籼稻93-11和粳稻日本晴DNA插入缺失差异片段揭示的水稻籼-粳分化

碱基的插入/缺失(InDel)引起DNA序列变化并形成了DNA片段长度多态,可以用作遗传标记.为了评价基于籼稻93-11和粳稻日本晴全基因组序列比对获得的差异片段而设计的InDel引物在鉴定籼稻和粳稻两种生态型以及研究稻属不同物种之间亲缘关系的意义,采用45对InDel引物,对来自亚洲10个国家的49份籼稻、43份粳稻品种和24份野生稻进行了检验.结果表明,其中41对InDel引物鉴定籼稻或粳稻品种的准确率高于80%.主成分分析散点图显示:籼稻与粳稻存在明显的遗传分化;含AA基因组的野生稻物种与籼稻品种存在较近的亲缘关系;非AA基因组的野生稻物种不存在明显的籼-粳分化.并且证明了基于籼稻93-11和粳稻日本晴全基因组序列比对获得的InDel差异片段设计的引物可以用于栽培稻籼稻和粳稻品种的鉴定以及籼-粳分化问题的研究,及探索稻属不同物种间的亲缘关系.

Differentiation of Indica-Japonica Rice Revealed by Insertion/deletion Fragments Obtained from Comparative Genomic Study of DNA Sequences between 93-11 (Indica) and Nipponbare (Japonica)

DNA polymorphisms resulted in nucleotide Insertion/Deletions in genomic sequences are the basis for developing InDel molecular markers.In order to validate the InDel primer pairs designed based on the comparative genomic study of DNA sequences between an Indica rice 93-11 and a Japonica rice Nipponbare,in identifying Indica and Japonica rice varieties, and studying wild Oryza species,49 Indica,43 Japonica and 24 wild rice accessions from 10 Asian countries using 45 InDel primer pairs were studied.The results indicated that of the 45 InDel primer pairs,41 can accurately identify Indica or Japonica rice varieties with the reliability over 80%.The scatter plotting data of the principal component analysis(PCA) indicated that(i) the InDel primer pairs can easily distinguish between Indica and japonica rice varieties,and indicate their genetic differentiation;(ii) the AAgenome wild rice species showed a close genetic relationship with the Indica rice varieties;and(iii) the non-AA genome wild rice species did not show evident differentiation into the Indica and Japonica types.It is concluded from the study that the InDel primer pairs based on 93-11 and Nipponbare can be useful for identifying Indica and Japonica rice varieties,and for studying genetic relationships of wild rice species,particularly related to the Indica-Japonica differentiation.