Miyashita N T, Kawabe A, Innan H
Laboratory of Plant Genetics, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502 Japan.
Genetics. 1999 Aug;152(4):1723-31. doi: 10.1093/genetics/152.4.1723.
To investigate the level and pattern of DNA variation of Arabidopsis thaliana at the entire genome level, AFLP analysis was conducted for 38 ecotypes distributed throughout the world. Ten pairs of selective primers were used to detect a total of 472 bands, of which 374 (79. 2%) were polymorphic. The frequency distribution of polymorphic bands was skewed toward an excess of singleton variation. On the basis of AFLP variation, nucleotide diversity for the entire genome was estimated to be 0.0106, which was within the range reported previously for specific nuclear genes. The frequency distribution of pairwise distance was bimodal because of an ecotype (Fl-3) with a large number of unique bands. Linkage disequilibrium between polymorphic AFLPs was tested. The proportion of significant linkage disequilibria was close to random expectation after neglecting the ecotype Fl-3. This result indicates that the effect of recombination could not be ignored in this selfing species. A neighbor-joining tree was constructed on the basis of the AFLP variation. This tree has a star-like topology and shows no clear association between ecotype and geographic origin, suggesting a recent spread of this plant species and limited migration between its habitats.
为了在全基因组水平上研究拟南芥DNA变异的水平和模式，对分布于世界各地的38个生态型进行了AFLP分析。使用10对选择性引物共检测到472条带，其中374条（79.2%）为多态性条带。多态性条带的频率分布偏向于单态变异过多。基于AFLP变异，估计全基因组的核苷酸多样性为0.0106，这在先前报道的特定核基因范围内。由于一个具有大量独特条带的生态型（Fl-3），成对距离的频率分布呈双峰。对多态性AFLP之间的连锁不平衡进行了测试。在忽略生态型Fl-3后，显著连锁不平衡的比例接近随机预期。这一结果表明，在这个自交物种中，重组的影响不可忽视。基于AFLP变异构建了邻接树。这棵树具有星状拓扑结构，生态型与地理起源之间没有明显关联，表明该植物物种近期有扩散，且其栖息地之间的迁移有限。
