川渝黔6个山羊品种mtDNA D-loop遗传多样性与系统进化研究
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摘要
我国四川、重庆和贵州地区气候温和,雨量充沛,山区和丘陵面积大,历史上由于交通闭塞,形成了具有浓郁地方特色的山羊品种。对其遗传多样性和系统进化的研究可以为开展山羊品种培育、保护和利用奠定基础。
本研究测定了我国川渝黔地区南江黄羊、成都麻羊、川东白山羊、板角山羊、贵州白山羊和黔北麻羊6个山羊品种以及1个引进品种波尔山羊共66个个体mtDNA D-loop环全序列,结合GenBank上的山羊mtDNA全序列和野山羊D环序列,采用软件DNAMAN、BioEdit、ClustalW、MEGA3.1、DnaSP、Arlequin2.0以及Network4.1对其进行了遗传多样性和起源进化分析。结果显示:
1.遗传多样性分析7个山羊品种66个个体的D环长度为1212bp或1213bp,长度变异是由于在1715bp处插入或缺失碱基C造成,共检测出116个多态性位点(83个简约信息位点,33个单一多态位点),其中300-700bp变异量多,其次是1000-1100bp。各品种碱基组成A+T(约55.7%)>C+G(约44.3%),转换发生率大于颠换,符合哺乳动物碱基组成特点。66个个体界定了50个单倍型,7个山羊品种有丰富的独享单倍型,单倍型多样度为0.9167-1.0000,核苷酸多样度为0.004125-0.023157,表明中国川渝黔地区山羊品种和波尔山羊的遗传多样性丰富。
2.品种的遗传分化用AMOVA分析,结果表明品种间的方差组分只占3.82%,品种内占96.18%,经检验品种间差异不显著(P>0.1),表明中国川渝黔地区家山羊品种间没有显著的遗传分化,表现弱的遗传结构。6个品种之间存在单倍型共享,各品种散布在网络图的各个支系,表明川渝黔地区山羊品种之间存在一定的基因交流。
3.品种间亲缘关系分析采用AMOVA分析方法,对分别基于D_a值、Dxy值和Fst值矩阵构建的NJ树比较分析,发现基于Dxy值矩阵构建的NJ树置信度最高。聚类结果为:南江黄羊先与川东白山羊聚为一类,再与板角山羊聚类,然后依次聚类与成都麻羊、贵州白山羊、黔北麻羊和波尔山羊。
4.起源分析对川渝黔地区6个山羊品种40个单倍型进行系统发育树和网络分析,结果表明,6个山羊品种的单倍型存在2个独立的支系(支系A和B),表明中国川渝黔地区山羊品种至少有2个母系起源。
5.支系B的起源本研究得出的支系B各条序列,结合已发表的17条亚洲五国(印度、巴基斯坦、蒙古、马来西亚和老挝)支系B的D环序列分析,中国山羊中支系B的单倍型间平均不配对差异值和核苷酸多样度为5.000000和0.007976,明显高于由亚洲五个国家组成的混合群体值3.338235和0.006940。表明山羊支系B很可能起源于中国。
In this study,the complete sequence of mitochondrial DNA(mtDNA)control region(CR,D-loop) was sequenced of 66 individuals from 7 domestic goat breeds(including 1 introduced breed-Boer goat)in Sichuan,Chongqing and Guizhou province.Based on goat's mtDNA whole sequnence and Capra goats' D-loop sequnences,the genetic variety,origion and divergence of these goats were analyzed by using DNAMAN,BioEdit,ClustalW,MEGA3.1,DNASP,Arlequin2.0 and Network4.1 softwares.The results showed that:
1.The goat complete sequence length of mtDNA D-loop CR was 1,212 bp or 1,213bp.The length difference was one insertion/deletionin on 1075 site.There were 116 polymorphic sites,with 83 parsimony informative polymorphic sites and 33 singleton polymorphic sites.Only 1 polymorphic site with three variants was found in our study.The largest number of site variants was in the sequence from 300bp to 700bp,and then from 1000bp to 1100bp.The base composition of D-loop complete sequence in the tested breeds was A+T(about 55.7%)＞C+G(about 44.3%).The number of transition was larger than that of transvertion.A total of 50 haplotypes were found,and the range of haplotype diversity and nucleotide diversity were 0.9167-1.0000 and 0.004125-0.023157,respectively.The results indicate that the goat genetic diversity in Sichuan,Chongqing and Guizhou province is very abundant.
2.The population genetic structure was studied by using AMOVA.The results showed that the variation was only 3.82%among groups,whereas 96.18%within breeds.There was no significant difference was found between breeds.The results indicate that 6 tested goat breeds have no significant heredity differentiation.
3.Three NJ trees of the 6 goat breeds were formed based on matrix D_a,Dxy and Fst.The result showed that the NJ tree based on matrix Dxy was the best.First,Nanjiang goat and Chuandong White goat was custered together,and then were Banjiao goat,Chengdu Grey goat,Guizhou White goat,Qianbei Grey goat and Boer goat.
4.There were 2 differenent lineages(A and B)in the tested goat breeds,by using phylogenetic and divergent goat mtDNA median network analysis.The results indicate that goat breeds in Sichuan, Chongqing and Guizhou province were origioned from two differenent ancestors.
5.The mean pairwise difference and nucleotide diversity between haplotypes from the Chinese goats are 5.000000 and 0.007976,whereas those from the five Asian countries(i.e.India,Pakistan,Mongolia, Malaysia and Laos)are 3.338235 and 0.006940,respectively.Our preliminary study indicated that mtDNA lineage B of goats was probably originated from China.
本研究测定了我国川渝黔地区南江黄羊、成都麻羊、川东白山羊、板角山羊、贵州白山羊和黔北麻羊6个山羊品种以及1个引进品种波尔山羊共66个个体mtDNA D-loop环全序列,结合GenBank上的山羊mtDNA全序列和野山羊D环序列,采用软件DNAMAN、BioEdit、ClustalW、MEGA3.1、DnaSP、Arlequin2.0以及Network4.1对其进行了遗传多样性和起源进化分析。结果显示:
1.遗传多样性分析7个山羊品种66个个体的D环长度为1212bp或1213bp,长度变异是由于在1715bp处插入或缺失碱基C造成,共检测出116个多态性位点(83个简约信息位点,33个单一多态位点),其中300-700bp变异量多,其次是1000-1100bp。各品种碱基组成A+T(约55.7%)>C+G(约44.3%),转换发生率大于颠换,符合哺乳动物碱基组成特点。66个个体界定了50个单倍型,7个山羊品种有丰富的独享单倍型,单倍型多样度为0.9167-1.0000,核苷酸多样度为0.004125-0.023157,表明中国川渝黔地区山羊品种和波尔山羊的遗传多样性丰富。
2.品种的遗传分化用AMOVA分析,结果表明品种间的方差组分只占3.82%,品种内占96.18%,经检验品种间差异不显著(P>0.1),表明中国川渝黔地区家山羊品种间没有显著的遗传分化,表现弱的遗传结构。6个品种之间存在单倍型共享,各品种散布在网络图的各个支系,表明川渝黔地区山羊品种之间存在一定的基因交流。
3.品种间亲缘关系分析采用AMOVA分析方法,对分别基于D_a值、Dxy值和Fst值矩阵构建的NJ树比较分析,发现基于Dxy值矩阵构建的NJ树置信度最高。聚类结果为:南江黄羊先与川东白山羊聚为一类,再与板角山羊聚类,然后依次聚类与成都麻羊、贵州白山羊、黔北麻羊和波尔山羊。
4.起源分析对川渝黔地区6个山羊品种40个单倍型进行系统发育树和网络分析,结果表明,6个山羊品种的单倍型存在2个独立的支系(支系A和B),表明中国川渝黔地区山羊品种至少有2个母系起源。
5.支系B的起源本研究得出的支系B各条序列,结合已发表的17条亚洲五国(印度、巴基斯坦、蒙古、马来西亚和老挝)支系B的D环序列分析,中国山羊中支系B的单倍型间平均不配对差异值和核苷酸多样度为5.000000和0.007976,明显高于由亚洲五个国家组成的混合群体值3.338235和0.006940。表明山羊支系B很可能起源于中国。
In this study,the complete sequence of mitochondrial DNA(mtDNA)control region(CR,D-loop) was sequenced of 66 individuals from 7 domestic goat breeds(including 1 introduced breed-Boer goat)in Sichuan,Chongqing and Guizhou province.Based on goat's mtDNA whole sequnence and Capra goats' D-loop sequnences,the genetic variety,origion and divergence of these goats were analyzed by using DNAMAN,BioEdit,ClustalW,MEGA3.1,DNASP,Arlequin2.0 and Network4.1 softwares.The results showed that:
1.The goat complete sequence length of mtDNA D-loop CR was 1,212 bp or 1,213bp.The length difference was one insertion/deletionin on 1075 site.There were 116 polymorphic sites,with 83 parsimony informative polymorphic sites and 33 singleton polymorphic sites.Only 1 polymorphic site with three variants was found in our study.The largest number of site variants was in the sequence from 300bp to 700bp,and then from 1000bp to 1100bp.The base composition of D-loop complete sequence in the tested breeds was A+T(about 55.7%)＞C+G(about 44.3%).The number of transition was larger than that of transvertion.A total of 50 haplotypes were found,and the range of haplotype diversity and nucleotide diversity were 0.9167-1.0000 and 0.004125-0.023157,respectively.The results indicate that the goat genetic diversity in Sichuan,Chongqing and Guizhou province is very abundant.
2.The population genetic structure was studied by using AMOVA.The results showed that the variation was only 3.82%among groups,whereas 96.18%within breeds.There was no significant difference was found between breeds.The results indicate that 6 tested goat breeds have no significant heredity differentiation.
3.Three NJ trees of the 6 goat breeds were formed based on matrix D_a,Dxy and Fst.The result showed that the NJ tree based on matrix Dxy was the best.First,Nanjiang goat and Chuandong White goat was custered together,and then were Banjiao goat,Chengdu Grey goat,Guizhou White goat,Qianbei Grey goat and Boer goat.
4.There were 2 differenent lineages(A and B)in the tested goat breeds,by using phylogenetic and divergent goat mtDNA median network analysis.The results indicate that goat breeds in Sichuan, Chongqing and Guizhou province were origioned from two differenent ancestors.
5.The mean pairwise difference and nucleotide diversity between haplotypes from the Chinese goats are 5.000000 and 0.007976,whereas those from the five Asian countries(i.e.India,Pakistan,Mongolia, Malaysia and Laos)are 3.338235 and 0.006940,respectively.Our preliminary study indicated that mtDNA lineage B of goats was probably originated from China.
引文
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