野牦牛及青海地方牦牛品种全线粒体基因组母系遗传多样性、分化及系统发育分析

doi:10.11843/j.issn.0366-6964.2022.05.010

畜牧兽医学报 ›› 2022, Vol. 53 ›› Issue (5): 1420-1430.doi: 10.11843/j.issn.0366-6964.2022.05.010

野牦牛及青海地方牦牛品种全线粒体基因组母系遗传多样性、分化及系统发育分析

李广祯^1,2, 马志杰^1,2*, 陈生梅^1,2, 雷初朝³, 李瑞哲^1,2, 谢银禄⁴, 晁生玉⁵

1. 青海大学畜牧兽医科学院, 西宁 810016;
2. 青海省高原家畜遗传资源保护与创新利用重点实验室, 西宁 810016;
3. 西北农林科技大学动物科技学院, 杨凌 712100;
4. 青海省格尔木市畜牧兽医站, 格尔木 816000;
5. 青海省海西州农业技术推广服务中心, 德令哈 817099

收稿日期:2021-09-22 出版日期:2022-05-23 发布日期:2022-05-25
通讯作者: 马志杰,主要从事动物遗传资源研究,E-mail:zhijiema@126.com
作者简介:李广祯(1997-),男,青海民和人,硕士生,主要从事动物遗传资源研究,E-mail:guangzhenli6228@126.com
基金资助:
国家自然科学基金(31960656)；中国科学院“西部之光”人才培养引进计划(“西部青年学者”)项目(3-1)

Maternal Genetic Diversity, Differentiation and Phylogeny of Mitogenome Sequence Variations of Wild Yak and Local Yak Breeds in Qinghai

LI Guangzhen^1,2, MA Zhijie^1,2*, CHEN Shengmei^1,2, LEI Chuzhao³, LI Ruizhe^1,2, XIE Yinlu⁴, CHAO Shengyu⁵

1. Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining 810016, China;
2. Key Laboratory of Plateau Livestock Genetic Resources Protection and Innovative Utilization, Xining 810016, China;
3. College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China;
4. Golmud Animal Husbandry and Veterinary Station in Qinghai, Golmud 816000, China;
5. Haixi Agricultural Technology Extension Service Center in Qinghai, Delingha 817099, China

Received:2021-09-22 Online:2022-05-23 Published:2022-05-25

摘要/Abstract

摘要： 旨在从分子水平上探究野牦牛及青海地方牦牛品种的母系遗传多样性、群体遗传结构、亲缘关系和遗传背景。本研究在测定青海省4个地方牦牛品种(即青海高原、环湖、雪多和玉树牦牛)22条全线粒体基因组(Mitogenome)序列的基础上，从GenBank下载了已公布的野牦牛及上述4个地方牦牛品种的142条相应序列，使用BioEdit 7.2.5、Arlequin 3.11和Network 10.1等软件对共计164条线粒体基因组序列进行综合分析。结果显示：1)根据序列间核苷酸变异共确定了115种单倍型，其中野牦牛和青海地方牦牛品种分别拥有22种和93种单倍型；在野牦牛和青海高原、环湖、雪多、玉树牦牛中分别检测到22、26、18、23、19种特有的单倍型。遗传多样性分析显示，野牦牛单倍型多样度最高(0.992 8±0.014 4)，且高于4个青海地方牦牛品种的单倍型多样度(0.973 1±0.007 7)；4个青海地方牦牛品种单倍型多样度大小依次为：雪多牦牛(0.988 5±0.012 6)、玉树牦牛(0.975 8±0.018 7)、青海高原牦牛(0.973 0±0.016 6)和环湖牦牛(0.939 3±0.027 8)。2)野牦牛与环湖牦牛之间的固定分化指数值(F_ST值)最大(0.041 2)，分化程度最高，而与玉树牦牛间的F_ST值最小(-0.008 8)，分化程度最低。青海4个地方牦牛品种中，雪多牦牛与青海高原牦牛之间F_ST值最大(0.035 8)，分化程度最高，而雪多牦牛与环湖牦牛间F_ST值最小(0.011 2)，分化程度最低。3)聚类分析显示，4个青海地方牦牛品种各自为1类，存在明显的母系遗传差异。相比而言，环湖牦牛和雪多牦牛聚类较近，青海高原牦牛和玉树牦牛聚类较近，而野牦牛与玉树牦牛聚类关系更近，各品种(群体)间的聚类结果与其分化程度、地理分布一致。4)系统发育分析表明，115种单倍型分布在3个大的母系遗传分支(即Mt-Ⅰ、Mt-Ⅱ和Mt-Ⅲ)，其中Mt-Ⅰ支系所占比例为72.17%，由A、B、E和F 4种单倍型组构成；Mt-Ⅱ支系包括C、D和H 3种单倍型组，占26.09%；而Mt-Ⅲ支系只包含G单倍型组，由雪多牦牛和野牦牛所拥有，所占比例为1.74%，提示牦牛有3个母系起源。综上所述，野牦牛和青海4个地方牦牛品种均具有丰富的母系遗传多样性，其多样性水平由高到低依次为野牦牛、雪多牦牛、玉树牦牛、青海高原牦牛和环湖牦牛。青海4个地方牦牛品种间及与野牦牛间的遗传分化程度均较弱，但各自拥有特有的母系遗传信息，存在明显的母系遗传差异。野牦牛和青海家牦牛品种由3个母系支系组成，推测牦牛有3个母系起源。

关键词: 牦牛, 线粒体基因组, 遗传多样性, 分化, 聚类关系, 系统发育

Abstract: The study aimed to explore the maternal genetic diversity, population structure, cluster relationship and genetic background of wild yak and local yak breeds in Qinghai at molecular level. The 22 mitogenome sequences of 4 local yak breeds in Qinghai (Qinghai Plateau, Huanhu, Xueduo and Yushu) were obtained, and 142 corresponding sequences from wild yak and the above 4 local yak breeds in Qinghai were downloaded from GenBank. A total of 164 mitogenome sequences were comprehensively analyzed by using BioEdit 7.2.5, Arlequin 3.11 and Network 10.1 softwares. The results showed that:1) A total of 115 haplotypes were identified based on nucleotide variation, among which 22 haplotypes were found in wild yak and 93 haplotypes were detected in Qinghai yak breeds. The 22, 26, 18, 23 and 19 haplotypes were detected in wild yak, Qinghai Plateau, Huanhu, Xueduo and Yushu yak breeds, respectively. Genetic diversity analysis showed that the haplotype diversity of wild yak was the highest (0.992 8±0.014 4), which was higher than that of 4 local yak breeds in Qinghai (0.973 1±0.007 7). The haplotype diversities of 4 local yak breeds were 0.988 5±0.012 6 (Xueduo yak), 0.975 8±0.018 7 (Yushu yak), 0.973 0±0.016 6 (Qinghai Plateau yak) and 0.939 3±0.027 8 (Huanhu yak), respectively. 2) The fixed index (F_ST) value between wild yak and Huanhu yak was the highest (0.041 2), while the lowest (-0.008 8) between wild yak and Yushu yak. Among the 4 local yak breeds, the F_ST value between Xuduo yak and Qinghai Plateau yak was the highest (0.035 8) and the differentiation degree was the highest, while the F_ST value between Xuduo yak and Huanhu yak was the lowest (0.011 2), inferring the lowest differentiation degree. 3) The clustering analysis showed that each of the 4 yak breeds was divided into one category, suggesting that there were significant maternal genetic differences among them. In contrast, the clustering of Huanhu and Xueduo yak was closer, while the clustering of Qinghai Plateau yak and Yushu yak was also closer. The clustering relationship between wild yak and Yushu yak was closer. The clustering results among breeds (populations) was consistent with their differentiation degree and geographical distribution. 4) Phylogenetic analysis showed that 115 haplotypes were distributed in 3 maternal lineages (Mt-Ⅰ, Mt-Ⅱ and Mt-Ⅲ). The proportion of Mt-Ⅰ clade was 72.17%, consisting of 4 haplogroups (A, B, E and F), and Mt-Ⅱ clade consisted of 3 haplogroups (C, D and H), accounting for 26.09%. Mt-Ⅲ clade contained only G haplogroup, which was owned by Xueduo yak and wild yak, accounting for 1.74%, suggesting that yak had 3 maternal origins. In summary, the wild yak and the 4 local yak breeds in Qinghai Province all have rich maternal genetic diversity, and the diversity levels from high to low are the wild yak, Xueduo yak, Yushu yak, Qinghai plateau yak and Huanhu yak. The genetic differentiations among the 5 yak breeds (population) are weak, and each breed(population) had unique maternal genetic information, there are significant maternal genetic difference among them. The wild yak and Qinghai domestic yak breeds are composed of 3 maternal lineages, and it is speculated that there are 3 maternal origins in yak.

Key words: yak, mitogenome, genetic diversity, differentiation, clustering relationship, phylogeny

中图分类号:

S823.85

李广祯, 马志杰, 陈生梅, 雷初朝, 李瑞哲, 谢银禄, 晁生玉. 野牦牛及青海地方牦牛品种全线粒体基因组母系遗传多样性、分化及系统发育分析[J]. 畜牧兽医学报, 2022, 53(5): 1420-1430.

LI Guangzhen, MA Zhijie, CHEN Shengmei, LEI Chuzhao, LI Ruizhe, XIE Yinlu, CHAO Shengyu. Maternal Genetic Diversity, Differentiation and Phylogeny of Mitogenome Sequence Variations of Wild Yak and Local Yak Breeds in Qinghai[J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(5): 1420-1430.

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野牦牛及青海地方牦牛品种全线粒体基因组母系遗传多样性、分化及系统发育分析

Maternal Genetic Diversity, Differentiation and Phylogeny of Mitogenome Sequence Variations of Wild Yak and Local Yak Breeds in Qinghai

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