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
Tóm tắt
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.
Tài liệu tham khảo
Backus EA, Serrano MS, Ranger CM (2005) Mechanisms of hopperburn: an overview of insect taxonomy, behavior and physiology. Annu Rev Entomol 50:125–151. https://doi.org/10.1146/annurev.ento.49.061802.123310
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. https://doi.org/10.1371/journal.pone.0003376
Bhatia D, Wing RA, Singh K (2013) Genotyping by sequencing, its implications and benefits. Crop Improv 40:101–111
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. https://doi.org/10.2135/cropsci2015.11.0693
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
Brar DS, Khush GS (1997) Alien introgression in rice. Plant Mol Biol 35:35–47. https://doi.org/10.1023/a:1005825519998
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 401–428
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. https://doi.org/10.1017/s0016672308009786
Cheng X, Zhu L, He G (2013) The understanding of molecular interaction between rice and brown planthopper. Mol Plant 6:621–634
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. https://doi.org/10.1073/pnas.0912139106
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. https://doi.org/10.1371/journal.pone.0019379
Fujita D, Kohli A, Horgan FG (2013) Rice resistance to planthoppers and leafhoppers. Crit Rev Plant Sci 32:162–191
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. https://doi.org/10.1007/s11032-012-9814-8
Heinrichs EA, Medrano FG, Rapusas HR (1985) Genetic Evaluation for Insect Resistance in Rice. International Rice Research Institute, Los Baños, pp 71–170
Heong KL, Hardy B (2009) Planthoppers: new threats to the sustainability of intensive rice production systems in Asia. International Rice Research Institute, Los Baños
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 1:48–51
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 78:222e231
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. https://doi.org/10.1002/ps.3437
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. https://doi.org/10.1016/j.gene.2015.02.026
Hu J, Xiao C, He Y (2016) Recent progress on the genetics and molecular breeding of brown planthopper resistance in rice. Rice 9:30
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. https://doi.org/10.1007/s001220000455
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 126:219–229
International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436:793–800. https://doi.org/10.1038/nature03895
IRRI (1996) Standard evaluation systems for rice. IRRI, Phillipines
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 37:217–221
Jena KK, Kim SM (2010) Current status of brown planthopper (BPH) resistance and genetics. Rice 3:161–171
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. https://doi.org/10.1007/s00122-005-0127-8
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. https://doi.org/10.1038/srep34376,2016
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 1:19–37
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 3–9
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 28:98–101
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. https://doi.org/10.1017/s1479262116000149
Li C, Zhou A, Sang T (2006) Genetic analysis of rice domestication syndrome with the wild annual species, Oryza nivara. New Phytol 170:185–194
Liang Y, Weilin Z (2016) Genetic and biochemical mechanisms of rice resistance to planthoppers. Plant Cell Rep 35:1559–1572
Ling KC, Tiongco ER, Aguiero VM (1978) Rice ragged stunt, a new virus disease. Plant Dis Rep 62:701–705
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. https://doi.org/10.1007/bf03187031
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. https://doi.org/10.1038/nbt.3069
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. https://doi.org/10.1186/1471-2164-15-674
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 233–244
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 124:495–504
Pathak MD, Cheng CH, Furtono ME (1969) Resistance to Nephotettix cincticeps and Nilaparvata lugens in varieties of rice. Nature 223:502–504
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 124:485–494
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. https://doi.org/10.1007/s00122-009-1125-z
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. https://doi.org/10.1038/srep37645,2016
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. https://doi.org/10.2135/cropsci2002.2112
Rivera CT, Ou SH, Lida TT (1966) Grassy stunt disease of Rice and its transmission by the planthopper Nilaparvata lugens Stal. Plant Dis Report 7:453–456
Sarao PS (2015) Integrated management of insect-pests of rice and basmati. Prog Farm 51:9–12
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. https://doi.org/10.1016/j.rsci.2016.06.005
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 129:109–117
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. https://doi.org/10.1038/srep11600
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 79:1003–1006
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. https://doi.org/10.1016/j.fcr.2010.10.004
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. https://doi.org/10.1038/srep05872
Thomson MJ (2014) High-throughput SNP genotyping to accelerate crop improvement. Plant Breed Biotechnol 2:195–212. https://doi.org/10.9787/pbb.2014.2.3.195
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. https://doi.org/10.1007/s00122-005-0097-x
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 5:108–112
Voorrips RE (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 93:77–78. https://doi.org/10.1093/jhered/93.1.77
Wang S, Basten CJ, Zeng ZB (2012) Windows QTL Cartographer 2.5. Department of Statistics, North Carolina State University, Raleigh. (http://statgen.ncsu.edu/qtlcart/WQTLCart.htm)
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. https://doi.org/10.1093/jxb/erv318
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 9:1–11
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 56–65
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. https://doi.org/10.1034/j.1601-5223.2002.1360106.x
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. https://doi.org/10.1007/s00122-004-1844-0
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. https://doi.org/10.1073/pnas.1614862113