Candidate defense genes from rice, barley, and maize and their association with qualitative and quantitative resistance in rice.

Candidate genes involved in both recognition (resistance gene analogs [RGAs]) and general plant defense (putative defense response [DR]) were used as molecular markers to test for association with resistance in rice to blast, bacterial blight (BB), sheath blight, and brown plant-hopper (BPH). The 118 marker loci were either polymerase chain reaction-based RGA markers or restriction fragment length polymorphism (RFLP) markers that included RGAs or putative DR genes from rice, barley, and maize. The markers were placed on an existing RFLP map generated from a mapping population of 116 doubled haploid (DH) lines derived from a cross between an improved indica rice cultivar, IR64, and a traditional japonica cultivar, Azucena. Most of the RGAs and DR genes detected a single locus with variable copy number and mapped on different chromosomes. Clusters of RGAs were observed, most notably on chromosome 11 where many known blast and BB resistance genes and quantitative trait loci (QTL) for blast, BB, sheath blight, and BPH were located. Major resistance genes and QTL for blast and BB resistance located on different chromosomes were associated with several candidate genes. Six putative QTL for BB were located on chromosomes 2, 3, 5, 7, and 8 and nine QTL for BPH resistance were located to chromosomes 3, 4, 6, 11, and 12. The alleles of QTL for BPH resistance were mostly from IR64 and each explained between 11.3 and 20.6% of the phenotypic variance. The alleles for BB resistance were only from the Azucena parent and each explained at least 8.4% of the variation. Several candidate RGA and DR gene markers were associated with QTL from the pathogens and pest. Several RGAs were mapped to BB QTL. Dihydrofolate reductase thymidylate synthase co-localized with two BPH QTL associated with plant response to feeding and also to blast QTL. Blast QTL also were associated with aldose reductase, oxalate oxidase, JAMyb (a jasmonic acid-induced Myb transcription factor), and peroxidase markers. The frame map provides reference points to select candidate genes for cosegregation analysis using other mapping populations, isogenic lines, and mutants.

[1]  T. Pryor,et al.  Genetic and molecular characterization of the maize rp3 rust resistance locus. , 2002, Genetics.

[2]  R. Nelson,et al.  Plant defense genes associated with quantitative resistance to potato late blight in Solanum phureja x dihaploid S. tuberosum hybrids. , 2002, Molecular plant-microbe interactions : MPMI.

[3]  Huanming Yang,et al.  A Draft Sequence of the Rice Genome (Oryza sativa L. ssp. indica) , 2002, Science.

[4]  Elena Boyko,et al.  A high-density cytogenetic map of the Aegilops tauschii genome incorporating retrotransposons and defense-related genes: insights into cereal chromosome structure and function , 2002, Plant Molecular Biology.

[5]  J. Leach,et al.  Vascular defense responses in rice: peroxidase accumulation in xylem parenchyma cells and xylem wall thickening. , 2001, Molecular plant-microbe interactions : MPMI.

[6]  R. Dixon.  Natural products and plant disease resistance , 2001, Nature.

[7]  M. Vicente,et al.  Cloning and mapping of resistance gene homologues in melon , 2001 .

[8]  Haiying Liang,et al.  Increased Septoria musiva resistance in transgenic hybrid poplar leaves expressing a wheat oxalate oxidase gene , 2001, Plant Molecular Biology.

[9]  B. Kang,et al.  A candidate gene approach identified phytoene synthase as the locus for mature fruit color in red pepper (Capsicum spp.) , 2001, Theoretical and Applied Genetics.

[10]  R. Wing,et al.  Chromosome landing at the bacterial blight resistance gene Xa4 locus using a deep coverage rice BAC library , 2001, Molecular Genetics and Genomics.

[11]  T. Thorup,et al.  Candidate gene analysis of organ pigmentation loci in the Solanaceae. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[12]  W. Zhai,et al.  Mapping quantitative trait loci controlling sheath blight resistance in two rice cultivars (Oryza sativa L.) , 2000, Theoretical and Applied Genetics.

[13]  L. Walling,et al.  The Myriad Plant Responses to Herbivores , 2000, Journal of Plant Growth Regulation.

[14]  K. Devos,et al.  Genome Relationships: The Grass Model in Current Research , 2000, Plant Cell.

[15]  P. Thoquet,et al.  Inheritance of partial resistance against Colletotrichum lindemuthianum in Phaseolus vulgaris and co-localization of quantitative trait loci with genes involved in specific resistance. , 2000, Molecular plant-microbe interactions : MPMI.

[16]  R. Fluhr,et al.  Divergent Evolution of Plant NBS-LRR Resistance Gene Homologues in Dicot and Cereal Genomes , 2000, Journal of Molecular Evolution.

[17]  Lishuang Shen,et al.  Mapping QTLs associated with drought avoidance in upland rice , 2000, Molecular Breeding.

[18]  D. Robertson,et al.  Mapping and expression of a bifunctional thymidylate synthase, dihydrofolate reductase gene from maize , 1999, Plant Molecular Biology.

[19]  V. Lefebvre,et al.  Disease resistance gene analogs as candidates for QTLs involved in pepper-pathogen interactions. , 1999, Genome.

[20]  N. Moran,et al.  Calibrating bacterial evolution. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[21]  R. Mago,et al.  Resistance gene analogues from rice: cloning, sequencing and mapping , 1999, Theoretical and Applied Genetics.

[22]  A. Melchinger,et al.  High-resolution mapping of loci conferring resistance to sugarcane mosaic virus in maize using RFLP, SSR, and AFLP markers , 1999, Molecular and General Genetics MGG.

[23]  M. Yano,et al.  RFLP- and physical mapping of resistance gene homologues in rice (O. sativa) and Barley (H. vulgare) , 1999, Theoretical and Applied Genetics.

[24]  B. Gill,et al.  Candidate gene analysis of quantitative disease resistance in wheat , 1999, Theoretical and Applied Genetics.

[25]  J. Pech,et al.  Purification and characterization of a NADPH-dependent aldehyde reductase from mung bean that detoxifies eutypine, a toxin from Eutypa lata , 1999 .

[26]  M. Cohen,et al.  Detection and analysis of QTLs for resistance to the brown planthopper, Nilaparvata lugens, in a doubled-haploid rice population , 1998, Theoretical and Applied Genetics.

[27]  P. Vos,et al.  The tomato Mi-1 gene confers resistance to both root-knot nematodes and potato aphids , 1998, Nature Biotechnology.

[28]  N. Ahmadi,et al.  Genetic basis and mapping of the resistance to rice yellow mottle virus. I. QTLs identification and relationship between resistance and plant morphology , 1998, Theoretical and Applied Genetics.

[29]  S. Seah,et al.  The isolation and mapping of disease resistance gene analogs in maize. , 1998, Molecular plant-microbe interactions : MPMI.

[30]  H. Leung,et al.  Genome scanning for resistance-gene analogs in rice, barley, and wheat by high-resolution electrophoresis , 1998, Theoretical and Applied Genetics.

[31]  I. Kaloshian,et al.  The nematode resistance gene Mi of tomato confers resistance against the potato aphid. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[32]  P. Ronald.  Resistance gene evolution. , 1998, Current opinion in plant biology.

[33]  J. Ellis,et al.  Structure and function of proteins controlling strain-specific pathogen resistance in plants. , 1998, Current opinion in plant biology.

[34]  J. Mikkelsen,et al.  Molecular characterization of the oxalate oxidase involved in the response of barley to the powdery mildew fungus. , 1998, Plant physiology.

[35]  B. R. Wiseman,et al.  Quantitative trait loci and metabolic pathways. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[36]  M. Yano,et al.  Rapid reorganization of resistance gene homologues in cereal genomes. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[37]  S. Muthukrishnan,et al.  Induction of thaumatin-like proteins (TLPs) in Rhizoctonia solani-infected rice and characterization of two new cDNA clones. , 1998, Physiologia plantarum.

[38]  I. Raskin,et al.  Activation of Host Defense Mechanisms by Elevated Production of H2O2 in Transgenic Plants , 1997, Plant physiology.

[39]  J. Leach,et al.  Differential induction of a peroxidase gene family during infection of rice by Xanthomonas oryzae pv. oryzae. , 1997, Molecular plant-microbe interactions : MPMI.

[40]  M. McMullen,et al.  Molecular mapping of a major gene conferring resistance to maize mosaic virus , 1997, Theoretical and Applied Genetics.

[41]  J. Nelson.  QGENE: software for marker-based genomic analysis and breeding , 1997, Molecular Breeding.

[42]  R. Dixon,et al.  THE OXIDATIVE BURST IN PLANT DISEASE RESISTANCE. , 1997, Annual review of plant physiology and plant molecular biology.

[43]  E. Finnegan,et al.  Inactivation of the flax rust resistance gene M associated with loss of a repeated unit within the leucine-rich repeat coding region. , 1997, The Plant cell.

[44]  P. Epple,et al.  Overexpression of an endogenous thionin enhances resistance of Arabidopsis against Fusarium oxysporum. , 1997, The Plant cell.

[45]  D. Leister,et al.  A PCR–based approach for isolating pathogen resistance genes from potato with potential for wide application in plants , 1996, Nature Genetics.

[46]  Y. G. Yu,et al.  Isolation of a superfamily of candidate disease-resistance genes in soybean based on a conserved nucleotide-binding site. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[47]  R. Shoemaker,et al.  Resistance gene analogs are conserved and clustered in soybean. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[48]  B. R. Wiseman,et al.  Quantitative trait loci and metabolic pathways: genetic control of the concentration of maysin, a corn earworm resistance factor, in maize silks. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[49]  A. Parco,et al.  Centromere mapping and orientation of the molecular linkage map of rice (Oryza sativa L.). , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[50]  M. E. Foley,et al.  Cloning and characterization of differentially expressed genes in imbibed dormant and afterripened Avena fatua embryos , 1995, Plant Molecular Biology.

[51]  H. Thordal-Christensen,et al.  Germin‐like oxalate oxidase, a H2O2‐producing enzyme, accumulates in barley attacked by the powdery mildew fungus , 1995 .

[52]  R. Dixon,et al.  Function of the oxidative burst in hypersensitive disease resistance. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[53]  B. Dumas,et al.  Tissue-Specific Expression of Germin-Like Oxalate Oxidase during Development and Fungal Infection of Barley Seedlings , 1995, Plant physiology.

[54]  D. Shah,et al.  Characterization and Expression of an Antifungal Zeamatin-like Protein (Zlp) Gene from Zea mays , 1994, Plant physiology.

[55]  J. Giraudat,et al.  RPS2 of Arabidopsis thaliana: a leucine-rich repeat class of plant disease resistance genes. , 1994, Science.

[56]  M. Mehdy.  Active Oxygen Species in Plant Defense against Pathogens , 1994, Plant physiology.

[57]  R. Nelson,et al.  RFLP mapping of genes conferring complete and partial resistance to blast in a durably resistant rice cultivar. , 1994, Genetics.

[58]  S. Tanksley,et al.  Comparative linkage maps of the rice and maize genomes. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[59]  H. Kindl,et al.  Disease resistance results from foreign phytoalexin expression in a novel plant , 1993, Nature.

[60]  S. Briggs,et al.  A Biochemical Phenotype for a Disease Resistance Gene of Maize. , 1992, The Plant cell.

[61]  J. Parlevliet,et al.  Residual effects of the Xa-4 resistance gene in three rice cultivars when exposed to a virulent isolate of Xanthomonas campestris pv. oryzae , 1991, Euphytica.

[62]  C. Woloshuk,et al.  Pathogen-induced proteins with inhibitory activity toward Phytophthora infestans. , 1991, The Plant cell.

[63]  R. P. Evans,et al.  The presence of a thaumatin-like protein, a chitinase and a glucanase among the pathogenesis-related proteins of potato () , 1990 .

[64]  M. Daly,et al.  MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. , 1987, Genomics.

[65]  R. Jorgensen,et al.  Ribosomal DNA spacer-length polymorphisms in barley: mendelian inheritance, chromosomal location, and population dynamics. , 1984, Proceedings of the National Academy of Sciences of the United States of America.

[66]  R. Fites,et al.  Thymidylate synthase activity from chlamydomonas cells and cultured tissues of Nicotiana, pinus, and daucus. , 1979, Plant physiology.

[67]  Susan McCouch,et al.  RFLP mapping of isozymes, RAPD and QTLs for grain shape, brown planthopper resistance in a doubled haploid rice population , 2004, Molecular Breeding.

[68]  E. Guiderdoni,et al.  Anther culture of tropical japonica × indica hybrids of rice (Oryza sativa L.) , 2004, Euphytica.

[69]  Q. Sun,et al.  Resistance gene complexes: evolution and utilization. , 2001, Annual review of phytopathology.

[70]  H. Leung,et al.  Mapping quantitative and qualitative disease resistance genes in a doubled haploid population of barley (Hordeum vulgare) , 2000, Theoretical and Applied Genetics.

[71]  N. Young.  QTL mapping and quantitative disease resistance in plants. , 1996, Annual review of phytopathology.

[72]  M. McMullen,et al.  Genomic organization of disease and insect resistance genes in maize , 1995 .

[73]  W. K. Roberts,et al.  Thaumatin-like pathogenesis-related proteins are antifungal , 1992 .

[74]  R. Hammerschmidt,et al.  Phenolic Compounds and Their Role in Disease Resistance , 1992 .

[75]  R. Dixon,et al.  Activation, structure, and organization of genes involved in microbial defense in plants. , 1990, Advances in genetics.

[76]  T. Martin.  Differences Between Compatible Parasite/Host Genotypes Involving the Pm4 Locus of Wheat and the Corresponding Genes in Erysiphe graminis f. sp. tritici , 1976 .

[77]  D. D. Kosambi.  The estimation of map distances from recombination values. , 1943 .