中国11个山羊品种遗传多样性与起源分化研究
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摘要
家畜品种资源是畜牧业可持续发展的基础,在畜牧业中占据越来越重要的地位,对家畜遗传多样性的研究有助于品种资源的保护和开发利用。山羊是家畜品种中适应性最广泛的动物之一,在地球上分布范围很广。山羊在人类的日常生活中占有重要的作用,为人类提供肉、奶、皮和绒等产品,是发展中国家牧民的重要经济来源。但是,学者们对于山羊的遗传和进化研究较少,据报道家山羊在历史上有两个驯化地,近东的新月区和巴基斯坦,中国的学者一般认为家山羊有两个祖先:佩刀状角的角羊骨羊(Capra aegagrus)和旋角羊骨羊(Capra falconeri)。
线粒体DNA(mtDNA)基因结构简单、稳定,但一级结构的碱基突变率却很高,在遗传过程中不发生重组,因而家畜一般能保持其祖先的类型不变。而且,mtDNA在遗传过程中遵守严格的母系遗传方式,因而一个个体的mtDNA类型就代表一个母系连锁群,这就大大减少了供试动物的数量。随着现代生物技术的发展,线粒体DNA测序是目前家畜分子进化和遗传多样性检测的最可靠和最常用分子标记之一。本试验测定了中国11个山羊品种(柴达木山羊、黄淮山羊、济宁青山羊、辽宁绒山羊、陇东黑山羊、南疆绒山羊、内蒙古绒山羊、西藏山羊、陕南白山羊和太行山羊)167个个体的线粒体DNA控制区HVI序列,结合GenBank上部分世界山羊品种资料进行分析,以期了解中国山羊的系统发育关系并以此作为品种资源保护、利用的客观依据。本研究所出结论如下:
1.中国11个山羊品种167个个体mtDNA D-loop区HVI序列长度为481 bp或480 bp,有3条序列长度为480 bp,主要是由于在序列的第239碱基处有1个碱基缺失,涉及到2只内蒙古绒山羊和1只陇东黑山羊。
2.中国山羊品种的167条mtDNA D-loop HVI序列共有126个多态位点,其中单一多态位点为27个,两碱基的简约信息位点为97个,三碱基的简约信息位点为2个,这表明中国山羊mtDNA D-loop HVI核苷酸变异丰富。
3.中国山羊品种的167条mtDNA D-loop HVI序列中,A、C、T和G的平均含量分别为:30.86%、22.13%、30.89%和16.14%。供试山羊各品种间核苷酸含量有差异,但差异不显著。A+T含量为61.73%,G+C含量为38.27%,A+T含量明显高于G+C含量,说明中国山羊GC含量符合哺乳动物核苷酸的组成比例。
4.中国山羊品种的167条mtDNA D-loop HVI序列共定义了121种单倍型,92种为品种特有单倍型,11种为品种间单倍型,18种为品种内单倍型。品种间和品种内单倍型的分布不平衡,H43、H68、H90和H107是较为古老的单倍型类型,中国山羊没有主流单倍型。
5.中国山羊品种mtDNA D-loop HVI序列的121种单倍型共有颠换位点8个,转换位点118个,转换/颠换率为15:1,说明中国山羊具有很强的转换偏倚性。但是山羊各品种内没有颠换,只有转换。
6.中国11个山羊品种的单倍型多样度范围为0.909~1.000,核苷酸的多样度范围为0.01 810~0.03 821,太行山羊不论是单倍型的多样度还是核苷酸的多样度,在供试山羊品种中数值都是最高的。山羊各品种间平均核苷酸差异数较大,变异范围为9.289~18.563,且品种间的Kimura双参数距离变异范围为0.021~0.047,说明中国山羊品种遗传多样性丰富。
7.中国山羊的121种mtDNA D-loop HVI单倍型聚类成A、B、C、D和一个新支系。新支系位于支系D和支系B之间,是由长度为480 bp的单倍型聚类而成,这是本研究的新发现。中国山羊为多母系遗传,品种内分化水平较低,品种间没有明显的遗传地理结构。与国外山羊序列比较发现中国山羊与国外山羊有广泛的基因交流。
8.根据mtDNA单倍型的系统发育分析和网络分析表明,中国山羊主要存在支系A和支系B两大母系起源,支系A和支系B在NJ树中出现的频率分别为86.78%和4.96%;支系C和支系D,出现的频率为3.31%,本试验新发现的新支系频率最低,为1.65%。
9.中国山羊群体核苷酸不配对分布呈现出一条三峰的波浪型曲线,说明中国山羊群体经历了三次大的群体扩张,第一次波峰最大,发生在核苷酸差异数为10~11之间,第二次波峰发生在核苷酸差异数为27~28之间,第三次波峰发生在核苷酸差异数为39~40之间。且所有序列Tajima D中性检验结果不显著(P>0.10或0.05Breed resource is the basis of sustaining development of animal production industry. China is one of the countries in the world which has the richest goat breed resources. But we have little knowledge on the origin, migration, evolution and breeds genetic status of Chinese indigenous goat breeds. Goat, one of the most adaptive livestock species, is distributed widely in the world, goat products such as meat, milk, skin and fiber are the main income for farmers in the developing countries. The origin of goat has long been considered a valuable research field in animal evolution. Some studies reported that wild goats were domesticated mainly in two zones in history, one was in the Fertile Crescent region of the Near East and the other was in Pakistan. Many Chinese researchers have done much work on the origin of goat and suggested the domestic goat progenitors were Capra aegagrus and Capra falconeri.
Mitochondrial DNA (mtDNA) is an important genetic marker because of its maternal inheritance without recombination and high mutation rate. Many mtDNA studies based on the D-loop control region analysis addressed questions of phylogeny and evolution. The research of livestock genetic diversity helps the conservation and utilization of animal breed resources. The sequencing of mtDNA is one of the most common and reliable molecular markers in detecting animal molecular evolution and genetic diversity.
In this article, HVI of mitochondrial DNA(mtDNA) control region(CR, D-loop) was sequenced in 167 individuals from 11 domestic goat breeds/strains raised in China (Chaidamu, Huanghuai, Jining grey, Liaoning cashmere, Longdong Black, Nanjiang Cashmere, Inner Mongolia Cashmere, Tibetan, Shaannan White, Taihang),downloading sequences from goat breeds from GenBank were carried out. The results will provide scientific basis for resource protection and utilization. The conclusions are as follows in this study.
1. The mtDNA D-loop HVI sequences, 480~481 bp in length were determined for 167 individual in 11 Chinese goat breeds, The variation was caused by the gaps of a pairwise in the 239 bp in the mtDNA D-loop HVI sequence . And only 3 samples was 480bp including 2 goats of Inner Mongolia Cashmere and 1 goat of Longdong Black.
2. The 167 mtDNA D-loop HVI sequences contained 126 variable sites, among them, singleton variable sites was 27, parsimony informative sites of two variants was 97 and parsimony informative sites of three variants was 2. The results indicate that the pairwise diversity of Chinese goats is very rich.
3. The average content of A, C, T and G was 30.86%, 22.13%, 30.89% and 16.14% respe- cttively. The nucleotide content of the experimental goat breeds was varient but was not significant. A+T and G+C of Chinese goat breeds was 61.73% and 38.27% respectively indicating the nucleotide content of Chinese goat was in accordance with the proportion of mammals.
4. Chinese goat breeds had 121 haplotypes but no mainstream type. 92 haplotypes was unique haplotypes. 11 haplotypes were shared among breeds and 18 haplotypes were shared within breeds. The distributions and frequencies were unequilibrium either among breeds or within breeds. NJ tree showed four haplotypes (H43, H68, H90 and H107) were the oldest.
5. The transition sites of mtDNA D-loop HVI sequences between the goat breeds were 8 and transversion sites were 118, the ratio of transitions to transversions was 15/1, suggesting Chinese goat has the high transition bias. But there were no transition within the goat breed.
6. 121 haplotypes with from 167 samples of 11 Chinese goat breeds were determined. The haplotype diversity and nucleotide diversity in 11 Chinese goat breeds were 0.909~1.000 and 0.01 810~0.03 821, respectively. The haplotype and nucleotide diversity of Taihang goat was the highest (1.000, 0.03 821 respectively). The average number of nucleotide differences variation was 9.289~18.563, The Kimura 2-parameter distance between breeds varied from 0.021~0.047. The results indicate that the genetic diversity of Chinese goats is very abundant.
7. NJ tree of Chinese goat analysis indicated there were 5 lineages including lineage A, B, C and D found before and a new lineage found in the article. The new lineage was clustered by the sequences of 480 bp. The new lineage was located between the lineage D and B. The result was first reported in Chinese goats. And there was no significant geographical structure in Chinese goat populations. Compared with the goats from the other nations, Chinese goats had a widely gene flow.
8. Phylogenetic analysis and a reduced median network analysis revealed two highly divergent goat mtDNA lineages A and B mainly. The frequency of the lineage A and B was 86.78% and 4.96%, respectively. Two additional lineages C and D are present in China at low frequency (3.31%) respectively. And the frequency of the new lineage was 1.65%.
9. The curve of nucleotide mismatch distributions in 11 domestic goat populations took on three unimodal. Pairwise differences ranged from 1 to 48. A major peak presented at 10~11 mutational differences, a secondary one at 27~28 differences and a third one at 39~40 differences. Lineage A showed unimodal distribution and undergo expansions. Lineage B showed near bimodal distribution and did not undergo expansion. Tajima's test of selective neutrality of Chinese goats was not significant (P>0.10 or 0.05
线粒体DNA(mtDNA)基因结构简单、稳定,但一级结构的碱基突变率却很高,在遗传过程中不发生重组,因而家畜一般能保持其祖先的类型不变。而且,mtDNA在遗传过程中遵守严格的母系遗传方式,因而一个个体的mtDNA类型就代表一个母系连锁群,这就大大减少了供试动物的数量。随着现代生物技术的发展,线粒体DNA测序是目前家畜分子进化和遗传多样性检测的最可靠和最常用分子标记之一。本试验测定了中国11个山羊品种(柴达木山羊、黄淮山羊、济宁青山羊、辽宁绒山羊、陇东黑山羊、南疆绒山羊、内蒙古绒山羊、西藏山羊、陕南白山羊和太行山羊)167个个体的线粒体DNA控制区HVI序列,结合GenBank上部分世界山羊品种资料进行分析,以期了解中国山羊的系统发育关系并以此作为品种资源保护、利用的客观依据。本研究所出结论如下:
1.中国11个山羊品种167个个体mtDNA D-loop区HVI序列长度为481 bp或480 bp,有3条序列长度为480 bp,主要是由于在序列的第239碱基处有1个碱基缺失,涉及到2只内蒙古绒山羊和1只陇东黑山羊。
2.中国山羊品种的167条mtDNA D-loop HVI序列共有126个多态位点,其中单一多态位点为27个,两碱基的简约信息位点为97个,三碱基的简约信息位点为2个,这表明中国山羊mtDNA D-loop HVI核苷酸变异丰富。
3.中国山羊品种的167条mtDNA D-loop HVI序列中,A、C、T和G的平均含量分别为:30.86%、22.13%、30.89%和16.14%。供试山羊各品种间核苷酸含量有差异,但差异不显著。A+T含量为61.73%,G+C含量为38.27%,A+T含量明显高于G+C含量,说明中国山羊GC含量符合哺乳动物核苷酸的组成比例。
4.中国山羊品种的167条mtDNA D-loop HVI序列共定义了121种单倍型,92种为品种特有单倍型,11种为品种间单倍型,18种为品种内单倍型。品种间和品种内单倍型的分布不平衡,H43、H68、H90和H107是较为古老的单倍型类型,中国山羊没有主流单倍型。
5.中国山羊品种mtDNA D-loop HVI序列的121种单倍型共有颠换位点8个,转换位点118个,转换/颠换率为15:1,说明中国山羊具有很强的转换偏倚性。但是山羊各品种内没有颠换,只有转换。
6.中国11个山羊品种的单倍型多样度范围为0.909~1.000,核苷酸的多样度范围为0.01 810~0.03 821,太行山羊不论是单倍型的多样度还是核苷酸的多样度,在供试山羊品种中数值都是最高的。山羊各品种间平均核苷酸差异数较大,变异范围为9.289~18.563,且品种间的Kimura双参数距离变异范围为0.021~0.047,说明中国山羊品种遗传多样性丰富。
7.中国山羊的121种mtDNA D-loop HVI单倍型聚类成A、B、C、D和一个新支系。新支系位于支系D和支系B之间,是由长度为480 bp的单倍型聚类而成,这是本研究的新发现。中国山羊为多母系遗传,品种内分化水平较低,品种间没有明显的遗传地理结构。与国外山羊序列比较发现中国山羊与国外山羊有广泛的基因交流。
8.根据mtDNA单倍型的系统发育分析和网络分析表明,中国山羊主要存在支系A和支系B两大母系起源,支系A和支系B在NJ树中出现的频率分别为86.78%和4.96%;支系C和支系D,出现的频率为3.31%,本试验新发现的新支系频率最低,为1.65%。
9.中国山羊群体核苷酸不配对分布呈现出一条三峰的波浪型曲线,说明中国山羊群体经历了三次大的群体扩张,第一次波峰最大,发生在核苷酸差异数为10~11之间,第二次波峰发生在核苷酸差异数为27~28之间,第三次波峰发生在核苷酸差异数为39~40之间。且所有序列Tajima D中性检验结果不显著(P>0.10或0.05
Mitochondrial DNA (mtDNA) is an important genetic marker because of its maternal inheritance without recombination and high mutation rate. Many mtDNA studies based on the D-loop control region analysis addressed questions of phylogeny and evolution. The research of livestock genetic diversity helps the conservation and utilization of animal breed resources. The sequencing of mtDNA is one of the most common and reliable molecular markers in detecting animal molecular evolution and genetic diversity.
In this article, HVI of mitochondrial DNA(mtDNA) control region(CR, D-loop) was sequenced in 167 individuals from 11 domestic goat breeds/strains raised in China (Chaidamu, Huanghuai, Jining grey, Liaoning cashmere, Longdong Black, Nanjiang Cashmere, Inner Mongolia Cashmere, Tibetan, Shaannan White, Taihang),downloading sequences from goat breeds from GenBank were carried out. The results will provide scientific basis for resource protection and utilization. The conclusions are as follows in this study.
1. The mtDNA D-loop HVI sequences, 480~481 bp in length were determined for 167 individual in 11 Chinese goat breeds, The variation was caused by the gaps of a pairwise in the 239 bp in the mtDNA D-loop HVI sequence . And only 3 samples was 480bp including 2 goats of Inner Mongolia Cashmere and 1 goat of Longdong Black.
2. The 167 mtDNA D-loop HVI sequences contained 126 variable sites, among them, singleton variable sites was 27, parsimony informative sites of two variants was 97 and parsimony informative sites of three variants was 2. The results indicate that the pairwise diversity of Chinese goats is very rich.
3. The average content of A, C, T and G was 30.86%, 22.13%, 30.89% and 16.14% respe- cttively. The nucleotide content of the experimental goat breeds was varient but was not significant. A+T and G+C of Chinese goat breeds was 61.73% and 38.27% respectively indicating the nucleotide content of Chinese goat was in accordance with the proportion of mammals.
4. Chinese goat breeds had 121 haplotypes but no mainstream type. 92 haplotypes was unique haplotypes. 11 haplotypes were shared among breeds and 18 haplotypes were shared within breeds. The distributions and frequencies were unequilibrium either among breeds or within breeds. NJ tree showed four haplotypes (H43, H68, H90 and H107) were the oldest.
5. The transition sites of mtDNA D-loop HVI sequences between the goat breeds were 8 and transversion sites were 118, the ratio of transitions to transversions was 15/1, suggesting Chinese goat has the high transition bias. But there were no transition within the goat breed.
6. 121 haplotypes with from 167 samples of 11 Chinese goat breeds were determined. The haplotype diversity and nucleotide diversity in 11 Chinese goat breeds were 0.909~1.000 and 0.01 810~0.03 821, respectively. The haplotype and nucleotide diversity of Taihang goat was the highest (1.000, 0.03 821 respectively). The average number of nucleotide differences variation was 9.289~18.563, The Kimura 2-parameter distance between breeds varied from 0.021~0.047. The results indicate that the genetic diversity of Chinese goats is very abundant.
7. NJ tree of Chinese goat analysis indicated there were 5 lineages including lineage A, B, C and D found before and a new lineage found in the article. The new lineage was clustered by the sequences of 480 bp. The new lineage was located between the lineage D and B. The result was first reported in Chinese goats. And there was no significant geographical structure in Chinese goat populations. Compared with the goats from the other nations, Chinese goats had a widely gene flow.
8. Phylogenetic analysis and a reduced median network analysis revealed two highly divergent goat mtDNA lineages A and B mainly. The frequency of the lineage A and B was 86.78% and 4.96%, respectively. Two additional lineages C and D are present in China at low frequency (3.31%) respectively. And the frequency of the new lineage was 1.65%.
9. The curve of nucleotide mismatch distributions in 11 domestic goat populations took on three unimodal. Pairwise differences ranged from 1 to 48. A major peak presented at 10~11 mutational differences, a secondary one at 27~28 differences and a third one at 39~40 differences. Lineage A showed unimodal distribution and undergo expansions. Lineage B showed near bimodal distribution and did not undergo expansion. Tajima's test of selective neutrality of Chinese goats was not significant (P>0.10 or 0.05
引文
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