Genome‐wide association study identifies an NLR gene that confers partial resistance to Magnaporthe oryzae in rice

Summary Because of the frequent breakdown of major resistance (R) genes, identification of new partial R genes against rice blast disease is an important goal of rice breeding. In this study, we used a core collection of the Rice Diversity Panel II (C‐RDP‐II), which contains 584 rice accessions and...

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Published in:Plant biotechnology journal 2020-06, Vol.18 (6), p.1376-1383
Main Authors: Liu, Ming‐Hao, Kang, Houxiang, Xu, Yucheng, Peng, Ye, Wang, Dan, Gao, Lijun, Wang, Xuli, Ning, Yuese, Wu, Jun, Liu, Wende, Li, Chengyun, Liu, Bin, Wang, Guo‐Liang
Format: Article
Language:English
Subjects:
Binding sites
Chromosome 4
Chromosomes
Cloning
CRISPR
Cultivars
Genes
Genetic engineering
Genome-wide association studies
Genomes
genome‐wide association study
Leucine
Magnaporthe oryzae
Nucleotides
partial resistance gene
pathogenic diversification
Phylogenetics
PiPR1
Plant breeding
Polymorphism
Population
Quantitative trait loci
Rice blast
Single-nucleotide polymorphism
Strains (organisms)
Transgenic plants
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Summary:Summary Because of the frequent breakdown of major resistance (R) genes, identification of new partial R genes against rice blast disease is an important goal of rice breeding. In this study, we used a core collection of the Rice Diversity Panel II (C‐RDP‐II), which contains 584 rice accessions and are genotyped with 700 000 single‐nucleotide polymorphism (SNP) markers. The C‐RDP‐II accessions were inoculated with three blast strains collected from different rice‐growing regions in China. Genome‐wide association study identified 27 loci associated with rice blast resistance (LABRs). Among them, 22 LABRs were not associated with any known blast R genes or QTLs. Interestingly, a nucleotide‐binding site leucine‐rich repeat (NLR) gene cluster exists in the LABR12 region on chromosome 4. One of the NLR genes is highly conserved in multiple partially resistant rice cultivars, and its expression is significantly up‐regulated at the early stages of rice blast infection. Knockout of this gene via CRISPR‐Cas9 in transgenic plants partially reduced blast resistance to four blast strains. The identification of this new non‐strain specific partial R gene, tentatively named rice blast Partial Resistance gene 1 (PiPR1), provides genetic material that will be useful for understanding the partial resistance mechanism and for breeding durably resistant cultivars against blast disease of rice.
ISSN:1467-7644
1467-7652
DOI:10.1111/pbi.13300