Skip to main content

Advertisement

SpringerLink
Log in

Fine mapping and analyses of R SC8 resistance candidate genes to soybean mosaic virus in soybean

  • Original Paper
  • Published:
Theoretical and Applied Genetics Aims and scope Submit manuscript

Abstract

Soybean mosaic virus (SMV) in soybean [Glycine max (L.) Merr.] is a destructive foliar disease in soybean-producing countries worldwide. In this study, F2, F2:3, and F7:11 recombinant inbred lines populations derived from Kefeng No.1 × Nannong 1138-2 were used to study inheritance and linkage mapping of the SMV strain SC8 resistance gene in Kefeng No.1. Results indicated that a single dominant gene (designated R SC8 ) controls resistance, which is located on chromosome 2 (MLG D1b). A mixed segregating population was developed by selfing two heterozygous plants (RHL153-1 and RHL153-2) at four markers adjacent to the locus and used in fine mapping R SC8 . In addition, two genomic-simple sequence repeats (SSR) markers BARCSOYSSR_02_0610 and BARCSOYSSR_02_0616 were identified that flank the two sides of R SC8 . Sequence analysis of the soybean genome indicated that the interval between the two genomic-SSR markers is 200 kb. QRT-PCR analysis of the candidate genes determined that five genes (Glyma02g13310, 13320, 13400, 13460, and 13470) are likely involved in soybean SMV resistance. These results will have utility in cloning, transferring, and pyramiding of the R SC8 through marker-assisted selection in soybean breeding programs.

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

Access this article

Log in via an institution

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

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  • Ade J, DeYoung BJ, Golstein C, Innes RW (2007) Indirect activation of a plant nucleiotide binding site-leucine-rich repeat protein by a bacterial protease. Proc Natl Acad Sci 104:2531–2536

    Article  CAS  PubMed  Google Scholar 

  • Babu M, Gagarinova AG, Brandle JE, Wang AM (2008) Association of the transcriptional response of soybean plants with soybean mosaic virus systemic infection. J Gen Virol 89:1069–1080

    Article  CAS  PubMed  Google Scholar 

  • Bai L, Li HC, Ma Y, Wang DG, Liu N, ZHi HJ (2009) Inheritance and gene mapping of resistance to soybean mosaic virus strain SC-11 in soybean. Soybean Sci 28:1–6

    Google Scholar 

  • Cheng H, Yang H, Zhang D, Gai JY, Yu DY (2010) Polymorphisms of soybean isoflavone synthase and flavanone 3-hydroxylase genes are associated with soybean mosaic virus resistance. Mol Breed 25:13–24

    Article  CAS  Google Scholar 

  • Cho ER, Goodman RM (1979) Strains of soybean mosaic virus: classification based on virulence in resistant soybean cultivars. Phytopathology 69:467–470

    Article  Google Scholar 

  • Cho ER, Goodman RM (1982) Evaluation of resistance in soybeans to soybean mosaic virus strains. Crop Sci 22:1133–1136

    Article  Google Scholar 

  • Choi BK, Koo JM, Ahn HJ, Yum HJ, Choi CW, Ryu KH, Chen PY, Tolin SA (2005) Emergence of Rsv-resistance breaking soybean mosaic virus isolates from Korean soybean cultivars. Virus Res 112:42–51

    Article  CAS  PubMed  Google Scholar 

  • Choi IY, Hyten DL, Matukumalli LK, Song QJ, Chaky JM, Quigley CY, Chase K, Lark KG, Reiter RS, Yoon MS (2007) A soybean transcript map: gene distribution, haplotype and single-nucleotide polymorphism analysis. Genetics 176:685–696

    Article  CAS  PubMed  Google Scholar 

  • Fu SX, Zhan Y, Zhi HJ, Gai JY, Yu DY (2006) Mapping of SMV resistance gene Rsc-7 by SSR markers in soybean. Genetica 128:63–69

    Article  CAS  PubMed  Google Scholar 

  • Gagarinova AG, Babu M, Poysa V, Hill JH, Wang A (2008) Identification and molecular characterization of two naturally occurring soybean mosaic virus isolates that are closely related but differ in their ability to overcome Rsv4 resistance. Virus Res 138:50–56

    Article  CAS  PubMed  Google Scholar 

  • Gore MA, Hayes AJ, Jeong SC, Yue YG, Buss GR, Saghai Maroof MA (2002) Mapping tightly linked genes controlling potyvirus infection at the Rsv1 and Rpv1 region in soybean. Genome 45:592–599

    Article  CAS  PubMed  Google Scholar 

  • Guo DQ, Zhi HJ, Wang YW, Gai JY, Zhou XA, Yang CL (2005) Identification and distribution of strains of soybean mosaic virus in middle and northern of Huang Huai Region of China. Soybean Sci 27:64–68

    Google Scholar 

  • Haley SD, Afanador LK, Miklas PN, Stavely JR, Kelly JD (1994) Heterogeneous inbred populations are useful as sources of near-isogenic lines for RAPD marker localization. Theor Appl Genet 88:337–342

    Article  CAS  Google Scholar 

  • Hayes AJ, Ma GR, Buss GR, Saghai Maroof MA (2000a) Molecular marker mapping of Rsv4, a gene conferring resistance to all known strains of soybean mosaic virus. Crop Sci 40:1434–1437

    Article  CAS  Google Scholar 

  • Hayes AJ, Yue YG, Saghai Maroof MA (2000b) Expression of two soybean resistance gene candidates shows divergence of paralogous single-copy genes. Theor Appl Genet 101:789–795

    Article  CAS  Google Scholar 

  • Hayes AJ, Jeong SC, Gore MA, Yu YG, Buss GR, Tolin SA, Saghai Maroof MA (2004) Recombination within a nucleotide-binding-site/leucine-rich-repeat gene cluster produces new variants conditioning resistance to soybean mosaic virus in soybeans. Genetics 166:493–503

    Article  CAS  PubMed  Google Scholar 

  • Hulbert SH, Webb CA, Smith SM, Sun Q (2001) Resistance gene complexes: evolution and utilization. Annu Rev Phytopathol 39:285–312

    Article  CAS  PubMed  Google Scholar 

  • Hwang TY, Moon JK, Yu S, Yang K, Mohankumar S, Yu YH, Lee YH, Kim HS, Kim HM, Saghai Maroof MA (2006) Application of comparative genomics in developing molecular markers tightly linked to the virus resistance gene Rsv4 in soybean. Genome 49:380–388

    Article  CAS  PubMed  Google Scholar 

  • Hwang TY, Sayama T, Takahashi M, Takada Y, Nakamoto Y, Funatsuki H, Hisano H, Sasamoto S, Sato S, Tabata S (2009) High-density integrated linkage map based on SSR markers in soybean. DNA Res 16:213–225

    Article  CAS  PubMed  Google Scholar 

  • Jeong SC, Saghai Maroof MA (2004) Detection and genotyping of SNPs tightly linked to two disease resistance loci, Rsv1 and Rsv3, of soybean. Plant Breed 123:305–310

    Article  CAS  Google Scholar 

  • Jeong SC, Hayes AJ, Biyashev RM, Saghai Maroof MA (2001) Diversity and evolution of a non-TIR-NBS sequence family that clusters to a chromosomal “hotspot” for disease resistance genes in soybean. Theor Appl Genet 103:406–414

    Article  CAS  Google Scholar 

  • Jeong SC, Kristipati S, Hayes AJ, Maughan PJ, Noffsinger SL, Gunduz I, Buss GR, Saghai Maroof MA (2002) Genetic and sequence analysis of markers tightly linked to the soybean mosaic virus resistance gene, Rsv3. Crop Sci 42:265–270

    Article  CAS  PubMed  Google Scholar 

  • Kobayashi S, Araki E, Osaki M, Khush GS, Fukuta Y (2006) Localization, validation, and characterization of plant-type QTLs on chromosomes 4 and 6 in rice (Oryza sativa L.). Field Crops Res 96:106–112

    Article  Google Scholar 

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

    Google Scholar 

  • Li HC, Zhi HJ, Gai JY, Guo DQ, Wang YW, Li K, Bai L, Yang H (2006) Inheritance and gene mapping of resistance to soybean mosaic virus strain SC14 in soybean. J Integr Plant Biol 48:1466–1472

    Article  CAS  Google Scholar 

  • Li K, Yang QH, Zhi HJ, Gai JY, Yu DY (2010) Identification and distribution of soybean mosaic virus strains in southern China. Plant Dis 94:351–357

    Article  Google Scholar 

  • Luan XY, Li ZF, Man WQ, Bai YN, Ma YS, Liu XL, Zheng BX, Du WG (2006) Identification of molecular markers linked to resistance for SMV3 in soybean. Mol Plant Breed 4:841–845

    CAS  Google Scholar 

  • Lupas A, van Dyke M, Stock J (1991) Predicting coiled coils from protein sequences. Science 252:1162–1164

    Article  CAS  Google Scholar 

  • Martin GB, Brommonschenkel SH, Chunwongse J, Frary A, Ganal MW, Spivey R, Wu T, Earle ED, Tanksley SD (1993) Map-based cloning of a protein kinase gene conferring disease resistance in tomato. Science 262:1432–1436

    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 using segregating populations. Proc Natl Acad Sci 88:9828–9832

    Article  CAS  PubMed  Google Scholar 

  • Missaoui AM, Ha BK, Phillips DV, Boerma HR (2007) Single nucleotide polymorphism detection of the Rcs3 gene for resistance to frogeye leaf spot in soybean. Crop Sci 47:1681–1690

    Article  CAS  Google Scholar 

  • Möhring S, Salamini F, Schneider K (2005) Multiplexed, linkage group-specific SNP marker sets for rapid genetic mapping and fingerprinting of sugar beet. Mol Breed 14:475–488

    Article  Google Scholar 

  • Ohkawa H, Imanishi H, Shiota N, Yamada T, Inui H, Ohkawa Y (1998) Molecular mechanisms of herbicide resistance with special emphasis on cytochrome P450 monooxygenases. Plant Biotechnol 15:173–176

    CAS  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Saghai Maroof MA, Jeong SC, Gunduz I, Tucker DM, Buss GR, Tolin SA (2008) Pyramiding of soybean mosaic virus resistance genes by marker-assisted selection. Crop Sci 48:517–526

    Article  Google Scholar 

  • Saghai Maroof MA, Tucker DM, Skoneczka JA, Bowman BC, Tripathy S, Tolin SA (2010) Fine mapping and candidate gene discovery of the soybean mosaic virus resistance gene, Rsv4. Plant genome 3:14–22

    Article  CAS  Google Scholar 

  • Shi AN, Chen PY, Li DX, Zheng CM, Zhang B, Hou AF (2009) Pyramiding multiple genes for resistance to soybean mosaic virus in soybean using molecular markers. Mol Breed 23:113–124

    Article  CAS  Google Scholar 

  • Shirasu K, Schulze Lefert P (2003) Complex formation, promiscuity and multi-functionality: protein interactions in disease-resistance pathways. Trends Plant Sci 8:252–258

    Article  CAS  PubMed  Google Scholar 

  • Song WY, Wang GL, Chen LL, Kim HS, Pi LY, Holsten T, Gardner J, Wang B, Zhai WX, Zhu LH (1995) A receptor kinase-like protein encoded by the rice disease resistance gene, Xa21. Science 270:1804–1806

    Article  CAS  PubMed  Google Scholar 

  • Song QJ, Marek LF, Shoemaker RC, Lark KG, Concibido VC, Delannay X, Specht JE, Cregan PB (2004) A new integrated genetic linkage map of the soybean. Theor Appl Genet 109:122–128

    Article  CAS  PubMed  Google Scholar 

  • Song QJ, Jia GF, Zhu YL, Grant D, Nelson RT, Hwang EY, Hyten DL, Cregan PB (2010) Abundance of SSR motifs and development of candidate polymorphic SSR markers (BARCSOYSSR_1.0) in soybean. Crop Sci 50:1950–1960

    Article  CAS  Google Scholar 

  • Su CF, Lu WG, Zhao TJ, Gai JY (2010) Verification and fine-mapping of QTLs conferring days to flowering in soybean using residual heterozygous lines. Chin Sci Bull 55:1–10

    Article  Google Scholar 

  • Sun X, Cao Y, Yang Z, Xu C, Li X, Wang S, Zhang Q (2004) Xa26, a gene conferring resistance to Xanthomonas oryzae pv. oryzae in rice, encodes an LRR receptor kinase-like protein. Plant J 37:517–527

    Article  CAS  PubMed  Google Scholar 

  • Van Ooijen JW, Voorrips RE (2001) JoinMap(R) 3.0, Software for the calculation of genetic linkage maps. Plant Res Int, Wageningen

    Google Scholar 

  • Van RL, Roth R, De PJ (2001) Identification of distinct specificity determinants in resistance protein Cf-4 allows construction of a Cf-9 mutant that confers recognition of avirulence protein AVR4. Plant Cell 13:273–285

    Google Scholar 

  • Voorrips RE (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 93:77–78

    Article  CAS  PubMed  Google Scholar 

  • Wang YJ (2001) Establishment and adjustment of RIL population and its application to map construction, mapping genes resistant to SMV and QTL analysis of agronomic and quality traits in soybeans. PhD thesis, Nanjing Agricultural University, China

  • Wang XQ, Gai JY, Pu ZQ (2003a) Classification and distribution of strains of soybean mosaic virus in middle and lower Huanghuai and Changjiang river valleys. Soybean Sci 22:102–107

    Google Scholar 

  • Wang YJ, Dongfang Y, Wang XQ, Yang YL, Yu DY, Gai JY, Wu XL, He CY, Zhang JS, Chen SY (2004) Mapping of five genes resistant to SMV strains in soybean. Acta Genet Sin 31:87–90

    Google Scholar 

  • Wang X, Gai J, Yu D (2003b) Inheritance of resistance to the SMV strain group SC8 in Kefeng No. 1. Soybean Sci 22:190–192

    Google Scholar 

  • Watanabe S, Hideshima R, Xia Z, Tsubokura Y, Sato S, Nakamoto Y, Yamanaka N, Takahashi R, Ishimoto M, Anai T (2009) Map-based cloning of the gene associated with the soybean maturity locus E3. Genetics 182:1251–1262

    Article  CAS  PubMed  Google Scholar 

  • Xia Z, Tsubokura Y, Hoshi M, Hanawa M, Yano C, Okamura K, Ahmed TA, Anai T, Watanabe S, Hayashi M (2007) An integrated high-density linkage map of soybean with RFLP, SSR, STS, and AFLP markers using a single F2 population. DNA Res 14:257–269

    Article  CAS  PubMed  Google Scholar 

  • Yamanaka N, Watanabe S, Toda K, Hayashi M, Fuchigami H, Takahashi R, Harada K (2005) Fine mapping of the FT1 locus for soybean flowering time using a residual heterozygous line derived from a recombinant inbred line. Theor Appl Genet 110:634–639

    Article  CAS  PubMed  Google Scholar 

  • Yang H, Huang YP, Zhi HJ, Yu DY (2010) Proteomics-based analysis of novel genes involved in response toward soybean mosaic virus infection. Mol Biol Rep. doi:10.1007/s11033-010-0135-x

  • Yu YG, Saghai Maroof MA, Buss GR, Maughan PJ, Tolin SA (1994) RFLP and microsatellite mapping of a gene for soybean mosaic virus resistance. Phytopathology 84:60–64

    Article  CAS  Google Scholar 

  • Yu YG, Buss GR, Saghai Maroof MA (1996) Isolation of a superfamily of candidate disease-resistance genes in soybean based on a conserved nucleotide-binding site. Proc Natl Acad Sci 93:11751–11756

    Article  CAS  PubMed  Google Scholar 

  • Zhang ZY, Chen SY, Gai JY (1999) Molecular markers linked to Rsa resistant to soybean mosaic virus. Chin Sci Bull 44:154–158

    Article  CAS  Google Scholar 

Download references

Acknowledgments

This work was supported by the State Key Basic Research and Development Plan of China (Grant No. 2006A10A111), the National Natural Science Foundation of China (Grant No. 30971815) and the MOE 111 Project (Grant No. B08025). We also thank Song Q. J. from Soybean Genomics and Improvement Laboratory, USDA-ARS for providing the SSR markers primer sequences.

Author information

Authors and Affiliations

  1. Soybean Research Institute, National Center for Soybean Improvement, National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095, Nanjing, China

    Dagang Wang, Ying Ma, Yongqing Yang, Ning Liu, Chunyan Li, Yingpei Song & Haijian Zhi

Authors
  1. Dagang Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ying Ma
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Yongqing Yang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Ning Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Chunyan Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Yingpei Song
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Haijian Zhi
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Haijian Zhi.

Additional information

Communicated by H. T. Nguyen.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Wang, D., Ma, Y., Yang, Y. et al. Fine mapping and analyses of R SC8 resistance candidate genes to soybean mosaic virus in soybean. Theor Appl Genet 122, 555–565 (2011). https://doi.org/10.1007/s00122-010-1469-4

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00122-010-1469-4

Keywords

Search

Navigation