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| 基于线粒体全基因组的柴达木牛母系遗传多样性、群体结构及系统发育分析 |
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魏旭东1,2, 刘瑞林1,2, 李瑞哲1,2, 张卫忠3, 王启辉4, 赵海明5, 郭卫兴6, 许正全4, 尕藏当周7, 韩赟8, 雷初朝9, 马志杰1,2
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1.青海大学 畜牧兽医科学院 青海省高原家畜遗传资源保护与创新利用重点实验室，青海 西宁 810016;2.农业农村部青藏高原畜禽遗传育种重点实验室，青海 西宁 810016;3.青海省格尔木市畜牧兽医站，青海 格尔木 816000;4.青海省格尔木市郭勒木德乡畜牧兽医站，青海 格尔木 816000;5.青海省格尔木市乌图美仁乡畜牧兽医站，青海 格尔木 816000;6.青海大学 畜牧兽医科学院 青海省高原家畜遗传资源保护与创新利用重点实验室;7.青海省都兰县宗加镇畜牧兽医站，青海 海西州 816102;8.青海省乌兰县畜牧兽医站，青海 海西州817100;9.西北农林科技大学 动物科技学院，陕西 杨陵 712100
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| 摘要: |
| 【目的】从全线粒体基因组水平探究柴达木牛的母系遗传多样性、群体结构及与其他黄牛品种间的遗传关系。【方法】采用全基因组重测序技术对60头柴达木牛进行重测序，获取每个个体的线粒体全基因组全序列，并从GenBank下载已公布的我国5个北方黄牛品种（即蒙古牛、西藏牛、哈萨克牛、延边牛和安西牛）和2个国外培育品种（荷斯坦牛和日本和牛）的共129条线粒体全基因组相应序列进行综合分析，以揭示柴达木牛线粒体基因组遗传变异，明确其母系遗传多样性水平、群体遗传结构组成、母系遗传背景及与我国北方部分地方黄牛品种、国外培育品种间的遗传关系。【结果】①60头柴达木牛线粒体全基因组序列比对分析共发现346个多态位点，其中单一多态位点51个，简约信息位点295个；根据序列间核苷酸变异共确定37种单倍型（H1~H37）。遗传多样性分析显示，柴达木牛线粒体基因组单倍型多样度为（0.981 0±0.006 0），核苷酸多样度为（0.003 3±0.000 2），提示其拥有丰富的母系遗传多样性。②系统发育分析表明，柴达木牛拥有普通牛和瘤牛2大母系支系，且以普通牛T支系为主，拥有T1、T2、T3、T4、I1和I2共6种亚单倍型组，提示柴达木牛拥有普通牛和瘤牛血统，有两个母系起源。③群体遗传分化分析表明，柴达木牛与蒙古牛、西藏牛、哈萨克牛、延边牛、日本和牛遗传分化程度均很弱，而与安西牛、荷斯坦牛达到中等遗传分化程度。④聚类分析显示，柴达木牛与蒙古牛聚类关系最近，与西藏牛、哈萨克牛、安西牛、延边牛聚类关系相对较近，与日本和牛、荷斯坦牛聚类关系较远，其聚类结果与分化程度基本一致。【结论】柴达木牛拥有丰富的母系遗传多样性，由普通牛和瘤牛两个母系支系组成，含有T1、T2、T3、T4、I1和I2共6种亚单倍型组，推测其有2个母系起源。柴达木牛与蒙古牛亲缘关系最近，与西藏牛、哈萨克牛、延边牛、安西牛遗传关系较近，而与日本和牛、荷斯坦牛遗传关系较远。 |
| 关键词: 柴达木牛 mtDNA 母系起源 群体结构 |
| DOI：10.13207/j.cnki.jnwafu.2025.01.001 |
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| 基金项目:青海省自然科学基金项目(2021-ZJ-914) |
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| Maternal genetic diversity,population structure and phylogenetic analysis of Qaidam cattle based on mitochondrial whole genome variations |
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WEI Xudong1,2, LIU Ruilin1,2, LI Ruizhe1,2, ZHANG Weizhong3, WANG Qihui4, ZHAO Haiming5, GUO Weixing1, XU Zhengquan4, GAZANG Dangzhou6, HAN Yun7, LEI Chuzhao8, MA Zhijie1,9
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1.Key Laboratory of Plateau Livestock Genetic Resources Protection and Innovative Utilization,Academy of Animal Science and Veterinary Medicine,Qinghai University,Xining，Qinghai 810061，China;2.Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau,;3.Station of Animal Science and Veterinary Medicine of Golmud City of Qinghai Province,Golmud，Qinghai 816000，China;4.Station of Animal Science and Veterinary Medicine of Golmud Town in Golmud City of Qinghai Province,Golmud，Qinghai 816000，China;5.Station of Animal Science and Veterinary Medicine of Wutumeiren Town in Golmud City of Qinghai Province,Golmud，Qinghai 816000，China;6.Station of Animal Science and Veterinary Medicine of Zongjia Town in Dulan County of Qinghai Province,Haixi，Qinghai 816102，China;7.Station of Animal Science and Veterinary Medicine of Wulan County of Qinghai Province,Haixi，Qinghai 817100，China;8.College of Animal Science and Technology,Northwest A&F University,Yangling，Shaanxi 712100，China;9.Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau,Ministry of Agriculture and Rural Affairs,Xining，Qinghai 810061，China
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| Abstract: |
| 【Objective】This study explored maternal genetic diversity,population structure and genetic relationship between Qaidam cattle and other cattle breeds at the genome level. 【Method】The whole genome resequencing technology was used for resequencing 60 Qaidam cattle to obtain the complete mitochondrial genome sequence of each individual.A total of 129 corresponding mitochondrial genome sequences from 5 northern cattle breeds (Mongolian cattle,Tibetan cattle,Kazakh cattle,Yanbian cattle and Anxi cattle) in China and 2 foreign breeds (Holstein cattle and Japanese Wagyu) were downloaded from GenBank for comprehensive analysis.【Result】(1) A total of 346 polymorphic loci were found in the alignment analysis of mitochondrial whole genome sequence of Qaidam cattle,including 51 single nucleotide mutation sites and 295 parsimony informative sites.A total of 37 haplotypes (H1-H37) were determined according to the nucleotide variation between sequences.Genetic diversity analysis showed that the haplotype diversity of the mitochondrial genome was (0.981 0±0.006 0),and the nucleotide diversity was (0.003 3±0.000 2）,suggesting that the genetic diversity of Qaidam cattle was relatively rich.(2) Phylogenetic analysis showed that Qaidam cattle had two maternal genetic branches of Bos taurus and Bos indicus,and the T branch was the main lineage.There were six sub-haplogroups of T1,T2,T3,T4,I1 and I2,suggesting that Qaidam cattle had two maternal origins of Bos taurus and Bos indicus.(3) The analysis of population genetic differentiation showed that the differentiation degree of Qaidam cattle was very weak with Mongolian cattle,Tibetan cattle,Kazakh cattle,Yanbian cattle and Japanese Wagyu,while it reached moderate genetic differentiation with Anxi cattle and Holstein cattle.Cluster analysis showed that Qaidam cattle had the closest clustering relationship with Mongolian cattle,relatively close to Tibetan cattle,Kazakh cattle,Anxi cattle and Yanbian cattle,and farthest from Japanese Wagyu and Holstein cattle.The clustering results were basically consistent with the degree of differentiation.【Conclusion】Qaidam cattle had rich maternal genetic diversity,which was composed of two maternal branches of Bos taurus and Bos indicus.It contained six sub-haplogroups of T1,T2,T3,T4,I1 and I2,and it was speculated to have two maternal origins.It was closely related to Mongolian cattle and genetically related to Tibetan cattle,Kazakh cattle,Yanbian cattle and Anxi cattle,while it was far with Japanese Wagyu and Holstein cattle. |
| Key words: Qaidam cattle mtDNA maternal origin population structure |
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