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Molecular screening for identification of blast resistance genes in North East and Eastern Indian rice germplasm (Oryza sativa L.) with PCR based makers

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Abstract

Molecular screening and genetic diversity of major rice blast resistance (R) genes were determined in 32 accessions of rice germplasm from North East and Eastern India with ten gene based single nucleotide polymorphisms and sequence tagged sites (STS) markers, namely z56592, zt56591, k39512, k3957, candidate gene marker, Pita3, YL155/YL87, YL183/YL87, Pb28, 195R-1 which showed close-set linkage to nine major rice blast resistance (R) genes, Piz, Piz-t, Pik, Pik-p, Pik-h, Pita/Pita-2, Pib and Pi9 and one susceptible pita gene. Among the 32 accessions, 13 were positive for Piz gene and six for Piz-t gene. Six accessions were positive for Pik gene, seven for Pik-p and 16 for Pik-h gene. One accession, Atte thima, was positive for three of Pik multiple genes. Out of 32, only two germplasm, Dudhraj and Nepali dhan, were detected with both Pita3 and YL155/YL87 marker for Pita/Pita-2 gene. The Pib gene appeared to be omnipresent and was detected in 31 of 32 germplasm with marker Pb28. The gene specific STS marker, 195R-1, for Pi9 gene produced positive bands in only two germplasm, Kalchatti and Bachi thima. The Uniform Blast Nursery (UBN) analysis showed that out of 32, six germplasm was resistant, ten moderately resistant and 16 germplasm were susceptible. Presence of Piz-t, Pita/Pita-2 and Pi9 gene ensured a resistant reaction in outdoor blast nursery whereas germplasm carrying Pib was susceptible when present alone. Presence of multiple genes, however, contributed to slow blasting resistance in the field. These results are useful in identification and incorporation of resistant genes from the germplasm into elite cultivars through marker assisted selection in rice breeding programs.

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Abbreviations

R:

Resistance

Avr:

Avirulent

SNPs:

Single nucleotide polymorphisms

STS:

Sequence tagged sites

UBN:

Uniform blast nursery

MR:

Moderately resistant

S:

Susceptible

MAS:

Marker assisted selection

NE:

North East

SES:

Standard evaluation system

DAS:

Days of sowing

References

  • Ashikawa I, Hayashi N, Yamane H, Kanamori H, Wu J, Matsumoto T, Ono K, Yano M (2008) Two adjacent nucleotide-binding site-leucine-rich repeat class genes are required to confer Pikm-specific rice blast resistance. Genetics 180:2267–2276

    Article  CAS  PubMed  Google Scholar 

  • Ballini E, Morel JB, Droc G, Price A, Courtois B, Notteghem JL, Tharreau D (2008) A genome-wide meta-analysis of rice blast resistance genes and quantitative trait loci provides new insights into partial and complete resistance. Mol Plant–Microbe Interact 21:859–868

    Article  CAS  PubMed  Google Scholar 

  • Bonman JM, Vergel de Dios TI, Khim MM (1986) Physiologic specialization of Pyricularia oryzae in the Philippines. Plant Disease 70:767–769

    Article  Google Scholar 

  • Bryan GT, Wu KS, Farrall L, Jia YL, 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 12:2033–2045

    CAS  PubMed Central  PubMed  Google Scholar 

  • Chen X, Shang J, Chen D, Lei C, Zou Y, Zhai W, Liu G, Xu J, Ling Z, Cao G, Ma B, Wang Y, Zhao X, Li S, Zhu L (2006) A B-lectin receptor kinase gene conferring rice blast resistance. Plant J 46:794–804

    Article  CAS  PubMed  Google Scholar 

  • Chen J, Shi Y, Liu W, Chai R, Fu Y, Zhuang J, Wu J (2011) A Pid3 allele from rice cultivar Gumei2 confers resistance to Magnaporthe oryzae. J Genet Genomics 38:209–216

    Article  CAS  PubMed  Google Scholar 

  • Das A, Soubam D, Singh PK, Thakur S, Singh NK, Sharma TR (2012) A novel blast resistance gene, Pi54rh cloned from wild species of rice, Oryza rhizomatis confers broad spectrum resistance to Magnaporthe oryzae. Funct Integr Genomics 12:215–228

    Article  CAS  PubMed  Google Scholar 

  • Deng Y, Zhu X, Shen Y, He Z (2006) Genetic characterization and Wne mapping of the blast resistance locus Pigm(t) tightly linked to Pi2 and Pi9 in a broad-spectrum resistant Chinese variety. Theor Appl Genet 113:705–713

    Article  CAS  PubMed  Google Scholar 

  • Flor HH (1971) Current status of gene-for-gene concept. Annu Rev Phytopathol 9:275–296

    Article  Google Scholar 

  • Fukuoka S, Saka N, Koga H, Ono K, Shimizu T, Ebana K, Hayashi N, Takahashi A, Hirochika H, Okuno K, Yano M (2009) Loss of function of a proline-containing protein confers durable disease resistance in rice. Science 325:998–1001

    Article  CAS  PubMed  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 108:212–220

    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, Inoue H, Kato T, Funao T, Shirota M, Shimizu T, Kanamori H, Yamane H, Hayano-Saito Y, Matsumoto T, Yano M, Takatsuji H (2010) Durable panicle blast-resistance gene Pb1 encodes an atypical CC-NBS-LRR protein and was generated by acquiring a promoter through local genome duplication. Plant J 64:498–510

    Article  CAS  PubMed  Google Scholar 

  • Hittalmani S, Parco A, Mew TW, 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 

  • Huang H, Huang L, Feng G, Wang S, Wang Y, Liu J, Jiang N, Yan W, Xu L, Sun P, Liu Z, Pan S, Liu X, Xiao Y, Liu E, Dai L, Wang G (2010) Molecular mapping of the new blast resistance genes Pi47 and Pi48 in the durably resistant local rice cultivar Xiangzi 3150. Phytopathology 101:620–626

    Article  Google Scholar 

  • Inukai T, Nelson RJ, Zeigler RS, Sarkarung S, Mackill DJ, Bobman JM, Takamure I, Kinoshita T (1994) Allelism of blast resistance genes in near-isogenic lines of rice. Phytopathology 84:1278–1283

    Article  Google Scholar 

  • Jeung JU, Kim BR, Cho YC, Han SS, Moon HP, Lee YT, Jena KK (2007) A novel gene, Pi40(t), linked to the DNA markers derived from NBS-LRR motifs confers broad spectrum of blast resistance in rice. Theor Appl Genet 115:1163–1177

    Article  CAS  PubMed  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 (2004a) Development of a SNLP marker from the Pi-ta blast resistance gene by tri-primer PCR. Euphytica 138:97–105

    Article  CAS  Google Scholar 

  • Jia Y, Wang Z, Fjellstrom RG, Moldenhauer KAK, Azam MA, Correll J, Lee FN, Xia Y, Rutger JN (2004b) Rice Pi-ta gene confers resistance to the major pathotypes of the rice blast fungus in the US. Phytopathology 94:296–301

    Article  CAS  PubMed  Google Scholar 

  • Kang S, Lebrun MH, Farrall L, Valent B (2001) Gain of virulence caused by insertion of a Pot3 transposon in a Magnaporthe grisea avirulence gene. Mol Plant–Microbe Interact 14:671–674

    Article  CAS  PubMed  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 Natl Inst Agrobiol Resour 2:13–39

    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

    Article  CAS  PubMed  Google Scholar 

  • Lin F, Chen S, Que Z, Wang L, Liu X, Pan Q (2007) The blast resistance gene Pi37 encodes a nucleotide binding site-leucine-rich repeat proteinand is a member of a resistance gene cluster on rice chromosome 1. Genetics 177:1871–1880

    Article  CAS  PubMed  Google Scholar 

  • Liu X, Lin F, Wang L, Pan Q (2007) The in silico map-based cloning of Pi36, a rice coiled-coil nucleotide-binding site leucine-rich repeat gene that confers race-specific resistance to the blast fungus. Genetics 176:2541–2549

    Article  CAS  PubMed  Google Scholar 

  • Liu J, Wang X, Mitchell T, Hu Y, Liu X, Dai L, Wang GL (2010) Recent progress and understanding of the molecular mechanisms of the rice-Magnaporthe oryzae interaction. Mol Plant Pathol 11:419–427

    Article  CAS  PubMed  Google Scholar 

  • Liu Y, Liu B, Bordeos A, Leung H, Zhu X, Wang G, Yang J, Leach JE (2013) Fine-mapping and molecular marker development for Pi56(t), a NBS-LRR gene conferring broad-spectrum resistance to Magnaporthe oryzae in rice. Theor Appl Genet 126:985–998

    Article  CAS  PubMed  Google Scholar 

  • Mackill DJ, Bonman JM (1992) Inheritance of blast resistance in near-isogenic lines of rice. Phytopathology 82:746–749

    Article  Google Scholar 

  • Mahender A, Swain DM, Gitishree D, Subudhi HN, Rao GJN (2012) Molecular analysis of native Manipur rice accessions for resistance against blast. Afr J of Biotech 11:1321–1329

    Article  CAS  Google Scholar 

  • McCouch SR, Nelson RJ, Tohme J, Zeigler RS (1994) Mapping of blast resistance genes in rice. In: Zeigler RS, Leong SA, Teng PS (eds) Rice blast disease. CAB International, Wallingford, pp 167–186

    Google Scholar 

  • Ngachan SV, Mohanty AK, Pattanayak A (2011) Status Paper on Rice in North East India–Rice in North East India. Rice Knowledge Management Portal pp 82. http://www.rkmp.co.in. Accessed 28 June 2011

  • Okuyama Y, Kanzaki H, Abe A, Yoshida K, Tamiru M, Saitoh H, Fujibe T, Matsumura H, Shenton M, Galam DC, Undan J, Ito A, Sone T, Terauchi R (2011) A multi-faceted genomics approach allows the isolation of rice Pia blast resistance gene consisting of two adjacent NBS-LRR protein genes. Plant J 66:467–479

    Article  CAS  PubMed  Google Scholar 

  • Qu S, Liu G, Zhou B, Bellizzi M, Zeng L, Dai L, Han B, Wang GL (2006) The broad spectrum blast resistance gene Pi9 encodes a nucleotide-binding site leucine-rich repeat protein and is a member of a multigene family in rice. Genetics 172:1901–1914

    Article  CAS  PubMed  Google Scholar 

  • RoyChowdhury M, Jia Y, Jackson A, Jia MH, Fjellstrom R, Cartwright R (2012a) Analysis of rice blast resistance gene Pi-z using pathogenicity assays and DNA markers. Euphytica 184:35–47

    Article  CAS  Google Scholar 

  • RoyChowdhury M, Jia Y, Jia MH, Fjellstrom B, Cartwright R (2012b) Identification of the rice blast resistance gene Pi-b in the national small grains collection. Phytopathology 102:700–706

    Article  CAS  PubMed  Google Scholar 

  • Rybka K, Miyamoto M, Ando I, Saito A, Kawasaki S (1997) High resolution mapping of the Indica-derived rice blast resistance genes II. Pi-ta2 and Pi-ta and a consideration of their origin. Mol Plant Microbe Interact 10:517–524

    Article  CAS  Google Scholar 

  • Shang J, Tao Y, Chen X, Zou Y, Lei C, Wang J, Li X, Zhao X, Zhang M, Lu Z, Xu J, Cheng Z, Wan J, Zhu L (2009) Identification of a new rice blast resistance gene, Pid3, by genome-wide comparison of paired nucleotide-binding site-leucine-rich repeat genes and their pseudogene alleles between the two sequenced rice genomes. Genetics 182:1303–1311

    Article  CAS  PubMed  Google Scholar 

  • Sharma TR, Madhav MS, Singh BK, Shanker P, Jana TK, Dalal V, Pandit A, Singh A, Gaikwad K, Upreti HC, Singh NK (2005) High-resolution mapping, cloning and molecular characterization of the Pi-kh gene of rice, which confers resistance to Magnaporthe grisea. Mol Genet Genomics 274:569–578

    Article  CAS  PubMed  Google Scholar 

  • Sharma TR, Rai AK, Gupta SK, Vijayan J, Devanna BN, Ray S (2012) Rice blast management through host-plant resistance: retrospect and prospects. Agric Res 1:37–52

    Article  Google Scholar 

  • Shikari AB, Khanna A, Krishnan SG, Singh UD, Rathour R, Tonapi V, Sharma TR, Nagarajan M, Prabhu KV, Singh AK (2013) Molecular analysis and phenotypic validation of blast resistance genes Pita and Pita 2 in landraces of rice (Oryza sativa L.). Indian J Genet 73:131–141

    CAS  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

    Article  PubMed Central  PubMed  Google Scholar 

  • Tang J, Zhu X, Wang Y, Liu L, Xu B, Li F, Fang J, Chu C (2011) Semi-dominant mutations in the CC-NB-LRR-type R gene, NLS1, lead to constitutive activation of defense responses in rice. Plant J 66:996–1007

    Article  CAS  PubMed  Google Scholar 

  • Tanksley SD, McCouch SR (1997) Seeds banks and molecular maps: unlocking genetic potential from the wild. Science 277:1063–1066

    Article  CAS  PubMed  Google Scholar 

  • Valent B (1990) Rice blast as a model system for plant pathology. Phytopathology 80:33–36

    Article  Google Scholar 

  • Valent B, Chumley FG (1994) A virulence genes and mechanism of genetic instability in the rice blast fungus. In: Zeigler RS, Leong SA, Teng PS (eds) Rice blast disease. CAB International, Wallingford, pp 111–134

    Google Scholar 

  • Valent B, Farrall L, Chumley FG (1991) Magnaporthe grisea genes for pathogenicity and virulence identified through a series of backcrosses. Genetics 127:87–101

    CAS  PubMed  Google Scholar 

  • Variar M, Vera Cruz CM, Carrillo MG, Bhatt JC, Sangar RBS (2009) Rice blast in India and strategies to develop durably resistant cultivars. In: Xiaofan W, Valent B (eds) Advances in genetics, genomics and control of rice blast disease. Springer, New York, pp 359–374

    Chapter  Google Scholar 

  • Wang ZX, Yano M, Yamanouchi 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 

  • Wang C, Hirano K, Kawasaki S (2002) Cloning of Pita-2 in the centromeric region of chr 12 with HEGS: high efficiency genome scanning. Third International Rice Blast Conference, p 25

  • 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 

  • Wang X, Fjellstrom RG, Jia Y, Yan W, Jia MH, Scheffer BE, Wu D, Shu Q, McClung AM (2010) Characterization of Pi-ta Blast resistance gene in an international rice core collection. Plant Breed 129:491–501

    CAS  Google Scholar 

  • Xia JQ, Correll JC, Lee FN, Marchetti MA, Rhoads DD (1993) DNA fingerprinting to examine microgeographic variation in the Magnaporhe grisea (Pyricularia grisea) population in two rice fields in Arkansas. Phytopathology 83:1029–1035

    Article  CAS  Google Scholar 

  • Xiao WM, Yang QY, Wang H, Guo T, Liu YZ, Zhu XY, Chen ZQ (2010) Identification and fine mapping of a resistance gene to Magnaporthe oryzae in a space-induced rice mutant. Mol Breed 28:303–312

    Article  Google Scholar 

  • Yaegashi H (1994) Use of resistant varieties and disease control for paddy rice. Agric Hortic 69:149–154

    Google Scholar 

  • Yang JY, Chen S, Zeng LX, Li YL, Chen Z, Li CY, Zhu XY (2009a) Race specificity of major rice blast resistance genes to Magnaporthe grisea isolates collected from indica rice in Guangdong. China Rice Sci. doi:CNKI.SUN.SDKE.0.2008.04.011

    Google Scholar 

  • Yang QZ, Lin F, Feng SJ, Wang L, Pan QH (2009b) Recent progress on molecular mapping and cloning of blast resistance genes in rice (Oryza sativa L.). Sci Agric Sin 42:1601–1615

    CAS  Google Scholar 

  • Yuan B, Zhai C, Wang W, Zeng X, Xu X, Hu H, Lin F, Wang L, Pan Q (2011) The Pik-p resistance to Magnaporthe oryzae in rice is mediated by a pair of closely linked CC-NBS-LRR genes. Theor Appl Genet 122:1017–1028

    Article  PubMed  Google Scholar 

  • Zhai C, Lin F, Dong Z, He X, Yuan B, Zeng X, Wang L, Pan Q (2011) The isolation and characterization of Pik, a rice blast resistance gene which emerged after rice domestication. New Phytol 189:321–334

    Article  CAS  PubMed  Google Scholar 

  • Zhou B, Qu S, Liu G, Dolan M, Sakai H, Lu G, Bellizzi M, Wang GL (2006) The eight amino-acid differences within three leucine-rich repeats between Pi2 and Piz-t resistance proteins determine the resistance specificity to Magnaporthe grisea. Mol Plant–Microbe Interact 19:1216–1228

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

The authors acknowledge the National Agriculture Innovative Project- Component 4, Indian Council of Agricultural Research (ICAR), on Allele mining blast resistance genes for financial support for this research. This work was performed at the Central Rainfed Upland Rice Research Station, Hazaribag, Jharkhand, India.

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  1. Central Rainfed Upland Rice Research Station (CRRI), Hazaribagh, 825301, Jharkhand, India

    Jahangir Imam, Shamshad Alam, Nimai P. Mandal & Mukund Variar

  2. Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, 124001, Haryana, India

    Jahangir Imam & Pratyoosh Shukla

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  1. Jahangir Imam
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Correspondence to Pratyoosh Shukla.

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Imam, J., Alam, S., Mandal, N.P. et al. Molecular screening for identification of blast resistance genes in North East and Eastern Indian rice germplasm (Oryza sativa L.) with PCR based makers. Euphytica 196, 199–211 (2014). https://doi.org/10.1007/s10681-013-1024-x

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