Development of PCR-based SNP markers for rice blast resistance genes at the Piz locus

Hayashi, Keiko; Hashimoto, Noriaki; Daigen, Masaaki; Ashikawa, Ikuo

doi:10.1007/s00122-003-1553-0

Cited by 280 publications

(171 citation statements)

References 26 publications

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“…S2) (27). The T1 or T2 generations of transgenic lines were used to evaluate blast resistance (28). Seeds from the T1 or T2 plants were tested in three independent replicates of a plate consisting of a 4 × 8 grid of pots, in which each pot contained approximately 10 seedlings of a given transformed line.…”

Section: Methodsmentioning

confidence: 99%

Rapidly evolving R genes in diverse grass species confer resistance to rice blast disease

Yang

Zhang

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

125

109

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We show that the genomes of maize, sorghum, and brachypodium contain genes that, when transformed into rice, confer resistance to rice blast disease. The genes are resistance genes (R genes) that encode proteins with nucleotide-binding site (NBS) and leucinerich repeat (LRR) domains (NBS-LRR proteins). By using criteria associated with rapid molecular evolution, we identified three rapidly evolving R-gene families in these species as well as in rice, and transformed a randomly chosen subset of these genes into rice strains known to be sensitive to rice blast disease caused by the fungus Magnaporthe oryzae. The transformed strains were then tested for sensitivity or resistance to 12 diverse strains of M. oryzae. A total of 15 functional blast R genes were identified among 60 NBS-LRR genes cloned from maize, sorghum, and brachypodium; and 13 blast R genes were obtained from 20 NBS-LRR paralogs in rice. These results show that abundant blast R genes occur not only within species but also among species, and that the R genes in the same rapidly evolving gene family can exhibit an effector response that confers resistance to rapidly evolving fungal pathogens. Neither conventional evolutionary conservation nor conventional evolutionary convergence supplies a satisfactory explanation of our findings. We suggest a unique mechanism termed "constrained divergence," in which R genes and pathogen effectors can follow only limited evolutionary pathways to increase fitness. Our results open avenues for R-gene identification that will help to elucidate R-gene vs. effector mechanisms and may yield new sources of durable pathogen resistance.

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Section: Methodsmentioning

confidence: 99%

Rapidly evolving R genes in diverse grass species confer resistance to rice blast disease

Yang

Zhang

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

125

109

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“…For example, at the Piz locus on chromosome 6, at least four genes have been identified (Liu et al 2002;Hayashi et al 2004) and three of them, Pi9, Pi2, and Pizt, have been cloned Zhou et al 2006). Structural comparisons of these cloned genes have provided information on the DNA region within these genes responsible for determining their distinct resistance specificities.…”

mentioning

confidence: 99%

Two Adjacent Nucleotide-Binding Site–Leucine-Rich Repeat Class Genes Are Required to Confer Pikm-Specific Rice Blast Resistance

Ashikawa

Hayashi

Yamane³

et al. 2008

Genetics

361

275

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The rice blast resistance gene Pikm was cloned by a map-based cloning strategy. High-resolution genetic mapping and sequencing of the gene region in the Pikm-containing cultivar Tsuyuake narrowed down the candidate region to a 131-kb genomic interval. Sequence analysis predicted two adjacently arranged resistance-like genes, Pikm1-TS and Pikm2-TS, within this candidate region. These genes encoded proteins with a nucleotide-binding site (NBS) and leucine-rich repeats (LRRs) and were considered the most probable candidates for Pikm. However, genetic complementation analysis of transgenic lines individually carrying these two genes negated the possibility that either Pikm1-TS or Pikm2-TS alone was Pikm. Instead, it was revealed that transgenic lines carrying both of these genes expressed blast resistance. The results of the complementation analysis and an evaluation of the resistance specificity of the transgenic lines to blast isolates demonstrated that Pikm-specific resistance is conferred by cooperation of Pikm1-TS and Pikm2-TS. Although these two genes are not homologous with each other, they both contain all the conserved motifs necessary for an NBS-LRR class gene to function independently as a resistance gene.

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“…It is a relatively new PCR-based method for the identification of previously known allelic mutations in the nucleic acid sequence. The method is based on the introduction of artificial mutations into the PCR-primer binding regions of the amplified DNA in an allele-specific manner, using allele-specific primers with mutagenic positions at different distances from the 3´ end, based on previous studies (21)(22)(23). This mismatch maximized the difference between the rate of substrate formation for the loci of the target alleles, and that of the non-target alleles.…”

Section: Discussionmentioning

confidence: 99%

Multiplex Mutagenically Separated Polymerase Chain Reaction Assay for Rapid Detection of Human Mitochondrial DNA Variations in Coding Area

Peng

Zhang

et al. 2008

Croat Med J

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Single nucleotide polymorphisms (SNPs) in mitochondrial DNA (mtDNA) are widely used as markers in population genetic studies and forensic analyses. Mitochondrial DNA is present in at least hundreds of copies in each cell (1), which is an additional advantage when small or degraded samples are the only source of DNA available for analysis (2-4). For identification of individuals in forensics, nucleotide sequencing of the two hypervariable regions (HVR) I Multiplex Mutagenically Separated Polymerase Chain Reaction Assay for Rapid Detection of Human Mitochondrial DNA Variations in Coding AreaRecently, it has been recognized that information in the mitochondrial DNA (mtDNA) coding region can provide additional forensic discrimination with respect to the standard typing of the D-loop region, increasing the forensic power of mtDNA testing, which is sometimes rather limited. In the present study, we simultaneously typed ten single nucleotide polymorphisms (SNP) in the coding region by use of mutagenically separated polymerase chain reaction (MS-PCR) in the Chinese Chengdu population. This technique, in which different-size allele-specific primers were used, specifically amplified both alleles of mtDNA in the same reaction. Subsequent gel electrophoresis showed ten of the allelic products of different loci. Using multiplex MS-PCR, 30 primers were added simultaneously into one reaction tube to identify ten SNPs. The mtDNA variations of 160 individuals from the Chinese Chengdu population were examined and classified into 18 haplotypes. The multiplex MS-PCR method is suitable for large-scale screening studies of mtDNA variability because it is both rapid and economical.

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Development of PCR-based SNP markers for rice blast resistance genes at the Piz locus

Cited by 280 publications

References 26 publications

Rapidly evolving R genes in diverse grass species confer resistance to rice blast disease

Rapidly evolving R genes in diverse grass species confer resistance to rice blast disease

Two Adjacent Nucleotide-Binding Site–Leucine-Rich Repeat Class Genes Are Required to Confer Pikm-Specific Rice Blast Resistance

Multiplex Mutagenically Separated Polymerase Chain Reaction Assay for Rapid Detection of Human Mitochondrial DNA Variations in Coding Area

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