National Laboratory of Protein Engineering and Plant Genetic Engineering, Peking-Yale Joint Center for Plant Molecular Genetics and AgroBiotechnology, College of Life Sciences, Peking University, Beijing, China.
BMC Plant Biol. 2010 Feb 8;10:22. doi: 10.1186/1471-2229-10-22.
In the studies incorporating worldwide sampling of A. thaliana populations, the samples from East Asia, especially from China, were very scattered; and the studies focused on global patterns of cpDNA genetic variation among accessions of A. thaliana are very few. In this study, chloroplast DNA sequence variability was used to infer phylogenetic relationships among Arabidopsis thaliana accessions from around the world, with the emphasis on samples from China.
A data set comprising 77 accessions of A. thaliana, including 19 field-collected Chinese accessions together with three related species (A. arenosa, A. suecica, and Olimarabidopsis cabulica) as the out-group, was compiled. The analysis of the nucleotide sequences showed that the 77 accessions of A. thaliana were partitioned into two major differentiated haplotype classes (MDHCs). The estimated divergence time of the two MDHCs was about 0.39 mya. Forty-nine haplotypes were detected among the 77 accessions, which exhibited nucleotide diversity (pi) of 0.00169. The Chinese populations along the Yangtze River were characterized by five haplotypes, and the two accessions collected from the middle range of the Altai Mountains in China shared six specific variable sites.
The dimorphism in the chloroplast DNA could be due to founder effects during late Pleistocene glaciations and interglacial periods, although introgression cannot be ruled out. The Chinese populations along the Yangtze River may have dispersed eastwards to their present-day locations from the Himalayas. These populations originated from a common ancestor, and a rapid demographic expansion began approximately 90,000 years ago. Two accessions collected from the middle range of the Altai Mountains in China may have survived in a local refugium during late Pleistocene glaciations. The natural populations from China with specific genetic characteristics enriched the gene pools of global A. thaliana collections.
在包含拟南芥全球采样的研究中，东亚地区的样本，尤其是来自中国的样本非常分散；而关注拟南芥样本间 cpDNA 遗传变异的全球模式的研究则非常少。本研究利用叶绿体 DNA 序列变异来推断世界各地拟南芥样本的系统发育关系，重点关注中国的样本。
我们构建了一个包含 77 个拟南芥样本的数据组，其中包括 19 个野外采集的中国样本，以及三个相关物种（A.arenosa、A.suecica 和 Olimarabidopsis cabulica）作为外群。核苷酸序列分析表明，这 77 个拟南芥样本被分为两个主要的分化单倍型类群（MDHCs）。两个 MDHC 之间的估计分化时间约为 0.39 百万年前。在 77 个样本中检测到 49 个单倍型，它们表现出核苷酸多样性（pi）为 0.00169。长江流域的中国种群有 5 种单倍型，而在中国阿尔泰山脉中段采集的两个样本共享 6 个特定的可变位点。
叶绿体 DNA 的二态性可能是由于晚更新世冰期和间冰期的奠基者效应造成的，尽管不能排除基因渗入的可能性。长江流域的中国种群可能是从喜马拉雅山脉向东扩散到现在的位置的。这些种群起源于一个共同的祖先，大约 9 万年前开始了快速的种群扩张。在中国阿尔泰山脉中段采集的两个样本可能在晚更新世冰期幸存于一个局部避难所。具有特定遗传特征的中国自然种群丰富了全球拟南芥群体的基因库。
