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Identification of the blast resistance gene Pit in rice cultivars using functional markers

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Abstract

DNA markers that allow for identification of resistance genes in rice germplasm have a great advantage in resistance breeding because they can assess the existence of the genes without laborious inoculation tests. Functional markers (FMs), which are designed from functional polymorphisms within the sequence of genes, are unaffected by nonfunctional allelic variation and make it possible to identify an individual gene. We previously showed that the resistance function of the rice blast resistance gene Pit in a resistant cultivar, K59, was mainly acquired by up-regulated promoter activity through the insertion of a long terminal repeat (LTR) retrotransposon upstream of Pit. Here, we developed PCR-based DNA markers derived from the LTR-retrotransposon sequence and used these markers to screen worldwide accessions of rice germplasm. We identified 5 cultivars with the LTR-retrotransposon insertion out of 68 rice accessions. The sequence and expression pattern of Pit in the five cultivars were the same as those in K59 and all showed Pit-mediated blast resistance. The results suggest that the functional Pit identified using the markers was derived from a common progenitor. Additionally, comparison of the Pit coding sequences between K59 and susceptible cultivars revealed that one nucleotide polymorphism, which caused an amino acid substitution, offered another target for a FM. These results indicate that our DNA markers should enhance prediction of Pit function and be applicable to a range of rice varieties/landraces cultivated in various regions worldwide and belonging to the temperate japonica, tropical japonica, and indica groups.

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References

  • Andersen JR, Lübberstedt T (2003) Functional markers in plants. Trends Plant Sci 8:554–560

    Article  CAS  PubMed  Google Scholar 

  • Babujee L, Gnanamanickam SS (2000) Molecular tools for characterization of rice blast pathogen (Magnaporthe grisea) population and molecular marker-assisted breeding for disease resistance. Curr Sci 78:248–257

    CAS  Google Scholar 

  • Bonman JM, Khush GS, Nelson RJ (1992) Breeding rice for resistance to pests. Annu Rev Phytopathol 30:507–528

    Article  Google Scholar 

  • Bryan GT, Wu KS, Farrall L, Jia Y, Hershey HP, McAdams SA, Faulk KN, Donaldson GK, Tarchini R, Valent B (2000) A single amino acid difference distinguishes resistant and susceptible alleles of the rice blast resistance gene Pi-ta. Plant cell 12:2033–2046

    Article  CAS  PubMed  Google Scholar 

  • Collard BC, Vera Cruz CM, McNally KL, Virk PS, Mackill DJ (2008) Rice molecular breeding laboratories in the genomics era: current status and future considerations. Int J Plant Genomics 2008:524847. doi:10.1155/2008/524847

    PubMed  Google Scholar 

  • DeYoung BJ, Innes RW (2006) Plant NBS-LRR proteins in pathogen sensing and host defense. Nat Immunol 7:1243–1249

    Article  CAS  PubMed  Google Scholar 

  • Ebron LA, Fukuta Y, Imbe T, Kato H, Yanoria JMT, Tsunematsu H, Khush GS, Yokoo M (2004) Estimation of genes in blast resistance in elite indica-type rice (Oryza sativa L.) varieties-bred at the International Rice Research Institute. Breed Sci 54:381–387

    Article  CAS  Google Scholar 

  • Hayashi K, Yoshida H (2009) Refunctionalization of the ancient rice blast disease resistance gene Pit by the recruitment of a retrotransposon as a promoter. Plant J 57:413–425

    Article  CAS  PubMed  Google Scholar 

  • Hayashi K, Hashimoto N, Daigen M, Ashikawa I (2004) Development of PCR-based SNP markers for rice blast resistance genes at the Piz locus. Theor Appl Genet 108:1212–1220

    Article  CAS  PubMed  Google Scholar 

  • Hayashi K, Yoshida H, Ashikawa I (2006) Development of PCR-based allele-specific and InDel marker sets for nine rice blast resistance genes. Theor Appl Genet 113:251–260

    Article  CAS  PubMed  Google Scholar 

  • Hayashi N, Kobayashi N, Vera Cruz CM, Fukuta Y (2009) Protocols for the sampling of diseased specimens and evaluation of blast disease in rice. JIRCAS Work Rep 63:17–33

    Google Scholar 

  • Hittalmani S, Parco A, Mew TV, Zeigler RS, Huang N (2000) Fine mapping and DNA marker-assisted pyramiding of the three major genes for blast resistance in rice. Theor Appl Genet 100:1121–1128

    Article  CAS  Google Scholar 

  • Ingvardsen CR, Schejbel B, Lübberstedt T (2008) Functional markers in resistance breeding. In: Lüttge U, Beyschlag W, Murata J (eds) Progress in botany, vol 69. Springer, Berlin, pp 61–87

    Chapter  Google Scholar 

  • Iyer AS, McCouch SR (2004) The rice bacterial blight resistance gene xa5 encodes a novel form of disease resistance. Mol Plant Microbe Interact 17:1348–1354

    Article  CAS  PubMed  Google Scholar 

  • Iyer AS, McCouch SR (2007) Functional markers for xa5-mediated resistance in rice (Oryza sativa L.). Mol Breed 19:291–296

    Article  Google Scholar 

  • Jena KK, Mackill DJ (2008) Molecular markers and their use in marker-assisted selection in rice. Crop Sci 48:1266–1276

    Article  Google Scholar 

  • Jia Y, Wang Z, Singh P (2002) Development of dominant rice blast Pi-ta resistance gene markers. Crop Sci 42:2145–2149

    Article  CAS  Google Scholar 

  • Jia Y, Bryan GT, Farrall L, Valent B (2003) Natural variation at the Pi-ta rice blast resistance locus. Phytopathology 93:1452–1459

    Article  CAS  PubMed  Google Scholar 

  • Jia Y, Redus M, Wang Z, Rutger JN (2004) Development of a SNLP marker from the Pi-ta blast resistance gene by tri-primer PCR. Euphytica 138:97–105

    Article  CAS  Google Scholar 

  • Kiyosawa S (1972) The inheritance of blast resistance transferred from some indica varieties in rice. Bull Nat Inst Agric Sci D23:69–96

    Google Scholar 

  • Kiyosawa S (1984) Establishment of differential varieties for pathogenicity test of rice blast fungus. Rice Genet Newsl 1:95–97

    Google Scholar 

  • Kiyosawa S, Orimoto Y, He YK, Ling ZZ (1983) Estimation of genotypes for blast resistance of rice varieties by testing with differential varieties. Oryza 20:216–222

    Google Scholar 

  • Kiyosawa S, Mackill DJ, Bonman JM, Tanaka Y, Ling ZZ (1986) An attempt of classification of world’s rice varieties based on reaction pattern to blast fungus strains. Bull Nat Inst Agric Resour 2:13–39

    Google Scholar 

  • Kojima Y, Ebana K, Fukuoka S, Nagamine T, Kawase M (2005) Development of an RFLP-based rice diversity research set of germplasm. Breed Sci 55:431–440

    Article  CAS  Google Scholar 

  • Kumar A, Bennetzen JL (1999) Plant retrotransposons. Annu Rev Genet 33:479–532

    Article  CAS  PubMed  Google Scholar 

  • Meyers BC, Kaushik S, Nandety RS (2005) Evolving disease resistance genes. Curr Opin Plant Biol 8:129–134

    Article  CAS  PubMed  Google Scholar 

  • Michelmore RW, Meyers BC (1998) Clusters of resistance genes in plants evolve by divergent selection and a birth-and-death process. Genome Res 8:1113–1130

    CAS  PubMed  Google Scholar 

  • Monosi B, Wisser RJ, Pennill L, Hulbert SH (2004) Full-genome analysis of resistance gene homologues in rice. Theor Appl Genet 109:1434–1447

    Article  CAS  PubMed  Google Scholar 

  • Noda T, Hayashi N, Du PV, Dinh HD, Lai Van E (1999) Distribution of pathogenic races of rice blast fungus in Vietnam. Ann Phytopathol Soc Jpn 65:526–530

    Google Scholar 

  • Osterberg MK, Shavorskaya O, Lascoux M, Lagercrantz U (2002) Naturally occurring indel variation in the Brassica nigra COL1 gene is associated with variation in flowering time. Genetics 161:299–306

    CAS  PubMed  Google Scholar 

  • Pearce SR, Stuart-Rogers C, Knox MR, Kumar A, Ellis THN, Flavell AJ (1999) Rapid isolation of plant Ty1-copia group retrotransposon LTR sequences for molecular marker studies. Plant J 19:711–717

    Article  CAS  PubMed  Google Scholar 

  • Sweeney MT, Thomson MJ, Cho YG, Park YJ, Williamson SH, Bustamante CD, McCouch SR (2007) Global dissemination of a single mutation conferring white pericarp in rice. PLoS Genet 3:e133

    Article  PubMed  Google Scholar 

  • Thornsberry JM, Goodman MM, Doebley J, Kresovich S, Nielsen D, Buckler ES 4th (2001) Dwarf8 polymorphisms associate with variation in flowering time. Nat Genet 28:286–289

    Article  CAS  PubMed  Google Scholar 

  • Tommasini L, Yahiaoui N, Srichumpa P, Keller B (2006) Development of functional markers specific for seven Pm3 resistance alleles and their validation in the bread wheat gene pool. Theor Appl Genet 114:165–175

    Article  CAS  PubMed  Google Scholar 

  • Tsugane K, Maekawa M, Takagi K, Takahara H, Qian Q, Eun CH, Iida S (2006) An active DNA transposon nDart causing leaf variegation and mutable dwarfism and its related elements in rice. Plant J 45:46–57

    Article  CAS  PubMed  Google Scholar 

  • Wang Z, Jia Y, Rutger JN, Xia Y (2007) Rapid survey for presence of a blast resistance gene Pi-ta in rice cultivars using the dominant DNA markers derived from portions of the Pi-ta gene. Plant Breed 126:36–42

    Article  CAS  Google Scholar 

  • Yahiaoui N, Srichumpa P, Dudler R, Keller B (2004) Genome analysis at different ploidy levels allows cloning of the powdery mildew resistance gene Pm3b from hexaploid wheat. Plant J 37:528–538

    Article  CAS  PubMed  Google Scholar 

  • Yasuda N, Noguchi MT, Fujita Y (2008) Induced rice resistance to blast varies as a function of Magnaporthe grisea avirulence genes. Plant Dis 92:1144–1149

    Article  Google Scholar 

  • Zhou T, Wang Y, Chen JQ, Araki H, Jing Z, Jiang K, Shen J, Tian D (2004) Genome-wide identification of NBS genes in japonica rice reveals significant expansion of divergent non-TIR NBS-LRR genes. Mol Genet Genomics 271:402–415

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

We thank Dr. T. Ashizawa and Dr. T. Nakajima for providing M. oryzae strains, and staff of our lab for their generous support. This work was partially supported by a Grant-in-Aid for Young Scientists (B) from the Ministry of Education, Culture, Sports, Science and Technology of Japan (21780009 to K. H.).

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Authors and Affiliations

  1. National Agricultural Research Center, National Agriculture and Food Research Organization (NARO), 3-1-1 Kannondai, Tsukuba, 305-8666, Japan

    K. Hayashi, N. Yasuda, Y. Fujita & S. Koizumi

  2. National Agricultural Research Center, National Agriculture and Food Research Organization (NARO), 1-2-1 Inada, Joetsu, 943-0193, Japan

    H. Yoshida

  3. National Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-18 Kannondai, Tsukuba, 305-8518, Japan

    H. Yoshida

Authors
  1. K. Hayashi
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  2. N. Yasuda
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  3. Y. Fujita
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  4. S. Koizumi
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  5. H. Yoshida
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Corresponding author

Correspondence to K. Hayashi.

Additional information

Communicated by L. Xiong.

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Supplemental Fig. 1

DNA polymorphisms and the sequencing peak figures in the Pit coding region of K59, Senshou and Tadukan. Open box at the top shows the coding region of Pit. The structural signatures of Pit are shown in the upper region of the figure. The numbers of the upper parts in panels indicate the positions of nucleotide substitutions. A hyphen positioned at the 1284th nucleotide shows a deletion mutation. Arrows indicate the peak that occurred for nucleotide substitutions or deletion mutations (TIFF 6902 kb)

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Hayashi, K., Yasuda, N., Fujita, Y. et al. Identification of the blast resistance gene Pit in rice cultivars using functional markers. Theor Appl Genet 121, 1357–1367 (2010). https://doi.org/10.1007/s00122-010-1393-7

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  • DOI: https://doi.org/10.1007/s00122-010-1393-7

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