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

doi:10.17520/biods.2021031

Abstract

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

Togtokh Mongke, Dongyi Bai, Tugeqin Bao, Ruoyang Zhao, Tana An, Aertengqimike Tiemuqier, Baoyindeligeer Mongkejargal, Has Soyoltiin, Manglai Dugarjaviin, Haige Han. Assessment of SNPs-based genomic diversity in different populations of Eastern Asian landrace horses[J]. Biodiv Sci, 2022, 30(5): 21031.

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URL: https://www.biodiversity-science.net/EN/10.17520/biods.2021031

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

Figures/Tables 5

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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

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