Genome-wide identification of R genes and exploitation of candidate RGA markers in rice  

作　　者：WANGXusheng WUWeiren JINGulei ZHUJun 

机构地区：[1]InstituteofBioinformatics,ZhejiangUniversity,Hangzhou310029,China [2]InstituteofBioinformatics,ZhejiangUniversity,Hangzhou310029,China//CollegeofCropScience,FujianAgricultureandForestryUniversity,Fuzhou350002,China [3]CollegeofCropScience,FujianAgricultureandForestryUniversity,Fuzhou350002,China

出　　处：《Chinese Science Bulletin》2005年第11期1120-1125,共6页

基　　金：the National High-Tech Research and Development Program of China(Grant Nos.2003AA207160&2002AA234031); the Natural Science Foundationof Fujian Province(Grant No.B9910011).

摘　　要：By scanning the whole genomic sequence of japonica rice using 45 known plant disease resistance (R) genes, we identified 2119 resistance gene homologs or ana- logs (RGAs) and verified that RGAs are not randomly dis- tributed but tend to cluster in the rice genome. The RGAs were classified into 21 families according to their functional domain based on Hidden Markov model (HMM). By com- paring the RGAs of japonica rice with the whole genomic sequence of indica rice, we found 702 RGAs allelic between the two subspecies and revealed that 671 (95.6%) of them have length difference (InDels) in their genomic sequences (including coding and non-coding regions) between the two subspecies, suggesting that RGAs are highly polymorphic between the two subspecies in rice. We also exploited 402 PCR-based and co-dominant candidate RGA markers by designing primer pairs on the regions flanking the InDels and validating them via e-PCR. The length differences of the candidate RGA markers between the two subspecies are from 1 to 742 bp, with an average of 10.26 bp. All related information of the RGAs is available from our web site (http://ibi.zju.edu.cn/RGAs/index.html).By scanning the whole genomic sequence of japonica rice using 45 known plantdisease resistance (R) genes, we identified 2119 resistance gene homologs or analogs (RGAs) andverified that RGAs are not randomly distributed but tend to cluster in the rice genome. The RGAswere classified into 21 families according to their functional domain based on Hidden Markov model(HMM). By comparing the RGAs of japonica rice with the whole genomic sequence of indica rice, wefound 702 RGAs allelic between the two subspecies and revealed that 671 (95.6%) of them have lengthdifference (InDels) in their genomic sequences (including coding and non-coding regions) between thetwo subspecies, suggesting that RGAs are highly polymorphic between the two subspecies in rice. Wealso exploited 402 PCR-based and co-dominant candidate RGA markers by designing primer pairs on theregions flanking the InDels and validating them via e-PCR. The length differences of the candidateRGA markers between the two subspecies are from 1 to 742 bp, with an average of 10.26 bp. Allrelated information of the RGAs is available from our web site(http:∥ibi.zju.edu.cn/RGAs/index.html).

关 键 词：基因组 R遗传因子 水稻 RGA 抵抗力基因 

分 类 号：S511[农业科学—作物学]