基于比较基因组学的宁强马与济州马遗传多样性及矮小体型的遗传基础研究

doi:10.11843/j.issn.0366-6964.2025.12.020

摘要/Abstract

摘要：

旨在比较分析宁强马和济州马的遗传多样性及矮小体型的遗传基础。本研究基于199匹现代家马的重测序数据比较分析了宁强马和济州马的遗传结构、遗传多样性和遗传分化，重点比较了矮小体型的遗传基础。群体结构分析显示，宁强马属于中国西南矮马，而济州马具有区别于西南矮马的祖先成分。核苷酸多样性、近交系数和ROH分析表明，济州马近期经历了较强的人工选育，遗传多样性较低，而宁强马具有较高的遗传多样性。此外，宁强马与德保矮马的遗传距离最近(F_ST=0.02)，而济州马与国内11个马品种均具有中等程度的遗传分化(F_ST>0.05)。全基因组选择扫描在宁强马和济州马基因组中检测到多个差异候选区域，鉴定到与生长发育(TBX5、TBX3、MEIS1、CECR2)和免疫(ADA2、AP3B1)相关的基因。综上，宁强马和济州马具有不同的祖先成分和选育程度，遗传分化明显，且矮小体型的遗传基础不同。这些结果对于深入了解世界矮马矮小性状的遗传基础以及中国马品种的保护和利用具有重要意义。

关键词: 宁强马, 济州马, 遗传多样性, 遗传分化, 矮小体型

Abstract:

This study aimed to comparatively analyze the genetic diversity and the genetic basis of small stature between Ningqiang ponies and Jeju ponies. This study compared and analyzed the genetic structure, genetic diversity, and genetic differentiation of Ningqiang ponies and Jeju ponies based on the whole-genome resequencing data from 199 modern domestic horses, focusing on comparing the genetic basis of small stature. Population structure analysis indicated that Ningqiang ponies belong to pony breeds of Southwestern China, while Jeju ponies had ancestral components that are distinct from those of the Southwestern ponies. Nucleotide diversity, inbreeding coefficient, and ROH analysis indicated that Jeju ponies had undergone strong artificial selection and breeding recently, with low genetic diversity, while Ningqiang ponies had high genetic diversity. Furthermore, the genetic distance between Ningqiang ponies and Debao ponies is the closest (F_ST=0.02), while Jeju ponies had a moderate degree of genetic differentiation from 11 domestic horse breeds (F_ST>0.05). Whole-genome selection scanning detected multiple differential candidate regions in the genomes of Ningqiang ponies and Jeju ponies, and identified genes related to growth and development (TBX5, TBX3, MEIS1, CECR2) and immunity (ADA2, AP3B1). In conclusion, Ningqiang ponies and Jeju ponies have different ancestral components and degrees of selection and breeding, with obvious genetic differentiation, and the genetic basis for small stature is also different. These results are of great significance for an in-depth understanding of the genetic basis of small stature traits in ponies and for the protection and utilization of horse breeds in China.

Key words: Ningqiang pony, Jeju pony, genetic diversity, genetic differentiation, small stature

中图分类号:

S821.2

韩家乐, 高峰, 孙珉浩, 虎巧燕, 丁枫怡, 党瑞华. 基于比较基因组学的宁强马与济州马遗传多样性及矮小体型的遗传基础研究[J]. 畜牧兽医学报, 2025, 56(12): 6167-6179.

HAN Jiale, GAO Feng, SUN Minhao, HU Qiaoyan, DING Fengyi, DANG Ruihua. Genetic Diversity and Genetic Basis of Small Stature in Ningqiang and Jeju Ponies Based on Comparative Genomics[J]. Acta Veterinaria et Zootechnica Sinica, 2025, 56(12): 6167-6179.

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分类 Classification	品种 Breed	样本量 Sample size	简称 Abbreviation	数据来源 Data source
矮马品种 Pony breed	宁强马 Ningqiang pony	30	NQ	自测
	宁强马 Ningqiang pony	7	NQ	下载
	德保矮马 Debao pony	26	DBP	下载
	建昌马 Jianchang pony	7	JC	下载
	济州马 Jeju pony	17	Jeju	下载
中/大型马品种 Medium/large horse breed	西藏马 Tibetan horse	19	Tibetan	下载
	蒙古马 Mongolian horse	13	MG	下载
	大通马 Datong horse	10	DT	下载
	焉耆马 Yanqi horse	6	YQ	下载
	柴达木马 Chaidamu horse	7	CDM	下载
	鄂伦春马 Erlunchun horse	6	ELC	下载
	河曲马 Hequ horse	3	HQ	下载
	伊犁马 Yili horse	6	YL	下载
	纯血马 Thoroughbred horse	42	THB	下载
	共计 Total	199

分类 Classification	品种 Breed	样本量 Sample size	简称 Abbreviation
矮马品种 Pony breed	宁强马 Ningqiang pony	10	NQ
	德保矮马 Debao pony	10	DB
	建昌马 Jianchang pony	7	JC
	济州马 Jeju pony	10	Jeju
中/大型马品种 Medium/large horse breed	西藏马 Tibetan horse	10	Tibetan
	蒙古马 Mongolian horse	10	MG
	大通马 Datong horse	10	DT
	焉耆马 Yanqi horse	6	YQ
	柴达木马 Chaidamu horse	7	CDM
	鄂伦春马 Erlunchun horse	6	ELC
	河曲马 Hequ horse	3	HQ
	伊犁马 Yili horse	6	YL
	纯血马 Thoroughbred horse	10	THB
	共计 Total	105

品种 Breed	核苷酸多样性Pi	近交系数 F_ROH	最小等位基因频率 MAF	平均He	平均Ne	平均PIC
DBP	0.001 225±0.000 685	0.157 129±0.054 012	0.087 7	0.130 1	1.198 7	0.109 6
Jeju	0.001 295±0.000 741	0.217 908±0.110 531	0.087 2	0.123 0	1.199 1	0.100 8
MG	0.001 220±0.000 681	0.145 031±0.020 740	0.085 5	0.126 3	1.193 9	0.106 0
NQ	0.001 427±0.000 776	0.137 709±0.029 427	0.095 9	0.141 4	1.217 5	0.118 6
THB	0.001 139±0.000 731	0.321 720±0.021 174	0.079 1	0.109 9	1.180 0	0.089 8
Tibetan	0.001 371±0.000 752	0.131 636±0.015 373	0.093 2	0.137 8	1.211 3	0.115 8
CDM	0.001 488±0.000 811	0.110 575±0.033 990	0.093 2	0.134 5	1.212 0	0.111 5
DT	0.001 521±0.000 816	0.124 623±0.018 812	0.095 9	0.140 3	1.217 7	0.117 2
ELC	0.001 091±0.000 671	0.176 318±0.041 788	0.077 8	0.109 9	1.177 1	0.090 1
HQ	0.001 324±0.000 778	0.129 265±0.002 492	0.080 7	0.109 9	1.182 9	0.088 7
JC	0.001 154±0.000 686	0.153 552±0.007 072	0.081 2	0.116 6	1.184 6	0.096 5
YL	0.001 251±0.000 700	0.138 762±0.013 515	0.083 6	0.120 1	1.190 1	0.099 3
YQ	0.001 206±0.000 698	0.147 195±0.004 891	0.082 4	0.117 9	1.187 5	0.097 3

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