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Association between molecular markers and blast resistance in an advanced backcross population of rice

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An advanced backcross population consisting of 80 BC3F3 lines derived from rice vars. Vandana/Moroberekan was analysed for blast resistance and genotyped with 50 candidate genes and 23 simple sequence repeat (SSR) markers. Six candidate defence response genes [thaumatin, three nucleotide-binding site-leucine-rich repeat sequences from maize and two resistance gene analogue (RGA) markers] and one SSR marker (RM21) were significantly associated with partial blast resistance in rice (P=0.01). These markers accounted for phenotypic variation ranging from 9.6% to 29.4% and contributed to 76% of the total variation of percentage diseased leaf area (DLA) observed under natural infection. Four candidate genes (oxalate oxidase, 14-3-3 protein and two RGA markers) and four SSR markers (RM21, RM168, RM215 and RM250) were significantly associated with resistance to a single pathogen isolate, PO6-6. Among these, two markers were for DLA, five for lesion number and one for lesion size. These markers accounted for 9.1–28.7% of the phenotypic variation. A moderate correlation (r=0.48, P<0.01) was found between the level of partial resistance measured in the greenhouse and that measured under natural conditions. Analysis of BC3F4 progeny using genotypes of BC3F3 confirmed the phenotypic contribution of these markers. Cluster analysis of DNA profiles showed that the BC3 population was genetically similar (>85%) to the recurrent parent Vandana. Although no obvious relationship between DNA profiles and resistant phenotypes was observed, three lines (VM19, VM46 and VM76) in a cluster with high similarity to Vandana (89–96%) expressed a high level of partial blast resistance in the field. Analysis of disease progress in the field confirmed the performance of selected lines based on greenhouse and nursery analyses. The advanced backcross progeny with resistance phenotypes tagged by markers will be useful for accumulating blast resistance in upland rice.

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References

  • Bai J, Pennill LA, Ning J, Lee SW, Ramalingam J, Webb CA, Zhao B, Sun Q, Nelson JC, Leach JE, Hulbert SH (2002) Diversity in nucleotide binding site-leucine-rich repeat genes in cereals. Genome Res 12:1871–1884

    Article  CAS  PubMed  Google Scholar 

  • Bent AF (1996) Plant disease resistance genes: function meets structure. Plant Cell 8:1757–1771

    CAS  Google Scholar 

  • Bonman JM, Vergael de Dios TI, Khin MM (1986) Physiological specialization of Pyricularia oryzae in the Philippines. Plant Dis 70:767–769

    Google Scholar 

  • Byrne PF, McMullen MD, Snook ME, Musket TA, Theuri JM, Widstrom NW, Wiseman BR, Coe EH (1996) Quantitative trait loci and metabolic pathways: genetic control of the concentration of maysin, a corn earworm resistance factor, in maize silks. Proc Natl Acad Sci USA 93:8820–8825

    CAS  PubMed  Google Scholar 

  • Cai D, Kleine M, Kifle S, Harloff H-J, Sandal NN, Marcker KA, Klein-Lankhorst RM, Salentijn EMA, Lange W, Stiekema WJ, Wyss U, Grundler FMW, Jung C (1997) Positional cloning of a gene for nematode resistance in sugar beet. Science 275:832–834

    CAS  PubMed  Google Scholar 

  • Causse MA, Fulton TM, Cho YG, Ahn SN, Chunwongse J, Wu K, Xiao J, Yu Z, Ronald PC, Harrington SE, Second G, McCouch SR, Tanksley D (1994) Saturated molecular map of the rice genome based on an interspecific backcross population. Genetics 138:1251–1274

    CAS  PubMed  Google Scholar 

  • Chen DH, Wang GL, Ronald PC (1997) Location of the rice resistance locus Pi5 (t) in Moroberekan by AFLP bulk segregation analysis. Rice Genet Newsl 14:95–98

    Google Scholar 

  • Chen DH, Dela Vina M, Inulai T, Mackill DJ, Ronald PC, Nelson RJ (1999) Molecular mapping of the blast resistance gene, Pi44(t), in a line derived from a durably resistant rice cultivar. Theor Appl Genet 98:1046–1053

    Article  CAS  Google Scholar 

  • Chen X, Temnykh S, Xu Y, Cho YG, McCouch SR (1997) Development of a microsatellite framework map providing genome-wide coverage in rice (Oryza sativa L.). Theor Appl Genet 95:553–567

    Article  CAS  Google Scholar 

  • Chen XM, Line RF, Leung H (1998) Genome scanning for conserve motifs of disease resistance genes in rice, barley, and wheat using high-resolution electrophoresis. Theor Appl Genet 97:345–355

    Article  CAS  Google Scholar 

  • Doebley J, Stec A, Wendel J, Edwards M (1990) Genetic and morphological analysis of a maize-teosinte F2 population: Implications for the origin of maize. Proc Natl Acad Sci USA 87:9888-9892

    CAS  PubMed  Google Scholar 

  • Faris JD, Li WL, Liu DJ, Chen PD, Gill BS (1999) Candidate gene analysis of quantitative disease resistance in wheat. Theor Appl Genet 98:219–225

    CAS  Google Scholar 

  • Huang JK, Wen L, Swegle M, Tran HC, Thin TH, Naylor HM, Muthukrishnan S, Reeck GR (1991) Nucleotide sequence of a rice genomic clone that encodes a class I endochitinase. Plant Mol Biol 16:479–480

    CAS  PubMed  Google Scholar 

  • International Rice Research Institute (1996) Standard evaluation system for rice, 4th edn. International Rice Research Institute, Manila, Philippines

  • Lamb C, Dixon RA (1997) The oxidative burst in plant disease resistance. Annu Rev Plant Physiol Plant Mol Biol 48:251–275

    CAS  Google Scholar 

  • Li ZK, Pinson SRM, Park WD, Paterson AH, Stansel JW (1997) Epistasis for three grain yield components in rice (Oryza sativa L.). Genetics 145:453–465

    CAS  PubMed  Google Scholar 

  • Li ZK, Luo LJ, Mei HW, Paterson AH, Zhao XH, Zhong DB, Wang YP, Yu XQ, Zhu L, Tabien A, Stansel JW, Ying CS (1999) A “defeated” rice resistance gene acts as a QTL against a virulent strain of Xanthomonas oryzae pv. oryzae. Mol Gen Genet 261:58–63

    CAS  PubMed  Google Scholar 

  • Martin GB, Brommonschenkel SH, Chunwongse J, Frary A, Ganal MW, Spivey R, Wu T, Earle ED, Tanksley SD (1993) Map-based cloning of a protein kinase gene conferring disease resistance in tomato. Science 262:1432–1435

    CAS  PubMed  Google Scholar 

  • Meyers BC, Kozik A, Griego A, Kuang H, Michelmore RW (2003) Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis . Plant Cell 15:809–834

    Article  CAS  PubMed  Google Scholar 

  • Murray MG, Thompson WF (1980) Rapid isolation of high-molecular-weight plant DNA. Nucleic Acids Res 8:4321–4325

    CAS  PubMed  Google Scholar 

  • Naqvi NI, Bonman JM, Mackill DJ, Nelson RJ, Chatto BB (1995) Identification of RAPD markers linked to a major blast resistance gene in rice. Mol Breed 1:341–348

    CAS  Google Scholar 

  • Panaud O, Chen X, McCouch SR (1996) Development of microsatellite markers and characterization of simple sequence length polymorphism (SSR) in rice (Oryza sativa L.). Mol Gen Genet 252:597–607

    Article  CAS  PubMed  Google Scholar 

  • Ramalingam J, Vera Cruz CM, Kukreja K, Chittoor JM, Wu J-L, Lee SW, Baraoidan MR, George ML, Cohen M, Hulbert S, Leach JE, Leung H (2003) Candidate resistance genes from rice, barley, and maize and their association with qualitative and quantitative resistance in rice. Mol Plant Microbe Interact 16:14–24

    CAS  PubMed  Google Scholar 

  • Rohlf FJ (1993) ntsys-pc: numerical taxonomy and multivariate analysis system, version 1.80. Exater Software, New York

  • Sambrook J, Fritch EF, Maniatis T (1989) Molecular cloning: a laboratory manual, 2nd edn. Cold Spring Harbor Laboratory Press, New York

    Google Scholar 

  • SAS Institute (1989) SAS/STAT user’s guide, version 6, 4th edn, vol 1 and 2. SAS Institute, Raleigh, N.C.

  • Schaffrath U, Zabbai F, Dudler R (2000) Characterization of RCI-1, a chloroplastic rice lipoxygenase whose synthesis is induced by chemical plant resistance activators. Eur J Biochem 267:5935–5942

    Article  CAS  PubMed  Google Scholar 

  • Shen KA, Meyers BC, Islam-Faridi MN, Chin DB, Stelly DM, Michelmore RW (1998) Resistance gene candidates identified by PCR with degenerate oligonucleotide primers map to clusters of resistance genes in lettuce. Mol Plant Microbe Interact 11:815–823

    CAS  PubMed  Google Scholar 

  • Shi ZX, Chen XM, Line RF, Leung H, Wellings CR (2001) Development of resistance gene analog polymorphism markers for the Yr9 gene resistance to wheat stripe rust. Genome 44:509–516

    CAS  PubMed  Google Scholar 

  • Song WY, Wang GL, Chen LL, Kim HS, Pi LY, Holsten T, Gardner J, Wang J, Zhai WX, Zhu LH, Fauquet C, Ronald P (1995) A receptor kinase-like protein encoded by the rice disease resistance gene, Xa21. Science 270:1804–1806

    CAS  PubMed  Google Scholar 

  • Tanksley SD, Nelson JC (1996) Advanced backcross QTL analysis: a method for the simultaneous discovery and transfer of valuable QTLs from unadapted germplasm into elite breeding lines. Theor Appl Genet 92:191–203

    Article  Google Scholar 

  • Toojinda T, Broers LH, Chen XM, Hayes PM, Kleinhofs A, Korte J, Kudrna D, Leung H, Line RF, Powell W, Ramsay L, Vivar H, Waugh R (2000) Mapping quantitative and qualitative disease resistance genes in a doubled haploid population of barley (Hordeum vulgare). Theor Appl Genet 101:580–589

    CAS  Google Scholar 

  • Veldboom LR, Lee M, Woodman WL (1994) Molecular marker-facilitated studies in an elite maize population: I. Linkage analysis and determination of QTL for morphological traits. Theor Appl Genet 88:7–16

    CAS  Google Scholar 

  • Wang G-L, Mackill DJ, Bonman JM, McCouch SR, Champoux MC, Nelson RJ (1994) RFLP mapping of genes conferring complete and partial resistance to blast in a durably resistant rice cultivar. Genetics 136:1421–1434

    CAS  PubMed  Google Scholar 

  • Wang G-L, Ruan D-L, Song W-Y, Sideris S, Chen L, Pi L-Y, Zhang S, Zhang Z, Fauquet C, Gaut BS, Whalen MC, Ronald PC (1998) Xa21D encodes a receptor-like molecule with a leucine-rich repeat domain that determines race-specific recognition and is subject to adaptive evolution. Plant Cell 10:765–779

    CAS  PubMed  Google Scholar 

  • Wang Z-X, Yano M, Yamanouch U, Iwamoto M, Monna L, Hayasaka H, Katayose Y, Sasaki T (1999) The Pib gene for rice blast resistance belongs to the nucleotide binding and leucine-rich repeat class of plant disease resistance genes. Plant J 19:55–64

    Article  PubMed  Google Scholar 

  • Yu SB, Li JX, Tan FY, Gao YJ, Li XH, Zhang QF, Saghai Maroof MA (1997) Importance of epstasis as the genetic basis of heterosis in an elite rice hybrid. Proc Natl Acad Sci USA 94:9226–9231

    CAS  PubMed  Google Scholar 

  • Zhang Z, Collings DB, Thordal-Christensen H (1995) Germin-like oxalate oxidase, a H2O2-producing enzyme, accumulates in barley attacked by the powdery mildew fungus. Plant J 8:139–145

    Article  CAS  Google Scholar 

  • Zhuang J-Y, Wu J-L, Chai R-Y, Fan Y-Y, Jin M-Z, Leung H, Zheng K-L (1998) Rapid identification of resistance gene analogs linked to two blast resistance genes in rice. Rice Genet Newsl 15:125–127

    Google Scholar 

  • Zhuang J-Y, Ma W-B, WuJ-L, Chai R-Y, Lu J, Fan Y-Y, Jin M-Z, Leung H, Zheng K-L (2002a) Mapping of leaf and neck blast resistance genes with resistance gene analog, RAPD and RFLP in rice. Euphytica 128:363–370

    Article  CAS  Google Scholar 

  • Zhuang J-Y, Fan Y-Y, Rao Z-M, Wu J-L, Xia Y-W, Zheng K-L (2002b) Analysis on additive effects and additive-by-additive epistatic effects of QTLs for yield traits in a recombinant inbred line population of rice. Theor Appl Genet 105:1137–1145

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

We thank many colleagues who provided the defence genes; Nollie Vera Cruz for helpful discussion, Noel Salac and Abe Ona for technical assistance, and Violeta Bartolome for help on statistical analysis. This work was supported in part by an IRRI research scholarship (J. Wu) and by the Asian Rice Biotechnology Network sponsored by the Asian Development Bank.

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Authors and Affiliations

  1. National Center for Rice Improvement, China National Rice Research Institute, 310006, Hangzhou, China

    J.-L. Wu & K.-L. Zheng

  2. Central Rainfed Upland Rice Research Station, 825 301, Hazaribag, Jharkhand, India

    P. K. Sinha & M. Variar

  3. Department of Plant Pathology, Kansas State University, Manhattan, KS 66506-5502, USA

    J. E. Leach

  4. CIRAD, Biotrop, Avenue Agropolis, 34398, Montpellier Cedex 5, France

    B. Courtois

  5. Entomology and Plant Pathology Division, International Rice Research Institute, DAPO P.O. Box 7777, Metro-Manila, Philippines

    J.-L. Wu & H. Leung

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  1. J.-L. Wu
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  2. P. K. Sinha
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  4. K.-L. Zheng
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Correspondence to H. Leung.

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Communicated by G. Wenzel

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Wu, JL., Sinha, P.K., Variar, M. et al. Association between molecular markers and blast resistance in an advanced backcross population of rice. Theor Appl Genet 108, 1024–1032 (2004). https://doi.org/10.1007/s00122-003-1528-1

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