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Background  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.    Results  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 (π) 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.    Conclusions  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.

The origin of populations of Arabidopsis thalianain China, based on the chloroplast DNA sequences