Yoshida K, Miyashita N T, Ishii T
Laboratory of Plant Genetics, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan.
Theor Appl Genet. 2004 Nov;109(7):1406-16. doi: 10.1007/s00122-004-1752-3. Epub 2004 Oct 6.
Nucleotide variation in the alcohol dehydrogenase (Adh1) locus region of the wild rice Oryza rufipogon and its related species was analysed to clarify the maintenance mechanism of DNA variation in Oryza species. The estimated nucleotide diversity in the Adh1 locus region of O. rufipogon was 0.002, which was one of the lowest values detected in nuclear loci of plant species investigated so far. Tests of neutrality detected significantly negative deviation from the neutral mutation model for the coding region, especially for replacement sites. When each of the ADH1 domains was considered, significance was detected only for the catalytic domain 1. These results suggest purifying selection in the Adh1 coding region. In the phylogenetic tree of Oryza species based on Adh1 variation, cultivated rice O. sativa subspp. japonica and indica were included in the cluster of O. rufipogon. The genetic distance of the Adh1 region between O. rufipogon and O. sativa was as low as the nucleotide diversity of O. rufipogon. These results imply that O. rufipogon and O. sativa cannot be classified based on the nucleotide variation of Adh1. No replacement divergence between O. rufipogon and the other three A-genome species (O. glumaepatula, O. barthii and O. meridionalis) were detected, indicating that ADH1 is conserved in the A-genome species. On the other hand, between O. rufipogon and the E-genome species O. australiensis, replacement changes were detected only in the catalytic domain 1. The difference in replacement substitutions between the A- and E-genome species may be related to adaptive changes in the ADH1 domains, reflecting environmental differences where the species encounter anaerobic stress.
分析了野生稻普通野生稻及其近缘物种乙醇脱氢酶（Adh1）基因座区域的核苷酸变异，以阐明水稻物种中DNA变异的维持机制。普通野生稻Adh1基因座区域的估计核苷酸多样性为0.002，这是迄今为止在植物物种核基因座中检测到的最低值之一。中性检验检测到编码区，特别是替换位点，显著偏离中性突变模型。当考虑ADH1的每个结构域时，仅在催化结构域1中检测到显著性。这些结果表明Adh1编码区存在纯化选择。在基于Adh1变异的水稻物种系统发育树中，栽培稻粳稻和籼稻被纳入普通野生稻聚类中。普通野生稻和栽培稻之间Adh1区域的遗传距离与普通野生稻的核苷酸多样性一样低。这些结果意味着普通野生稻和栽培稻不能根据Adh1的核苷酸变异进行分类。未检测到普通野生稻与其他三个A基因组物种（阔叶野生稻、非洲栽培稻和南方野生稻）之间的替换分歧，表明ADH1在A基因组物种中是保守的。另一方面，在普通野生稻和E基因组物种澳洲野生稻之间，仅在催化结构域1中检测到替换变化。A基因组和E基因组物种之间替换替代的差异可能与ADH1结构域的适应性变化有关，反映了物种遇到厌氧胁迫的环境差异。
