喀喇昆仑-帕米尔地区牦牛mtDNA D-loop区遗传多样性及系统发育分析

doi:10.16431/j.cnki.1671-7236.2020.08.016

摘要/Abstract

摘要： 为明确喀喇昆仑-帕米尔地区牦牛遗传多样性水平、遗传分化和系统进化地位，本研究选择mtDNA D-loop区序列作为分子标记，采用PCR直接测序和生物信息学方法分析喀喇昆仑-帕米尔地区牦牛mtDNA D-loop区序列特征和遗传多样性，利用GenBank中牦牛序列，采用最大似然法构建系统发育树和中介网络关系。结果显示，喀喇昆仑-帕米尔地区牦牛mtDNA D-loop序列富含A、T碱基，AT含量为61.2%，存在63个多态位点，占核苷酸总数的7.04%，平均单倍型多样性（Hd）为0.806，平均核苷酸多样性（π）为0.01528，平均核苷酸差异数（K）为13.509，表明喀喇昆仑-帕米尔地区牦牛遗传多样性丰富；系统发育分析显示，中国境内牦牛形成两大分支，细分为6个小进化支，存在两个母系起源，表明喀喇昆仑-帕米尔地区牦牛拥有两个不同的母系起源；中介网络关系分析显示，喀喇昆仑-帕米尔地区牦牛与其他品种牦牛单倍型共享较少，在分支C中喀喇昆仑-帕米尔地区牦牛群体所占比例较大，且与野牦牛共享。喀喇昆仑-帕米尔地区牦牛群体具有较独特的遗传背景，推测可能是从早期野牦牛驯化而来。建议加大该区域牦牛品种的认定和品种标准的制定，加强对该区域牦牛遗传资源的保护；根据群体现状，引入野血牦牛进行提纯复壮，防止品种退化和遗传多样性降低；减少外来牦牛品种的引进而无序杂交，以确保优质牦牛品种资源的本品种特性。

关键词: 喀喇昆仑-帕米尔地区; 牦牛; mtDNA D-loop; 遗传多样性; 系统发育

Abstract: This experiment was conducted to clarify the genetic diversity,genetic differentiation and phylogenetic status of yak in Karakoram-Pamir area.The mtDNA D-loop region sequence was selected as a molecular marker,and the sequence and genetic diversity of the mtDNA D-loop region of yak in Karakoram-Pamir area were analyzed by PCR direct sequencing and bioinformatics methods.The yak sequence in GenBank was used.The maximum likelihood method was used to construct the phylogenetic tree and the intermediary network relationship.The results showed that the mtDNA D-loop sequence of yak in Karakoram-Pamir area was rich in A and T bases,with AT content of 61.2%,and there were 63 polymorphic loci,accounting for 7.04% of the total number of nucleotides.The results indicated that A and T bases were rich in the mtDNA D-loop sequences at 61.2%.There were 63 mutation sites,accounting for 7.04% of all nucleotides,The average haplotype diversity (Hd) was 0.806,the average nucleotide diversity (π) was 0.01528,and the average nucleotide difference (K) was 13.509,indicating that the yak was rich in genetic diversity in Karakoram-Pamir area;Through phylogenetic analysis,there were two branches in yak in China,forming two branches and six small clades.The yak in Karakoram-Pamir area involved in this study had two different maternal origins.Additionally,yak in the Karakoram-Pamir area was less shared with other breeds of yak haplotypes.In the branch C,the yak group in the Karakoram-Pamir area accounts for a large proportion and was shared with wild yak.The yak population in Karakoram-Pamir area had a unique genetic background,which might be the result of early domestication of wild yaks.It was suggested to increase the identification of yak breeds and the formulation of breed standards in this area,and strengthen the protection of yak genetic resources in this area.According to the current situation of the population,wild blood yaks were introduced for purification and rejuvenation to prevent breed degeneration and decrease of genetic diversity.The introduction of foreign yak breeds and disorderly hybridization were reduced to ensure the characteristics of this breed of high-quality yak breed resources.

Key words: Karakoram-Pamir area; yak; mtDNA D-loop; genetic diversity; phylogeny

中图分类号:

S823.8

李静, 郭丽君, 王莉, 胡平, 肖逸, 韩建林, 王玉涛. 喀喇昆仑-帕米尔地区牦牛mtDNA D-loop区遗传多样性及系统发育分析[J]. 中国畜牧兽医, 2020, 47(8): 2481-2492.

LI Jing, GUO Lijun, WANG Li, HU Ping, XIAO Yi, HAN Jianlin, WANG Yutao. Analyses of Genetic Diversity and Phylogeny of mtDNA D-loop from Yak in Karakoram-Pamir Area[J]. China Animal Husbandry and Veterinary Medicine, 2020, 47(8): 2481-2492.

参考文献

[1] BAI J L.Phylotaxonomic position of Tianzhu white yak (Poephagus grunniens) based on nucleotide sequences of multiple subunits of cytochromecoxidase[J].Journal of Applied Animal Research,2014,43(4):431-438.
[2] LAI S J,CHEN S Y,LIU Y P,et al.Mitochondrial DNA sequence diversity and origin of Chinese domestic[J].Yak Animal Genetics,2007,38(1):77-80
[3] 施奇静,王静,孙军平,等.中国牦牛资源保护及可持续利用:驯化与品种培育[J].家畜生态学报,2016,37(1):81-86. SHI Q J,WANG J,SUN J P,et al.Conservation and sustainable utilization of yak resources of China:Domestication and breed[J].Journal of Domestic Animal Ecology,2016,37(1):81-86.(in Chinese)
[4] GUO S,SAVOLAINEN P,SU J,et al.Origin of mitochondrial DNA diversity of domestic yaks[J].BMC Evolutionary Biology,2006,73(6):1-13.
[5] 孟庆辉,陈永杏,董红敏,等.牦牛分布特点及其种群数量[J].家畜生态学报,2017,38(3):80-85. MENG Q H,CHEN Y X,DONG H M,et al.The distribution characteristics and population of yak[J].Journal of Domestic Animal Ecology,2017,38(3):80-85.(in Chinese)
[6] QI X B,HAN J L,ROGER B,et al.Understanding the Yak Pastoralism in Central Asian Highlands:Mitochondrial DNA Evidence for Origin,Domestication and Dispersal of Domestic Yak[M].London (UK):Taylor & Francis,2008.
[7] 胡丹,钟金城,柴志欣.新疆塔什库尔干牦牛mtDNA Cytb基因和D-Loop区遗传多样性及系统进化分析[J].家畜生态学报,2018,39(11):11-16. HU D,ZHONG J C,CHAI Z X.Genetic diversity and phyletic evolution on mtDNA Cytb gene and D-Loop region of Taxkorgan yak[J].Journal of Domestic Animal Ecology,2018,39(11):11-16.(in Chinese)
[8] 李静,王莉,道敏,等.喀喇昆仑-帕米尔地区牦牛mtDNA Cytb遗传多样性及系统发育分析[J].生物技术进展,2019,9(5):509-517. LI J,WANG L,DAO M,et al.Genetic diversity and phylogenetic analysis on mtDNA Cytb in yak of Karakorum-Pamir region[J].Progress in Biotechnology,2019,9(5):509-517.(in Chinese)
[9] 马志杰.牦牛父系遗传多样性及起源研究[D].杨凌:西北农林科技大学,2019. MA Z J.Study on the paternal genetic diversity and origin of the yak (Bos grunniens)[D].Yangling:Northwest A&F University,2019.
[10] WANG Z F,SHEN X,LIU B,et al.Phylogeographical analyses of domestic and wild yaks based on mitochondrial DNA:New data and reappraisal[J].Journal of Biogeography,2010,37(12):2332-2344.
[11] GU Z L,ZHAO X B,LI N,et al.Complete sequence of the yak (Bos grunniens) mitochondrial genome and its evolutionary relationship with other ruminants[J].Molecular Phylogenetics and Evolution,2007,42(1):248-255.
[12] BASANG W D,AN T W,DANJIU L B,et al.Diversity analysis of Chinese Tibetan Naqu yak (Bos grunniens) populations using mtDNA[J].Pakistan Journal of Zoology,2018,50(6):2051-2057.
[13] KIERSTEIN G,VALLINOTO M,SILVA A,et al.Analysis of mitochondrial D-loop region casts new light on domestic water buffalo (Bubalus bubalis) phylogeny[J].Molecular Phylogenetics and Evolution,2004,30(2):308-324.
[14] 马志杰,钟金城,韩建林,等.野牦牛(Bos grunniens mutus) mtDNA D-Loop区的遗传多样性[J].生态学报,2009,29(9):4798-4803. MA Z J,ZHONG J C,HAN J L,et al.Genetic diversity in the mtDNA D-Loop region of wild yak (Bos grunniens mutus)[J].Acta Ecologica Sinica,2009,29(9):4798-4803.(in Chinese)
[15] 张成福,徐利娟,姬秋梅,等.西藏牦牛mtDNA D-loop区的遗传多样性及其遗传分化[J].生态学报,2012,32(5):1387-1395. ZHANG C F,XU L J,JI Q M,et al.Genetic diversity and evolution relationship on mtDNA D-loop in Tibetan yaks[J].Acta Ecologica Sinica,2012,32(5):1387-1395.(in Chinese)
[16] 成述儒,曾玉峰,王欣荣,等.甘肃境内6个牦牛群体mtDNA D-环序列遗传多样性与聚类分析[J].华北农学报,2014,29(3):16-21. CHENG S R,ZENG Y F,WANG X R,et al.Genetic diversity and cluster analysis of six yak populations in Gansu province using mitochondrial D-loop sequence[J].Acta Agriculturae Boreali-Sinica,2014,29(3):16-21.(in Chinese)
[17] 涂世英,汪琦,柴志欣,等.中甸牦牛mtDNA D-loop区遗传多样性及系统进化分析[J].中国草食动物科学,2016,36(3):5-10. TU S Y,WANG Q,CHAI Z X,et al.Analysis on genetic diversity and phyletic evolution of mitochondrial DNA D-loop region from Zhongdian yak[J].China Herbivore Science,2016,36(3):5-10.(in Chinese)
[18] 郭松长,祁得林,陈桂华,等.家牦牛线粒体DNA(mtDNA)遗传多样性及其分类[J].生态学报,2008,28(9):4286-4294. GUO S C,QI D L,CHEN G H,et al.Genetic diversity and classification of domestic yak inferrded from mitochondrial DNA sequences[J].Acta Ecologica Sinica,2008,28(9):4286-4294.(in Chinese)
[19] 曾玉峰.甘肃境内6个牦牛群体mtDNA D-环序列和微卫星遗传多样性与聚类分析[D].兰州:甘肃农业大学,2013. ZENG Y F.Cluster and genetic diversity analysis of six yak populations in Gansu province using mitochondrial D-Loop sequence and microsatellite marker[D].Lanzhou:Gansu Agricultural University,2013.(in Chinese)
[20] 赖松家.中国三个牛种遗传多样性和分子系统进化研究[D].雅安:四川农业大学,2004. LAI S J.Study on genetic diversity and molecular phylogeny in Chinese three species of cattle[D].Ya'an:Sichuan Agricultural University,2004.(in Chinese)
[21] 赖松家,王玲,刘益平,等.中国部分牦牛品种线粒体DNA遗传多态性研究[J].遗传学报,2005,32(5):463-470. LAI S J,WANG L,LIU Y P,et al.Study on genetic polymorphisms of mitochondrial DNA in some yak breeds in China[J].Journal of Genetics and Genomics,2005,32(5):463-470.(in Chinese)