中国蒙古马的遗传多样性与系统发育及起源研究
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摘要
目前,对于中国蒙古马何处起源、如何驯化和遗传结构怎样等问题的答案还知之甚少。而且,以Cytb (Cytochrome b)基因来确定家马系统发育结构很少见诸报道,对于中国蒙古马和纯血马间的遗传差异更是未曾见过详细报道。一方面,为了确定中国蒙古马、三河马和纯血马共六个类群的遗传关系,探讨它们的驯化过程,我们对CKM(肌肉型肌酸激酶)第二内含子和线粒体DNA (mitochondrial DNA, mtDNA) D-loop区序列的变异进行研究；另一方面,为了进一步弄清世界各地家马的遗传结构、起源和驯化过程,并尽力确定其系统发育结构,我们对本研究获得的36条中国蒙古马、三河马、纯血马Cytb基因全序列和GenBank中提交的世界各地家马的全序列进行了深入的分析。具体结果如下：
(1)关于CKM序列
纯血马与其余中国家马类群间的差异较大,而中国家马类群间的差异较小,表明纯血马与中国家马间的品种形成历史、育种措施和起源截然不同。三河马和中国蒙古马的遗传关系非常相近,而且,二者间的渐渗(杂交)现象非常严重。三河马和乌审马需要尽快进行卓有成效的保护。
(2)关于Cytb序列
根据UPGMA树和最小跨度树(MST, Minimum Spanning Tree)的结构,将所有的家马Cytb单倍型划分为A-F六个单倍型群。而且,各单倍型群间的FST、平均差异数和矫正平均差异数值都达到了差异显著水平(p<0.01),进一步支持了单倍型群确定的正确性。A单倍型群是最古老的单倍型群,表明该单倍型群是最原始或者最早发生驯化的家马单倍型群。所有的单倍型群和Cytb的所有序列都显示家马历史上经历过群体扩张事件。中国蒙古马是多重母系来源的,经历过群体扩张,且具有非常丰富的遗传多样性,表明蒙古地区可能也是家马的驯化地之一。
首次通过将219条各品种家马Cytb全序列根据地理区域划分为北美、西欧、东欧、中东、中亚、东亚6个类群,来比较母系遗传结构差异。结果表明：北美类群和亚洲类群之间差异较显著,而其余类群间则差异不显著,一方面说明亚欧大陆各地区马种之间母系基因渗透现象比较严重;另一方面一定程度上支持北美马种来自欧洲的论断。构建的Median Joining网络聚类图显示,所有家马的母系起源于A-G7个单倍型群,进一步支持家马多重母系起源的观点。并且,家马各单倍型群都是由多个地理区间上分布的家马混杂而成的,未发现由单独一种地理区间的家马构成的单倍型群,即地理位置、母系构成以及母性起源之间没有明显的相互关系。
(3)关于D-loop区序列
单倍型多样性和核苷酸多样性的最小值都出现在巴尔虎马类群中,表明该蒙古马类群亟需进行有效的保护。几乎所有家马类群间的遗传差异都是显著的,尤其巴尔虎马、纯血马和锡尼河马与其余家马类群间的差异都十分显著(p<0.01)。而且,中国蒙古马、三河马、纯血马三个品种共六个类群的家马都揭示有数个母系来源。还有,三河马和中国蒙古马间的渐渗(杂交)现象非常严峻,表明三河马也亟需进行有效的品种保护。中国蒙古马和三河马这两个内蒙古地区的家马品种经分析显现出较纯血马更近的亲缘关系,表明蒙古地区和英格兰地区的这两地的家马具有截然不同的品种形成历史、育种措施或者母系起源。另外,结果还显示锡尼河马在内蒙古家马类群中具有最远的遗传距离。
To date, the questions of origins (where), domestication (how), and genetic structure (what) of Chinese Mongolian horses are poorly understood. Furthermore, there have been sparse reports on the phylogenetic structure determination for horse Cytb (Cytochrome b) gene, and no reports on the genetic differences between the Chinese Mongolian horses and the Thoroughbreds. On the one hand, in order to determine their genetic structure, understand their genetic relationships, and explore their domestication processes, we performed two extensive surveys of both creatine kinase (muscle isoenzyme; CKM) intronic sequences variations and mtDNA D-loop variations among six populations of indigenous Chinese Mongolian horses, cultivated Sanhe horses, and imported Thoroughbreds; On the other hand, in order to obtain more knowledge of the genetic structure, origin, and domestication processes of worldwide horses, and try to determine their phylogenetic structure, we performed two extensive surveies of Cytb sequence diversity from new acquired36sequences, together with the other published sequences deposited in GenBank. The detailed results are as follows:
(1) With respect to CKM sequences
The differences between the Thoroughbred population and other Chinese horse populations were large, but only small differences were observed among Chinese horse populations, suggesting that the domestication history, breeding measures, and origins of these horse populations are completely different. Results suggest that Sanhe and Chinese Mongolian horses are very closely related and the ingression (interbreeding) between the Chinese Mongolian and Sanhe horse is serious. Our results suggest that the Sanhe horse and Wushen horse require prompt and powerful protection.
(2) With respect to Cytb sequences
According to the structure of UPGMA tree and Minimum Spanning Tree (MST), the haplotypes were divided into A-G six haplogroups, and the significant p values (p<0.01) of FST, the average number of pairwise differences and the corrected average pairwise differences between haplogroup populations'values supporting the trueness and accuracy of the haplogroup determination. The A haplogroup is the most ancient clade in horses, indicating it's the primary and original domestic clade in horses. All the clades and the total data set of Cytb sequences showed the horses have undergone population expansion event in the history. Results suggest that Chinese Mongolian horses originated multiply; also underwent population expansion and possess great genetic diversity, indicating the Mongolian region maybe one of the domesticated places of horses.
By dividing the total219horse Cytb sequences into North American (NA), West European (WE), East European (EE), Middle East (ME), Central Asian (CA) and East Asian (EA) groups, we analyzed the differences of horse maternal structure in different geographic areas based on Cytb sequences for the first time. It was shown that the significant differences were only observed between NA group and three Asian groups. On the one hand, it indicated that the ingression within the horses in the Eurasian continent was great; on the other hand, it supported the assertion that the domesticated NA horses originated from Europe to some extent. Seven distinct haplogroups (A-G) were revealed in the founded Median Joining network, supporting the multiple maternal origins of the horses. Moreover, all the seven horse haplogroups were composed of horses from several different geographic regions. Besides, there was no obvious correspondence between the geographic regions, maternal structure, and maternal origins among all the domesticated horses around the world.
(3) With respect to D-loop sequences
The results show that the lowest haplotype diversity and nucleotide diversity values were both emerged in Baerhu horse population, implicating this Mongolian horse population required an urgent powerful protection. The D-loop sequences were examined and differences between all population pairs were observed and almost all were significant, especially, Baerhu, Thoroughbred, and Xinihe populations are significantly different from others (p<0.01). Furthermore, it was revealed that there are several maternal origins in the three researched horse breeds and in all the six horse populations. Moreover, the ingression between Chinese Mongolian horse and Sanhe horse is in a remarkably serious condition, suggesting that the Sanhe horses need a prompt and powerful protection as well. It was also revealed that the two different horse breeds in Inner Mongolia are more closely related to each other than to Thoroughbred, indicating the domestication history, breeding measures or origins are completely different. Additionally, the results show that the Xinihe horse population has the farthest genetic distance among Inner Mongolian horse populations.
(1)关于CKM序列
纯血马与其余中国家马类群间的差异较大,而中国家马类群间的差异较小,表明纯血马与中国家马间的品种形成历史、育种措施和起源截然不同。三河马和中国蒙古马的遗传关系非常相近,而且,二者间的渐渗(杂交)现象非常严重。三河马和乌审马需要尽快进行卓有成效的保护。
(2)关于Cytb序列
根据UPGMA树和最小跨度树(MST, Minimum Spanning Tree)的结构,将所有的家马Cytb单倍型划分为A-F六个单倍型群。而且,各单倍型群间的FST、平均差异数和矫正平均差异数值都达到了差异显著水平(p<0.01),进一步支持了单倍型群确定的正确性。A单倍型群是最古老的单倍型群,表明该单倍型群是最原始或者最早发生驯化的家马单倍型群。所有的单倍型群和Cytb的所有序列都显示家马历史上经历过群体扩张事件。中国蒙古马是多重母系来源的,经历过群体扩张,且具有非常丰富的遗传多样性,表明蒙古地区可能也是家马的驯化地之一。
首次通过将219条各品种家马Cytb全序列根据地理区域划分为北美、西欧、东欧、中东、中亚、东亚6个类群,来比较母系遗传结构差异。结果表明：北美类群和亚洲类群之间差异较显著,而其余类群间则差异不显著,一方面说明亚欧大陆各地区马种之间母系基因渗透现象比较严重;另一方面一定程度上支持北美马种来自欧洲的论断。构建的Median Joining网络聚类图显示,所有家马的母系起源于A-G7个单倍型群,进一步支持家马多重母系起源的观点。并且,家马各单倍型群都是由多个地理区间上分布的家马混杂而成的,未发现由单独一种地理区间的家马构成的单倍型群,即地理位置、母系构成以及母性起源之间没有明显的相互关系。
(3)关于D-loop区序列
单倍型多样性和核苷酸多样性的最小值都出现在巴尔虎马类群中,表明该蒙古马类群亟需进行有效的保护。几乎所有家马类群间的遗传差异都是显著的,尤其巴尔虎马、纯血马和锡尼河马与其余家马类群间的差异都十分显著(p<0.01)。而且,中国蒙古马、三河马、纯血马三个品种共六个类群的家马都揭示有数个母系来源。还有,三河马和中国蒙古马间的渐渗(杂交)现象非常严峻,表明三河马也亟需进行有效的品种保护。中国蒙古马和三河马这两个内蒙古地区的家马品种经分析显现出较纯血马更近的亲缘关系,表明蒙古地区和英格兰地区的这两地的家马具有截然不同的品种形成历史、育种措施或者母系起源。另外,结果还显示锡尼河马在内蒙古家马类群中具有最远的遗传距离。
To date, the questions of origins (where), domestication (how), and genetic structure (what) of Chinese Mongolian horses are poorly understood. Furthermore, there have been sparse reports on the phylogenetic structure determination for horse Cytb (Cytochrome b) gene, and no reports on the genetic differences between the Chinese Mongolian horses and the Thoroughbreds. On the one hand, in order to determine their genetic structure, understand their genetic relationships, and explore their domestication processes, we performed two extensive surveys of both creatine kinase (muscle isoenzyme; CKM) intronic sequences variations and mtDNA D-loop variations among six populations of indigenous Chinese Mongolian horses, cultivated Sanhe horses, and imported Thoroughbreds; On the other hand, in order to obtain more knowledge of the genetic structure, origin, and domestication processes of worldwide horses, and try to determine their phylogenetic structure, we performed two extensive surveies of Cytb sequence diversity from new acquired36sequences, together with the other published sequences deposited in GenBank. The detailed results are as follows:
(1) With respect to CKM sequences
The differences between the Thoroughbred population and other Chinese horse populations were large, but only small differences were observed among Chinese horse populations, suggesting that the domestication history, breeding measures, and origins of these horse populations are completely different. Results suggest that Sanhe and Chinese Mongolian horses are very closely related and the ingression (interbreeding) between the Chinese Mongolian and Sanhe horse is serious. Our results suggest that the Sanhe horse and Wushen horse require prompt and powerful protection.
(2) With respect to Cytb sequences
According to the structure of UPGMA tree and Minimum Spanning Tree (MST), the haplotypes were divided into A-G six haplogroups, and the significant p values (p<0.01) of FST, the average number of pairwise differences and the corrected average pairwise differences between haplogroup populations'values supporting the trueness and accuracy of the haplogroup determination. The A haplogroup is the most ancient clade in horses, indicating it's the primary and original domestic clade in horses. All the clades and the total data set of Cytb sequences showed the horses have undergone population expansion event in the history. Results suggest that Chinese Mongolian horses originated multiply; also underwent population expansion and possess great genetic diversity, indicating the Mongolian region maybe one of the domesticated places of horses.
By dividing the total219horse Cytb sequences into North American (NA), West European (WE), East European (EE), Middle East (ME), Central Asian (CA) and East Asian (EA) groups, we analyzed the differences of horse maternal structure in different geographic areas based on Cytb sequences for the first time. It was shown that the significant differences were only observed between NA group and three Asian groups. On the one hand, it indicated that the ingression within the horses in the Eurasian continent was great; on the other hand, it supported the assertion that the domesticated NA horses originated from Europe to some extent. Seven distinct haplogroups (A-G) were revealed in the founded Median Joining network, supporting the multiple maternal origins of the horses. Moreover, all the seven horse haplogroups were composed of horses from several different geographic regions. Besides, there was no obvious correspondence between the geographic regions, maternal structure, and maternal origins among all the domesticated horses around the world.
(3) With respect to D-loop sequences
The results show that the lowest haplotype diversity and nucleotide diversity values were both emerged in Baerhu horse population, implicating this Mongolian horse population required an urgent powerful protection. The D-loop sequences were examined and differences between all population pairs were observed and almost all were significant, especially, Baerhu, Thoroughbred, and Xinihe populations are significantly different from others (p<0.01). Furthermore, it was revealed that there are several maternal origins in the three researched horse breeds and in all the six horse populations. Moreover, the ingression between Chinese Mongolian horse and Sanhe horse is in a remarkably serious condition, suggesting that the Sanhe horses need a prompt and powerful protection as well. It was also revealed that the two different horse breeds in Inner Mongolia are more closely related to each other than to Thoroughbred, indicating the domestication history, breeding measures or origins are completely different. Additionally, the results show that the Xinihe horse population has the farthest genetic distance among Inner Mongolian horse populations.
引文
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