南阳牛生长性状相关基因组区域全基因组关联分析

doi:10.16431/j.cnki.1671-7236.2020.01.009

中国畜牧兽医 ›› 2020, Vol. 47 ›› Issue (1): 74-82.doi: 10.16431/j.cnki.1671-7236.2020.01.009

南阳牛生长性状相关基因组区域全基因组关联分析

吕世杰¹, 陈付英¹, 张子敬¹, 施巧婷¹, 辛晓玲¹, 楚秋霞¹, 李文军¹, 柏中林², 王二耀¹, 徐照学¹

1. 河南省农业科学院畜牧兽医研究所, 郑州 450002;
2. 泌阳县动物疫病预防控制中心, 驻马店 463700

收稿日期:2019-05-05 出版日期:2020-01-20 发布日期:2020-01-17
通讯作者: 王二耀, 徐照学 E-mail:wangeryao666@qq.com;xuzhaoxue11@163.com
作者简介:吕世杰(1989-),男,河南三门峡人,博士,研究方向:动物遗传育种与繁殖,E-mail:sjlyu@outlook.com;陈付英(1973-),女,河南南阳人,博士,副研究员,研究方向:黄牛分子育种,E-mail:fychen2004@sina.com吕世杰和陈付英对本文具有同等贡献,并列为第一作者
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）；河南省畜禽繁育与营养调控重点实验室

Genomic Regions Associated with Growth Traits in Nanyang Cattle Using Genome-wide Association Analysis

LYU Shijie¹, CHEN Fuying¹, ZHANG Zijing¹, SHI Qiaoting¹, XIN Xiaoling¹, CHU Qiuxia¹, LI Wenjun¹, BAI Zhonglin², WANG Eryao¹, XU Zhaoxue¹

1. Institute of Animal Science and Veterinary Medicine, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China;
2. Center of Animal Disease Prevention and Control of Biyang, Zhumadian 463700, China

Received:2019-05-05 Online:2020-01-20 Published:2020-01-17

摘要/Abstract

摘要： 本研究旨在筛选和鉴定与南阳牛生长性状相关的基因组区域和候选基因，从而更好地了解牛生长性状的遗传机制。试验共采集71头南阳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。对每头个体初生重及不同月龄（6、12、18、24、36）的体重、体高、体斜长、胸围和坐骨端宽及每6个月体增重等生长性状进行全基因组关联分析；获得显著相关的基因组区域后，对其中基因进行功能注释以筛选候选基因。结果显示，共获得141 755个筛选后的SNPs，通过全基因组关联分析鉴定出5个分别与12月龄体重（8号染色体：17 320 634~17 347 720 bp）、12月龄胸围（2号染色体：15 063 190~15 155 309 bp）、24月龄体斜长（11号染色体：60 727 342~81 425 987 bp）、36月龄坐骨端宽（14号染色体：15 635 762~15 643 272 bp）和12~18月龄体增重（26号染色体：40 456 192~40 456 477 bp）等生长性状显著相关的基因组区域（LOD≥6.35）。通过对5个基因组区域内的186个基因进行功能注释，共筛选得到11号染色体上的8个基因（BMP10、IFT172、SDC1、TCF23、TRIM54、RAB1A、VPS54和GDF7）与骨生长、肌肉发育和生长调控有关，建议其可优先作为牛生长性状相关候选基因进行进一步验证。

关键词: 南阳牛; 生长性状; SLAF-seq; 全基因组关联分析; 候选基因

Abstract: The aim of this study was to screen and identify the genomic regions and candidate genes related to growth traits of Nanyang cattle,so as to better understand the genetic mechanism of growth traits.Blood samples of 71 Nanyang cattle were collected and used to extract genomic DNA.The specific-locus amplified fragment sequencing (SLAF-seq) technology was used to obtain genome-wide SNP markers and classify the genotypes of experimental individuals.A genome-wide association analysis (GWAS) was carried out for several growth traits consisting of body weight (BW),body height (BH),body length (BL),chest girth (CG),ischium width (IW) and body weight gain (BWG).BW,BH,BL,CG and IW of every individual were measured in every six months from birth to 36 months of age.BWG was calculated as the difference between subsequent body weight measurements with 6-month interval.Gene annotation was performed for the genes within the identified genomic regions to prioritize candidate genes.After filtering,141 755 SNPs remained for the GWAS.5 genomic regions (LOD ≥ 6.35) significantly associated with BW at 12 months of age(chromosome 8:17 320 634-17 347 720 bp),CG at 12 months of age (chromosome2:15 063 190-15 155 309 bp),BL at 24 months of age (chromosome 11:60 727 342-81 425 987 bp),IW at 36 months of age (chromosome 14:15 635 762-15 643 272 bp) and BWG between 12 and 18 months of age (chromosome 26:40 456 192-40 456 477 bp) were identified,respectively.8 genes (BMP10,IFT172,SDC1,TCF23,TRIM54,RAB1A,VPS54 and GDF7) on chromosome 11 were screened out by functional annotation of 186 genes in 5 genomic regions,which were related to bone growth,muscle development and growth regulation.It was suggested that they could be used as candidate genes for growth traits of cattle for further verification.

Key words: Nanyang cattle; growth traits; SLAF-seq; GWAS; candidate gene

中图分类号:

S813.3

吕世杰, 陈付英, 张子敬, 施巧婷, 辛晓玲, 楚秋霞, 李文军, 柏中林, 王二耀, 徐照学. 南阳牛生长性状相关基因组区域全基因组关联分析[J]. 中国畜牧兽医, 2020, 47(1): 74-82.

LYU Shijie, CHEN Fuying, ZHANG Zijing, SHI Qiaoting, XIN Xiaoling, CHU Qiuxia, LI Wenjun, BAI Zhonglin, WANG Eryao, XU Zhaoxue. Genomic Regions Associated with Growth Traits in Nanyang Cattle Using Genome-wide Association Analysis[J]. China Animal Husbandry and Veterinary Medicine, 2020, 47(1): 74-82.

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南阳牛生长性状相关基因组区域全基因组关联分析

Genomic Regions Associated with Growth Traits in Nanyang Cattle Using Genome-wide Association Analysis

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