Theoretical and Applied Genetics

, Volume 131, Issue 5, pp 1163–1171 | Cite as

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

  • Kishor Kumar
  • Preetinder Singh Sarao
  • Dharminder Bhatia
  • Kumari Neelam
  • Amanpreet Kaur
  • Gurjeet Singh Mangat
  • Darshan Singh Brar
  • Kuldeep Singh
Original Article


Key message

A BPH-resistant locus designated as Bph34 identified in Oryza nivara acc. IRGC104646 on long arm of chromosome 4 using high-resolution mapping with 50 K SNP chip. BPH resistance contributed by locus showed dominant inheritance in F2 and F3. The Bph34 locus is 91 kb in size and contains 11 candidate genes. In addition to SNP markers, SSR markers, RM16994 and RM17007 co-segregated with the BPH resistance. These two SSR markers can facilitate marker-assisted transfer of the Bph34 locus into elite rice cultivars in all labs.


Brown planthopper (BPH, Nilaparvata lugen Stål) is one of the most destructive insects of rice (Oryza sativa L.) causing significant yield losses annually. Exploiting host plant resistance to BPH and incorporating resistant genes in susceptible commercial cultivars is economical and environmentally friendly approach to manage this pest. Here, we report high-resolution mapping of a novel genetic locus for resistance to BPH, designated as Bph34 on long arm of rice chromosome 4. The locus was mapped using an interspecific F2 population derived from a cross between susceptible indica cultivar PR122 and BPH-resistant wild species, O. nivara acc. IRGC104646. Inheritance studies performed using F2 and F2:3 populations revealed the presence of single dominant gene. Construction of high-density linkage map using 50 K SNP chip (OsSNPnks) followed by QTL mapping identified single major locus at 28.8 LOD score between SNP markers, AX-95952039 and AX-95921548. The major locus contributing resistance to BPH designated as Bph34 and explained 68.3% of total phenotypic variance. The Bph34 locus is 91 Kb in size on Nipponbare reference genome-IRGSP-1.0 and contains 11 candidate genes. In addition to associated SNP markers, two SSR markers, RM16994 and RM17007, also co-segregated with the Bph34 which can be used efficiently for markers assisted transfer into elite rice cultivars across the labs.



Financial grant from Indian Council of Agricultural Research (ICAR), New Delhi under project “Niche Area of Excellence in Wheat and Rice, PC 2198” is highly acknowledged.

Compliance with ethical standards

Conflict of interest

Authors declare no conflict of interest.

Supplementary material

122_2018_3069_MOESM1_ESM.pdf (116 kb)
Fig. S1 High-density SNP-based linkage map generated using Affymetrix Axiom 50 K SNP chip based genotyping of interspecific F2 population derived from O. sativa cv. PR122 and O. nivara acc. IRGC104646 showing; (a) chromosome 1-6 (b) chromosome 7-12 (PDF 115 kb)
122_2018_3069_MOESM2_ESM.pdf (68 kb)
Supplementary material 2 (PDF 68 kb)
122_2018_3069_MOESM3_ESM.tif (179 kb)
Fig. S2 PCR amplification with Bph34 linked SSR markers showing differences in alleles in 1 = PR122, 2 = O. nivara acc. IRGC104646, 3 = Swarnlata, 4 = Balamawee on 2.5% agarose gel, L indicates the marker lane. (TIFF 178 kb)
122_2018_3069_MOESM4_ESM.tif (495 kb)
Fig. S3 Selected F2 recombinants and parental lines, PR122 and O. nivara acc. IRGC104646 indicating recombination events in the Bph34 region along with their mean BPH resistance scores, where A-allele homozygous for PR122; B-allele homozygous for O. nivara acc. IRGC104646 and H- heterozygotes (TIFF 495 kb)
122_2018_3069_MOESM5_ESM.tif (215 kb)
Fig. S4 Agarose gel showing amplification of linked SSR marker RM17014 in F3: BC1F1 plants, parental bands corresponding to PR122 and O. nivara acc. IRGC104646 are marked (TIFF 215 kb)
122_2018_3069_MOESM6_ESM.docx (19 kb)
Supplementary material 6 (DOCX 20 kb)


  1. Backus EA, Serrano MS, Ranger CM (2005) Mechanisms of hopperburn: an overview of insect taxonomy, behavior and physiology. Annu Rev Entomol 50:125–151. CrossRefPubMedGoogle Scholar
  2. Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, Selker EU, Cresko WA, Johnson EA (2008) Rapid SNP discovery and genetic mapping using sequenced rad markers. PLoS One. PubMedPubMedCentralGoogle Scholar
  3. Bhatia D, Wing RA, Singh K (2013) Genotyping by sequencing, its implications and benefits. Crop Improv 40:101–111Google Scholar
  4. Bhatia D, Joshi S, Das A, Vikal Y, Sahi GK, Neelam K, Kaur K, Singh K (2017) Introgression of yield component traits in rice (Oryza sativa ssp. indica) through interspecific hybridization. Crop Sci 57:1–17. CrossRefGoogle Scholar
  5. 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 15:122–140CrossRefGoogle Scholar
  6. Brar DS, Khush GS (1997) Alien introgression in rice. Plant Mol Biol 35:35–47. CrossRefPubMedGoogle Scholar
  7. Brar DS, Virk PS, Jena KK, Khush GS (2009) Breeding for resistance to planthoppers in rice. In: Heong KL, Hardy B (eds) Planthoppers: new threats to the sustainability of intensive rice production systems in Asia. International Rice Research Institute, Los Baños, pp 401–428Google Scholar
  8. Cheema KK, Grewal NK, Vikal Y, Sharma R, Lore JS, Das A, Bhatia D, Gupta V, Bharaj TS, Singh K (2008) A novel bacterial blight resistance gene from Oryza nivara mapped to 38 kb region on chromosome 4L and transferred to O. sativa (L.). Genet Res 90:397–407. CrossRefGoogle Scholar
  9. Cheng X, Zhu L, He G (2013) The understanding of molecular interaction between rice and brown planthopper. Mol Plant 6:621–634CrossRefPubMedGoogle Scholar
  10. Du B, Zhang W, Liu B et al (2009) Identification and characterization of Bph14, a gene conferring resistance to brown planthopper in rice. Proc Natl Acad Sci USA 106:22163–22168. CrossRefPubMedPubMedCentralGoogle Scholar
  11. Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One. PubMedPubMedCentralGoogle Scholar
  12. Fujita D, Kohli A, Horgan FG (2013) Rice resistance to planthoppers and leafhoppers. Crit Rev Plant Sci 32:162–191CrossRefGoogle Scholar
  13. He J, Liu Y, Liu Y, Jiang L, Wu H, Kang H, Liu S, Chen L, Liu X, Cheng X, Wan J (2013) High-resolution mapping of brown planthopper (BPH) resistance gene Bph27(t) in rice (Oryza sativa L.). Mol Breed 31:549–557. CrossRefGoogle Scholar
  14. Heinrichs EA, Medrano FG, Rapusas HR (1985) Genetic Evaluation for Insect Resistance in Rice. International Rice Research Institute, Los Baños, pp 71–170Google Scholar
  15. Heong KL, Hardy B (2009) Planthoppers: new threats to the sustainability of intensive rice production systems in Asia. International Rice Research Institute, Los BañosGoogle Scholar
  16. Hirabayashi H, Kaji R, Angeles ER, Ogawa T, Brar DS, Khush GS (1999) RFLP analysis of a new gene for resistance to brown planthopper derived from O. officinalis on rice chromosome 4. Breed Res 1:48–51Google Scholar
  17. Horgan FG, Ramal AF, Bentur JS et al (2015) Virulence of brown planthopper (Nilaparvata lugens) populations from South and South East Asia against resistant rice varieties. Crop Prot 78:222e231CrossRefGoogle Scholar
  18. Hu J, Cheng M, Gao G et al (2013) Pyramiding and evaluation of three dominant brown planthopper resistance genes in the elite indica rice 9311 and its hybrids. Pest Manag Sci 69:802–808. CrossRefPubMedGoogle Scholar
  19. Hu J, Xiao C, Cheng M et al (2015) A new finely mapped Oryza australiensis-derived QTL in rice confers resistance to brown planthopper. Gene 561:132–137. CrossRefPubMedGoogle Scholar
  20. Hu J, Xiao C, He Y (2016) Recent progress on the genetics and molecular breeding of brown planthopper resistance in rice. Rice 9:30CrossRefPubMedPubMedCentralGoogle Scholar
  21. Huang Z, He G, Shu L, Li X, Zhang Q (2001) Identification and mapping of two brown planthopper resistance genes in rice. Theor Appl Genet 102:929–934. CrossRefGoogle Scholar
  22. Huang D, Qiu Y, Zhang Y, Huang F, Meng J, Wei S et al (2012) Fine mapping and characterization of BPH27, a brown planthopper resistance gene from wild rice (Oryza rufipogon Griff.). Theor Appl Genet 126:219–229CrossRefPubMedGoogle Scholar
  23. International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436:793–800. CrossRefGoogle Scholar
  24. IRRI (1996) Standard evaluation systems for rice. IRRI, PhillipinesGoogle Scholar
  25. Ishii T, Brar DS, Multani DS, Khush GS (1994) Molecular tagging of genes for brown planthopper resistance and earliness introgressed from Oryza australiensis into cultivated rice, O. sativa. Genome 37:217–221CrossRefPubMedGoogle Scholar
  26. Jena KK, Kim SM (2010) Current status of brown planthopper (BPH) resistance and genetics. Rice 3:161–171CrossRefGoogle Scholar
  27. Jena KK, Jeung JU, Lee JH et al (2006) High-resolution mapping of a new brown planthopper (BPH) resistance gene, Bph18(t), and marker-assisted selection for BPH resistance in rice (Oryza sativa L.). Theor Appl Genet 112:288–297. CrossRefPubMedGoogle Scholar
  28. Ji H, Kim S, Kim YH 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.,2016 CrossRefPubMedPubMedCentralGoogle Scholar
  29. Kenmore PE, Carino FO, Perez CA, Dyck VA, Gutierrez AP (1984) Population regulation of the rice brown planthopper (Nilaparvata lugens Stål) within rice fields in the Philippines. J Plant Prot 1:19–37Google Scholar
  30. Khush GS, Ling KC, Aquino RC, Aquiero VM (1977) Breeding for resistance to grassy stunt in rice. In: Proceedings of 3rd international Congress SABRAO, Canberra, Australia, pp 3–9Google Scholar
  31. Kumar H, Maurya RP, Tiwari SN (2012) Studies on antibiosis mechanism of resistance in rice against brown planthopper Nilaparvata lugens (Stål). Ann Plant Prot Sci 28:98–101Google Scholar
  32. Kumari N, Lore JS, Kaur K, Pathania S, Kumar K, Sahi G, Mangat GS, Singh K (2016) Identification of resistance sources in wild species of rice against two recently evolved pathotypes of Xanthomonas oryzae pv oryzae. Plant Genet Resour. Google Scholar
  33. Li C, Zhou A, Sang T (2006) Genetic analysis of rice domestication syndrome with the wild annual species, Oryza nivara. New Phytol 170:185–194CrossRefPubMedGoogle Scholar
  34. Liang Y, Weilin Z (2016) Genetic and biochemical mechanisms of rice resistance to planthoppers. Plant Cell Rep 35:1559–1572CrossRefGoogle Scholar
  35. Ling KC, Tiongco ER, Aguiero VM (1978) Rice ragged stunt, a new virus disease. Plant Dis Rep 62:701–705Google Scholar
  36. Liu G, Yan H, Fu Q, Qian Zhang Z, Zhai W, Zhu L (2001) Mapping of a new gene for brown planthopper resistance in cultivated rice introgressed from Oryza eichingeri. Chin Sci Bull 46:1459–1462. CrossRefGoogle Scholar
  37. Liu Y, Wu H, Chen H, Liu Y, He J, Kang H, Sun Z, Pan G, Wang Q, Hu J, Zhou F, Zhou K, Zheng X, Ren Y, Chen L, Wang Y, Zhao Z, Lin Q, Wu F, Zhang X, Guo X, Cheng X, Jiang L, Wu C, Wang H, Wan J (2015) A gene cluster encoding lectin receptor kinases confers broad-spectrum and durable insect resistance in rice. Nat Biotechnol 33:301–305. CrossRefPubMedGoogle Scholar
  38. Lv W, Du B, Shangguan X et al (2014) BAC and RNA sequencing reveal the brown planthopper resistance gene BPH15 in a recombination cold spot that mediates a unique defense mechanism. BMC Genom 15:674. CrossRefGoogle Scholar
  39. Matsumura M, Takeuchi H, Satoh M, Sanasa-Morimura S, Otuka A, Watanabe T, Thanh DV (2009) Current status of insecticide resistance in rice planthoppers. In: Heong KL, Hardy B (eds) Planthoppers: new threats to the sustainability of intensive rice production systems in Asia. International Rice Research Institute, Los Baños, pp 233–244Google Scholar
  40. Myint KKM, Fujita D, Matsumura M, Sonoda T, Yoshimura A, Yasui H (2012) Mapping and pyramiding of two major genes for resistance to the brown planthopper (Nilaparvata lugens Stål) in the rice cultivar ADR52. Theor Appl Genet 124:495–504CrossRefPubMedGoogle Scholar
  41. Pathak MD, Cheng CH, Furtono ME (1969) Resistance to Nephotettix cincticeps and Nilaparvata lugens in varieties of rice. Nature 223:502–504CrossRefGoogle Scholar
  42. Qiu Y, Guo J, Jing S (2012) Development and characterization of japonica rice lines carrying the brown planthopper-resistance genes BPH12 and BPH6. Theor Appl Genet 124:485–494CrossRefPubMedGoogle Scholar
  43. Rahman ML, Jiang W, Chu SH et al (2009) High-resolution mapping of two rice brown planthopper resistance genes, Bph20(t) and Bph21(t), originating from Oryza minuta. Theor Appl Genet 119:1237–1246. CrossRefPubMedGoogle Scholar
  44. Ren J, Gao F, Wu X et al (2016) Bph32, a novel gene encoding an unknown SCR domain-containing protein, confers resistance against the brown planthopper in rice. Sci Rep 6:37645.,2016 CrossRefPubMedPubMedCentralGoogle Scholar
  45. Renganayaki K, Fritz AK, Sadasivam S et al (2002) Mapping and progress toward map-based cloning of brown planthopper biotype-4 resistance gene introgressed from Oryza officinalis into cultivated rice, O. sativa. Crop Sci 42:2112–2117. CrossRefGoogle Scholar
  46. Rivera CT, Ou SH, Lida TT (1966) Grassy stunt disease of Rice and its transmission by the planthopper Nilaparvata lugens Stal. Plant Dis Report 7:453–456Google Scholar
  47. Sarao PS (2015) Integrated management of insect-pests of rice and basmati. Prog Farm 51:9–12Google Scholar
  48. Sarao PS, Sahi GK, Neelam K et al (2016) Donors for resistance to brown planthopper Nilaparvata lugens (Stål) from wild rice species. Rice Sci 23:219–224. CrossRefGoogle Scholar
  49. Sharma N, Ketipearachchi Y, Murata K et al (2003) RFLP/AFLP mapping of a brown planthopper (Nilaparvata lugens Stål) resistance gene Bph1 in rice. Euphytica 129:109–117CrossRefGoogle Scholar
  50. Singh N, Jayaswal PK, Panda K et al (2015) Single-copy gene based 50 K SNP chip for genetic studies and molecular breeding in rice. Sci Rep 5:11600. CrossRefPubMedPubMedCentralGoogle Scholar
  51. Srivastava C, Chander S, Sinha SR, Palta RK (2009) Toxicity of various insecticides against Delhi and Palla population of brown planthopper (Nilaparvata lugens). Indian J Agric Sci 79:1003–1006Google Scholar
  52. Suh JP, Yang SJ, Jeung JU et al (2011) Development of elite breeding lines conferring Bph18 gene-derived resistance to brown planthopper (BPH) by marker-assisted selection and genome-wide background analysis in japonica rice (Oryza sativa L.). Field Crop Res 120:215–222. CrossRefGoogle Scholar
  53. Tamura Y, Hattori M, Yoshioka H et al (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. CrossRefPubMedPubMedCentralGoogle Scholar
  54. Thomson MJ (2014) High-throughput SNP genotyping to accelerate crop improvement. Plant Breed Biotechnol 2:195–212. CrossRefGoogle Scholar
  55. Van Os H, Stam P, Visser RGF, Van Eck HJ (2005) RECORD: a novel method for ordering loci on a genetic linkage map. Theor Appl Genet 112:30–40. CrossRefPubMedGoogle Scholar
  56. Vikal Y, Das A, Patra B, Goel RK, Sidhu JS, Singh K (2007) Identification of new sources of bacterial blight (Xanthomonas oryzae pv. oryzae) resistance in wild Oryza species and O. glaberrima. Plant Genet Resour 5:108–112CrossRefGoogle Scholar
  57. Voorrips RE (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 93:77–78. CrossRefPubMedGoogle Scholar
  58. Wang S, Basten CJ, Zeng ZB (2012) Windows QTL Cartographer 2.5. Department of Statistics, North Carolina State University, Raleigh. (
  59. Wang Y, Cao L, Zhang Y et al (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. CrossRefPubMedPubMedCentralGoogle Scholar
  60. Wei J, Hu W, Liu Q, Cheng X, Tong M, Zhu L, Chen R, He G (2009) Understanding rice plant resistance to the brown planthopper (Nilaparvata lugens): a proteomic approach. Proteomics 9:1–11CrossRefGoogle Scholar
  61. Wu MT, Li CP, Chen JR, Huang SH, Ku HM (2009) Mapping of brown planthopper resistance gene introgressed from Oryza nivara into cultivated rice, O. sativa. In: Proceedings of the international symposium on rice research in the era of global warming, October 6–7, 2009, Taichung, Taiwan, pp 56–65Google Scholar
  62. Yang H, Ren X, Weng Q et al (2002) Molecular mapping and genetic analysis of a rice brown planthopper (Nilaparvata lugens Stål) resistance gene. Hereditas 136:39–43. CrossRefPubMedGoogle Scholar
  63. Yang H, You A, Yang Z et al (2004) High-resolution genetic mapping at the Bph15 locus for brown planthopper resistance in rice (Oryza sativa L.). Theor Appl Genet 110:182–191. CrossRefPubMedGoogle Scholar
  64. Zhao Y, Huang J, Wang Z et al (2016) Allelic diversity in an NLR gene BPH9 enables rice to combat planthopper variation. Proc Natl Acad Sci USA 113:12850–12855. CrossRefPubMedCentralGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.School of Agricultural BiotechnologyPunjab Agricultural UniversityLudhianaIndia
  2. 2.Department of Plant Breeding and GeneticsPunjab Agricultural UniversityLudhianaIndia
  3. 3.ICAR-National Bureau of Plant Genetic ResourcesNew DelhiIndia

Personalised recommendations