Theoretical and Applied Genetics

, Volume 127, Issue 1, pp 113–124 | Cite as

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

  • V. S. A. K. Sama
  • Nidhi Rawat
  • R. M. Sundaram
  • Kudapa Himabindu
  • Bhaskar S. Naik
  • B. C. Viraktamath
  • Jagadish S. Bentur
Original Paper

Abstract

Key message

We report here tagging and fine-mapping ofgm3gene, 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.

Supplementary material

122_2013_2205_MOESM1_ESM.tif (206 kb)
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. Lanes1 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 (602 kb)
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)
122_2013_2205_MOESM3_ESM.xlsx (18 kb)
Supplementary material 1 (XLSX 18 kb)

References

  1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1997) Basic local alignment search tool. J Mol Biol 2l5:403–4l0Google Scholar
  2. 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 12:1871–1884PubMedCrossRefGoogle Scholar
  3. Bentur JS, Kalode MB (1996) Hypersensitive reaction and induced resistance in rice against Asian rice gall midge Orseolia oryzae. Entomol Exp Appl 78:77–81CrossRefGoogle Scholar
  4. 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 20Google Scholar
  5. 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 86Google Scholar
  6. 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 10:1468–1472CrossRefGoogle Scholar
  7. 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 92:6597–6601PubMedCrossRefGoogle Scholar
  8. 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 95:553–567CrossRefGoogle Scholar
  9. 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 195Google Scholar
  10. Dellaporta SL, Wood J, Hicks JB (1983) A plant DNA mini preparation. Plant Mol Biol Report 1:19–21CrossRefGoogle Scholar
  11. DeYoung BJ, Innes RW (2006) Plant NBS-LRR proteins in pathogen sensing and host defense. Nat Immunol 7:1243–1249PubMedCentralPubMedCrossRefGoogle Scholar
  12. 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 6:246–249CrossRefGoogle Scholar
  13. 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 106:22163–22168PubMedCrossRefGoogle Scholar
  14. Fujita D, Kohli A, Horgan FG (2013) Rice resistance to planthoppers and leafhoppers. Crit Rev Plant Sci 32:162–191CrossRefGoogle Scholar
  15. Hammond-Kosack KE, Parker JE (2003) Deciphering plant pathogen communication: fresh perspectives for molecular resistance breeding. Curr Opin Biotechnol 14:177–193PubMedCrossRefGoogle Scholar
  16. 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 55:141–149PubMedCrossRefGoogle Scholar
  17. 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 241Google Scholar
  18. 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:l79–187Google Scholar
  19. Iyer AS, McCouch SR (2004) The rice bacterial blight resistance gene xa5 encodes a novel form of disease resistance. Mol Plant Microbe In 17:1348–1354CrossRefGoogle Scholar
  20. Iyr-Pascuzzi AS, McCouch SR (2007) Recessive resistance genes and the Oryza sativa-Xanthomonas oryze pv. oryzae pathosystem. Mol Plant Microbe Interact 20:731–739CrossRefGoogle Scholar
  21. 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 109:1377–1384PubMedCrossRefGoogle Scholar
  22. Jena KK, Kim SM (2010) Current status of brown plant hopper (BPH) resistance and genetics. Rice 3:161–171CrossRefGoogle Scholar
  23. 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 64:733–739Google Scholar
  24. 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 81Google Scholar
  25. 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 103:953–961CrossRefGoogle Scholar
  26. Kumar A, Shrivastava MN, Shukla BC (1998) Inheritance and allelic relationship of gall midge biotype-1 resistance gene(s) in some new donors. Oryza 35:70–73Google Scholar
  27. Kumar A, Shrivastava MN, Shukla BC (1999) A new gene for resistance to gall midge in rice cultivar RP2333-156-8. Rice Genet Newslett 16:85–87Google Scholar
  28. 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 1:174–181PubMedCrossRefGoogle Scholar
  29. 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 181:1627–1638PubMedCrossRefGoogle Scholar
  30. Meyers BC, Kozik A, Griego A, Kuang H, Michelmore RW (2003) Genome-wide analysis of NBS–LRR-encoding genes in Arabidopsis. Plant Cell 15:809–834PubMedCentralPubMedCrossRefGoogle Scholar
  31. 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 88:9828–9832PubMedCrossRefGoogle Scholar
  32. 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 87:782–788PubMedCrossRefGoogle Scholar
  33. 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 18:2082–2093PubMedCentralPubMedCrossRefGoogle Scholar
  34. 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 27:129–135CrossRefGoogle Scholar
  35. 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 12:249–264PubMedCrossRefGoogle Scholar
  36. 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 63:122–130PubMedCrossRefGoogle Scholar
  37. 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 95:9750–9754PubMedCrossRefGoogle Scholar
  38. 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 86:123–133PubMedCrossRefGoogle Scholar
  39. 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 187:393–400CrossRefGoogle Scholar
  40. Sambrook J, Russell DW (2001) Molecular cloning: a laboratory manual Cold Spring Harbor, 3rd edn. Cold Spring Harbor laboratory, New York, pp 540–546Google Scholar
  41. 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 105:691–698PubMedCrossRefGoogle Scholar
  42. 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 37:517–527PubMedCrossRefGoogle Scholar
  43. 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 160:411–422CrossRefGoogle Scholar
  44. 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 10:175PubMedCentralPubMedCrossRefGoogle Scholar
  45. 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 18:13–14Google Scholar
  46. 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 65:313–314Google Scholar
  47. 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 23:567–576PubMedCrossRefGoogle Scholar
  48. 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 26:207–211Google Scholar
  49. 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 123:235–240CrossRefGoogle Scholar
  50. White FF, Yang B (2009) Host and pathogen factors controlling the rice-Xanthomonas oryzae interaction. Plant Physiol 150:1677–1686PubMedCentralPubMedCrossRefGoogle Scholar
  51. 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 109–129Google Scholar
  52. 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 113:1347–1355PubMedCrossRefGoogle Scholar
  53. 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 5:405–413Google Scholar
  54. 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 95:1663–1668PubMedCrossRefGoogle Scholar
  55. 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 11:78PubMedCentralPubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • V. S. A. K. Sama
    • 1
    • 2
  • Nidhi Rawat
    • 1
  • R. M. Sundaram
    • 1
  • Kudapa Himabindu
    • 1
    • 2
  • Bhaskar S. Naik
    • 1
  • B. C. Viraktamath
    • 1
  • Jagadish S. Bentur
    • 1
    • 3
  1. 1.Directorate of Rice ResearchHyderabadIndia
  2. 2.International Crops Research Institute for the Semi-Arid TropicsPatancheruIndia
  3. 3.Agri Biotech FoundationHyderabadIndia

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