Skip to main content
SpringerLink
Log in

Current status on mapping of genes for resistance to leaf- and neck-blast disease in rice

  • Review Article
  • Published:
3 Biotech Aims and scope Submit manuscript

Abstract

Blast disease caused by fungal pathogen Pyricularia oryzae is a major threat to rice productivity worldwide. The rice-blast pathogen can infect both leaves and panicle neck nodes. Nearly, 118 genes for resistance to leaf blast have been identified and 25 of these have been molecularly characterized. A great majority of these genes encode nucleotide-binding site–leucine-rich repeat (NBS–LRR) proteins and are organized into clusters as allelic or tightly linked genes. Compared to ever expanding list of leaf-blast-resistance genes, a few major genes mediating protection to neck blast have been identified. A great majority of the genetic studies conducted with the genotypes differing in the degree of susceptibility/resistance to neck blast have suggested quantitative inheritance for the trait. Several reports on co-localization of gene/QTLs for leaf- and neck-blast resistance in rice genome have suggested the existence of common genes for resistance to both phases of the disease albeit inconsistencies in the genomic positions leaf- and neck-blast-resistance genes in some instances have presented the contrasting scenario. There is a strong evidence to suggest that developmentally regulated expression of many blast-resistance genes is a key determinant deciding their effectiveness against leaf or neck blast. Testing of currently characterized leaf-blast-resistance genes for their reaction to neck blast is required to expand the existing repertoire resistance genes against neck blast. Current developments in the understanding of molecular basis of host–pathogen interactions in rice-blast pathosystem offer novel possibilities for achieving durable resistance to blast through exploitation of natural or genetically engineered loss-of-function alleles of host susceptibility genes.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1

Similar content being viewed by others

References

  • Aglawe SB, Umakanth B, Rama Devi SJS, Vishalakshi B, Bhadana VP, Sharma SK, Sharma PK, Kumar S, Prasad MS, Madhav MS (2017) Identification of novel QTLs conferring field resistance for rice leaf and neck blast from an unique landrace of India. Gene Rep 7:35–42

    Google Scholar 

  • Ahn SN, Kim YK, Hong HC, Han SS, Choi HC, McCouch SR, Moon HP (1997) Mapping of genes conferring resistance to Korean isolates of rice blast fungus using DNA markers. Korean J Breed 29(4):416–423

    Google Scholar 

  • Ahn SN, Kim YK, Hong HC, Han SS, Kwon SJ, Choi HC, Moon HP, McCouch SR (2000) Molecular mapping of a new gene for resistance to rice blast (Pyricularia grisea Sacc.). Euphytica 116:17–22

    CAS  Google Scholar 

  • 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 Pik-m specific rice blast resistance. Genetics 180:2267–2276

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ashkani S, Rafil MY, Shabanimofrad M, Miah G, Sahebi M, Azizi P, Tanweer FA, Akhtar MS, Nasehi A (2015) Molecular breeding strategy and challenges towards the improvement of blast disease resistance in rice crop. Front Plant Sci 6:1–14

    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(7):859–868

    CAS  PubMed  Google Scholar 

  • Barman SR, Gowda M, Venu RC, Chattoo BB (2004) Identification of a major blast resistance gene in the rice cultivar Tetep. Plant Breed 123:300–302

    CAS  Google Scholar 

  • Berruyer R, Adreit H, Milazzo J, Gaillard S, Berger A, Dioh W, Lebrun MH, Tharreau D (2003) Identification and fine mapping of Pi33 the rice resistance gene corresponding to the Magnaporthe grisea avirulence gene ACE1. Theor Appl Genet 107:1139–1147

    CAS  PubMed  Google Scholar 

  • Brunner S, Hurni S, Streckeisen P, Mayr G, Albrecht M, Yahiaoui N, Keller B (2010) Intragenic allele pyramiding combines different specificities of wheat Pm3 resistance alleles. Plant J 6:433–445

    Google Scholar 

  • Bryan GT, Wu KS, Farrall L, Jia Y, Hershey HP, McAdams SA, 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  PubMed Central  Google Scholar 

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

    CAS  PubMed  PubMed Central  Google Scholar 

  • Chauhan R, Farman M, Zhang HB, Leong S (2002) Genetic and physical mapping of a rice blast resistance locus Pi-CO39(t) that corresponds to the avirulence gene AVR1-CO39 of Magnaporthe grisea. Mol Genet Genom 267:603–612

    CAS  Google Scholar 

  • Chen X, Temnykh S, Xu Y, Gho 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

    CAS  Google Scholar 

  • Chen DH, Vina MD, Inukai 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

    CAS  Google Scholar 

  • Chen XW, Li SG, Xu JC, Zhai WX, Ling ZZ, Ma BT, Wang YP, Wang WM, Cao G, Ma YQ, Shang JJ, Zhao XF, Zhou KD, Zhu LH (2004) Identification of two blast resistance genes in a rice variety Digu. J Phytopathol 152:77–85

    CAS  Google Scholar 

  • Chen S, Wang L, Que ZQ, Pan R, Pan Q (2005) Genetic and physical mapping of Pi37(t), a new gene conferring resistance to rice blast in the famous cultivar St. No. 1. Theor Appl Genet 111:1563–1570

    CAS  PubMed  Google Scholar 

  • Chen XW, Shang JJ, Chen DX, Lei CL, Zou Y, Zhai WX, Liu GZ, Xu JC, Ling ZZ, Cao G, Ma BT, Wang YP, Zhao XF, Li SG, Zhu LH (2006) A B-lectin receptor kinase gene conferring rice blast resistance. Plant J 46:794–804

    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 Gumei 2 confers resistance to Magnaporthe oryzae. J Genet Genom 38:209–216

    CAS  Google Scholar 

  • Chen S, Su J, Han J, Wang W, Wang C, Yang J, Zeng L, Wang X, Zhu X, Yang C (2014) Resistance spectrum assay and fine mapping of the blast resistance gene from a rice experimental line, IRBLta2-Re. Euphytica 195:209–216

    CAS  Google Scholar 

  • Chen J, Peng P, Tian J, He Y, Zhang L, Liu Z, Yin D, Zhang Z (2015) Pike, a rice blast resistance allele consist of two adjacent NBS-LRR genes, was identified as a novel allele at the Pik locus. Mol Breed 35:117

    CAS  Google Scholar 

  • Cho YG, Ishii T, Emnykh S, Chen X, Lipovich L, McCouch SR, Park WO, Ayres N, Cartinhour S (2000) Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativa L.). Theor Appl Genet 100:697–712

    Google Scholar 

  • Deng Y, Zhu X, Shen Y, He Z (2006) Genetic characterization and fine 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

    CAS  PubMed  Google Scholar 

  • Deng Y, Zhu X, Xu J, Chen H, He Z (2009) Map-based cloning and breeding application of a broad-spectrum resistance gene Pigm to rice blast. In: Wang GL, Valent B (eds) Advances in genetics, genomics and control of rice blast disease. Springer, Dordrecht, pp 161–171

    Google Scholar 

  • Dong L, Liu S, Xu P, Deng W, Li X, Tharreau D, Li J, Zhou J, Wang Q, Tao D, Yang Q (2017) Fine mapping of Pi57(t) conferring broad spectrum resistance against Magnaporthe oryzae in introgression line IL-E1454 derived from Oryza longistaminata. PLoS One 12(10):e0186201

    PubMed  PubMed Central  Google Scholar 

  • Dwinita WU, Sugiono M, Hajrial A, Asep S, Ida H (2008) Blast resistance genes in wild rice Oryza rufipogon and rice cultivar IR64. Indones J Agric Sci 1:71–76

    Google Scholar 

  • Ebitani T, Hayashi N, Omoteno M, Ozaki H, Yano M, Morikawa M, Fukuta Y (2011) Characterization of Pil3, a blast resistance gene that maps to chromosome 6 in indica rice (Oryza sativa L. variety, Kasalath). Breed Sci 61:251–259

    CAS  Google Scholar 

  • Ellur RK, Khanna A, Yadav A, Pathania S, Rajashekara H, Singh VK, Krishnan SG, Bhowmick PK, Nagarajan M, Vinod KK, Prakash G (2016) Improvement of Basmati rice varieties for resistance to blast and bacterial blight diseases using marker assisted backcross breeding. Plant Sci 242:330–341

    CAS  PubMed  Google Scholar 

  • Endo T, Yamaguchi M, Kaji R, Nakagomi K, Yokogami M, Nakamura T, Ishikawa G, Yonimaru J, Nishio T (2012) Close linkage of a blast resistance gene, Pias(t), with a bacterial leaf blight resistance gene, Xa1-as(t), in a rice cultivar ‘Asominori’. Breed Sci 62:334

    CAS  PubMed  PubMed Central  Google Scholar 

  • Fang N, Wang R, He W, Yin C, Guan C, Chen H, Huang J, Wang J, Bao Y, Zhang H (2016) QTL mapping of panicle blast resistance in japonica landrace Heikezijing and its application in rice breeding. Mol Breed 36:171–179

    Google Scholar 

  • Fjellstrom R, Conaway-Bormans CA, McClung AM, Marchetti MA, Shank AR, Park WD (2004) Development of DNA markers suitable for marker assisted selection of three genes conferring resistance to multiple pathotypes. Crop Sci 44:1790–1798

    CAS  Google Scholar 

  • Fuentes LJ, Correa-Victoria FJ, Escobar F, Prado G, Aricapa G, Duque MC, Tohme J (2008) Identification of microsatellite markers linked to the blast resistance gene Pi-1(t) in rice. Euphytica 160:295–304

    CAS  Google Scholar 

  • Fujii K, Hayano-Saito Y, Saito K, Sugiura N, Hayashi N, Tsuji T, Izawa T, Iwasaki M (2000) Identification of a RFLP marker tightly linked to the panicle blast resistance gene Pb1 in rice. Breed Sci 50(3):183–188

    CAS  Google Scholar 

  • Fukuoka S, Okuno K (2001) QTL analysis and mapping of pi21 a recessive gene for field resistance to rice blast in Japanese upland rice. Theor Appl Genet 103:85–190

    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

    CAS  PubMed  Google Scholar 

  • Fukuta Y (2004) The Pish blast resistance gene of rice (Oryza sativa L.) is located on the long arm of chromosome 1. Japan International Research Center for Agricultural Sciences (JIRCAS), Annual Report, pp 46–47

  • Gowda M, Roy-Barman S, Chattoo BB (2006) Molecular mapping of a novel blast resistance gene Pi38 in rice using SSLP and AFLP markers. Plant Breed 125:596–599

    CAS  Google Scholar 

  • Harushima Y et al (1998) A high-density rice genetic linkage map with 2275 markers using a single F2 population. Genetics 148:479–494

    CAS  PubMed  PubMed Central  Google Scholar 

  • Hayasaka H, Miyao A, Yano M, Matsunaga K, Sasaki T (1996) RFLP mapping of a rice blast resistance gene Pik. Breed Sci 46:68

    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

    CAS  PubMed  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

    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

    CAS  PubMed  Google Scholar 

  • He WW, Fang NY, Wang RS, Wu YY, Zen GY, Guan CH, Chen H, Huang J, Wang JF, Bao YM, Zhang HS (2017) Fine mapping of a new race-specific blast resistance gene, Pi-hk2, in japonica Heikezijing from Taihu region of China. Phytopathology 107:84–91

    CAS  PubMed  Google Scholar 

  • Hittalmani S, Parco A, Mew TV, 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(7):1121–1128

    CAS  Google Scholar 

  • Hittalmani S, Srinivasachary BP, Shashidhar HE (2003) Identifying major genes and QTLs for field resistance to neck blast in rice. In: Khush GS et al (eds) Advances in rice genetics. Rice Genetics Collection, Los Banos, pp 248–250

    Google Scholar 

  • Hu J, Chang X, Zou L, Tang W, Wu W (2018) Identification and fine mapping of Bph33, a new brown planthopper resistance gene in rice (Oryza sativa L.). Rice 11:55

    PubMed  PubMed Central  Google Scholar 

  • Hua L, Wu J, Chen C, Wu W, He X, Lin F, Wang L, Ashikawa I, Matsumoto T, Wang L, Pan Q (2012) The isolation of Pi1, an allele at the Pik locus which confers broad spectrum resistance to rice blast. Theor Appl Genet 125(5):1047–1055

    CAS  PubMed  Google Scholar 

  • Huang H et al (2011) Molecular mapping of the new blast resistance genes Pi47 and Pi48 in the durably resistant local rice cultivar Xiangzi 3150. Phytopathology 101:620–626

    PubMed  Google Scholar 

  • Inoue T, Zhong HS, Miyao A, Ashikawa I, Monna L, Fukuoka S, Miyadera N, Nagamura Y, Kurata K, Sasaki T, Minobe Y (1994) Sequence tagged sites (STSs) as standard landmarks in the rice genome. Theor Appl Genet 89:728–734

    CAS  PubMed  Google Scholar 

  • Ishihara T, Saito YH, Oide S, Ebana K, La NT, Hayashi K, Ashizawa T, Suzuki F, Koizumi S (2014) Quantitative trait locus analysis of resistance to panicle blast in the rice cultivar Miyazakimochi. Rice 7:2

    PubMed  PubMed Central  Google Scholar 

  • Jeon JS, Chen D, Yi GH, Wang GL, Ronald PC (2003) Genetic and physical mapping of Pi5(t) a locus associated with broad-spectrum resistance to rice blast. Mol Genet Genom 269:280–289

    CAS  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 blast resistance in rice. Theor Appl Genet 115:1163–1177

    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

    CAS  Google Scholar 

  • Jiang J, Wang S (2002) Identification of a 118 kb DNA fragment containing the locus of blast resistance gene Pi-2(t) in rice. Mol Genet Genom 268:249–252

    CAS  Google Scholar 

  • Jiang N et al (2012) Molecular mapping of the Pi2/9 allelic gene Pi2-2 conferring broad-spectrum resistance to Magnaporthe oryzae in the rice cultivar Jefferson. Rice 5:1–7

    Google Scholar 

  • Joshi S, Dhatwalia S, Kaachra A, Sharma KD, Rathour R (2019) Genetic and physical mapping of a new rice blast resistance specificity Pi-67 from a broad spectrum resistant genotype Tetep. Euphytica 215:9. https://doi.org/10.1007/s10681-018-2332-y

    Article  CAS  Google Scholar 

  • Kaji R, Ogawa T (1996) RFLP mapping of a blast resistance gene Pi-km in rice. Breed Sci 46(Suppl. 1):70

    Google Scholar 

  • Kaji R, Ogawa T, Nishimura M (1997) RFLP mapping of a blast resistance gene, Pit, in rice. Breed Sci 47(Suppl. 1):37

    Google Scholar 

  • Khanna A, Sharma V, Ellur RK, Shikari AB, Krishnan SG, Singh UD, Prakash G, Sharma TR, Rathour R, Variar M, Prashanthi SK (2015) Development and evaluation of near-isogenic lines for major blast resistance gene(s) in Basmati rice. Theor Appl Genet 128(7):1243–1259

    CAS  PubMed  Google Scholar 

  • Kim DM, Ju HG, Yang P, Han SS, Roh JH, Ahn SN (2011) Mapping and race specific reaction of the resistance gene Pi45(t) in rice. Korean J Breed Sci 43:42–49

    Google Scholar 

  • Kiyosawa S (1967) Genetic studies on host-pathogen relationship in the rice blast disease. In: Proceedings of symposium of rice diseases and their control by growing resistant varieties and other measures. Tokyo, pp 137–153

  • Koide Y, Telebanco-Yanoria MJ, Fukuta Y, Kobayashi N (2013) Detection of novel blast resistance genes Pi58(t) and Pi59(t) in a Myanmar rice landrace based on a standard differential system. Mol Breed 32:241–252

    CAS  Google Scholar 

  • KoideY Telebanco-Yanoria MJ, Pena FD, Fukuta Y, Kobayashi N (2011) Characterization of rice blast isolates by the differential system and their application for mapping a resistance gene, Pi19 (t). J Phytopathol 159:85–93

    Google Scholar 

  • Kumar P, Pathania S, Katoch P, Sharma TR, Plaha P, Rathour R (2010) Genetic and physical mapping of blast resistance gene Pi-42(t) on the short arm of rice chromosome 12. Mol Breed 25:217–228

    CAS  Google Scholar 

  • Lee S, Wamishe Y, Jia Y, Liu G, Jia MH (2009a) Identification of two major resistance genes against race 1E–1k Magnoporthe oryzae in the indica rice cultivar Zhe733. Mol Breed 24:127–134

    CAS  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 (2009b) Rice Pi5 mediated resistance to Magnaporthe oryzae requires the presence of two Nucleotide-Binding-Leucine-Rich-Repeat genes. Genetics 181:1627–1638

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lei CL, Huang DY, Li W, Wang LJ, Liu ZL, Wang XT, Shi K, Cheng ZJ, Zhang X, Ling ZZ, Wan JM (2005) Molecular mapping of a blast resistance gene in an indica rice cultivar Yanxian No. 1. Rice Genet Newsl 22:76–77

    Google Scholar 

  • Lei C, Hao K, Yang Y, Ma J, Wang S, Wang J, Cheng Z, Zhao S, Zhang X, Guo X, Wang C, Wan J (2013) Identification and fine mapping of two blast resistance genes in rice cultivar 93-11. Crop J 1:2–14

    Google Scholar 

  • Li LY, Wang L, Jing JX, Li ZQ, Lin F, Huang LF, Pan QH (2007) The Pik-m gene, conferring stable resistance to isolates of Magnaporthe oryzae was finely mapped in a crossover cold region on rice chromosome 11. Mol Breed 20:179–188

    CAS  Google Scholar 

  • Li W, Lei C, Cheng Z, Jia Y, Huang D, Wang J, Wang J, Zhang X, Su N, Guo X, Zhai H, Wan J (2008) Identification of SSR markers for a broad-spectrum blast resistance gene Pi20(t) for marker assisted breeding. Mol Breed 22:141–149

    CAS  Google Scholar 

  • Li W et al (2017) A natural allele of a transcription factor in rice confers broad-spectrum blast resistance. Cell 114:116–126

    Google Scholar 

  • Liang Z, Wang L, Pan Q (2016) A new recessive gene conferring resistance against rice blast. Rice 9:47

    PubMed  PubMed Central  Google Scholar 

  • Lin F, Chen S, Que Z, Wang L, Liu X (2007a) The blast resistance gene Pi37 encodes an NBS-LRR protein and is a member of a resistance gene cluster on rice chromosome 1. Genetics 177:1871–1880

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lin LY, Jing JX, Li ZQ, Lin F, Huang LF, Pan QH (2007b) A high-resolution map of the rice blast resistance gene Pi15 constructed by sequence-ready markers. Plant Breed 126:287–290

    CAS  Google Scholar 

  • Liu B, Zhang S, Zhu X, Yang Q, Wu S, Mei M, Mauleon R, Leach J, Mew T, Leung H (2004) Candidate defense genes as predictors of quantitative blast resistance in rice. Mol Plant Microbe Interact 17:1146–1152

    CAS  PubMed  Google Scholar 

  • Liu XQ, Wang L, Chen S, Lin F, Pan QH (2005) Genetic and physical mapping of Pi36(t) a novel rice blast resistance gene located on rice chromosome 8. Mol Genet Genom 274:394–401

    CAS  Google Scholar 

  • Liu X, Lin F, Wang L, Pan Q (2007a) 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

    CAS  PubMed  PubMed Central  Google Scholar 

  • Liu X, Yang Q, Lin F, Hua L, Wang C, Wang L, Pan Q (2007b) Identification and fine mapping of Pi39(t) a major gene conferring the broad-spectrum resistance to Magnaporthe oryzae. Mol Genet Genom 278:403–410

    CAS  Google Scholar 

  • Liu Y, Liu B, Zhu X, Yang J, Bordeos A, Wang G, Leach JE, Leung H (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(4):985–998

    CAS  PubMed  Google Scholar 

  • Lv Q, Huang Z, Xu X, Tang L, Liu H, Wang C, Zhou Z, Xin Y, Xing J, Peng Z, Li X, Zheng T, Zhu L (2017) Allelic variation of the rice blast resistance gene Pid3 in cultivated rice worldwide. Sci Rep 7:10362

    PubMed  PubMed Central  Google Scholar 

  • Ma J et al (2015) Pi64, encoding a novel CC-NBS-LRR protein, confers resistance to leaf and neck blast in rice. Mol Plant Microbe Interact 28(5):558–568

    CAS  PubMed  Google Scholar 

  • Mackill DJ, Zhang Z, Redona ED, Colowit PM (1996) Level of polymorphism and genetic mapping of AFLP markers in rice. Genome 39:969–977

    CAS  PubMed  Google Scholar 

  • McCouch SR, Kochert G, Yu ZH, Wang ZY, Khush GS, Coffman WR, Tanksley SD (1988) Molecular mapping of rice chromosomes. Theor Appl Genet 76(6):815–829

    CAS  PubMed  Google Scholar 

  • McCouch SR et al (2002) Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Res 9(6):199–207

    CAS  PubMed  Google Scholar 

  • Mekwatanakarn P, Kositratana W, Levy M, Zeigler RS (2000) Pathotype and avirulence gene diversity in Thailand as determined by rice lines near-isogenic for major resistance genes. Plant Dis 84:60–70

    PubMed  Google Scholar 

  • Moldenhauer KAK, Lee FN, Norman RJ, Helms RS, Wells BR, Dilday RH, Rohman PC, Marchetti MA (1990) Registration of “Katy” rice. Crop Sci 30:747–748

    Google Scholar 

  • Monna L, Miyao A, Inoue T, Fukuoka S, Yamazaki M, Zhong HS, Sasaki T, Minobe Y (1994) Determination of RAPD markers in rice and their conversion into sequence tagged sites (STSs) and STS-specific primers. DNA Res 1:139–148

    CAS  PubMed  Google Scholar 

  • Naqvi NI, Chattoo BB (1996) Molecular genetic analysis and sequence characterized amplified region-assisted selection of blast resistance in rice. Rice Genet 3:570–576

    Google Scholar 

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

    CAS  Google Scholar 

  • Nguyen TTT, Koizumi S, La TN, Zenbayashi KS, AshizawaT Yasuda N, Imazaki I, Miyasaka A (2006) Pi35(t) a new gene conferring partial resistance to leaf blast in the rice cultivar Hokkai 188. Theor Appl Genet 113:697–704

    CAS  PubMed  Google Scholar 

  • Noenplab A, Vanavichit A, Toojinda T, Sirithunyad P, Tragoonrung S, Sriprakhon S, Vongsaprom C (2006) QTL mapping for leaf and neck blast resistance in Khao Dawk Mali 105 and Jao Hom Nin recombinant inbred lines. Sci Asia 32:133–142

    CAS  Google Scholar 

  • 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 multifaceted genomics approach allows the isolation of the rice Pia blast resistance gene consisting of two adjacent NBS-LRR protein genes. Plant J 66:467–479

    CAS  PubMed  Google Scholar 

  • Pan Q, Wang L, Ikehashi H, Tanisaka T (1996a) Identification of a new blast resistance gene in the indica rice cultivar Kasalath using Japanese differential cultivars and isozyme markers. Phytopathology 86:1071–1075

    Google Scholar 

  • Pan QH, Tanisaka T, Ikehashi H (1996b) Studies on the genetics and breeding of blast resistance in rice VI. Gene analysis for the blast resistance of two Yunnan native cultivars GA20 and GA25. Breed Sci 46(Suppl. 2):70

    Google Scholar 

  • Pan QH, Wang L, Ikehashi H, Yamagata H, Tanisaka T (1998) Identification of two new genes conferring resistance to rice blast in the Chinese native cultivar ‘Maowangu’. Plant Breed 117:27–31

    Google Scholar 

  • Pan QH, Wang L, Tanisaka T (1999) A new blast resistance gene identified in the Indian native rice cultivar Aus373 through allelism and linkage tests. Plant Pathol 48(2):288–293

    CAS  Google Scholar 

  • Parco A (1995) STS markers for the blast resistance gene Pi-1(t). Rice Genome 4:9

    Google Scholar 

  • Puri KD, Shreshta SM, Chhetri GBK, Joshi KD (2009) Leaf and neck blast resistance reaction in Tropical rice lines under greenhouse condition. Euphytica 165(3):523–532

    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

    CAS  PubMed  PubMed Central  Google Scholar 

  • Rathour R, Singh BM, Plaha P (2006) Virulence structure of the Magnaporthe grisea rice population from the Northwestern Himalayas. Phytoparasitica 34(3):281–291

    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-ta 2 and Pi-ta and a consideration of their origin. Mol Plant Microbe Interact 10:517–524

    CAS  Google Scholar 

  • Sallaud C, Lorieux M, Roumen E, Tharreau D, Berruyer R, Svestasrani P, Garsmeur O, Ghesquiere A, Notteghem JL (2003) Identification of five new blast resistance genes in the highly blast resistant rice variety IR64 using a QTL mapping strategy. Theor Appl Genet 106:794–803

    CAS  PubMed  Google Scholar 

  • Sasaki R (1922) Existence of strains in rice blast fungus. Int J Plant Prot Tokoyo 9:631–644

    Google Scholar 

  • Sesma A, Osbourn AE (2004) The rice leaf blast pathogen undergoes developmental processes typical of root-infecting fungi. Nature 431:582–586

    CAS  PubMed  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

    CAS  PubMed  PubMed Central  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-k h gene of rice, which confers resistance to Magnaporthe grisea. Mol Genet Genom 274:569–578

    CAS  Google Scholar 

  • Shi BH, Zhang JH, Zheng YM, Liu YQ, Vera Cruz CM, Zheng TQ, Zhao MF (2012) Identification of a new resistance gene Pi-Da(t) from Dacca6 against rice blast fungus Magnaporthe oryzae in Jin23B background. Mol Breed 30:1089–1096

    CAS  Google Scholar 

  • Singh VK et al (2012) Incorporation of blast resistance into “PRR78”, an elite Basmati rice restorer line, through marker assisted backcross breeding. Field Crops Res 128:8–16

    Google Scholar 

  • Singh WH, Kapila RK, Sharma TR, Rathour R (2015) Genetic and physical mapping of a new allele of Pik locus from japonica rice ‘Liziangxintuanheigu’. Euphytica 205:889–901

    CAS  Google Scholar 

  • Sirithunya P, Tragoonrung S, Vanavichit A, Pa-In N, Vongsaprom C, Toojinda T (2002) Quantitative Trait loci associated with leaf and neck blast resistance in recombinant inbred line population of rice (Oryza sativa). DNA Res 9:79–88

    CAS  PubMed  Google Scholar 

  • Srivastava D, Shamim M, Kumar M, Mishra A, Pandey P, Kumar D, Yadav P, Siddiqui MH, Singh KN (2017) Current status of conventional and molecular interventions for blast resistance in rice. Rice Sci 24(6):299–321

    Google Scholar 

  • Sun P, Liu J, Wang Y, Jiang N, Wang S, Dai Y, Gao J, Li Z, Pan S, Wang D, Li W, Liu X, Xiao Y, Liu E, Wang GL, Dai L (2013) Molecular mapping of the blast resistance gene Pi49 in the durably resistant rice cultivar Mowanggu. Euphytica 192:45–54

    CAS  Google Scholar 

  • Sun H, Wu L, Guo L, Song F, Zheng Z, Cheng Z (2016) Genetic analysis and molecular mapping of Pitb with broad-spectrum resistance to Magnaporthe oryzae in rice. Euphytica 209:547–554

    CAS  Google Scholar 

  • Tabien RE, Li Z, Paterson AH, Marchetti MA, Stansel JW, Pinson SRM (2000) Mapping of four rice blast resistance genes from Lemont and Teqing and evaluation of their combinatorial effect for field resistance. Theor Appl Genet 101:1215–1225

    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

    PubMed  PubMed Central  Google Scholar 

  • Takehisa H, Yasuda M, Fukuta Y, Kobayashi N, Hayashi N, Nakashita H, Abe T, Sato T (2009) Genetic analysis of resistance genes in an Indica-type rice (Oryza sativa L.), Kasalath, using DNA markers. Breed Sci 59:253–260

    CAS  Google Scholar 

  • Talbot NJ (2003) On the trail of a cereal killer: exploring the biology of Magnaporthe grisea. Annu Rev Microbiol 57:177–202

    CAS  PubMed  Google Scholar 

  • Terashima T, Fukuoka S, Saka N, Kudo S (2008) Mapping of a blast field resistance gene Pi39(t) of elite rice strain Chubu 111. Plant Breed 127:485–489

    Google Scholar 

  • Vasudevan K, Vera Cruz CM, Gruissem W, Bhullar NK (2014) Large scale germplasm screening for identification of novel rice blast resistance sources. Front Plant Sci 5:505. https://doi.org/10.3389/fpls.2014.00505

    Article  PubMed  PubMed Central  Google Scholar 

  • Vasudevan K, Gruissem W, Bhullar NK (2015) Identification of novel alleles of the rice blast resistance gene Pi54. Sci Rep 5:15678. https://doi.org/10.1038/srep15678

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang GL, 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  PubMed Central  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

    PubMed  Google Scholar 

  • Wang L, Xu X, Lin F, Pan Q (2009) Characterization of rice blast resistance genes in the Pik cluster and fine mapping of the Pik-p locus. Phytopathology 99:900–905

    CAS  PubMed  Google Scholar 

  • Wang Y et al (2012) Molecular mapping of the blast resistance genes Pi2-1 and Pi51(t) in the durably resistant rice Tianjingyeshengdao. Phytopathology 102:779–786

    CAS  PubMed  Google Scholar 

  • Wang Y, Zhao JM, Zhang LX, Wang P, Wang SW, Wang H, Wang XX, Liu ZH, Zheng WJ (2015) Analysis of the diversity and function of the alleles of the rice blast resistance genes Piz-t, Pita and Pik in 24 rice cultivars. J Integr Agric. https://doi.org/10.1016/s2095-3119(15)61207-2

    Article  Google Scholar 

  • Wang F, Wang C, Liu P, Lei C, Hao W, Gao Y, Liu YG, Zhao K (2016a) Enhanced rice blast resistance by CRISPR/Cas9-targeted mutagenesis of the ERF transcription factor gene OsERF922. PLoS One 11:e0154027

    PubMed  PubMed Central  Google Scholar 

  • Wang R, Fang W, Guan C, He W, Bao Y, Zhang H (2016b) Characterization and fine mapping of a blast resistant gene Pi-jnw1 from the japonica rice landrace Jiangnanwan. PLoS One 11(12):e0169417

    PubMed  PubMed Central  Google Scholar 

  • Wu KS, Martinez C, Lentini Z, Tohme J, Chumley FG, Scolnik PA, Valent B (1996) Cloning a blast resistance gene by chromosome walking. In: Khush GS (ed) Proceedings of the third international rice genetics symposium. IRRI, Manila, Philippines, pp 669–674

    Google Scholar 

  • Wu JL, Fan YY, Li DB, Zheng KL, Leung H, Zhuang JY (2005) Genetic control of rice blast resistance in the durably resistant cultivar Gumei 2 against multiple isolates. Theor Appl Genet 111:50–56

    CAS  PubMed  Google Scholar 

  • Wu YY, Bao YM, Xie LJ, Su YY, Chu RZ, He WW, Huang J, Wang JF, Zhang HS (2013) Fine mapping and identification of blast resistance gene Pi-hk1 in a broad-spectrum resistant japonica rice landrace. Phytopathology 103(11):1162–1168

    CAS  PubMed  Google Scholar 

  • Xiao W, Yang Q, Wang H, Guo T, Liu Y, Zhu X, Chen Z (2011) Identification and fine mapping of a resistance gene to Magnaporthe oryzae in a space-induced rice mutant. Mol Breed 28:303–312

    CAS  Google Scholar 

  • Xiao W, Yang Q, Wang H, Duan J, Guo T, Liu Y, Zhu X, Chen Z (2012) Identification and fine mapping of a major R gene to Magnaporthe oryzae in a broad-spectrum resistant germplasm in rice. Mol Breed 30:1715–1726

    CAS  Google Scholar 

  • Xiao W, Yang Q, Sun D, Wang H, Guo T, Liu Y, Zhu X, Chen Z (2015) Identification of three major R genes responsible for broad-spectrum blast resistance in an indica rice accession. Mol Breed 35:49

    CAS  Google Scholar 

  • Xiu-Ying H, Liu X, Wang L, Wang L, Lin F, Cheng Y, Pan Q (2012) Identification of the novel recessive gene pi55(t) conferring resistance to Magnaporthe oryzae. Sci China Life Sci 55(2):141–149

    Google Scholar 

  • Xu X, Chen H, Fujimura T, Kawasaki S (2008a) Fine mapping of a strong QTL of field resistance against rice blast Pikahei-1(t) from upland rice Kahei utilizing a novel resistance evaluation system in the greenhouse. Theor Appl Genet 117:997–1008

    PubMed  Google Scholar 

  • Xu X, Hayashi N, Wang CT, Kato H, Fujimura T, Kawasaki S (2008b) Efficient authentic fine mapping of the rice blast resistance gene Pik-h in the Pik cluster, using new Pik-h differentiating isolates. Mol Breed 22:289–299

    CAS  Google Scholar 

  • Xu X, Hayashi N, Wang CT, Fukuoka S, Kawasaki S, Takasuji H, Jiang CJ (2014) Rice blast resistance gene Pikahei-1(t), a member of a resistance gene cluster on chromosome 4, encodes a nucleotide-binding site and leucine-rich repeat protein. Mol Breed 34:691–700

    CAS  Google Scholar 

  • Yadav MK, Aravindan S, Ngangkham U, Subudhi HN, Bag MK, Adak T, Munda S, Samantaray S, Jena M (2017) Use of molecular markers in identification and characterization of resistance to rice blast in India. PLoS One 12(4):e0176236. https://doi.org/10.1371/journal.pone.0176236

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yang Q, Lin F, Wang L, Pan Q (2009) Identification and mapping of Pi41 a major gene conferring resistance to rice blast in the Oryza sativa subspecies indica reference cultivar 93-11. Theor Appl Genet 118:1027–1034

    CAS  PubMed  Google Scholar 

  • Yu ZH, Mackill DJ, Bonman JM, Tanskley SD (1991) Tagging of blast resistance in rice via linkage to RFLP markers. Theor Appl Genet 81:471–476

    CAS  PubMed  Google Scholar 

  • Yu ZH, Mackill DJ, Bonman JM, McCouch SR, Guiderdoni E, Notteghem JL, Tanksley SD (1996) Molecular mapping of genes for resistance to rice blast (Pyricularia grisea Sacc.). Theor Appl Genet 93:859–863

    CAS  PubMed  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

    PubMed  Google Scholar 

  • Zenbayashi K, Fukuoka S, Katagiri S, Fujisawa M, Matsumoto T, Ashizawa T, Koizumi S (2007) Genetic and physical mapping of the partial resistance gene Pi34 to blast in rice. Phytopathology 97:598–602

    Google Scholar 

  • Zeng XS, Yang XF, Zhao ZH, Lin F, Wang L, Pan Q (2011) Characterization and fine mapping of the rice blast resistance gene Pia. Sci China Life Sci 54:372–378

    CAS  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

    CAS  PubMed  Google Scholar 

  • Zhao H, Wang X, Jia Y, Minkenberg B, Wheatley M, Fan J, Jia MH, Famoso A, Edwards D, Wamishe Y, Valent B, Wang GL, Yang Y (2018) The rice blast resistance gene Ptr encodes an atypical protein required for broad-spectrum disease resistance. Nat Commun. https://doi.org/10.1038/s41467-018-04369-4

    Article  PubMed  PubMed Central  Google Scholar 

  • Zheng W, Wang Y, Wang L, Ma Z, Zhao J, Wang P, Zhang L, Liu Z, Lu X (2016) Genetic mapping and molecular marker development for Pi65(t), a novel broad-spectrum resistance gene to rice blast using next-generation sequencing. Theor Appl Genet 129:1035–1044

    CAS  PubMed  Google Scholar 

  • Zhou JH, Wang JL, Xu JC, Lei CL, Ling ZZ (2004) Identification and mapping of a rice blast resistance gene Pi-g(t) in the cultivar Guangchangzhan. Plant Pathol 53(2):191–196

    CAS  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

    CAS  PubMed  Google Scholar 

  • Zhou X et al (2018) Loss of function of a rice TPR-domain RNA-binding protein confers broad-spectrum disease resistance. Proc Natl Acad Sci USA 115(12):3174–3179

    CAS  PubMed  Google Scholar 

  • Zhu M, Wang L, Pan Q (2004) Identification and characterization of a new blast resistance gene located on rice chromosome 1 through linkage and differential analyses. Phytopathology 94:515–519

    CAS  PubMed  Google Scholar 

  • Zhu X, Chen S, Yang J, Zhou S, Zeng L, Han J, Jing S, Ling W, Pan Q (2012) The identification of Pi50(t), a new member of the rice blast resistance Pi2/Pi9 multigene family. Theor Appl Genet 124:1295–1304

    CAS  PubMed  Google Scholar 

  • Zhuang JY, Lu J, Qian HR, Lin HX, Zheng KL (1998) Tagging of blast resistance gene(s) to DNA markers and marker-assisted selection (MAS) in rice improvement. In: IAEA-TECDOC:1010. International Atomic Energy Agency (IAEA)

  • Zhuang JY, Ma WB, Wu JL, Chai RY, Lu J, Fan YY, Jin MZ, Leung H, Zheng KL (2002) Mapping of leaf and neck blast resistance genes with resistance gene analog, RAPD and RFLP in rice. Euphytica 128(3):363–370

    CAS  Google Scholar 

Download references

Acknowledgements

The senior author gratefully acknowledges the Inspire Fellowship received from the Department of Science and Technology, Ministry of Science and Technology, Government of India for her Ph.D programme.

Author information

Authors and Affiliations

  1. Department of Agricultural Biotechnology, CSK Himachal Pradesh Agricultural University, Palampur, Himachal Pradesh, 176062, India

    S. Kalia & R. Rathour

Authors
  1. S. Kalia
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. R. Rathour
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

SK formulated the initial draft and RR corrected and wrote the final manuscript.

Corresponding author

Correspondence to R. Rathour.

Ethics declarations

Conflict of interest

The authors have no conflict of interest to declare.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Kalia, S., Rathour, R. Current status on mapping of genes for resistance to leaf- and neck-blast disease in rice. 3 Biotech 9, 209 (2019). https://doi.org/10.1007/s13205-019-1738-0

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s13205-019-1738-0

Keywords

Search

Navigation