Skip to main content
Log in

Mapping of a novel recessive brown planthopper resistance gene bph46 from wild rice (Oryza nivara)

  • Research
  • Published:
Euphytica Aims and scope Submit manuscript

Abstract

Rice production is severely threatened by frequent outbreaks of Brown planthopper (BPH), Nilaparvata lugens (Stảl.) biotypes globally. On this account, host-plant resistance serves as an important strategy to reduce the damage caused by BPH. The wild species of rice Oryza nivara accession IRGC 93198 showed consistent resistance reaction against BPH biotype 4 for 5 consecutive years of screening under the greenhouse conditions. The mapping of the BPH resistance gene from Oryza nivara accession IRGC 93198 was conducted using BC2F2 and BC2F3 progenies. Out of 239 BC2F2 plants, 65 plants were resistant (1-3 score), and 174 plants (5, 7, and 9 score) were susceptible, thus fitting the segregation ratio of 3:1 (Susceptible: Resistant). The BC2F3 progenies segregated in 1:2:1 confirming that the resistance from O. nivara is governed by a single recessive gene. Bulked segregant analysis (BSA) identified genomic region on the short arm of chromosome 4 to be associated with BPH resistance. Molecular mapping performed on BC2F2 population identified a QTL on chromosome 4 within the marker interval RM16285 and RM6314 explaining phenotypic variance of 27% at LOD 22.34. The linked marker RM6659 was found efficient in demarcating the susceptible from resistant lines when applied on the panel of rice cultivars, hence can be used for marker assisted selection in crop breeding. The previously identified BPH-resistant genes located on chromosome 4 were found susceptible to the BPH biotype 4 screening test. This specifies bph46 to be a novel gene that can be deployed as a valuable donor in BPH resistance breeding programs.

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

Access this article

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

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

References

  • Alam SN, Cohen MB (1998) Detection and analysis of QTLs for resistance to the brown planthopper, Nilaparvata lugens, in a doubled-haploid rice population. Theor Appl Genet 97:1370–1379

    Article  CAS  Google Scholar 

  • Balakrishnan D, Laha GS, Arra Y, Surapaneni M, Beerelli K, Ladhalakshmi D, Srinivas PM, Subba Rao LV, Sundaram RM, Neelamraju S (2022) Identification of novel major and minor quantitative trait loci associated with bacterial blight resistance in rice from Oryza nivara-derived wild introgression lines. Plant Breed 141(6):756–770

    Article  CAS  Google Scholar 

  • Bao YY, Zhang CX (2019) Recent advances in molecular biology research of a rice pest, the brown planthopper. J Integr Agric 18(4):716–728

    Article  CAS  Google Scholar 

  • Bhasin H, Bhatia D, Raghuvanshi S, Lore JS, Sahi GK, Kaur B, Vikal Y, Singh K (2012) New PCR-based sequence-tagged site marker for bacterial blight resistance gene Xa38 of rice. Mol Breed 30:607–611

    Article  CAS  Google Scholar 

  • Bottrell DG, Schoenly KG (2012) Resurrecting the ghost of green revolutions past: the brown planthopper as a recurring threat to high-yielding rice production in tropical Asia. J Asia Pac Entomol 15:122–140

    Article  Google Scholar 

  • Brar DS, Singh K (2011) Oryza in Wild crop relatives: Genomic and breeding resources: Cereals. In: Kole C (ed) pp 321–326

  • Cabauatan PQ, Cabunagan RC, Choi IR (2009) Rice viruses transmitted by the brown planthopper Nilaparvata lugens Stål. Planthoppers: new threats to the sustainability of intensive rice production systems in Asia Los Baños (Philippines). Int Rice Res Inst, pp 357–368

  • Cheng L, Wang Y, Meng L, Hu X, Cui Y, Sun Y et al (2012) Identification of salt-tolerant QTLs with strong genetic background effect using two sets of reciprocal introgression lines in rice. Genome 55:45–55. https://doi.org/10.1139/g11-075

    Article  CAS  PubMed  Google Scholar 

  • Cheng X, Wu Y, Guo J, Du B, Chen R, Zhu L, He G (2013) A rice lectin receptor-like kinase that is involved in innate immune responses also contributes to seed germination. Plant J 76:687–698. https://doi.org/10.1111/tpj.12328

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Deen R, Ramesh K, Padmavathi G, Viraktamath BC, Ram T (2017) Mapping of brown planthopper [Nilaparvata lugens (Stål)] resistance gene (bph 5) in rice (Oryza sativa L.). Euphytica 213:1–14

    Article  CAS  Google Scholar 

  • Du B, Zhang W, Liu B, Hu J, Wei Z, Shi Z, He R, Zhu L, Chen R, Han B et al (2009) Identification and characterization of Bph14, a gene conferring resistance to brown planthopper in rice. PNAS 106:22163–22168. https://doi.org/10.1073/pnas.0912139106

    Article  PubMed  PubMed Central  Google Scholar 

  • Du B, Chen R, Guo J, He G (2020) Current understanding of the genomic, genetic, and molecular control of insect resistance in rice. Mol Breed 40:24. https://doi.org/10.1007/s11032-020-1103-3

    Article  CAS  Google Scholar 

  • Eizenga GC, Bryant RJ, Agrama HA, Mackill DJ (2016) Evaluation of a M-202 x Oryza nivara advanced backcross mapping population for seedling vigor, yield components and quality. Euphytica 208:157–171

    Article  Google Scholar 

  • Fujita D, Doi K, Yoshimura A, Yasui H (2004) Introgression of a resistance gene for green rice leafhopper from Oryza nivara into cultivated rice, Oryza sativa L. Rice Genet Newsl 21:64–66

    Google Scholar 

  • Guo J, Xu C, Wu D, Zhao Y, Qiu Y, Wang X, Ouyang Y, Cai B, Liu X, Jing S et al (2018) Bph6 encodes an exocyst-localized protein and confers broad resistance to planthoppers in rice. Nat Genet 50:297–306. https://doi.org/10.1038/s41588-018-0039-6

    Article  CAS  PubMed  Google Scholar 

  • He J, Liu YQ, Liu YL, Jiang L, Wu H, Kang HY, Liu SJ, Chen LM, Liu X, Cheng XN, Wan JM (2013) High-resolution mapping of brown planthopper (BPH) resistance gene Bph27(t) in rice (Oryza sativa L.). Mol Breed 31:549–557

    Article  CAS  Google Scholar 

  • Heinrichs EA, Medrano FG, Rapusas HR (1985) Genetic evaluation for insect resistance in rice. Int Rice Res Inst, pp 71–142

  • Horgan FG, Ramal AF, Bentur JS, Kumar R, Bhanu KV, Sarao PS, Iswanto EH, Chien HV, Phyu MH, Bernal CC, Almazan ML, Alam MZ, Lu Z, Huang SH (2015) Virulence of brown planthopper (Nilaparvata lugens) populations from South and South East Asia against resistant rice varieties. Crop Prot 78:222–231. https://doi.org/10.1016/j.cropro.2015.09.014

    Article  Google Scholar 

  • Hori K, Suzuki K, Ishikawa H, Nonoue Y, Nagata K, Fukuoka S et al (2021) Genomic regions involved in differences in eating and cooking quality other than Wx and Alk genes between indica and japonica rice cultivars. Rice 14:8. https://doi.org/10.1186/s12284-020-00447-8

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hu J, Chang X, Zou L et al (2018) Identification and fine mapping of Bph33, a new brown planthopper resistance gene in rice (Oryza sativa L.). Rice 11:55. https://doi.org/10.1186/s12284-018-0249-7

    Article  PubMed  PubMed Central  Google Scholar 

  • Huang D, Qiu Y, Zhang Y, Huang F, Meng J, Wei S, Li R, Chen B (2013) Fine mapping and characterization of BPH27, a brown planthopper resistance gene from wild rice (Oryza rufipogon Griff.). Theor Appl Genet 126:219–229

    Article  CAS  PubMed  Google Scholar 

  • International Rice Research Institute (IRRI) (1996) Standard evaluation system for rice. Int Rice Res Inst, Los Baños, pp 30–31

  • Jairin J, Sansen K, Wongboon W, Kothcharerk J (2010) Detection of a brown planthopper resistance gene bph4 at the same chromosomal position of Bph3 using two different genetic backgrounds of rice. Breed Sci 60(1):71–75

    Article  CAS  Google Scholar 

  • Ji H, Kim SR, Kim YH, Suh JP, Park HM, Sreenivasulu N, Misra G, Kim SM, Hechanova SL, Kim H et al (2016) Map-based cloning and characterization of the BPH18 gene from wild rice conferring resistance to brown planthopper (BPH) insect pest. Sci Rep 6:34376. https://doi.org/10.1038/srep34376

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jing S, Zhao Y, Du B, Chen R, Zhu L, He G (2017) Genomics of interaction between the brown planthopper and rice. Curr Opin Insect Sci 19:82–87. https://doi.org/10.1016/j.cois.2017.03.005

    Article  PubMed  Google Scholar 

  • Kaur P, Neelam K, Sarao PS, Babbar A, Kumar K, Vikal Y, Khanna R, Kaur R, Mangat GS, Singh K (2022) Molecular mapping and transfer of a novel brown planthopper resistance gene bph42 from Oryza rufipogon (Griff.) to cultivated rice (Oryza sativa L.). Mol Biol Rep 49(9):8597–8606. https://doi.org/10.1007/s11033-022-07692-8

    Article  CAS  PubMed  Google Scholar 

  • Ketipearachchi Y, Kaneda C, Nakamura C (1998) Adaptation of the brown planthopper (BPH), Nilaparvata lugens (Stal) (Homoptera: Delphacidae), to BPH resistant rice cultivars carrying bph8 or Bph9. Appl Entomol Zool 33:497–505. https://doi.org/10.1303/aez.33.497

    Article  Google Scholar 

  • Khush GS (1977) Disease and insect resistance in rice. Adv in Agron 29:265–341

    Article  Google Scholar 

  • Khush GS, Coffman WR (1977) Genetic evaluation and utilization (GEU) program. Theor Appl Genet 51:97–110. https://doi.org/10.1007/BF00273821

    Article  CAS  PubMed  Google Scholar 

  • Khush GS, Karim AR, Angeles EG (1985) Genetics of resistance of rice cultivar ARC10550 to Bangladesh brown planthopper biotype. J Genet 64(2):121–125

    Article  Google Scholar 

  • Kumar PN, Sujatha K, Laha GS, Rao KS, Mishra B, Viraktamath BC, Hari Y, Reddy CS, Balachandran SM, Ram T, Madhav MS, Rani NS, Neeraja CN, Reddy GA, Shaik H, Sundaram RM (2012) Identification and fine-mapping of Xa33, a novel gene for resistance to Xanthomonas Oryzae pv. oryzae. Phytopathol 102:222–228

    Article  CAS  Google Scholar 

  • Kumar K, Sarao PS, Bhatia D, Neelam K, Kaur A, Mangat GS, Brar DS, Singh K (2018) High-resolution genetic mapping of a novel brown planthopper resistance locus, Bph34 in Oryza sativa L. X Oryza nivara (Sharma & Shastry) derived interspecific F2 population. Theor Appl Genet 131:1163–1171

    Article  CAS  PubMed  Google Scholar 

  • Li C, Zhou A, Sang T (2006) Rice domestication by reducing shattering. Science 311:1936–1939

    Article  CAS  PubMed  Google Scholar 

  • Li Z, Xue Y, Zhou H, Li Y, Usman B, Jiao X, Wang X, Liu F, Qin B, Li R, Qiu Y (2019) High-resolution mapping and breeding application of a novel brown planthopper resistance gene derived from wild rice (Oryza rufipogon Griff). Rice. https://doi.org/10.1186/s12284-019-0289-7

    Article  PubMed  PubMed Central  Google Scholar 

  • Liu Y, Wu H, Chen H, Liu Y, He J, Kang H, Sun Z, Pan G, Wang Q, Hu J et al (2015) A gene cluster encoding lectin receptor kinases confers broad-spectrum and durable insect resistance in rice. Nat Biotechnol 33:301–305. https://doi.org/10.1038/nbt.3069

    Article  CAS  PubMed  Google Scholar 

  • Ma X, Fu Y, Zhao X et al (2016) Genomic structure analysis of a set of Oryza nivara introgression lines and identification of yield-associated QTLs using whole-genome resequencing. Sci Rep 6:27425. https://doi.org/10.1038/srep27425

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Meng L, Li H, Zhang L, Wang J (2015) QTL IciMapping: integrated software for genetic linkage map construction and quantitative trait locus mapping in biparental populations. Crop J 3:269–283

    Article  Google Scholar 

  • Michelmore RW, Paran KRV (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 

  • Mishra A, Barik SR, Pandit E, Yadav SS, Das SR, Pradhan K (2022) Genetics, mechanisms and deployment of brown planthopper resistance genes in rice. CRC Crit Rev Plant Sci 41:91–127

    Article  CAS  Google Scholar 

  • Mohanty SK, Panda RS, Mohapatra SL, Nanda A, Behera L, Jena M, Sahu RK, Sahu SC, Mohapatra T (2017) Identification of novel quantitative trait loci associated with brown planthopper resistance in the rice landrace Salkathi. Euphytica. https://doi.org/10.1007/s10681-017-1835-2

    Article  Google Scholar 

  • Nguyen CD, Zheng SH, Sanada-Morimura S, Matsumura M, Yasui H, Fujita D (2021) Substitution mapping and characterization of brown planthopper resistance genes from indica rice variety, “PTB33” (Oryza sativa L.). Breed Sci 71:497–509

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ookawa T, Aoba R, Yamamoto T, Ueda T, Takai T, Fukuoka S et al (2016) Precise estimation of genomic regions controlling lodging resistance using a set of reciprocal chromosome segment substitution lines in rice. Sci Rep 6:30572. https://doi.org/10.1038/srep30572

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Orjuela J, Garavito A, Bouniol M, Arbelaez JD, Moreno L, Kimball J, Wilson G, Rami JF, Tohme J, McCouch SR, Lorieux M (2010) A universal core genetic map for rice. Theor Appl Genet 120:563–572

    Article  CAS  PubMed  Google Scholar 

  • Qiu Y, Guo J, Jing S, Zhu L, He G (2010) High-resolution mapping of the brown planthopper resistance gene Bph6 in rice and characterizing its resistance in the 9311 and Nipponbare near isogenic backgrounds. Theor Appl Genet 121:1601–1611

    Article  PubMed  Google Scholar 

  • Qiu X, Chen K, Lv W, Ou X, Zhu Y, Xing D et al (2017) Examining two sets of introgression lines reveals background-independent and stably expressed QTL that improve grain appearance quality in rice (Oryza sativa L.). Theor Appl Genet 130:951–967. https://doi.org/10.1007/s00122-017-2862-z

    Article  PubMed  PubMed Central  Google Scholar 

  • Rahman ML, Jiang W, Chu SH, Qiao Y, Ham TH, Woo MK, Lee J, Khanam S, Chin JH, Jeung JU, Brar DS, Jena KK, Koh HJ (2009) High-resolution mapping of two brown planthopper resistance genes, Bph20(t) and Bph21(t), originating from Oryza minuta. Theor Appl Genet 119:1237–1246

    Article  PubMed  Google Scholar 

  • Ren J, Gao F, Wu X, Lu X, Zeng L, Lv J, Su X, Luo H, Ren G (2016) Bph32, a novel gene encoding an unknown SCR domain-containing protein, confers resistance against the brown planthopper in rice. Sci Rep 6:37645. https://doi.org/10.1038/srep37645

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Saghai-Maroof MA, Soliman KM, Jorgensen RA, Allard RW (1984) Ribosomal DNA spacer length polymorphism in barley: Mendelian inheritance, chromosomal location and population dynamics. Proc Natl Acad Sci USA 81:8014–8018

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sani Haliru B, Rafii MY, Mazlan N, Ramlee SI, Muhammad I, Silas Akos I, Halidu J, Swaray S, Rini Bashir Y (2020) Recent strategies for detection and improvement of brown planthopper resistance genes in rice: a review. Plants 9(9):1202. https://doi.org/10.3390/plants9091202

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sarao PS, Sahi GK, Neelam K, Mangat GS, Patra BC, Singh K (2016) Donors for resistance to brown planthopper Nilaparvata lugens (Stål) from wild rice species. Rice Sci 23:219–224

    Article  Google Scholar 

  • Sen S, Chakraborty R, Kalita P (2020) Rice—not just a staple food: a comprehensive review on its phytochemicals and therapeutic potential. Trends Food Sci Technol 97:265–285. https://doi.org/10.1016/j.tifs.2020.01.022

    Article  CAS  Google Scholar 

  • Shi S, Wang H, Nie L, Tan D, Zhou C, Zhang Q, Li Y, Du B, Guo J, Huang J et al (2021) Bph30 confers resistance to brown planthopper by fortifying sclerenchyma in rice leaf sheaths. Mol Plant 14:1714–1732. https://doi.org/10.1016/j.molp.2021.07.004

    Article  CAS  PubMed  Google Scholar 

  • Singh K, Neelam K, Kaur K (2016) Broadening the genetic base of grain cereals. p 27. https://doi.org/10.1007/978-81-322-3613-9_3

  • Sogawa K (2015) Planthopper outbreaks in different paddy ecosystems in Asia: man-made hopper plagues that threatened the green revolution in rice. In: Heong K, Cheng J, Escalada M (eds) Rice planthoppers. Springer, Dordrecht, pp 33–63. https://doi.org/10.1007/978-94-017-9535-7_2

    Chapter  Google Scholar 

  • Sun LH, Su CC, Wang CM, Zhai HQ, Wan JM (2005) Mapping of a major resistance gene to the brown planthopper in the rice cultivar Rathu Heenati. Breed Sci 55:391–396

    Article  CAS  Google Scholar 

  • Swamy BP, Kaladhar K, Reddy GA, Viraktamath BC, Sarla N (2014) Mapping and introgression of QTL for yield and related traits in two backcross populations derived from Oryza sativa cv. Swarna and two accessions of O. nivara. J Genet 93:643–654

    Article  PubMed  Google Scholar 

  • Takai T, Ikka T, Kondo K, Nonoue Y, Ono N, Arai-Sanoh Y et al (2014) Genetic mechanisms underlying yield potential in the rice high-yielding cultivar Takanari, based on reciprocal chromosome segment substitution lines. BMC Plant Biol 14:295. https://doi.org/10.1186/s12870-014-0295-2

    Article  PubMed  PubMed Central  Google Scholar 

  • Tamura Y, Hattori M, Yoshioka H, Yoshioka M, Takahashi A, Wu J, Sentoku N, Yasui H (2014) Map-based cloning and characterization of a brown planthopper resistance gene BPH26 from Oryza sativa L. ssp. indica cultivar ADR52. Sci Rep 4:5872. https://doi.org/10.1038/srep05872

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Temnykh S, Park WD, Ayres N, Cartinhour S, Hauck N, Lipovich L, Cho YG, Ishii T, McCouch SR (2000) Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.). Theor Appl Genet 100:697–712

    Article  CAS  Google Scholar 

  • Wang Y, Cao L, Zhang Y, Cao C, Liu F, Huang F, Qiu Y, Li R, Luo X (2015) Map-based cloning and characterization of BPH29, a B3 domain-containing recessive gene conferring brown planthopper resistance in rice. J Exp Bot 66:6035–6045. https://doi.org/10.1093/jxb/erv318

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang H, Shi S, Guo Q, Nie L, Du B, Chen R, Zhu L, He G (2018) High-resolution mapping of a gene conferring strong antibiosis to brown planthopper and developing resistant near-isogenic lines in 9311 backgrounds. Mol Breed 38:107. https://doi.org/10.1007/s11032-018-0859-1

    Article  CAS  Google Scholar 

  • Wang X, Han Y, Zhang Y, Deng B, Wu B, Guo X, Qin Y, Fang Y, Liu F, Qin B, Luo J, Li R (2021) QTL mapping integrated with BSA-Seq analysis identifies a novel gene conferring resistance to brown planthopper from common wild rice (Oryza rufipogon Griff). Euphytica. https://doi.org/10.21203/rs.3.rs-478718/v1

    Article  Google Scholar 

  • Yang HY, Ren X, Weng QM, Zhu LL, He GC (2002) Molecular mapping and genetic analysis of a rice brown planthopper (Nilaparvata lugens Stål) resistance gene. Hereditas 136:39–43

    Article  PubMed  Google Scholar 

  • Yang HY, You AQ, Yang ZF, Zhang FT, He RF, Zhu LL, He GC (2004) High-resolution genetic mapping at the Bph15 locus for brown planthopper resistance in rice (Oryza sativa L.). Theor Appl Genet 110:182–191

    Article  CAS  PubMed  Google Scholar 

  • Zhao Y, Huang J, Wang Z, Jing S, Wang Y, Ouyang Y, Cai B, Xin XF, Liu X, Zhang C et al (2016) Allelic diversity in an NLR gene BPH9 enables rice to combat planthopper variation. Proc Natl Acad Sci 113:12850–12855. https://doi.org/10.1073/pnas.1614862113

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhou C, Zhang Q, Chen Y, Huang J, Guo Q, Li Y, Wang W, Qiu Y, Guan W, Zhang J et al (2021) Balancing selection and wild gene pool contribute to resistance in global rice germplasm against planthopper. J Integr Plant Biol 63:1695–1711. https://doi.org/10.1016/j.molp.2021.07.004

    Article  CAS  PubMed  Google Scholar 

Download references

Funding

the funding was provided by ICAR (No. CS/18(12)/2015-O&P).

Author information

Authors and Affiliations

Authors

Contributions

Authors’ contribution All authors contributed to the study. Kumari Neelam, Kuldeep Singh, Yogesh Vikal conceptualized the research, proofreading of the manuscript, Preetinder Singh Sarao maintained the BPH biotype 4 and helped in the screening of mapping population, Pavneet Kaur, Kumari Neelam, renu Khanna: Genotyping, data analysis, writing of the original draft, Pavneet Kaur, Yashika Walia Dhir, Navneet Singh Saini performed phenotyping of mapping population against BPH biotype 4. All co-authors approved this manuscript before submission.

Corresponding author

Correspondence to Kumari Neelam.

Ethics declarations

Conflict of interest

All authors declare that they have no conflict of interest.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Kaur, P., Neelam, K., Sarao, P.S. et al. Mapping of a novel recessive brown planthopper resistance gene bph46 from wild rice (Oryza nivara). Euphytica 220, 61 (2024). https://doi.org/10.1007/s10681-024-03316-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s10681-024-03316-3

Keywords

Navigation