title: 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.
abstract: 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.
authors.affiliation: State Key Laboratory of Plant Genomics and National Plant Gene Research Centre, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Junjun
authors.initials: J
authors.lastname: Shang
authors.forename: Yong
authors.initials: Y
authors.lastname: Tao
authors.forename: Xuewei
authors.initials: X
authors.lastname: Chen
authors.forename: Yan
authors.initials: Y
authors.lastname: Zou
authors.forename: Cailin
authors.initials: C
authors.lastname: Lei
authors.forename: Jing
authors.initials: J
authors.lastname: Wang
authors.forename: Xiaobing
authors.initials: X
authors.lastname: Li
authors.forename: Xianfeng
authors.initials: X
authors.lastname: Zhao
authors.forename: Meijun
authors.initials: M
authors.lastname: Zhang
authors.forename: Zhike
authors.initials: Z
authors.lastname: Lu
authors.forename: Jichen
authors.initials: J
authors.lastname: Xu
authors.forename: Zhukuan
authors.initials: Z
authors.lastname: Cheng
authors.forename: Jianmin
authors.initials: J
authors.lastname: Wan
authors.forename: Lihuang
authors.initials: L
authors.lastname: Zhu
mesh_terms: D000483:Alleles; D001483:Base Sequence; D017343:Genes, Plant; D049810:Genetic Speciation; D018745:Genome, Plant / Q000235:genetics*; D008969:Molecular Sequence Data; D012275:Oryza / Q000235:genetics*; D011544:Pseudogenes