卡拉麦里山蒙古野驴遗传多样性与遗传结构分析

doi:10.11843/j.issn.0366-6964.2025.10.018

畜牧兽医学报 ›› 2025, Vol. 56 ›› Issue (10): 4973-4987.doi: 10.11843/j.issn.0366-6964.2025.10.018

卡拉麦里山蒙古野驴遗传多样性与遗传结构分析

李亚旋¹(), 邵长亮², 高浩冉¹, 伍金山¹, 徐梦琦¹, 王一鹏¹, 刘皓君¹, 苏靖宇¹, 陈俊华¹, 李梦欣¹, 马英杰¹^,*(), 单文娟¹^,*()

1. 新疆大学生命科学与技术学院，新疆生物资源基因工程重点实验室，乌鲁木齐 830046
2. 卡拉麦里山有蹄类野生动物自然保护区管理中心，乌鲁木齐 830000

收稿日期:2025-03-11 出版日期:2025-10-23 发布日期:2025-11-01
通讯作者: 马英杰,单文娟 E-mail:107552201006@stu.xju.edu.cn;mayingjie@xju.edu.cn;swj@xju.edu.cn
作者简介:李亚旋(1997-)，女，重庆人，硕士生，主要从事分子遗传学研究，E-mail：107552201006@stu.xju.edu.cn
基金资助:
新疆维吾尔自治区科技计划项目-中央引导地方科技发展专项(ZYYD2024ZY04)；国家自然科学基金(32400406; 32260116)

Genetic Diversity and Structure Analysis of the Equus hemionus hemionus in Kalamaili

LI Yaxuan¹(), SHAO Changliang², GAO Haoran¹, WU Jinshan¹, XU Mengqi¹, WANG Yipeng¹, LIU Haojun¹, SU Jingyu¹, CHEN Junhua¹, LI Mengxin¹, MA Yingjie¹^,*(), SHAN Wenjuan¹^,*()

1. Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Sciences and Technology, Xinjiang University, Urumqi 830046, China
2. Management Center, Mt. Kalamaili Ungulate Nature Reserve, Urumqi 830000, China

Received:2025-03-11 Online:2025-10-23 Published:2025-11-01
Contact: MA Yingjie, SHAN Wenjuan E-mail:107552201006@stu.xju.edu.cn;mayingjie@xju.edu.cn;swj@xju.edu.cn

摘要/Abstract

摘要：

旨在综合评估新疆卡拉麦里山有蹄类野生动物自然保护区(以下简称：卡山)蒙古野驴种群的遗传多样性与遗传结构，提供保护管理的分子遗传学依据。本研究采用非损伤性取样法，通过PCR扩增及测序技术，对卡山161份成功提取基因组DNA的蒙古野驴新鲜粪便样本进行个体识别、遗传多样性指标计算和遗传结构分析。结果显示：基于10个微卫星位点检测到159头遗传学上相互独立的蒙古野驴个体共123个等位基因，平均多态信息含量PIC=0.634，平均观测杂合度Ho=0.533，平均期望杂合度He=0.658，近交系数Fis=0.140(P < 0.01)。CYTB、D-LOOP及串联基因(CYTB+D-LOOP)单倍型多样性分别为0.63、0.82、0.84，核苷酸多样性Pi分别为0.005 24、0.020 63、0.012 54，卡山蒙古野驴种群的遗传多样性指标低于蒙古国蒙古野驴种群，高于伊朗、印度、土库曼斯坦的蒙古野驴种群，综合评估其遗传多样性处于中等偏上水平。遗传结构与系统发育分析，当K=2时，卡山蒙古野驴种群有最优群体结构划分。线粒体系统发育和单倍型网络分布分析揭示：卡山蒙古野驴内部的2个主要支系(Clade Ⅰ、Clade Ⅱ)均与蒙古国蒙古野驴种群具有较近的亲缘关系，共享单倍型Hap 21、Hap 23、Hap 24。群体历史动态分析，微卫星基因频率呈“L”型分布，线粒体中性检验Tajima’s D、Fu’s Fs均为正值(P>0.05)，错配分布呈多峰分布，贝叶斯天际线趋势相对平缓，两类分子标记均表明卡山蒙古野驴种群未经历扩张或收缩，处于稳定状态。综合分析，卡山蒙古野驴种群具有较高的遗传多样性水平，种群内部存在2个祖先血统，且当前种群数量稳定。本研究结果为卡山蒙古野驴后续可持续保护提供了分子遗传学依据，有助于制定科学合理的保护管理措施。

关键词: 微卫星, 线粒体, 蒙古野驴指名亚种, 遗传多样性, 遗传结构

Abstract:

The study aimed to comprehensively evaluate the genetic diversity and genetic structure of the E. h. hemionus in Kalamaili Mountain Ungulate Wildlife Nature Reserve in Xinjiang (hereinafter referred to as "Kalamaili") and provide molecular genetic evidence for their conservation and management. This study employed non-invasive sampling methods, PCR amplification and sequencing techniques to analyze 161 freshly collected fecal samples with successfully extracted genomic DNA. Individual identification, genetic diversity indices, and genetic structure were evaluated. The results revealed that, based on 10 microsatellite loci, 159 genetically distinct individuals were identified, harboring 123 alleles in total. The average polymorphic information content (PIC) was 0.634, observed heterozygosity (Ho) was 0.533, expected heterozygosity (He) was 0.658, and the inbreeding coefficient (Fis) was 0.140 (P < 0.01). For mitochondrial markers, haplotype diversities (Hd) of CYTB, D-LOOP, and the concatenated gene (CYTB+D-LOOP) were 0.63, 0.82, and 0.84, respectively. The nucleotide diversities (Pi) were 0.005 24, 0.020 63, and 0.012 54, respectively. The genetic diversity of the E. h. hemionus population in Kalamaili was lower than that of population in Mongolia but higher than those in Iran, Indian, and Turkmenistan population, indicating an overall moderate-to-high level of genetic diversity. Genetic structure and phylogenetic analysis revealed that when K=2, the Kalamaili population had the optimal genetic structure division. Mitochondrial phylogenetic and haplotype network distribution analyses showed that the two major clades (Clade Ⅰ and Clade Ⅱ) within the Kalamaili population were closely related to the population in Mongolia, sharing haplotypes Hap 21, Hap 23 and Hap 24. Demographic analysis showed an "L"-shaped distribution of microsatellite allele frequencies, while mitochondrial neutrality tests (Tajima's D and Fu's Fs) yielded non-significant positive values (P>0.05). Mismatch distribution exhibits multimodal pattern, and Bayesian skyline plot indicated a relatively flat trend, collectively suggesting that the Kalamaili E. h. hemionus population has not undergone recent expansion or decline. In conclusion, the Kalamaili E. h. hemionus population exhibits high genetic diversity, with two ancestral lineages present and currently maintains a stable population size. These findings provide a molecular genetic basis for future conservation strategies and support evidence-based management decisions for the sustainable protection of this species.

Key words: microsatellite, mitochondrial, Equus hemionus hemionus, genetic diversity, genetic structure

中图分类号:

S822.2

李亚旋, 邵长亮, 高浩冉, 伍金山, 徐梦琦, 王一鹏, 刘皓君, 苏靖宇, 陈俊华, 李梦欣, 马英杰, 单文娟. 卡拉麦里山蒙古野驴遗传多样性与遗传结构分析[J]. 畜牧兽医学报, 2025, 56(10): 4973-4987.

LI Yaxuan, SHAO Changliang, GAO Haoran, WU Jinshan, XU Mengqi, WANG Yipeng, LIU Haojun, SU Jingyu, CHEN Junhua, LI Mengxin, MA Yingjie, SHAN Wenjuan. Genetic Diversity and Structure Analysis of the Equus hemionus hemionus in Kalamaili[J]. Acta Veterinaria et Zootechnica Sinica, 2025, 56(10): 4973-4987.

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位点 Locus	荧光 Dye	引物序列(5'→3') Primers sequence	等位基因大小/bp Allele range	退火温度/℃ Annealing temperature
AHT040	HEX	GCAAGTTCAGCACCTCCCT TTTATGACACCTGCTGAGAACG	230	58
COR053	HEX	AATTGACTGTGGAAGCCTTG GGCTGAGGAGTAAGCTGAAAG	173~197	55
AHT021	TAMRA	TCCAAGTTGCTGAATGGATC ACGGCCTGATTCTCTCTTTG	199~215	58
HMS02	FAM	ACGGTGGCAACTGCCAAGGAAG CTTGCAGTCGAATGTGTATTAAATG	218~236	63
1CA41	TAMRA	CTGGTCAGGCCTATTACCCA AGATATTGGGGGCGGAAG	245	58
1CA25	HEX	TCCAATTTTCCCCAATGGTA CTGCATTTTGACAATGGTGG	206	58
1CA43	FAM	ATGGCATGATTTGCTTCTCC TGGAAACAACCTAAATGTCCA	122	58
COR082	HEX	GCTTTTGTTTCTCAATCCTAGC TGAAGTCAAATCCCTGCTTC	196~226	58
1CA32	TAMRA	AGTTACCAAATGTCGCATTGC TTCATCTGTAAAATGGGCAGG	107	58
1CA44	TAMRA	GGCAGCACACCAAATCAAGT TCCTGCAAAACAACAGAGGA	203	58

基因 Gene	引物(5'→3') Primer	扩增条件 Annealing condition
CYTB	AACTGCAGTCATCTCCGGTTTACAAGAC CGAAGCTTGATATGAAAAACCATCGTTG	95 ℃ 4 min; 35 cycles: 95 ℃ 30 s, 50 ℃ 30 s, 72 ℃ 30 s; 72 ℃ 5 min.
CYTB^*	ATGACAAACATCCGAAAGTC ACTACAGGGACTCTTCACTT
D-LOOP	CTTGTAAACCAGGAAAGGGGGAAAC ATTTAGAGGGCATTCTCACTGGGAT	95 ℃ 4 min; 35 cycles: 95 ℃ 30 s, 60 ℃ 30 s, 72 ℃ 30 s; 72 ℃ 5 min.

位点 Locus	个体数 N	等位基因数Na	有效等位基因数Ne	香农指数 I	多态信息含量PIC	观测杂合度Ho	期望杂合度He	近交系数 Fis	哈迪-温伯格平衡检测 P-value HWE
AHT40	159	22	8.032	2.391	0.864	0.711	0.875	0.159^**	0.000^**
COR053	159	20	8.689	2.387	0.874	0.736	0.885	0.109^**	0.016^*
AHT021	159	16	6.303	2.234	0.829	0.698	0.841	0.166^**	0.000^**
HMS2	159	14	5.896	1.992	0.810	0.836	0.830	-0.010	0.466
1CA41	159	13	4.715	1.825	0.757	0.547	0.788	0.196^**	0.000^**
1CA25	159	10	2.079	1.087	0.483	0.321	0.519	0.323^**	0.000^**
1CA43	159	10	1.515	0.835	0.331	0.277	0.340	0.103^*	0.035^*
COR082	159	9	3.709	1.548	0.696	0.654	0.730	0.072	0.000^**
1CA32	159	6	2.213	1.076	0.500	0.522	0.548	0.045	0.000^**
1CA44	159	3	1.283	0.393	0.198	0.025	0.221	0.826^**	0.000^**
Mean	159	12.3	4.444	1.577	0.634	0.533	0.658	0.140^**	/
SE	0	1.88	0.858	0.222		0.080	0.075	0.080	/

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卡拉麦里山蒙古野驴遗传多样性与遗传结构分析

Genetic Diversity and Structure Analysis of the Equus hemionus hemionus in Kalamaili

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