Ishii T, Xu Y, McCouch S R
Department of Plant Breeding, Cornell University, Ithaca, NY 14853-1901, USA.
Genome. 2001 Aug;44(4):658-66.
Simple sequence length polymorphism analysis was carried out to reveal microsatellite variation and to clarify the phylogenetic relationships among A-genome species of rice. Total DNA from 29 cultivars (23 Oryza sativa and 6 O. glaberrima) and 30 accessions of wild A-genome species (12 O. rufipogon, 5 O. glumaepatula, 2 O. longistaminata, 6 O. meridionalis, and 5 O. barthii) was used as a template for PCR to detect 24 nuclear and 10 chloroplast microsatellite loci. Microsatellite allelic diversity was examined based on amplified banding patterns. Microsatellites amplified clearly in all 59 accessions, with an average of 18.4 alleles per locus. The polymorphism information content (PIC) value ranged from 0.85 to 0.94, with an average of 0.89. At the species level, high average PIC values were observed in O. sativa (0.79) and O. rufipogon (0.80). For chloroplast microsatellites, the average number of alleles per locus and the average PIC value were 2.9 and 0.38, respectively. While the magnitude of diversity was much greater for nuclear microsatellites than for chloroplast microsatellites, they showed parallel patterns of differentiation for each taxonomic group. Using the ratio of common alleles (estimated as size of amplified fragments) as a similarity index, the average percentages of common microsatellite alleles were calculated between taxa. For both nuclear and chloroplast microsatellites, O. sativa showed the highest similarity values to O. rufipogon, and O. glaberrima was most similar to O. barthii. These data support previous evidence that these cultivars originated from the corresponding wild ancestral species.
进行了简单序列长度多态性分析，以揭示微卫星变异并阐明水稻A基因组物种之间的系统发育关系。来自29个栽培品种（23个亚洲栽培稻和6个非洲栽培稻）和30份野生A基因组物种材料（12份普通野生稻、5份长雄蕊野生稻、2份长花药野生稻、6份南方野生稻和5份巴蒂野生稻）的总DNA用作PCR模板，以检测24个核微卫星位点和10个叶绿体微卫星位点。基于扩增条带模式检查微卫星等位基因多样性。微卫星在所有59份材料中均清晰扩增，每个位点平均有18.4个等位基因。多态性信息含量（PIC）值范围为0.85至0.94，平均为0.89。在物种水平上，亚洲栽培稻（0.79）和普通野生稻（0.80）的平均PIC值较高。对于叶绿体微卫星，每个位点的等位基因平均数和平均PIC值分别为2.9和0.38。虽然核微卫星的多样性程度比叶绿体微卫星大得多，但它们在每个分类组中都显示出平行的分化模式。使用共同等位基因的比例（以扩增片段大小估计）作为相似性指数，计算了不同分类单元之间共同微卫星等位基因的平均百分比。对于核微卫星和叶绿体微卫星，亚洲栽培稻与普通野生稻的相似性值最高，而非洲栽培稻与巴蒂野生稻最相似。这些数据支持了先前的证据，即这些栽培品种起源于相应的野生祖先物种。
