selection in Angus Cattle Using SLAF-seq[J]. Acta Veterinaria et Zootechnica Sinica, 2020, 51(4): 713-721.

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利用简化基因组测序筛选安格斯牛生长相关的受选择基因

Identification of Growth-Related Genes under Selection in Angus Cattle Using SLAF-seq

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