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The in Silico Map-Based Cloning of Pi36, a Rice Coiled-Coil–Nucleotide-Binding Site–Leucine-Rich Repeat Gene That Confers Race-Specific Resistance to the Blast Fungus

Laboratory of Plant Resistasnce and Genetics, College of Resources and Environmental Sciences, South China Agricultural University, Guangzhou 510642, China.
Genetics (Impact Factor: 4.87). 09/2007; 176(4):2541-9. DOI: 10.1534/genetics.107.075465
Source: PubMed

ABSTRACT The indica rice variety Kasalath carries Pi36, a gene that determines resistance to Chinese isolates of rice blast and that has been located to a 17-kb interval on chromosome 8. The genomic sequence of the reference japonica variety Nipponbare was used for an in silico prediction of the resistance (R) gene content of the interval and hence for the identification of candidate gene(s) for Pi36. Three such sequences, which all had both a nucleotide-binding site and a leucine-rich repeat motif, were present. The three candidate genes were amplified from the genomic DNA of a number of varieties by long-range PCR, and the resulting amplicons were inserted into pCAMBIA1300 and/or pYLTAC27 vectors to determine sequence polymorphisms correlated to the resistance phenotype and to perform transgenic complementation tests. Constructs containing each candidate gene were transformed into the blast-susceptible variety Q1063, which allowed the identification of Pi36-3 as the functional gene, with the other two candidates being probable pseudogenes. The Pi36-encoded protein is composed of 1056 amino acids, with a single substitution event (Asp to Ser) at residue 590 associated with the resistant phenotype. Pi36 is a single-copy gene in rice and is more closely related to the barley powdery mildew resistance genes Mla1 and Mla6 than to the rice blast R genes Pita, Pib, Pi9, and Piz-t. An RT-PCR analysis showed that Pi36 is constitutively expressed in Kasalath.

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    • "However, choosing the right resistance genes to be used in the breeding process can be a daunting task, since not all genes are equally effective due to genetic variation in the pathogen in the target area. Thanks to genetic analysis using molecular markers, the number of known blast resistance genes has rapidly grown in the last decade: at present , more than 50 genes have been identified and 8 of these have been cloned [7] [8]. Except for the Pi21 gene, most of the resistant genes are dominant [9]. "
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    • "4); Pi-9 (Qu et al., 2006), Pi2 (Zhou et al., 2006), Piz-t (Zhou et al., 2006), Pid2 (Chen et al., 2006), Pid3 (Shang et al., 2009); Pi25 (Chen et al., 2011) (Chr. 6); Pi-36 (Liu et al., 2007) (Chr. 8); Pi5 (Lee et al., 2009) (Chr. "
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    ABSTRACT: Allele mining is a promising way to dissect naturally occurring allelic variants of candidate genes with essential agronomic qualities. With the identification, isolation and characterisation of blast resistance genes in rice, it is now possible to dissect the actual allelic variants of these genes within an array of rice cultivars via allele mining. Multiple alleles from the complex locus serve as a reservoir of variation to generate functional genes. The routine sequence exchange is one of the main mechanisms of R gene evolution and development. Allele mining for resistance genes can be an important method to identify additional resistance alleles and new haplotypes along with the development of allele-specific markers for use in marker-assisted selection. Allele mining can be visualised as a vital link between effective utilisation of genetic and genomic resources in genomics-driven modern plant breeding. This review studies the actual concepts and potential of mining approaches for the discovery of alleles and their utilisation for blast resistance genes in rice. The details provided here will be important to provide the rice breeder with a worthwhile introduction to allele mining and its methodology for breakthrough discovery of fresh alleles hidden in hereditary diversity, which is vital for crop improvement.
    Current issues in molecular biology 02/2015; 17:57-74. · 6.00 Impact Factor
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    • "4); Pi-9 (Qu et al., 2006), Pi2 (Zhou et al., 2006), Piz-t (Zhou et al., 2006), Pid2 (Chen et al., 2006), Pid3 (Shang et al., 2009); Pi25 (Chen et al., 2011) (Chr. 6); Pi-36 (Liu et al., 2007) (Chr. 8); Pi5 (Lee et al., 2009) (Chr. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Allele mining is a promising way to dissect naturally occurring allelic variants of candidate genes with essential agronomic qualities. With the identification, isolation and characterisation of blast resistance genes in rice, it is now possible to dissect the actual allelic variants of these genes within an array of rice cultivars via allele mining. Multiple alleles from the complex locus serve as a reservoir of variation to generate functional genes. The routine sequence exchange is one of the main mechanisms of R gene evolution and development. Allele mining for resistance genes can be an important method to identify additional resistance alleles and new haplotypes along with the development of allele-specific markers for use in marker-assisted selection. Allele mining can be visualised as a vital link between effective utilisation of genetic and genomic resources in genomics-driven modern plant breeding. This review studies the actual concepts and potential of mining approaches for the discovery of alleles and their utilisation for blast resistance genes in rice. The details provided here will be important to provide the rice breeder with a worthwhile introduction to allele mining and its methodology for breakthrough discovery of fresh alleles hidden in hereditary diversity, which is vital for crop improvement.
    Current issues in molecular biology 01/2015; 17:57-74. · 6.00 Impact Factor
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