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A putative candidate for the recessive gall midge resistance gene gm3 in rice identified and validated

Abstract

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We report here tagging and fine-mapping of gm3 gene, development of a functional marker for it and its use in marker-assisted selection.

Abstract

The recessive rice gall midge resistance gene, gm3 identified in the rice breeding line RP2068-18-3-5 confers resistance against five of the seven Indian biotypes of the Asian rice gall midge Orseolia oryzae. We report here tagging and fine-mapping of gm3 gene, development of a functional marker for it and demonstrated its use in marker-assisted selection (MAS). A mapping population consisting of 302 F10 recombinant inbred lines derived from the cross TN1 (susceptible)/RP2068-18-3-5, was screened against gall midge biotype 4 (GMB4) and analyzed with a set of 89 polymorphic SSR markers distributed uniformly across the rice genome. Two SSR markers, RM17480 and gm3SSR4, located on chromosome 4L displayed high degree of co-segregation with the trait phenotype and flanked the gene. In silico analysis of the genomic region spanning these two markers contained 62 putatively expressed genes, including a gene encoding an NB-ARC (NBS-LRR) domain containing protein. A fragment of this gene was amplified with the designed marker, NBcloning 0.9 Kb from the two susceptible TN1, Improved Samba Mahsuri (B95-1) and two resistant cultivars, RP 2068-18-3-5 and Phalguna (with Gm2 gene). The amplicons were observed to be polymorphic between the susceptible and resistant genotypes and hence were cloned and sequenced. A new primer, gm3del3, which was designed based on sequence polymorphism, amplified fragments with distinct size polymorphism among RP2068-18-3-5, Phalguna and TN1 and B95-1 and displayed no recombination in the entire mapping population. Expression of the candidate NB-ARC gene in the susceptible TN1 and the resistant RP2068-18-3-5 plants following infestation with GMB4 was analyzed, through real-time reverse transcription PCR. Results showed twofold enhanced expression in RP2068-18-3-5 plants, but not in TN1 plants, 120 h after infestation. Amino acid sequence and structure analysis of the proteins coded by different alleles of gm3 gene showed deletion of eight amino acids due to an early stop codon in RP2068-18-3-5 resulting in a change in the functional domain of the protein. The gm3del3 was used as a functional marker for introgression of gm3 gene into the genetic background of the elite bacterial blight resistant cultivar Improved Samba Mahsuri (B95-1) through MAS.

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References

  • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1997) Basic local alignment search tool. J Mol Biol 2l5:403–4l0

    Google Scholar 

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

    CAS  PubMed  Article  Google Scholar 

  • Bentur JS, Kalode MB (1996) Hypersensitive reaction and induced resistance in rice against Asian rice gall midge Orseolia oryzae. Entomol Exp Appl 78:77–81

    Article  Google Scholar 

  • Bentur JS, Pasalu IC, Sarma NP, PrasadaRao U, Mishra B (2003) Gall midge resistance in rice. DRR Research Paper Series 01/2003. Directorate of Rice Research, Hyderabad, p 20

    Google Scholar 

  • Bentur JS, Padma Kumari AP, Jhansi Lakshmi V, Padmavathi CH, Kondala Rao Y, Amudhan S, Pasalu IC (2011) Insect resistance in rice. DRR Technical bulletin 51/2011 Directorate of Rice Research, India, p 86

    Google Scholar 

  • Biradar SK, Sundaram RM, Thirumurugan T, Bentur JS, Amudhan S, Shenoy VV, Mishra B, Bennet J, Sarma NP (2004) Identification of flanking SSR markers for a major rice gall midge resistance gene Gm1 and their validation. Theor Appl Genet 10:1468–1472

    Article  Google Scholar 

  • Century KS, Holub EB, Staskawicz BJ (1995) NDRI, a locus of Arabidopsis thaliana that is required for disease resistance to both a bacterial and a fungal pathogen. Proc Natl Acad Sci USA 92:6597–6601

    CAS  PubMed  Article  Google Scholar 

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

    CAS  Article  Google Scholar 

  • Cohen MB, Bentur JS, Gould F (2004) Durable deployment of gall midge-resistant varieties. In: Bennett J, Bentur JS, Pasalu IC, Krislmaiah K (eds) New approaches to gall midge resistance in rice. Proceedings of the International Workshop, November 1998. International Rice Research Institute and Indian Council of Agricultural Research, Los Banos (Philippines), Hyderabad, India, pp 195

  • Dellaporta SL, Wood J, Hicks JB (1983) A plant DNA mini preparation. Plant Mol Biol Report 1:19–21

    CAS  Article  Google Scholar 

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

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  • Dickinson MJ, Jones DA, Jones JDG (1993) Close linkage between the Cf-2/Cf-5 and Mi resistance loci in tamato. Mol Plant Microbe Interact 6:246–249

    Article  Google Scholar 

  • Du B, Zhang WL, Liu BF, Hu J, Wei Z, Shi ZY, He RF, Zhu LL, Chen RZ, Han B, He G (2009) Identification and characterization of Bph14, a gene conferring resistance to brown plant hopper in rice. Proc Natl Acad Sci USA 106:22163–22168

    CAS  PubMed  Article  Google Scholar 

  • Fujita D, Kohli A, Horgan FG (2013) Rice resistance to planthoppers and leafhoppers. Crit Rev Plant Sci 32:162–191

    CAS  Article  Google Scholar 

  • Hammond-Kosack KE, Parker JE (2003) Deciphering plant pathogen communication: fresh perspectives for molecular resistance breeding. Curr Opin Biotechnol 14:177–193

    CAS  PubMed  Article  Google Scholar 

  • He X, Liu X, Wang L, Wang L, Lin F, Cheng Y, Chen Z, Liao Y, Pan Q (2012) Identification of the novel recessive gene pi55(t) conferring resistance to Magnaporthe oryzae. Sci China Life Sci 55:141–149

    CAS  PubMed  Article  Google Scholar 

  • Himabindu K (2009) Identification, tagging and mapping of rice gall midge resistance genes using microsatellite markers. PhD thesis, Acharya Nagarjuna University, Guntur, Andhra Pradesh, India, pp 241

  • Himabindu K, Suneetha K, Sama VSAK, Bentur JS (2010) A new rice gall midge resistance gene in the breeding line CR57-MR1523, mapping with flanking markers and development of NILs. Euphytica l74:l79–187

    Google Scholar 

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

    CAS  Article  Google Scholar 

  • Iyr-Pascuzzi AS, McCouch SR (2007) Recessive resistance genes and the Oryza sativa-Xanthomonas oryze pv. oryzae pathosystem. Mol Plant Microbe Interact 20:731–739

    Article  Google Scholar 

  • Jain A, Ariyadasa R, Kumar A, Srivastava MN, Mohan M, Nair S (2004) Tagging and mapping of a rice gall midge resistance gene, Gm8, and development of SCARs for use in marker aided selection and gene pyramiding. Theor Appl Genet 109:1377–1384

    CAS  PubMed  Article  Google Scholar 

  • Jena KK, Kim SM (2010) Current status of brown plant hopper (BPH) resistance and genetics. Rice 3:161–171

    Article  Google Scholar 

  • Kalode MB, Pophaly DJ, Kasi Viswanathan PR, Sreeramulu M (1977) Studies on resistance and mass rearing of rice gall midge, Orseolia oryzae (Wood-Mason) Madras Agric J 64:733–739

    Google Scholar 

  • Katiyar SK, Verulkar SB, Adsul G, Dhundre M, Chandel G, Bennett J (2000) Molecular markers for gall midge resistance genes in rice: Stage set for MAS and map based gene cloning. In: Abstracts 4th international rice genetics symposium, International Rice Research Institute, Philippines, 22–27 October 2000, pp 81

  • Katiyar SK, Tan Y, Huang B, Chandel G, Xu Y, Zhang Y, Xie Z, Bennett J (2001) Molecular mapping of gene Gm-6(t) which confers resistance against four biotypes of Asian rice gall midge in China. Theor Appl Genet 103:953–961

    CAS  Article  Google Scholar 

  • Kumar A, Shrivastava MN, Shukla BC (1998) Inheritance and allelic relationship of gall midge biotype-1 resistance gene(s) in some new donors. Oryza 35:70–73

    Google Scholar 

  • Kumar A, Shrivastava MN, Shukla BC (1999) A new gene for resistance to gall midge in rice cultivar RP2333-156-8. Rice Genet Newslett 16:85–87

    Google Scholar 

  • Lander ES, Green P, Abrahamson J, Barlow A, Daly MG, Lincoln SE, Newburg L (1987) MAPMAKER: an interactive computer package for constructing primary genetic maps of experimental and natural populations. Genomics 1:174–181

    CAS  PubMed  Article  Google Scholar 

  • Lee SK, Song MY, Seo YS, Kim HK, Ko S, Cao PJ, Suh JP, Yi G, Roh JH, Lee S, An G, Hahn TR, Wang GL, Ronald P, Jeon JS (2009) Rice Pi5-mediated resistance to Magnaporthe oryzae requires the presence of two coiled-coil-nucleotide-binding-leucine-rich repeat genes. Genetics 181:1627–1638

    CAS  PubMed  Article  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

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  • Michelmore RW, Paran I, Kasseri RV (1991) Identification of markers linked to disease resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions using segregating populations. Proc Nat Acad Sci USA 88:9828–9832

    CAS  PubMed  Article  Google Scholar 

  • Mohan M, Nair S, Bentur JS, PrasadaRao U, Bennett J (1994) RFLP and RAPD mapping of the rice Gm2 gene that confers resistance to biotype 1 of gall midge (Orseolia oryzae). Theor Appl Genet 87:782–788

    CAS  PubMed  Article  Google Scholar 

  • Rairdan GJ, Moffett P (2006) Distinct domains in the ARC region of the potato resistance protein Rx mediate LRR binding and inhibition of activation. Plant Cell 18:2082–2093

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  • Ramkumar G, Srinivasarao K, MadanMohan K, Sudershan I, Sivaranjani AKP, Gopalkrishna K, Viraktamath BC, Madhav MS (2011) Development and validation of functional marker targeting an InDel in the major rice blast disease resistance gene Pi54 (Pikh). Mol Breed 27:129–135

    Article  Google Scholar 

  • Rawat N, Neeraja CN, Sundaram RM, Nair S, Bentur JS (2012) A novel mechanism of gall midge resistance in the rice variety Kavya revealed by microarray analysis. Funct Integr Genomics 12:249–264

    CAS  PubMed  Article  Google Scholar 

  • Rawat N, Himabindu K, Neeraja CN, Nair S, Bentur JS (2013) Suppressive subtraction hybridization reveals that rice gall midge attack elicits plant-pathogen-like responses in rice. Plant Physiol Biochem 63:122–130

    CAS  PubMed  Article  Google Scholar 

  • Rossi M, Goggin FL, Milligan SB, Kaloshian I, Ullman DE, Williamson VM (1998) The nematode resistance gene Mi of tomato confers resistance against the potato aphid. Proc Nat Acad Sci USA 95:9750–9754

    CAS  PubMed  Article  Google Scholar 

  • Salmeron JM, Oldroyd EDG, Rommens CMT, Scoofield SR, Kim HS, Lavelle DT, Dahlbeck D, Staskawicz BJ (1996) Tamato Prf is a member of the leucine-rich repeat class of plant disease resistance genes and lies embeded with in pto kinase gene cluster. Cell 86:123–133

    CAS  PubMed  Article  Google Scholar 

  • Sama VSAK, Himabindu K, Naik BS, Sundaram RM, Viraktamath BC, Bentur JS (2012) Mapping and MAS breeding of an allelic gene to the Gm8 for resistance to Asian rice gall midge. Euphytica 187:393–400

    CAS  Article  Google Scholar 

  • Sambrook J, Russell DW (2001) Molecular cloning: a laboratory manual Cold Spring Harbor, 3rd edn. Cold Spring Harbor laboratory, New York, pp 540–546

    Google Scholar 

  • Sardesai N, Kumar A, Rajyashri KR, Nair S, Mohan M (2002) Identification and mapping of an AFLP marker lined to Gm7, a gall midge resistance gene and its conversion to a SCAR marker for its utility in marker aided selection in rice. Theor Appl Genet 105:691–698

    CAS  PubMed  Article  Google Scholar 

  • Sun X, Cao Y, Yang Z, Xu C, Li X, Wang S, Zhang Q (2004) Xa26, a gene conferring resistance to Xanthomonas oryzae pv oryzae in rice, encodes a LRR receptor like kinase protein. Plant J 37:517–527

    CAS  PubMed  Article  Google Scholar 

  • Sundaram RM, Manne RV, Biradar SK, Laha GS, Ashok Reddy G, Shoba Rani N, Sarma NP, Sonti RV (2008) Marker assisted introgression of bacterial blight resistance in Samba Mahsuri, an elite indica rice variety. Euphytica 160:411–422

    Article  Google Scholar 

  • Takahashi A, Hayashi N, Miyao A, Hirochika H (2010) Unique features of the rice blast resistance Pish locus revealed by large scale retrotransposon-tagging. BMC Plant Biol 10:175

    PubMed Central  PubMed  Article  Google Scholar 

  • Tan Y, Pan Y, Zhang Y, Lixix Z, Xu Y (1993) Resistance to gall midge (GM) Orseolia oryzae in Chinese rice verieties compared with varieties from other countries. Int Rice Res Notes 18:13–14

    Google Scholar 

  • Tiwari S, Bentur JS, Mishra B, Kumar AA, Kole C (2005) Reaction of gene differential rice varieties against gall midge Orseolia oryzae (Wood-Mason) biotypes in the greenhouse. Indian J Genet 65:313–314

    Google Scholar 

  • van der Vossen EA, van der Voort JN, Kanyuka K, Bendahmane A, Sandbrink H, Baulcombe DC, Bakker J, Stiekema WJ, Klein-Lankhorst RM (2000) Homologues of a single resistance-gene cluster in potato confer resistance to distinct pathogen: a virus and a nematode. Plant J 23:567–576

    PubMed  Article  Google Scholar 

  • Vijayalakshmi P, Amudhan S, Himabindu K, Cheralu C, Bentur JS (2006) A new biotype of the Asian rice gall midge Orseolia oryzae (Diptera: Cecidomyiidae) characterized from the Warangal population in Andhra Pradesh, India. Int J Trop Insect Sci 26:207–211

    Google Scholar 

  • Wang C, Wen G, Lin X, Liu X, Zhang D (2009) Identification and fine mapping of the new bacterial blight resistance gene, Xa31 (t), in rice. Eur J Plant Pathol 123:235–240

    CAS  Article  Google Scholar 

  • White FF, Yang B (2009) Host and pathogen factors controlling the rice-Xanthomonas oryzae interaction. Plant Physiol 150:1677–1686

    CAS  PubMed Central  PubMed  Article  Google Scholar 

  • Widowsky DA, O’Toole JC (1996) Prioritizing rice research agenda for eastern India. In: Evanson RE, Herdt HM (eds) Rice research in Asia: progress and priorities. International Rice Research Institute, Manila, pp 109–129

    Google Scholar 

  • Xiang Y, Cao Y, Xu C, Li X, Wang S (2006) Xa3, conferring resistance for rice bacterial blight and encoding a receptor kinase like protein, is the same as Xa26. Theor Appl Genet 113:1347–1355

    CAS  PubMed  Article  Google Scholar 

  • Yasala AK, Rawat N, Sama VSAK, Himabindu K, Sundaram RM, Bentur JS (2012) In silico analysis for gene content in rice genomic regions mapped for the gall midge resistance genes. Plant Omics J 5:405–413

    CAS  Google Scholar 

  • Yoshimura S, Yamanouchi U, Katayose Y, Toki S, Wang Z-X, Kono I, Kurata N, Yano M, Iwata N, Sasaki T (1998) Expression of Xa1, a bacterial blight resistance gene in rice induced by bacterial inoculation. Proc Natl Acad Sci USA 95:1663–1668

    CAS  PubMed  Article  Google Scholar 

  • Zhou Y-L, Xu M-R, Zhao M-F, Xie X-W, Zhu L-H, Fu B-Y, Li Z-K (2010) Genome-wide gene responses in a transgenic rice line carrying the maize resistance gene Rxo1 to the rice bacterial streak pathogen Xanthomonas oryzae pv. Oryzicola. BMC Genomics 11:78

    PubMed Central  PubMed  Article  Google Scholar 

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Acknowledgments

We thank the Project Director, Directorate of Rice Research, Hyderabad, for facilities and encouragement. This work was supported by a research grant (F.No.BT/AB/FG-2(PH-II)(4A)/2009) from the Department of Biotechnology, Government of India.

Conflict of interest

We declare that none of the authors has any conflict of interest with reference to the publication of results contained in the manuscript.

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We declare that we have followed the highest standards of ethical practices in reporting the results of our research contained in this paper.

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Correspondence to Jagadish S. Bentur.

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Communicated by Y. Xu.

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122_2013_2205_MOESM1_ESM.tif

Fig. 7 Genotyping for foreground selection of the target genes in selected introgressed lines. a xa13 markers, b Xa21 markers, c xa5 markers, d gm3 marker. Lanes 1 Recipient parent B95-1 with xa5+xa13+Xa21 genes, 2 Donor parent RP2068-18-3-5 with gm3 gene, 3 BC2F2 plant# 14, 4 BC2F2 plant #5. Note that BC2F2 plant had xa13, Xa21 and gm3 gene in homozygous condition (TIFF 206 kb)

122_2013_2205_MOESM2_ESM.tif

Fig. 8 Seed samples of the recipient parent B95-1 (a) and of BC2F2 plant#5 derived line (b). Both the samples fit the group medium slender type (TIFF 234 kb)

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Sama, V.S.A.K., Rawat, N., Sundaram, R.M. et al. A putative candidate for the recessive gall midge resistance gene gm3 in rice identified and validated. Theor Appl Genet 127, 113–124 (2014). https://doi.org/10.1007/s00122-013-2205-7

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Keywords

  • Simple Sequence Repeat Marker
  • Bacterial Blight
  • Gall Midge
  • Blast Resistance Gene
  • Bacterial Blight Resistance