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

Abstract

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

CLC Number:

S822.2

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

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