Sequence divergence of rice microsatellites in Oryza and other plant species
Sequence divergence of rice microsatellites in Oryza and other plant species
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DOI：
10.1007/s00438-002-0739-5
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发表时间：
2002-11-01
影响因子：
3.1
通讯作者：
McCouch, SR
中科院分区：
文献类型：
--
作者：
Chen, X;Cho, YG;McCouch, SR
为了确定微卫星座位的遗传变异基础，对11对用于扩增水稻微卫星标记的引物对12个植物样本进行了扩增能力以及扩增产物的电泳性和基于序列的多态性的评估，这些样本包括来自水稻属6个不同物种的代表和来自玉米(玉米)、小麦(小麦)和拟南芥(Arabiopsis)的各1个基因型。在水稻BB/CC和CC基因组中扩增出了73%(8/11)的扩增产物，在其他属中扩增出27%(3/11)的扩增产物。从所有属中扩增出的七个DNA片段中，有三个被确定为与它们的水稻同源。使用聚丙烯酰胺凝胶电泳法共检测到115个扩增片段，并将这些扩增片段聚为74个不同的电泳型。对108个扩增片段进行测序，发现了大小一致的情况，揭示了13个新的基于序列的变异。物种内的等位基因多样性主要是由于微卫星区域重复数的变化，但插入/缺失(INDELs)和碱基替换的频率随着样品之间遗传距离的增加而增加。这项研究表明，在涉及密切相关个体的研究中，电形态大小多态是衡量遗传差异的适当指标，但当在较长时间尺度上进行系统发育或进化推断时，在序列水平上评估SSR变异是必不可少的。
To determine the basis of genetic variation at microsatellite loci, eleven primer pairs, developed to amplify microsatellite markers in rice, were evaluated for their ability to amplify a PCR product and for both electromorphic and sequence-based polymorphism of the resulting products in 12 plant samples, including representatives from six different species within the genus Oryza and one genotype each from Zea (maize), Triticum (wheat) and Arabidopsis. PCR amplification was reliable in the four O. sativa samples as well as in the closely related Oryza relatives with AA genomes, while only 73% (8/11) of primers amplified in the BB/CC and CC genomes of Oryza, and 27% (3/11) amplified in the other genera. Three out of seven DNA fragments that were amplified from all genera were determined to be orthologous to their rice counterparts. A total of 115 amplicons were detected using polyacrylamide gel electrophoresis and these clustered into 74 distinct electromorphs. Sequencing of 108 amplicons revealed size homoplasy, exposing 13 new sequence-based variants. Allelic diversity within a species was predominantly due to changes in the number of repeats in the microsatellite region, but the frequency of insertions/deletions (indels) and base substitutions increased as the genetic distance between samples increased. This study suggests that electromorph size polymorphism is an adequate measure of genetic difference in studies involving closely-related individuals, but that when phylogenetic or evolutionary inferences are being made over longer time scales, evaluation of SSR variation at the sequence level is essential.