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Fine mapping and identification of candidate rice genes associated with qSTV11 SG, a major QTL for rice stripe disease resistance

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Abstract

Rice stripe disease, caused by rice stripe virus (RSV) is a serious constraint to rice production in subtropical regions of East Asia. We performed fine mapping of a RSV resistance QTL on chromosome 11, qSTV11 SG, using near-isogenic lines (NILs, BC6F4) derived from a cross between the highly resistant variety, Shingwang, and the highly susceptible variety, Ilpum, using 11 insertion and deletion (InDel) markers. qSTV11 SG was localized to a 150-kb region between InDel 11 (17.86 Mbp) and InDel 5 (18.01 Mbp). Among the two markers in this region, InDel 7 is diagnostic of RSV resistance in 55 Korean japonica and indica rice varieties. InDel 7 could also distinguish the allele type of Nagdong, Shingwang, Mudgo, and Pe-bi-hun from Zenith harboring the Stv-b i allele. As a result, qSTV11 SG is likely to be the Stv-b i allele. There were 21 genes in the 150-kb region harboring the qSTV11 SG locus. Three of these genes, LOC_Os11g31430, LOC_Os11g31450, and LOC_Os11g31470, were exclusively expressed in the susceptible variety. These expression profiles were consistent with the quantitative nature along with incomplete dominance of RSV resistance. Sequencing of these genes showed that there were several amino acid substitutions between susceptible and resistant varieties. Putative functions of these candidate genes for qSTV11 SG are discussed.

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References

  • Albar L, Bangratz-Reyser M, Hébrard E, Ndjiondjop MN, Jones M, Ghesquière A (2006) Mutations in the eIF (iso)4G translation initiation factor confer high resistance of rice to Rice yellow mottle virus. Plant J 47:417–426

    Article  PubMed  CAS  Google Scholar 

  • Bohnsack MT, Czaplinski K, Gorlich D (2004) Exportin 5 is a RanGTP-dependent dsRNA-binding protein that mediates nuclear export of pre-miRNAs. RNA 10:185–191

    Article  PubMed  CAS  Google Scholar 

  • Bollman KM, Aukerman MJ, Park MY, Hunter C, Berardini TZ, Poethig RS (2003) HASTY, the Arabidopsis ortholog of exportin 5/MSN5, regulates phase change and morphogenesis. Development 130:1493–1504

    Article  PubMed  CAS  Google Scholar 

  • Calado A, Treichel N, Muller EC, Otto A, Kutay U (2002) Exportin-5-mediated nuclear export of eukaryotic elongation factor 1A and tRNA. EMBO J 21:6216–6224

    Article  PubMed  CAS  Google Scholar 

  • Chung BJ (1974) Studies on the occurrence, host range, transmission, and control of rice stripe disease in Korea. Kor J Plant Prot 13(4):181–204

    Google Scholar 

  • Chung KY, Park RK, Chung KS, Lee SK, Jeon BT, Jin YD (1975) A new high yielding rice variety resistant to rice stripe virus ‘Milyang 15 (Nagdong)’. Res Rept NYAES 17(c):17–24. (in Korean)

    Google Scholar 

  • Ding XL, Jiang L, Liu SJ, Wan JM (2004) QTL analysis for rice stripe disease resistance gene using recombinant inbred lines derived from crossing of Kinmaze and DV85. Acta Genetica Sin 31:287–292

    CAS  Google Scholar 

  • Ding XL, Jiang L, Zhang YX, Sun DZ, Zhai HQ, Wan JM (2005) Detection and analysis of QTL for resistance to stripe disease in rice, using backcross inbred lines. Acta Agron Sin 31(8):1041–1046 (in Chinese with English Abstract)

    CAS  Google Scholar 

  • Du P, Wu J, Zhang J, Zhao S, Zheng H, Gao G, Wei L, Li Y (2011) Viral infection induces expression of novel phased microRNAs from conserved cellular microRNA precursors. PLoS Pathog 7:e1002176

    Article  PubMed  CAS  Google Scholar 

  • Falk BW, Tsai JH (1998) Biology and molecular biology of viruses in the genus Tenuivirus. Annu Rev Phytopathol 36:139–163

    Article  PubMed  CAS  Google Scholar 

  • German-Retana S, Walter J, Doublet B, Roudet-Tavert G, Nicaise V, Lecampion C, Houvenaghel MC, Robigalia C, Michon T, LeGall O (2008) Mutational analysis of plant cap-binding protein eIF4E reveals key amino acids involved in biochemical functions and Potyvirus infection. J Virol 82:7601–7612

    Article  PubMed  CAS  Google Scholar 

  • Hayano-Saito Y, Tsuji T, Fujii K, Saito K, Iwasaki M, Saito A (1998) Localization of the rice stripe disease resistance gene, Stvb-i, by graphical genotyping and linkage analyses with molecular markers. Theor Appl Genet 96:1044–1049

    Article  CAS  Google Scholar 

  • Hayano-Saito Y, Saito K, Hujii K, Touyama T, Tsuji T, Sugiura N, Izawa T, Iwasaki M (2000a) SCAR marker for selection of the rice stripe resistance gene Stvb-i. Breed Res 2(2):67–72 (in Japanese with English Abstract)

    Article  Google Scholar 

  • Hayano-Saito Y, Saito K, Nakamura S, Kawasaki S, Iwasaki M (2000b) Fine physical mapping of the rice stripe resistance gene locus, Stvb-i. Theor Appl Genet 101:59–63

    Article  CAS  Google Scholar 

  • Hemmes H, Lakatos L, Goldbach R, Burgyan J, Prins M (2007) The NS3 protein of Rice hoja blanca tenuivirus suppresses RNA silencing in plant and insect hosts by efficiently binding both siRNAs and miRNAs. RNA 13:1079–1089

    Article  PubMed  CAS  Google Scholar 

  • Ikeda R, Kaneda C (1982) Genetic relationships of brown planthopper resistance to dwarf and stripe disease resistance in rice. Jpn J Breed 32:177–185

    Google Scholar 

  • Kang BC, Yeam I, Frantz JD, Murphy JF, Jahn M (2005) The pvr1 locus in Capsicum encodes a translation initiation factor eIF4E that interacts with Tobacco etch virus VPg. Plant J 42:392–405

    Article  PubMed  CAS  Google Scholar 

  • Kwak DY, Lee BC, Choi I, Yeo US, Cho JH, Lee JY, Song YC, Yun YN, Park DS, Kang HW, Nam MH, Lee JH (2011) Identification of a major QTL, qSTV11 SG, associated with resistance to rice stripe virus disease originated from Shingwangbyeo in rice (Oryza Sativa L.). Korean J Breed Sci 43(5):396–401

    Google Scholar 

  • Lee BC, Yoon YN, Hong SJ, Hong YK, Kwak DY, Lee JH, Yeo US, Kang HW, Hwang HG (2008) Analysis on the Occurrence of Rice stripe virus. Res Plant Dis 14(3):210–213

    Article  Google Scholar 

  • Lee JH, Muhsin M, Atienza GA, Kwak DY, Kim SM, De Leon TB, Angeles ER, Coloquio E, Kondoh H, Satoh K, Cabunagan RC, Cabauatan PQ, Kikuchi S, Leung H, Choi IR (2010) Single nucleotide polymorphisms in a gene for Translation Initiation Factor (eIF4G) of rice (Oryza sativa) associated with resistance to rice tungro spherical virus. MPMI 23(1):29–38

    Article  PubMed  CAS  Google Scholar 

  • Léonard S, Plante D, Wittmann S, Daigneault N, Fortin MC, Lalibereté JF (2000) Complex formation between Potyvirus Vpg and translation eukaryotic initiation factor 4E correlates with virus infectivity. J Virol 74:7730–7737

    Article  PubMed  Google Scholar 

  • Lu L, Du Z, Qin M, Wang P, Lan H, Niu X, Jia D, Xie L, Lin Q et al (2009) Pc4, a putative movement protein of rice stripe virus, interacts with a type I DnaJ protein and a small Hsp of rice. Virus Genes 38:320–327

    Article  PubMed  CAS  Google Scholar 

  • Lund E, Guttinger S, Calado A, Dahlberg JE, Kutay U (2004) Nuclear export of microRNA precursors. Science 303:95–98

    Article  PubMed  CAS  Google Scholar 

  • Maeda H, Nemoto H, Yagi T, Fukuta Y (1999) QTL analysis for rice stripe disease resistance using recombinant inbred lines (RILs) derived from crossing between Milyang and Akihikari. In: China. Association of Agricultural Science, China National Rice Research Institute, China National Hybrid Rice Research and Development Center, China Foundation for Agricultural Science and Education. Prospects of Rice Genetics and Breeding for the 21st Century: Paper Collection of International Rice genetics and Breeding Symposium. China Agricultural Science and Technology Press, Beijing, pp 53–57

  • Maeda H, Sugisawa T, Nemoto H, Sunohara Y (2004) QTL analysis for rice stripe resistance in the Japanese upland rice Kanto 72. Breed Sci 54:19–26

    Article  CAS  Google Scholar 

  • Maule AJ, Caranta C, Boulton MI (2007) Sources of natural resistance to plant viruses: status and prospects. Mol Plant Pathol 8:223–231

    Article  PubMed  CAS  Google Scholar 

  • Miyoshi H, Suehiro N, Tomoo K, Muto S, Takahashi T, Tsukamoto T, Ohmori T, Natsuaki T (2006) Binding analyses for the interaction between plant virus genome-linked protein (VPg) and plant translational initiation factors. Biochemie 88:329–340

    Article  CAS  Google Scholar 

  • Nault LR (1994) Transmission biology, vector specificity and evolution of planthopper-transmitted plant viruses. In: Denno RE, Perfect TJ (eds) Planthopper, their ecology and management. Chapman and Hall, New York, pp 429–448

    Google Scholar 

  • Olsen AN, Ernst HA, Leggio LL, Skriver K (2004) NAC transcription factors: structurally distinct, functionally diverse. Trends Plant Sci 10:1360–1385

    Google Scholar 

  • Ou SH (1972) Virus diseases. In: Diseases Rice (ed) pp. Commonwealth Mycological Institute, Surrey, pp 14–22

    Google Scholar 

  • Park MY, Wu G, Gonzalez-Sulser A, Vaucheret H, Scott Poethig R (2005) Nuclear processing and export of microRNAs in Arabidopsis. PNAS 102:3691–3696

    Article  PubMed  CAS  Google Scholar 

  • Schaad MC, Anderberg RJ, Carrington JC (2000) Strain-specific interaction of the tobacco etch virus NIa protein with the translation initiation factor eIF4E in the yeast two hybrid system. Virology 234:84–92

    Google Scholar 

  • Shen YJ, Jiang H, Jin JP, Zhang ZB, He YY, Wang G, Wang C, Qian L, Li X, Yu QB, Liu HJ, Chen DH, Gao JH, Huang H, Shi TL, Yang ZN (2004) Development of genome-wide DNA polymorphism database for map-based cloning of rice genes. Plant Physiol 135:1198–1205

    Article  PubMed  CAS  Google Scholar 

  • Shimizu T, Toriyama S, Takahashi M, Akutsu K, Yoneyama K (1996) Non-viral sequences at the 59 termini of mRNAs derived from virus-sense and virus-complementary sequences of the ambisense RNA segments of rice stripe tenuivirus. J Gen Virol 77:541–546

    Article  PubMed  CAS  Google Scholar 

  • Takahashi Y, Omura T, Shohara K, Tsuchizaki T (1991) Comparison of four serological methods for practical detection of ten viruses of rice in plants and insects. Plant Dis 75:458–461

    Article  CAS  Google Scholar 

  • Toriyama S (1995) Viruses and molecular biology of Tenuivirus. In: Singh RP, Singh US, Kohmoto K (eds) Pathogenesis and Host Specificity in Plant Diseases, Viruses and Viroids, vol 3. Pergamon, Oxford, p 211–223

  • Washino O, Toriyama K, Ezuka A, Sakurai Y (1968) Studies on the breeding of rice varieties resistance to stripe disease. III. Genetic studies on resistance to stripe in foreign varieties. Jpn J Breed 17:167–172

    Google Scholar 

  • Washio O, Ezuka A, Sakurai Y, Toriyama K (1968a) Studies on the breeding of rice varieties resistant to rice stripe disease. II. Genetic study on resistance to stripe disease in Japanese upland rice. Jpn J Breed 18:96–101

    Google Scholar 

  • Washio O, Ezuka A, Sakurai Y, Toriyama K (1968b) Studies on the breeding of rice varieties resistant to rice stripe disease. III. Genetic studies on resistance to stripe in foreign varieties. Jpn J Breed 18:167–172

    Google Scholar 

  • Washio O, Ezuka A, Sakurai Y, Toriyama K (1968c) Testing method for, genetics of and breeding for resistance to rice stripe disease. Bull Chugoku Natl Agric Exp Stn A16:39–197

    Google Scholar 

  • Wu SJ, Zhong H, Zhou Y, Zuo H, Zhou LH, Zhu JY, Ji CQ, Gu SL, Gu MH, Liang GH (2009) Identification of QTLs for the resistance to rice stripe virus in the indica rice variety Dular. Euphytica 165:557–565

    Article  Google Scholar 

  • Wu X, Zuo S, Chen Z, Zhang Y, Zhu J, Ma N, Tang J, Chu C, Pan X (2011) Fine mapping of qSTV11 TQ, a major gene conferring resistance to rice stripe disease. Theor Appl Genet 122:915–923

    Article  PubMed  Google Scholar 

  • Xie RK, Mao BH, Wang YD, Zhao Y, Zhen YL (2005) The incidence and control of rice stripe in indica hybrid rice. Hybrid Rice 20:48–49

    Google Scholar 

  • Xiong R, Wu J, Zhou Y, Zhou X (2008) Identification of a movement protein of the tenuivirus rice stripe virus. J Virol 82:12304–12311

    Article  PubMed  CAS  Google Scholar 

  • Xiong R, Wu J, Zhou Y, Zhou X (2009) Characterization and subcellular localization of an RNA silencing suppressor encoded by rice stripe tenuivirus. Virology 387:29–40

    Article  PubMed  CAS  Google Scholar 

  • Xu SB, Tao YF, Yang ZQ, Chu JY (2002) A simple and rapid method used for silver staining and gel preservation. Hereditas 24:336–338

    Google Scholar 

  • Yeam I, Cavatorta JR, Ripoll DR, Kang BC, Jahn MM (2007) Functional dissection of naturally occurring amino acid substitutions in eIF4E that confers recessive Potyvirus resistance in plants. Plant Cell 19:2913–2928

    Article  PubMed  CAS  Google Scholar 

  • Yoshii M, Nishikiori M, Tomita K, Yoshioka N, Kozuka R, Naito S, Ishikawa M (2004) The Arabidopsis Cucumovirus Multiplication 1 and 2 loci encode translation initiation factors 4E and 4G. J Virol 78:6102–6111

    Article  PubMed  CAS  Google Scholar 

  • Zhang SX, Li L, Wang XF, Zhou GH (2007) Transmission of rice stripe virus acquired form frozen infected leaves by the small brown planthopper (Laodelphax striatellus Fallen). J Virol Methods 146:359–362

    Article  PubMed  CAS  Google Scholar 

  • Zhao F, Cai Z, Hu T, Yao H, Wang L, Dong N, Wang B, Ru Z, Zhai W (2010) Genetic analysis and molecular mapping of a novel gene conferring resistance to rice stripe virus. Plant Mol Biol Rep 28:512–518

    Article  Google Scholar 

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Acknowledgments

This study was supported by grants from the Rural Development Administration (PJ0086852012).

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Authors and Affiliations

  1. National Institute of Crop Science, Milyang, 627-803, Korea

    Tackmin Kwon, Jong-Hee Lee, Soo-Kwon Park, Un-Ha Hwang, Jun-Hyun Cho, Do-Yeon Kwak, Yeong-Nam Youn, Un-Sang Yeo, You-Chun Song, Hang-Won Kang, Min-Hee Nam & Dong-Soo Park

  2. Dong-A University, 37 Nakdong-Daero, Busan, Korea

    Jaesung Nam

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  1. Tackmin Kwon
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  2. Jong-Hee Lee
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Correspondence to Dong-Soo Park.

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Communicated by M. Wissuwa.

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Kwon, T., Lee, JH., Park, SK. et al. Fine mapping and identification of candidate rice genes associated with qSTV11 SG, a major QTL for rice stripe disease resistance. Theor Appl Genet 125, 1033–1046 (2012). https://doi.org/10.1007/s00122-012-1893-8

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