Identification of a New Rice Blast Resistance Gene, Pid3, by Genomewide Comparison of Paired Nucleotide-Binding Site–Leucine-Rich Repeat Genes and Their Pseudogene Alleles Between the Two Sequenced Rice Genomes

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Junjun Shang, Yong Tao, Xuewei Chen, Yan Zou, Cailin Lei, Jing Wang, Xiaobing Li, Xianfeng Zhao, Meijun Zhang, Zhike Lu, Jichen Xu, Zhukuan Cheng, Jianmin Wan, Lihuang Zhu
Genetics, 2009, 182(4): 1303-1311  DOI: 10.1534/genetics.109.102871;      追溯原文......本站官方QQ群:62473826

Rice blast, caused by Magnaporthe oryzae, is one of the most devastating diseases. The two major subspecies of Asian cultivated rice (Oryza sativa L.), indica and japonica, have shown obvious differences in rice blast resistance, but the genomic basis that underlies the difference is not clear. We performed a genomewide comparison of the major class of resistant gene family, the nucleotide-binding site–leucine-rich repeat (NBS–LRR) gene family, between 93-11 (indica) and Nipponbare (japonica) with a focus on their pseudogene members. We found great differences in either constitution or distribution of pseudogenes between the two genomes. According to this comparison, we designed the PCR-based molecular markers specific to the Nipponbare NBS–LRR pseudogene alleles and used them as cosegregation markers for blast susceptibility in a segregation population from a cross between a rice blast-resistant indica variety and a susceptible japonica variety. Through this approach, we identified a new blast resistance gene, Pid3, in the indica variety, Digu. The allelic Pid3 loci in most of the tested japonica varieties were identified as pseudogenes due to a nonsense mutation at the nucleotide position 2208 starting from the translation initiation site. However, this mutation was not found in any of the tested indica varieties, African cultivated rice varieties, or AA genome-containing wild rice species. These results suggest that the pseudogenization of Pid3 in japonica occurred after the divergence of indica and japonica.

通过2个已知基因组序列水稻的全基因组核苷酸结合位点和富含亮氨酸重复基因与其等位假基因的成对比对分离一个新的稻瘟病抗性基因Pid3

由Mgnaporthe oryzae引起的稻瘟病是最具毁灭性的植物病害之一。尽管亚洲栽培稻(Oryza sativa L.)的两个亚种,籼稻(indica)和粳稻(japonica)对稻瘟病表现出的抗性截然不同,但是造成这种差异的基因组基础却并不清楚。作者在全基因范围内对93-11(籼稻)和日本晴(粳稻)中主要的一类抗病基因家族——核苷酸结合位点和富含亮氨酸重复(NBS-LRR)基因家族中的假基因成员进行了比对。作者发现在这两个基因组上假基因的分布和结构都存在巨大的差异。根据全基因组比对结果,作者设计了大量基于PCR的分子标记,用以特异性扩增日本晴的的NBS-LRR假基因成员。这些标记与稻瘟病感病性状是共分离的,因而可以用来对由抗病籼稻和感病粳稻为父母本获得的后代分离群体的抗感情况进行鉴定。通过这种策略,我们在籼稻品种地谷中分离了一个新的抗稻瘟病基因Pid3。在大部分被测的粳稻品种中Pid3基因转录起始位点开始的第2208位核苷酸处的无义突变导致了粳稻中的Pid3基因成为了假基因。同时,这个位点的突变却没有在籼稻、非洲栽培稻或是AA组的野生稻中被检测到。这些结果都说明粳稻品种Pid3假基因化是发生在籼粳分化以后的。
结果:93-11与日本晴间全基因组NBS-LRR基因比对 利用NBS-LRR假基因为分子标记鉴定一个未知的抗性基因位点 Pid3基因的克隆及功能研究 比较籼稻、粳稻和野生稻中Pid3基因无义突变位点


基因列表
  稻瘟病抗性基因 Pi25; Pid3
  稻瘟病抗性基因 Pi-d3