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Analysis of a major rice blast resistance gene in the rice restorer line Hanghui 1179

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Abstract

Rice blast, caused by the fungal pathogen Magnaporthe oryzae, is one of the most devastating diseases of rice (Oryza sativa) worldwide. Identification and utilization of resistance genes in rice breeding is considered to be an effective and economical method to control this disease. Hanghui 1179 (HH1179) is a new native rice restorer line developed in South China. The hybrids derived from HH1179 show broad-spectrum resistance against rice blast in South China, and a further understanding of the genetic resistance in HH1179 will provide useful information for breeding resistant cultivars. In the present study, we used bulked segregant analysis combined with specific-length amplified fragment sequencing to identify a dominant gene from HH1179 that provides resistance against the rice blast isolate GD13-14. Association analysis indicated that the resistance gene is located on chromosome 6 and we mapped the target gene to a 100.8 kb region (between markers InDel-8 and RM19818) that contains the Pi2/Pi9/Piz/Piz-t/Pi50 gene cluster. Candidate gene prediction and cDNA sequencing indicated that the target resistance gene in HH1179 is Pi2. Our findings will be valuable for resistance breeding with restorer line HH1179.

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References

  • Chen H, Chen B, Zhang D, Xie Y, Zhang Q (2001) Pathotypes of Pyricularia grisea in rice fields of central and southern China. Plant Dis 85:843–850

    Article  Google Scholar 

  • Chen X, Li S, Xu J, Zhai W, Ling Z, Ma B, Wang Y, Wang W, Cao G, Ma Y, Shang J, Zhao X, Zhou K, Zhu L (2004) Identification of two blast resistance genes in a rice variety, Digu. J Phytopathol 152:77–85

    Article  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

    Article  CAS  Google Scholar 

  • Chen S, Su J, Hua L, Wang W, Wang C, Yang J, Zeng L, Zhu X (2015) Genetic analysis and gene identification of restorer line Huazhan against rice blast. Acta Phytopathol Sin 45(6):598–605 (in Chinese)

    Google Scholar 

  • Chen S, Wang W, Su J, Wang C, Feng A, Yang J, Zeng L, Zhu X (2016) Rapid identification of rice blast resistance gene by specific length amplified fragment sequencing. Biotechnol Biotechnol Equip 30(3):462–468

    Article  CAS  Google Scholar 

  • Collard BCY, Mackill DJ (2008) Marker-assisted selection: an approach for precision plant breeding in the twenty-first century. Philos Trans R Soc Lond B 363(1491):557–572

    Article  CAS  Google Scholar 

  • Dai L, Wu J, Li X, Wang X, Liu X, Jantasuriyarat C, Kudrna D, Yu Y, Wing R, Han B, Zhou B, Wang G (2010) Genomic structure and evolution of the Pi2/9 locus in wild rice species. Theor Appl Genet 121:295–309

    Article  CAS  PubMed  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

    Article  CAS  PubMed  Google Scholar 

  • Deng Y, Zhai K, Xie Z, Dongyong Yang D, Zhu X, Liu J, Wang W, Qin P, Yang Y, Zhang G, Li Q, Zhang J, Wu S, Milazzo J, Mao B, Wang E, Xie H, Tharreau D, He Z (2017) Epigenetic regulation of antagonistic receptors confers rice blast resistance with yield balance. Science. doi:10.1126/science.aai8898

    Google Scholar 

  • Devanna NB, Vijayan J, Sharma TR (2014) The blast resistance gene Pi54of cloned from Oryza officinalis interacts with Avr-Pi54 through its novel non-LRR domains. PLoS ONE 9(8):e104840

    Article  PubMed  PubMed Central  Google Scholar 

  • Fjellstrom R, McClung AM, Shank AR (2006) SSR markers closely linked to the Pi-z locus are useful for selection of blast resistance in a broad array of rice Germplasm. Mol Breed 17(2):149–157

    Article  CAS  Google Scholar 

  • Fukuoka S, Yamamoto S, Mizobuchi R, Yamanouchi U, Ono K, Kitazawa N, Yasuda N, Fujita Y, Nguyen T, Koizumi S, Sugimoto K, Matsumoto T, Yano M (2014) Multiple functional polymorphisms in a single disease resistance gene in rice enhance durable resistance to blast. Sci Rep 4:4550

    Article  Google Scholar 

  • Han Y, Zhao X, Liu D, Li Y, Lightfoot DA, Yang Z, Zhao L, Zhou G, Wang Z, Huang L, Zhang Z, Qiu L, Zheng H, Li W (2016) Domestication footprints anchor genomic regions of agronomic importance in soybeans. N Phytol 209(2):871–884

    Article  CAS  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(2):251–260

    Article  CAS  PubMed  Google Scholar 

  • Huang X, Feng Q, Qian Q, Zhao Q, Wang L, Wang A, Guan J, Fan D, Weng Q, Huang T, Dong G, Sang T, Han B (2009) High-throughput genotyping by whole-genome resequencing. Genome Res 19:1068–1076

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Huang J, Si W, Deng Q, Li P, Yang S (2014) Rapid evolution of avirulence genes in rice blast fungus Magnaporthe oryzae. BMC Genet 15:45

    Article  PubMed  PubMed Central  Google Scholar 

  • Inukai T, Nelson RJ, Zeigler RS, Sarkarung S, Mackill DJ, Bonman JM, Takamure I, Kinoshita T (1994) Allelism of blast resistance genes in near-isogenic lines of rice. Phytopathology 84(11):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, 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 

  • Kosambi DD (1944) The estimation of map distances from recombination values. Ann Eugen 12:172–175

    Article  Google Scholar 

  • Liang D, Chen M, Qi X, Xu Q, Zhou F, Chen X (2016) QTL mapping by SLAF-seq and expression analysis of candidate genes for aphid resistance in cucumber. Front Plant Sci 7:1000

    PubMed  PubMed Central  Google Scholar 

  • Liu G, Lu G, Zeng L, Wang G (2002) Two broad-spectrum blast resistance genes, Pi9(t) and Pi2(t), are physically linked on rice chromosome 6. Mol Genet Genomics 267:472–480

    Article  CAS  PubMed  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(10):1146–1152

    Article  CAS  PubMed  Google Scholar 

  • Liu Y, Qi S, Young N, Olsen K, Caicedo A, Jia Y (2015) Characterization of resistance genes to rice blast fungus. Mol Breed 35:52

    Article  Google Scholar 

  • Ma J, Lei C, Xu X, Hao K, Wang J, Cheng Z, Ma X, Ma J, Zhou K, Zhang X, Guo X, Wu F, Lin Q, Wang C, Zhai H, Wang H, Wan J (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

    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 

  • Miah G, Rafii MY, Ismail MR, Puteh AB, Rahim HA, Asfaliza R, Latif MA (2013) Blast resistance in rice: a review of conventional breeding to molecular approaches. Mol Biol Rep 40:2369–2388

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Montaldo HH, Meza-Herrera CA (1998) Use of molecular markers and major genes in the genetic improvement of livestock. Electron J Biotechnol 2:83–89

    Article  Google Scholar 

  • Murray MG, Thompson WK (1980) Rapid isolation of high molecular-weight plant DNA. Nucleic Acids Res 8:4321–4325

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ou SH (1980) Pathogen variability and host resistance in rice blast disease. Annu Rev Phytopathol 18:167–187

    Article  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  PubMed Central  Google Scholar 

  • Sawada H, Sugihara M, Takagaki M, Nagayama K (2004) Monitoring and characterization of Magnaporthe grisea isolates with decreased sensitivity to scytalone dehydratase inhibitors. Pest Manag Sci 60:777–785

    Article  CAS  PubMed  Google Scholar 

  • Schlötterer C, Tobler R, Kofler R, Nolte V (2014) Sequencing pools of individuals—mining genome-wide polymorphism data without big funding. Nat Rev Genet 15:749–763

    Article  PubMed  Google Scholar 

  • Shang J, Tao Y, Chen XW, 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 blast resistance gene, Pid3, by genome-wide comparison of paired NBS-LRR genes and their pseudogene alleles between the two sequenced rice genome. Genetics 182(4):1303–1311

    Article  CAS  PubMed  PubMed Central  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(3):79–88

    Article  CAS  PubMed  Google Scholar 

  • Su J, Wang W, Han J, Chen S, Wang C, Zeng L, Feng A, Yang J, Zhou B, Zhu X (2015) Functional divergence of duplicated genes results in a novel blast resistance gene Pi50 at the Pi2/9 locus. Theor Appl Genet 128:2213–2225

    Article  CAS  PubMed  Google Scholar 

  • Sun X, Liu D, Zhang X, Li W, Liu H, Hong W, Jiang C, Guan N, Ma C, Zeng H (2013) SLAF-seq: an efficient method of large-scale de novo SNP discovery and genotyping using high-throughput sequencing. PLoS ONE 8(3):e58700

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  Google Scholar 

  • The Standard Evaluation System for rice (SES). Edited by International Rice Research Institute, 1996

  • Vengadessan V, Rai KN, Kannan Bapu JR, Hash CT, Bhattacharjee R, Senthilvel S, Vinayan MT, Nepolean T (2013) Construction of genetic linkage map and QTL analysis of sink-size traits in Pearl Millet (Pennisetum glaucum). ISRN Genet 2013:1–15

    Article  Google Scholar 

  • Wang G, 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 

  • Xia C, Chen L, Rong T, Li R, Xiang Y, Wang P, Liu C, Dong X, Liu B, Zhao D, Wei R, Lan H (2015) Identification of a new maize inflorescence meristem mutant and association analysis using SLAF-seq method. Euphytica 202:35–44

    Article  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(4):1715–1726

    Article  CAS  Google Scholar 

  • Yang J, Chen S, Zeng L, Li Y, Chen Z, Li C, Zhu X (2008) Race specificity of major rice blast resistance genes to Magnaporthe grisea isolates collected from indica rice in Guangdong, China. Rice Sci 15:311–318

    Article  Google Scholar 

  • Zeigler RS, Leong SA, Teng PS (1994) Rice blast disease. CAB International Mycological Institute, Kew

    Google Scholar 

  • Zhang Y, Wang L, Xin H, Li D, Ma C, Ding X, Hong W, Zhang X (2013) Construction of a high-density genetic map for sesame based on large scale marker development by specific length amplified fragment (SLAF) sequencing. BMC Plant Biol 13:141

    Article  PubMed  PubMed Central  Google Scholar 

  • Zhang D, Li H, Wang J, Zhang H, Hu Z, Chu S, Lv H, Yu D (2016a) High-density genetic mapping identifies new major loci for tolerance to low-phosphorus stress in soybean. Front Plant Sci 7:372

    PubMed  PubMed Central  Google Scholar 

  • Zhang Z, Shang H, Shi Y, Huang L, Li J, Ge Q, Gong J, Liu A, Chen T, Wang D, Wang Y, Palanga KK, Muhammad J, Li W, Lu Q, Deng X, Tan Y, Song W, Cai J, Li P, Rashid H, Gong W, Yuan Y (2016b) Construction of a high-density genetic map by specific locus amplified fragment sequencing (SLAF-seq) and its application to quantitative trait loci (QTL) analysis for boll weight in upland cotton (Gossypium hirsutum). BMC Plant Biol 16:79

    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

    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 

  • Zhu X, Chen S, Yang J, Zhou S, Zeng L, Han J, Su J, Wang L, Pan Q (2012) The identification of Pi50(t), a new member of the rice blast resistance Pi2/Pi9 multigene family. Theor Appl Genet 124(7):1295–1304

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

This research was supported by Grants from the National Key Technology Research and Development Program of China (No. 2016YFD0102102), the Guangdong Science and Technology Projects (2015A020209142, 2013B020301011), and the Special Fund for Modern Agricultural Industry Technology System of Guangdong Province.

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  1. Jiyong Zhou and Wuming Xiao have contributed equally to this work.

Authors and Affiliations

  1. National Engineering Research Center of Plant Space Breeding, South China Agricultural University, Guangzhou, 510642, China

    Jiyong Zhou, Wuming Xiao & Zhiqiang Chen

  2. Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China

    Wenjuan Wang, Aiqing Feng, Xiaoyuan Zhu & Shen Chen

  3. Guangdong Agricultural Technology Extension Station, Guangzhou, China

    Jiyong Zhou

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  1. Jiyong Zhou
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  2. Wuming Xiao
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  3. Wenjuan Wang
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Correspondence to Shen Chen or Zhiqiang Chen.

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Zhou, J., Xiao, W., Wang, W. et al. Analysis of a major rice blast resistance gene in the rice restorer line Hanghui 1179. Euphytica 213, 143 (2017). https://doi.org/10.1007/s10681-017-1932-2

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