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

机译：水稻R基因全基因组鉴定和候选RGA标记的开发

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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 analogs (RGAs) and verified that RGAs are not randomly distributed 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 comparing 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).
机译：通过使用45种已知的植物抗病性（R）基因扫描粳稻的整个基因组序列，我们鉴定了2119个抗病基因同源物或类似物（RGA），并验证了RGA不是随机分布的，而是倾向于在水稻基因组中聚集。根据隐马尔可夫模型（HMM），RGA根据其功能域分为21个家族。通过将粳稻的RGA与in稻的整个基因组序列进行比较，我们发现两个亚种之间有702个RGA等位基因，发现其中的671个（95.6％）在其基因组序列（包括编码序列和非编码序列）中具有长度差异（InDels）。两个亚种之间的编码区），表明RGA在水稻两个亚种之间具有高度多态性。我们还通过在InDel两侧的区域上设计引物对并通过e-PCR验证了它们，开发了402个基于PCR的共显性候选RGA标记。两个亚种之间候选RGA标记的长度差异为1至742 bp，平均为10.26 bp。有关RGA的所有相关信息，请访问我们的网站（http：∥ibi.zju.edu.cn/ RGAs / index.html）。

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