基于基因组SNPs对东亚家马不同群体遗传多样性的评估

doi:10.17520/biods.2021031

生物多样性 ›› 2022, Vol. 30 ›› Issue (5): 21031. DOI: 10.17520/biods.2021031

• 研究报告: 遗传多样性 • 下一篇

基于基因组SNPs对东亚家马不同群体遗传多样性的评估

陶克涛, 白东义, 图格琴, 赵若阳, 安塔娜, 铁木齐尔·阿尔腾齐米克, 宝音德力格尔, 哈斯, 芒来(), 韩海格()

内蒙古农业大学动物科学学院内蒙古自治区马属动物遗传育种与繁殖重点实验室, 呼和浩特 010018

收稿日期:2021-07-20 接受日期:2022-04-29 出版日期:2022-05-20 发布日期:2022-05-20
通讯作者: 芒来,韩海格
作者简介:hanhaige@imau.edu.cn
* E-mail: dmanglai@163.com;
基金资助:
国家自然科学基金项目(31961143025);国家自然科学基金项目(31960657);内蒙古自然基金项目(2021BS03040)

Assessment of SNPs-based genomic diversity in different populations of Eastern Asian landrace horses

Togtokh Mongke, Dongyi Bai, Tugeqin Bao, Ruoyang Zhao, Tana An, Aertengqimike Tiemuqier, Baoyindeligeer Mongkejargal, Has Soyoltiin, Manglai Dugarjaviin(), Haige Han()

Inner Mongolia Key Laboratory of Equus Genetics, Breeding and Reproduction, College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018

Received:2021-07-20 Accepted:2022-04-29 Online:2022-05-20 Published:2022-05-20
Contact: Manglai Dugarjaviin,Haige Han

摘要/Abstract

摘要：

家马地方品种的遗传多样性是动态演变的, 并与其育种模式息息相关; 在过去约300年中, 育种者培育了具突出表型特征的标准化培育品种, 该类型品种对家马地方品种的繁育产生了巨大影响, 这是导致家马地方品种遗传多样性下降及遗传分化的主要因素之一。本研究采集了5个东亚家马地方品种(蒙古马、哈萨克马、河曲马、藏马和西南马)、2个西亚家马品种(阿拉伯马和阿哈尔捷金马)以及2个欧洲家马品种(设特兰矮马和克莱斯黛尔马)的70个样品, 并整合之前所发表的100匹内蒙古地区家马不同群体单核苷酸多态性(SNPs)数据集, 通过全基因组重测序和生物信息学方法分析了东亚家马不同群体的遗传多样性。研究发现东亚家马地方品种具有较丰富的遗传多样性, 相比欧洲和西亚品种产生了显著的遗传分化, 其中蒙古高原群体的遗传多样性最为丰富; 受杂交改良影响, 内蒙古不同群体间产生了一定程度的遗传分化; 河曲马和藏马的遗传背景最为单一, 受引种杂交繁育影响较小。本研究评估了东亚家马地方品种的遗传多样性分布格局和演化特征, 可为建立家马地方种质核心保护群体以及培育新品种提供遗传学理论支持。

关键词: 东亚家马地方品种, 遗传多样性, 遗传分化, 引种繁育, 遗传资源保护

Abstract

Aims: The genetic diversity within landrace horse breeds changes over time and is greatly affected by breeding strategies. In the past 300 years, standardized horse breeds have been bred for prominent traits, and these breeds have been then largely introduced to improve the landrace populations which has been resulted in the reduced genetic diversity or genetic differentiation within landrace population. The aim of this study was to assess the genetic diversity of Eastern Asian landrace horse populations which will constitute the basis for the conservation of landrace horse genomic resources as well as breeding of new strain of horses.

Methods: Here we sequenced the whole genome of 70 horses from five Eastern Asian horse breeds (Hequ horse and Tibetan horse, Southwest horse, Mongolian horse, and Kazakh horse), two Western Asian breeds (Arabian horse, Akhal-Teke horse), and two European breeds (Shetland pony and Clydesdale horse). This newly generated data was combined with 100 previously published Inner Mongolian horse SNPs data to investigate the genomic diversity of the Asian landrace horse breeds.

Results: Our results suggest that the Eastern Asian landrace horse breeds have significant genetic differentiation and higher genetic diversity compared with non-Eastern Asian horse breeds. In particular, the Inner Mongolian horse populations showed the highest genetic diversity, and genetic differentiation has been observed among the populations sampled in Inner Mongolia Autonomous Region, China, which may reflect the exotic genetic influence on the genetic improving some of the local populations, such as Baicha iron hoof horse and Abag horse populations. There was no observation of this gene flow in the Hequ horse and Tibetan horse.

Conclusion: The genetic diversity of landrace horses changes and even decreases through hybridization between native and introduced modern standardized horse breeds. The wild ancestral population of domestic horses is now wholly extinct; therefore, it is imperative to maintain and protect the genetic diversity of landrace horses. The expansion of the modern standardized horse bloodlines has contributed to genetic diversity decreases and genetic differentiation increases in landrace horses. The Eastern Asian landrace horse breeds have higher genetic diversity, and endangered Baicha iron hoof horse and Abag horse have occurred significant genetic differentiation trend from the Mongolian horse population. Genetic swamping is the major concern for small population horses, therefore, the genetic conservation of Baicha iron hoof horse warrants particular attention.

Key words: Eastern Asian horse breeds, genetic diversity, genetic differentiation, introduction and breeding, genetic resources conservation

陶克涛, 白东义, 图格琴, 赵若阳, 安塔娜, 铁木齐尔·阿尔腾齐米克, 宝音德力格尔, 哈斯, 芒来, 韩海格 (2022) 基于基因组SNPs对东亚家马不同群体遗传多样性的评估. 生物多样性, 30, 21031. DOI: 10.17520/biods.2021031.

Togtokh Mongke, Dongyi Bai, Tugeqin Bao, Ruoyang Zhao, Tana An, Aertengqimike Tiemuqier, Baoyindeligeer Mongkejargal, Has Soyoltiin, Manglai Dugarjaviin, Haige Han (2022) Assessment of SNPs-based genomic diversity in different populations of Eastern Asian landrace horses. Biodiversity Science, 30, 21031. DOI: 10.17520/biods.2021031.

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链接本文: https://www.biodiversity-science.net/CN/10.17520/biods.2021031

https://www.biodiversity-science.net/CN/Y2022/V30/I5/21031

图/表 5

表1 本研究所使用样品来源及其近交系数和期望杂合度信息

Table 1 Information on collection source, inbreeding coefficient (F) and expected heterozygosity (He) of samples used in this study

品种/群体 Breed/Population	样品代号 Code	采样地 Sampling region	样本量 Sample size	近交系数 Inbreeding coefficient (F)	期望杂合度 Expected heterozygosity (H_e)	数据来源 Data source
藏马 Tibetan horse	TIB	西藏那曲 Nagqu, Tibet, China	7	0.031	0.246	本研究 Present study
河曲马 Hequ horse	HQ	青海省河南蒙古族自治县 Henan Mongol Autonomous County, Qinghai, China	6	0.045	0.239	本研究 Present study
西南马 Southwest horse	SW	云南丽江 Lijiang, Yunnan, China	7	0.043	0.247	本研究 Present study
蒙古马 Mongolian horse	MN	乌兰巴托市, 蒙古国 Ulaanbaatar, Mongolia	13	0.017	0.261	本研究 Present study
乌珠穆沁马 Ujimqin horse	UJM	内蒙古锡林郭勒盟 Xilingol League, Inner Mongolia, China	3 21	0.029	0.266	本研究 Present study; Han et al, 2019a
乌审马 Uxin horse	UX	内蒙古鄂尔多斯市乌审旗 Uxin Banner, Inner Mongolia, China	3 22	0.042	0.266	本研究 Present study; Han et al, 2019a
百岔铁蹄马 Baicha iron hoof horse	BCIH	内蒙古赤峰市克什克腾旗 Hexigten Banner, Inner Mongolia, China	2 19	0.019	0.264	本研究 Present study; Han et al, 2019a
三河马 Sanhe horse	SH	内蒙古呼伦贝尔市 Hulunbuir, Inner Mongolia, China	23	-0.003	0.269	Han et al, 2019a
阿巴嘎黑马 Abag horse	AB	内蒙古锡林郭勒盟阿巴嘎旗 Abag Banner, Inner Mongolia, China	15	0.027	0.251	Han et al, 2019a
哈萨克马 Kazakh horse	KZ	新疆塔城地区 Tacheng, Xinjiang, China	6	0.00028	0.252	本研究 Present study
阿拉伯马 Arabian horse	ARR	北京 Beijing, China	5	0.108	0.213	本研究 Present study
设特兰矮马 Shetland pony	STL	内蒙古鄂尔多斯市可汗御马苑 Ordos, Inner Mongolia, China	5	0.120	0.221	本研究 Present study
阿哈尔捷金马 Akhal-Teke horse	AKTK	内蒙古太仆寺旗 Taibus Banner, Inner Mongolia, China	5	0.07	0.223	本研究 Present study
克莱斯戴尔马 Clydesdale horse	DRT	内蒙古鄂尔多斯市可汗御马苑 Ordos, Inner Mongolia, China	5	0.24	0.227	本研究 Present study
总计 Total	14群体 14 populations		167个体 167 individuals

表1 本研究所使用样品来源及其近交系数和期望杂合度信息

Table 1 Information on collection source, inbreeding coefficient (F) and expected heterozygosity (He) of samples used in this study

品种/群体 Breed/Population	样品代号 Code	采样地 Sampling region	样本量 Sample size	近交系数 Inbreeding coefficient (F)	期望杂合度 Expected heterozygosity (H_e)	数据来源 Data source
藏马 Tibetan horse	TIB	西藏那曲 Nagqu, Tibet, China	7	0.031	0.246	本研究 Present study
河曲马 Hequ horse	HQ	青海省河南蒙古族自治县 Henan Mongol Autonomous County, Qinghai, China	6	0.045	0.239	本研究 Present study
西南马 Southwest horse	SW	云南丽江 Lijiang, Yunnan, China	7	0.043	0.247	本研究 Present study
蒙古马 Mongolian horse	MN	乌兰巴托市, 蒙古国 Ulaanbaatar, Mongolia	13	0.017	0.261	本研究 Present study
乌珠穆沁马 Ujimqin horse	UJM	内蒙古锡林郭勒盟 Xilingol League, Inner Mongolia, China	3 21	0.029	0.266	本研究 Present study; Han et al, 2019a
乌审马 Uxin horse	UX	内蒙古鄂尔多斯市乌审旗 Uxin Banner, Inner Mongolia, China	3 22	0.042	0.266	本研究 Present study; Han et al, 2019a
百岔铁蹄马 Baicha iron hoof horse	BCIH	内蒙古赤峰市克什克腾旗 Hexigten Banner, Inner Mongolia, China	2 19	0.019	0.264	本研究 Present study; Han et al, 2019a
三河马 Sanhe horse	SH	内蒙古呼伦贝尔市 Hulunbuir, Inner Mongolia, China	23	-0.003	0.269	Han et al, 2019a
阿巴嘎黑马 Abag horse	AB	内蒙古锡林郭勒盟阿巴嘎旗 Abag Banner, Inner Mongolia, China	15	0.027	0.251	Han et al, 2019a
哈萨克马 Kazakh horse	KZ	新疆塔城地区 Tacheng, Xinjiang, China	6	0.00028	0.252	本研究 Present study
阿拉伯马 Arabian horse	ARR	北京 Beijing, China	5	0.108	0.213	本研究 Present study
设特兰矮马 Shetland pony	STL	内蒙古鄂尔多斯市可汗御马苑 Ordos, Inner Mongolia, China	5	0.120	0.221	本研究 Present study
阿哈尔捷金马 Akhal-Teke horse	AKTK	内蒙古太仆寺旗 Taibus Banner, Inner Mongolia, China	5	0.07	0.223	本研究 Present study
克莱斯戴尔马 Clydesdale horse	DRT	内蒙古鄂尔多斯市可汗御马苑 Ordos, Inner Mongolia, China	5	0.24	0.227	本研究 Present study
总计 Total	14群体 14 populations		167个体 167 individuals

图1 样品基因组ROH长度(MB)统计。MN: 蒙古马; STL:设特兰矮马; KZ: 哈萨克马; SH: 三河马; BCIH: 百岔铁蹄马; TIB: 藏马; SW: 西南马; HQ: 河曲马; UX: 乌审马; UJM: 乌珠穆沁马; AB: 阿巴嘎黑马; AKTK: 阿哈尔捷金马; ARR: 阿拉伯马; DRT: 克莱斯戴尔马。

Fig. 1 The sum of ROH length (MB) per individual genome in each population of horse samples. MN, Mongolian horse; STL, Shetland pony; KZ, Kazakh horse; SH, Sanhe horse; BCIH, Baicha iron hoof horse; TIB, Tibetan horse; SW, Southwest horse; HQ, Hequ horse; UX, Uxin horse; UJM, Ujimqin horse; AB, Abag horse; AKTK, Akhal-Teke horse; ARR, Arabian horse; DRT, Clydesdale horse.

图2 167个样品PC1和PC2的主成分分析(PCA)。AB: 阿巴嘎黑马; AKTK: 阿哈尔捷金马; ARR: 阿拉伯马; BCIH: 百岔铁蹄马; SW: 西南马; DRT: 克莱斯戴尔马; HQ: 河曲马; KZ: 哈萨克马; MN: 蒙古马; SH: 三河马; STL: 设特兰矮马; TIB: 藏马; UJM: 乌珠穆沁马; UX: 乌审马。

Fig. 2 Principal component analysis (PCA) plot for PC1 and PC2 comprising 167 individuals. AB, Abag horse; AKTK, Akhal-Teke horse; ARR, Arabian horse; BCIH, Baicha iron hoof horse; SW, Southwest horse; DRT, Clydesdale horse; HQ, Hequ horse; KZ, Kazakh horse; MN, Mongolian horse; SH, Sanhe horse; STL, Shetland pony; TIB, Tibetan horse; UJM, Ujimqin horse; UX, Uxin horse.

图3 基于最大似然法构建的14个家马群体系统发育树。比例尺展示了样品协方差矩阵中元素的10倍平均标准差(10 s.e.)。

Fig. 3 Phylogenetic tree of 14 horse populations based on maximum likelihood (ML). The scale bar shows 10 times the average standard error of the entries in the sample covariance matrix (10 s.e.).

图4 基于最大似然法构建的14个家马群体遗传结构。HQ: 河曲马; TIB: 藏马; SW: 西南马; MN: 蒙古马; UX: 乌审马; UJM: 乌珠穆沁马; SH: 三河马; AB: 阿巴嘎黑马; BCIH: 百岔铁蹄马; ARR: 阿拉伯马; AKTK: 阿哈尔捷金马; KZ: 哈萨克马; STL: 设特兰矮马; DRT: 克莱斯黛尔马。

Fig. 4 Genetic structure of 14 horse populations based on maximum likelihood (ML). HQ, Hequ horse; TIB, Tibetan horse; SW, Southwest horse; MN, Mongolian horse; UX, Uxin horse; UJM, Ujimqin horse; SH, Sanhe horse; AB, Abag horse; BCIH, Baicha iron hoof horse; ARR, Arabian horse; AKTK, Akhal-Teke horse; KZ, Kazakh horse; STL, Shetland pony; DRT, Clydesdale horse.

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基于基因组SNPs对东亚家马不同群体遗传多样性的评估

Assessment of SNPs-based genomic diversity in different populations of Eastern Asian landrace horses

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