Efficient indica and japonica rice identification based on the InDel molecular method:Its implication in rice breeding and evolutionary research  

作　　者：Bao-Rong Lu Xingxing Cai Xin Jin 

机构地区：[1]Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science,Fudan University, Shanghai 200433, China

出　　处：《Progress in Natural Science:Materials International》2009年第10期1241-1252,共12页自然科学进展·国际材料（英文版）

基　　金：supported by the National Basic Research Program of China(Grant No.2006CB100205);the National Natural Science Foundation of China(Grant No.2007ZD001);the Shanghai Commission of Science and Technology(Grant No.08JC1401700)

摘　　要：An efficient molecular method for the accurate and efficient identification of indica and japonica rice was created based on the poly-morphisms 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 indiea 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.An efficient molecular method for the accurate and efficient identification of indica and japonica rice was created based on the poly-morphisms 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.

关 键 词：Cultivated rice Wild Oryza INDEL Molecular marker indica-japonica identification Neutrality test 

分 类 号：S511[农业科学—作物学] S511.03