Efficient indica and japonica rice identification based on the InDel molecular method: Its implication in rice breeding and evolutionary research
Efficient indica and japonica rice identification based on the InDel molecular method: Its implication in rice breeding and evolutionary research
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基于InDel分子方法的籼粳稻高效鉴定及其在水稻育种和进化研究中的意义
DOI：
10.1016/j.pnsc.2009.01.011
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发表时间：
2009-10-10
影响因子：
4.7
通讯作者：
Jin, Xin
中科院分区：
文献类型：
--
作者：
Lu, Bao-Rong;Cai, Xingxing;Jin, Xin
根据基本局部比对搜索工具(BLAST)获得的插入/缺失(Indel)DNA片段对水稻(93-11)和日本晴(Nipponbard)全基因组序列的多态性，建立了一种准确、高效地鉴定水稻的分子生物学方法。利用聚合酶链式反应(PCR)和聚丙烯酰胺凝胶电泳法(PAGE)对包括93-11和日本晴在内的44个典型水稻品种的45个Indel基因座进行了验证。对不同Indel基因座的数据矩阵进行了中立性检验，结果表明，34个Indel基因座与水稻品种间的分化密切相关。对来自11个亚洲国家的栽培水稻品种和12个不同来源的野生稻品种进行的更广泛的分析证实，通过计算水稻基因组中不同Indel基因座上不同Indel基因座上特定于水稻或水稻的等位基因的平均频率，可以准确地确定水稻的籼稻和粳稻特征。这种方法被命名为“INDELL分子指数”，它结合了分子和统计方法来确定水稻品种的籼型和粳型特征。与传统的以形态为基础的方法相比，Indel分子指数提供了一种非常准确、快速、简单、高效的鉴定方法。此外，Indel指数还可以用来判断野生稻种的籼型或粳型特征，极大地扩展了该方法的适用性。INDELL分子指数为在水稻育种中有效选择合适的水稻种质提供了一种新的工具。这也为研究不同环境条件下水稻的起源、进化和遗传分化提供了一个新的模式。(C)2009年中国和中国科学院国家自然科学基金。爱思唯尔有限公司出版，《科学》中国出版社出版。版权所有。
An efficient molecular method for the accurate and efficient identification of indica and japonica rice was created based on the polymorphisms of insertion/deletion (InDel) DNA fragments obtained from the basic local alignment search tool (BLAST) to the entire genomic sequences of indica (93-11) and japonica rice (Nipponbare). The 45 InDel loci were validated experimentally by the polymerase chain reaction (PCR) and polyacrylamide gel electrophoresis (PAGE) in 44 typical indica and japonica rice varieties, including 93-11 and Nipponbare. A neutrality test of the data matrix generated from electrophoretic banding patterns of various InDel loci indicated that 34 InDel loci were strongly associated with the differentiation of indica and japonica rice. More extensive analyses involving cultivated rice varieties from 11 Asian countries, and 12 wild Oryza species with various origins confirmed that indica and japonica characteristics could accurately be determined via calculating the average frequency of indica- or japonica-specific alleles on different InDel loci across the rice genome. This method was named as the "InDel molecular index" that combines molecular and statistical methods in determining the indica and japonica characteristics of rice varieties. Compared with the traditional methods based essentially on morphology, the InDel molecular index provides a very accurate, rapid, simple, and efficient method for identifying indica and japonica rice. In addition, the InDel index can be used to determine indica or japonica characteristics of wild Oryza species, which largely extends the utility of this method. The InDel molecular index provides a new tool for the effective selection of appropriate indica or japonica rice germplasm in rice breeding. It also offers a novel model for the study of the origin, evolution, and genetic differentiation of indica and japonica rice adapted to various environmental changes. (C) 2009 National Natural Science Foundation of China and Chinese Academy of Sciences. Published by Elsevier Limited and Science in China Press. All rights reserved.