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Single nucleotide polymorphism markers for rapid detection of the Rsv4 locus for soybean mosaic virus resistance in diverse germplasm

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Abstract

Soybean mosaic virus (SMV) causes a substantial decrease in soybean yield and reduction of seed quality. The most effective management strategy to control the virus is the deployment of host resistance. Seven SMV strains and three independent multi-allelic loci for SMV resistance have been identified previously. The goal of this research was to detect single nucleotide polymorphisms (SNPs) associated with SMV resistance at the Rsv4 locus. Ten soybean accessions, with confirmed resistance genes, were used for sequencing the candidate gene Glyma.02g121400. Alignment of these sequences revealed three SNPs displaying 100% consistency for genotypes carrying the Rsv4 gene. These SNPs were applied for a rapid screen of diverse soybean germplasm using the Sequenom iPLEX Gold platform, phenotyped with SMV-G1 and G7 strains to determine phenotype and classified into several groups carrying the proposed R-gene. The population of V94-5152 (Rsv4) × Lee 68 (rsv) was screened using novel SNPs to create a genetic map with improved resolution to determine the location of the Rsv4. To observe the recombination frequencies within the population, three additional SNPs on both sides of the Glyma.02g121400 gene were added. A linkage map revealed a distance of 3.6 cM between the Rsv4 locus and the closest SNP, thus shifting the putative Rsv4 region downstream on chromosome 2. With this region, five candidate genes have been proposed. The genomic position of the discovered SNPs, linked to the Rsv4, could increase screening precision and accelerate breeding efforts to develop multi-strain-resistant crops.

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References

  • Buss GR, Ma G, Chen P, Tolin SA (1997) Registration of V94-5152 soybean germplasm resistant to soybean mosaic potyvirus. Crop Sci 37:1987–1988. doi:10.2135/cropsci1997.0011183X003700060068x

    Article  Google Scholar 

  • Buzzell RI, Tu JC (1989) Inheritance of a soybean stem-tip necrosis reaction to soybean mosaic virus. J Hered 80:400–401

    Google Scholar 

  • Carrington JC, Whitham SA (1998) Viral invasion and host defense: strategies and counter-strategies. Curr Opin Plant Biol 1:336–341. doi:10.1016/1369-5266(88)80056-6

    Article  CAS  PubMed  Google Scholar 

  • Chen P, Buss GR, Roane CW, Tolin SA (1991) Allelism among genes for resistance to soybean mosaic virus in strain differential soybean cultivars. Crop Sci 31:305–309. doi:10.2135/cropsci1991.0011183X003100020015x

    Article  Google Scholar 

  • Chen P, Buss GR, Roane CW, Tolin SA (1994) Inheritance in soybean of resistant and necrotic reactions to soybean mosaic virus strains. Crop Sci 34:414–422. doi:10.2135/cropsci1994.0011183X003400020021x

    Article  Google Scholar 

  • Cho EK, Goodman RM (1979) Strains of soybean mosaic virus: classification based on virulence in resistant soybean cultivars. Phytopathology 69:467–470. doi:10.1094/Phyto-69-467

    Article  Google Scholar 

  • Doerks T, Huber S, Buchner E, Bork P (2002) BSD: a novel domain in transcription factors and synapse-associated proteins. Trends Biochem Sci 27(4):168–170. doi:10.1016/S0968-0004(01)02042-4

    Article  CAS  PubMed  Google Scholar 

  • Doyle JJ, Doyle JL (1990) Isolation of plant DNA from fresh tissue. Focus 12:13–15

    Google Scholar 

  • Engelman JA, Luo J, Cantley LC (2006) The evolution of phosphatidylinositol 3-kinases as regulators of growth and metabolism. Nat Rev Genet 7(8):606–619. doi:10.1038/nrg1879

    Article  CAS  PubMed  Google Scholar 

  • Grant D, Nelson RT, Cannon SB, Shoemaker RC (2010) SoyBase, the USDA-ARS soybean genetics and genomics database. Nucl Acids Res 38(1):843–846. doi:10.1093/nar/gkp798

    Article  Google Scholar 

  • Gunduz I, Buss GR, Chen P, Tolin SA (2004) Genetic and phenotypic analysis of soybean mosaic virus resistance in PI 88788 soybean. Phytopathology 94:687–692. doi:10.1094/Phyto.2004.94.7.687

    Article  PubMed  Google Scholar 

  • Hayes AJ, Ma G, Buss GR, Saghai Maroof MA (2000) Molecular marker mapping of Rsv4, a gene conferring resistance to all known strains of soybean mosaic virus. Crop Sci 40:1434–1437. doi:10.2135/cropsci2000.4051434x

    Article  CAS  Google Scholar 

  • Hill JH (1999) Soybean mosaic virus. In: Hartman GL, Sinclair JB, Rupe JC (eds) Compendium of soybean diseases, 4th edn. Am Phytopathol Soc Press, St. Paul, MN, pp. 70–71

    Google Scholar 

  • Hwang TY, Moon JK, Yu S, Yang K, Mohankumar S, Yu YH, Lee YH, Kim HS, Kim HM, Saghai Maroof MA, Jeong SC (2006) Application of comparative genomics in developing molecular markers tightly linked to the virus resistance gene Rsv4 in soybean. Gemome 49(4):380–388. doi:10.1139/g05-111

    CAS  Google Scholar 

  • Ilut DC, Lipka AE, Jeong N, Bae DN, Kim DH, Kim JH, Redekar N, Yang K, Park W, Kang ST, Kim N, Moon JK, Saghai Maroof MA, Gore MA, Jeong SC (2015) Identification of haplotypes at the Rsv4 genomic region in soybean associated with durable resistance to soybean mosaic virus. Theor Appl Genet 9:1–16. doi:10.1007/s00122-015-2640-8

    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 

  • Kiihl RAS, Hartwig EE (1979) Inheritance of reaction to soybean mosaic virus in soybeans. Crop Sci 19:372–375. doi:10.2135/cropsci1979.0011183X001900030024x

    Article  Google Scholar 

  • Li D, Chen P, Alloatti J, Shi A, Chen YF (2010) Identification of new alleles for resistance to soybean mosaic virus in soybean. Crop Sci 50:649–655. doi:10.2135/cropsci2009.06.0302

    Article  Google Scholar 

  • Li D, Chen P, Shi A, Shakiba E, Gergerich R, Chen Y (2009) Temperature affects expression of symptoms induced by soybean mosaic virus in homozygous and heterozygous plants. J Hered 100(3):348–354. doi:10.1093/jhered/esn109

    Article  CAS  PubMed  Google Scholar 

  • Li K, Ren R, Adhimoolan K, Gao L, Yuan Y, Liu Z, Zhong Y, Zhi H (2015) Genetic analysis and identification of two soybean mosaic virus resistance genes Rsc18A and Rsc18B in soybeans. Plant Breed. In press

  • Liao L, Chen P, Rajcan I, Buss GR, Tolin SA (2011) Genetic analysis of ‘8101’ soybean containing three genes for resistance to soybean mosaic virus (SMV). Crop Sci 51:503–511. doi:10.2135/cropsci2010.02.0113

    Article  CAS  Google Scholar 

  • Ma G, Chen P, Buss GR, Tolin SA (1995) Genetic characteristics of two genes for resistance to soybean mosaic virus in PI 486355 soybean. Theor Appl Genet 91:907–914. doi:10.1093/jhered/esh059

    CAS  PubMed  Google Scholar 

  • Ma G, Chen P, Buss GR, Tolin SA (2002) Complementary action of two independent dominant genes in Columbia soybean for resistance to soybean mosaic virus. J Hered 93:179–184. doi:10.1093/jhered/93.3.179

    Article  CAS  PubMed  Google Scholar 

  • Ma G, Chen P, Buss GR, Tolin SA (2003) Genetic study of a lethal necrosis to soybean mosaic virus in PI 507389 soybean. J Hered 94:205–211. doi:10.1093/jhered/esg059

    Article  CAS  PubMed  Google Scholar 

  • Marone D, Russo MA, Laido G, De Leonardis AM, Mastrangelo AM (2013) Plant nucleotide binding site-leucine-rich repeat (NBS-LRR) genes: active guardians in host defense responses. Int J Mol Sci 14(4):7302–7326. doi:10.3390/ijms14047302

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ren Q, Pfeiffer TW, Ghabrial SA (1997) Soybean mosaic virus incidence level and infection time: interaction effects on soybean. Crop Sci 37:1706–1711. doi:10.2135/cropsci1997.0011183X003700060005x

    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 3:1–9. doi:10.3835/plantgenome2009.07.0020

    Article  Google Scholar 

  • Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J, Xu D, Hellsten U, May GD, Yu Y, Sakurai T, Umezawa T, Bhattacharyya MK, Sandhu D, Valliyodan B, Lindquist E, Peto M, Grant D, Shu S, Goodstein D, Barry K, Futrell-Griggs M, Abernathy B, Du J, Tian Z, Zhu L, Gill N, Joshi T, Libault M, Sethuraman A, Zhang XC, Shinozaki K, Nguyen HT, Wing RA, Cregan P, Specht J, Grimwood J, Rokhsar D, Stacey G, Shoemaker RC, Jackson SA (2010) Genome sequence of the palaeopolyploid soybean. Nature 463:178–183. doi:10.1038/nature08670

    Article  CAS  PubMed  Google Scholar 

  • Semagn K, Babu R, Hearne S, Olsen M (2014) Single nucleotide polymorphism genotyping using kompetitive allele specific PCR (KASP): overview of the technology and its application in crop improvement. Mol Breed 33:1–14. doi:10.1007/s11032-013-9917-x

    Article  CAS  Google Scholar 

  • Shakiba E, Chen P, Gergerich R, Li S, Dombek D, Brye K, Shi A (2012a) Reaction of commercial soybean cultivars from the mid-south to soybean mosaic virus. Crop Sci 52:1990–1997. doi:10.2135/cropsci2011.04.0221

    Article  Google Scholar 

  • Shakiba E, Chen P, Li D, Brye K, Dong D (2012b) Two novel alleles at the Rsv3 locus for resistance to soybean mosaic virus in PI 399091 and PI 61947 soybeans. Crop Sci 52:2587–2594. doi:10.2135/cropsci2012.01.0010

    Article  CAS  Google Scholar 

  • Shakiba E, Chen P, Brye K, Shi A (2013) Inheritance and allelism of resistance to soybean mosaic virus in Corsica and Beeson. Crop Sci 53:1455–1463. doi:10.2135/cropsci2012.01.0006

    Article  Google Scholar 

  • Shi A, Chen P, Vierling R, Li D, Zheng C (2012) Identification of soybean mosaic virus resistance alleles in Jindou 1 soybean. Euphytica 192:181–187. doi:10.1007/s10681-012-0816-8

    Article  Google Scholar 

  • Shi A, Chen P, Vierling R, Zheng C, Li D, Dong D, Shakiba E, Cervantez I (2011) Multiplex single nucleotide polymorphism (SNP) assay for detection of soybean mosaic virus resistance genes in soybean. Theor Appl Genet 122:445–457. doi:10.1007/s00122-010-1459-6

    Article  CAS  PubMed  Google Scholar 

  • Suh SJ, Bowman BC, Jeong N, Yang K, Kastl C, Tolin SA, Saghai Maroof MA, Jeong SC (2011) The Rsv3 locus conferring resistance to soybean mosaic virus is associated with a cluster of coiled-coil nucleotide-binding leucine-rich repeat genes. Plant Genome 4:55–64. doi:10.3835/plantgenome2010.11.0024

    Article  Google Scholar 

  • Tolin SA (1999) Diseases caused by viruses: compendium of soybean diseases. APS Press, St. Paul, MN, USA

    Google Scholar 

  • Wang D, Ma Y, Yang Y, Liu N, Li C, Song Y, Zhi H (2011) Fine mapping and analyses of R SC8 resistance candidate genes to soybean mosaic virus in soybean. Theor Appl Genet 122:555–565. doi:10.1007/s00122-010-1469-4

    Article  PubMed  Google Scholar 

  • Yan H, Wang H, Cheng H, Hu Z, Chu S, Zhang G, Yu D (2015) Detection and fine-mapping of SC7 resistance genes via linkage and association analysis in soybean. Integr Plant Biol 57(8):722–729. doi:10.1111/jipb.12323

    Article  CAS  Google Scholar 

  • 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. doi:10.1094/Phyto-84-6

    Article  CAS  Google Scholar 

  • Zheng C, Chen P, Gergerich RC (2005) Characterization of resistance to soybean mosaic virus in diverse soybean germplasm. Crop Sci 45:2503–2509. doi:10.2135/cropsci2005.0114

    Article  Google Scholar 

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Acknowledgments

We would like to acknowledge Dr. Randall Nelson (USDA-ARS) and Dr. Bo Zhang (Virginia Tech University) for providing the soybean seeds used in this study. We also thank Dr. Sue Tolin (Virginia Tech University) for providing SMV strains. This work was supported by the United Soybean Board and Arkansas Soybean Promotion Board.

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Authors and Affiliations

  1. Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, 72701, USA

    Mariola Klepadlo, Pengyin Chen, Richard E. Mason & Vibha Srivastava

  2. Department of Horticulture, University of Arkansas, Fayetteville, AR, 72701, USA

    Ainong Shi

  3. Department of Plant Pathology, University of Arkansas, Fayetteville, AR, 72701, USA

    Ken L. Korth

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  1. Mariola Klepadlo
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  2. Pengyin Chen
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Correspondence to Pengyin Chen.

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Klepadlo, M., Chen, P., Shi, A. et al. Single nucleotide polymorphism markers for rapid detection of the Rsv4 locus for soybean mosaic virus resistance in diverse germplasm. Mol Breeding 37, 10 (2017). https://doi.org/10.1007/s11032-016-0595-3

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