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Fine mapping the soybean aphid resistance gene Rag1 in soybean

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Abstract

The soybean aphid (Aphis glycines Matsumura) is an important soybean [Glycine max (L.) Merr.] pest in North America. The dominant aphid resistance gene Rag1 was previously mapped from the cultivar ‘Dowling’ to a 12 cM marker interval on soybean chromosome 7 (formerly linkage group M). The development of additional genetic markers mapping closer to Rag1 was needed to accurately position the gene to improve the effectiveness of marker-assisted selection (MAS) and to eventually clone it. The objectives of this study were to identify single nucleotide polymorphisms (SNPs) near Rag1 and to position these SNPs relative to Rag1. To generate a fine map of the Rag1 interval, 824 BC4F2 and 1,000 BC4F3 plants segregating for the gene were screened with markers flanking Rag1. Plants with recombination events close to the gene were tested with SNPs identified in previous studies along with new SNPs identified from the preliminary Williams 82 draft soybean genome shotgun sequence using direct re-sequencing and gene-scanning melt-curve analysis. Progeny of these recombinant plants were evaluated for aphid resistance. These efforts resulted in the mapping of Rag1 between the two SNP markers 46169.7 and 21A, which corresponds to a physical distance on the Williams 82 8× draft assembly (Glyma1.01) of 115 kilobase pair (kb). Several candidate genes for Rag1 are present within the 115-kb interval. The markers identified in this study that are closely linked to Rag1 will be a useful resource in MAS for this important aphid resistance gene.

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Abbreviations

bp:

Base pair

kb:

Kilobase pair

LG:

Linkage group

MAS:

Marker-assisted selection

MCA:

Melting curve assay

PCR:

Polymerase chain reaction

SSR:

Simple sequence repeat

SNP:

Single nucleotide polymorphism

STS:

Sequence tagged site

References

  • Bell-Johnson B, Garvey G, Johnson J, Lightfoot D, Meksem K (1998) Biotechnology approaches to improving resistance to SCN and SDS: methods for high-throughput marker-assisted selection. Soybean Genet Newsl 25:115–117

    Google Scholar 

  • Burd JD, Porter DR (2006) Biotypic diversity in greenbug (Hemiptera: Aphididae): characterizing new virulence and host associations. J Econ Entomol 99:959–965

    Article  PubMed  Google Scholar 

  • Choi IY, Hyten DL, Matukumalli LK, Song Q, Chaky JM, Quigley CV, Chase K, Lark KG, Reiter RS, Yoon MS, Hwang EY, Yi SI, Young ND, Shoemaker RC, van Tassell CP, Specht JE, Cregan PB (2007) A soybean transcript map: gene distribution, haplotype and single-nucleotide polymorphism analysis. Genetics 176:685–696

    Article  CAS  PubMed  Google Scholar 

  • Craigmiles JP, Hartwig EE, Sij JW (1978) Registration of ‘Dowling’ soybeans. Crop Sci 18:1094

    Article  Google Scholar 

  • Cregan PB, Quigley CV (1997) Simple sequence repeat DNA marker analysis. In: Caetano-Anolles G, Gresshoff PM (eds) DNA markers: protocols, applications and overview. Wiley, New York, pp 173–185

    Google Scholar 

  • Dogimont C, Bendahmane A, Pitrat M, Burget-Bigeard E, Hagen L, Le Menn A, Pauquet J, Rousselle P, Caboche M, Chovelon V (2009) Gene resistant to Aphis gossypii. US Patent 7,576,264, 18 Aug 2009

  • Fehr WR, Caviness CE, Burmood DT, Pennington JS (1971) Stage of development descriptions for soybeans, Glycine max (L.) Merrill. Crop Sci 11:929–931

    Google Scholar 

  • Francia E, Tacconi G, Crosatti C, Barabaschi D, Bulgarelli D, Dall’Aglio E, Valè G (2005) Marker assisted selection in crop plants. Plant Cell Tissue Organ Cult 82:317–342

    Article  CAS  Google Scholar 

  • Gupta P, Varshney RK, Sharma PC, Ramesh B (1999) Molecular markers and their applications in wheat breeding. Plant Breed 118:369–390

    Article  CAS  Google Scholar 

  • Haley SD, Peairs FB, Walker CB, Rudolph JB, Randolph TL (2004) Occurrence of a new Russian wheat aphid biotype in Colorado. Crop Sci 44:1589–1592

    Article  Google Scholar 

  • Hartman GL, Domier LL, Wax LM, Helm CG, Onstad DW, Shaw JT, Solter LF, Voegtlin DJ, D’Arcy CJ, Gray ME, Steffy KL, Orwick PL (2001) Occurrence and distribution of Aphis glycines on soybean in Illinois in 2000 and its potential control. http://www.plantmanagementnetwork.org/pub/php/brief/aphisglycines/. Accessed 06 Mar 2009

  • Hill CB, Li Y, Hartman GL (2004) Resistance to the soybean aphid in soybean germplasm. Crop Sci 44:98–106

    Google Scholar 

  • Hill CB, Li Y, Hartman GL (2006a) A single dominant gene for resistance to the soybean aphid in the soybean cultivar Dowling. Crop Sci 46:1601–1605

    Article  Google Scholar 

  • Hill CB, Li Y, Hartman GL (2006b) Soybean aphid resistance in soybean Jackson is controlled by a single dominant gene. Crop Sci 46:1606–1608

    Article  CAS  Google Scholar 

  • Hill CB, Kim KS, Crull L, Diers BW, Hartman GL (2009) Inheritance of resistance to the soybean aphid in soybean PI 200538. Crop Sci 49:1193–1200

    Article  CAS  Google Scholar 

  • Hyten DL, Song Q, Zhu Y, Choi IY, Nelson RL, Costa JM et al (2006) Impacts of genetic bottlenecks on soybean genome diversity. Proc Natl Acad Sci USA 103:16666–16671

    Article  CAS  PubMed  Google Scholar 

  • Hyten DL, Song Q, Choi I-Y, Yoon M-S, Specht JE, Matukumalli LK, Nelson RL, Shoemaker RC, Young ND, Cregan PB (2008) High-throughput genotyping with the GoldenGate assay in the complex genome of soybean. Theor Appl Genet 116:945–952

    Article  CAS  PubMed  Google Scholar 

  • Hyten DL, Choi I-Y, Song Q, Specht JE, Carter TE, Shoemaker RC, Hwang E-Y, Matukumalli LK, Cregan PB (2009a) A high density integrated genetic linkage map of soybean and the development of a 1,536 Universal Soy Linkage Panel for QTL mapping. Crop Sci (in press)

  • Hyten DL, Smith J, Frederick RD, Tucker ML, Song Q, Cregan PB (2009b) Bulked segregant analysis using the GoldenGate assay to locate the Rpp3 locus that confers resistance to soybean rust in soybean. Crop Sci 49:265–271

    Article  CAS  Google Scholar 

  • Kaczorowski KA, Kim KS, Diers BW, Hudson ME (2008) Microarray-based genetic mapping using soybean near-isogenic lines and generation of SNP markers in the Rag1 aphid-resistance interval. Plant Genome 1:89–98

    Article  CAS  Google Scholar 

  • Keim P, Shoemaker RC (1988) A rapid protocol for isolating soybean DNA. Soybean Genet Newsl 15:150–152

    Google Scholar 

  • Kim KS, Hill CB, Hartman GL, Mian MAR, Diers BW (2008) Discovery of soybean aphid biotypes. Crop Sci 48:923–928

    Article  Google Scholar 

  • Klingler J, Creasy R, Gao LL, Nair RM, Calix AS, Jacob HS, Edwards OR, Singh KB (2005) Aphid resistance in Medicago truncatula involves antixenosis and phloem-specific, inducible antibiosis, and maps to a single locus flanked by NBS-LRR resistance gene analogs. Plant Physiol 137:1445–1455

    Article  CAS  PubMed  Google Scholar 

  • Lee SH, Walker DR, Cregan PB, Boerma HR (2004) Comparison of four flow cytometric SNP detection assays and their use in plant improvement. Theor Appl Genet 110:167–174

    Article  CAS  PubMed  Google Scholar 

  • Li Y, Hill CB, Carlson SR, Diers BW, Hartman GL (2007) Soybean aphid resistance in the soybean cultivars Dowling and Jackson map to linkage group M. Mol Breed 19:25–34

    Article  CAS  Google Scholar 

  • Li Y, Zou J, Li M, Bilgin DD, Vodkin LO, Hartman GL, Clough SJ (2008) Soybean defense responses to the soybean aphid. New Phytol 179(1):185–195

    Article  CAS  PubMed  Google Scholar 

  • Mensah C, DiFonzo C, Wang D (2008) Inheritance of soybean aphid resistance in PI 567541B and PI 567598B. Crop Sci 48:1759–1763

    Article  Google Scholar 

  • Mian MAR, Kang ST, Beil SE, Hammond RB (2008) Genetic linkage mapping of the soybean aphid resistance gene in PI 243540. Theor Appl Genet 117:955–962

    Article  CAS  Google Scholar 

  • Michel AP, Zhang W, Jung JK, Kang ST, Mian MAR (2009) Population genetic structure of Aphis glycines. Environ Entomol 38:1301–1311

    Article  PubMed  Google Scholar 

  • Milligan SB, Bodeau J, Yaghoobi J, Kaloshian I, Zabel P, Williamson VM (1998) The root knot nematode resistance gene Mi from tomato is a member of the leucine zipper, nucleotide binding, leucine-rich-repeat family of plant genes. Plant Cell 10:1307–1320

    Article  CAS  PubMed  Google Scholar 

  • Mohan M, Nair S, Bhagwat A, Krishna TG, Yano M, Bhatia CR, Sasaki T (1997) Genome mapping, molecular markers and marker-assisted selection in crop plants. Mol Breed 3:87–103

    Article  CAS  Google Scholar 

  • Nickell CD, Noel GR, Cary TR, Leitz RA (1998) Registration of ‘Dwight’ soybean. Crop Sci 38:1398

    Google Scholar 

  • Nickell CD, Noel GR, Cary TR, Thomas DJ, Diers BW (2001) Registration of ‘Loda’ soybean. Crop Sci 41:589–590

    Article  Google Scholar 

  • Rossi M, Goggin FL, Milligan SB, Kaloshian I, Ullman DE, Williamson VM (1998) The nematode resistance gene Mi of tomato confers resistance against the potato aphid. Proc Natl Acad Sci USA 95:9750–9754

    Article  CAS  PubMed  Google Scholar 

  • SAS Institute (2002) The SAS system for Windows. Release 9.00. SAS Institute, Cary

    Google Scholar 

  • Schork NJ, Fallin D, Lanchbury JS (2000) Single nucleotide polymorphisms and the future of genetic epidemiology. Clin Genet 58:250–264

    Article  CAS  PubMed  Google Scholar 

  • Van Ooijen JW, Voorrips RE (2001) JoinMap 3.0 software for the calculation of genetic linkage maps. Plant Research International, Wageningen

    Google Scholar 

  • Venette RC, Ragsdale DW (2004) Assessing the invasion by soybean aphid (Homoptera: Aphididae) where will it end? Ann Entomol Soc Am 97:219–226

    Article  Google Scholar 

  • Zhang G, Gu C, Wang D (2009) Molecular mapping of soybean aphid resistance genes in PI 567541B. Theor Appl Genet 118:473–482

    Article  CAS  PubMed  Google Scholar 

  • Zhu Y, Song QJ, Hyten DL, Van Tassell CP, Matukumalli LK, Grimm DR, Hyatt SM, Fickus EW, Young ND, Cregan PB (2003) Single-nucleotide polymorphism in soybean. Genetics 163:1123–1134

    CAS  PubMed  Google Scholar 

Download references

Acknowledgments

This work was supported by soybean check-off funding from the Illinois Soybean Association, the United Soybean Board, and the USDA CSREES grant #AG2006-34488-16915 to MEH and BD.

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Authors and Affiliations

  1. Department of Crop Sciences, University of Illinois, Urbana, IL, 61801, USA

    Ki-Seung Kim, Stephanie Bellendir, Curtis B. Hill, Matthew E. Hudson & Brian W. Diers

  2. USDA-ARS, Purdue University, West Lafayette, IN, 47907, USA

    Karen A. Hudson

  3. USDA-ARS, University of Illinois, Urbana, IL, 61801, USA

    Glen L. Hartman

  4. Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD, 20705, USA

    David L. Hyten

Authors
  1. Ki-Seung Kim
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  2. Stephanie Bellendir
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  3. Karen A. Hudson
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  4. Curtis B. Hill
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  5. Glen L. Hartman
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  6. David L. Hyten
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  7. Matthew E. Hudson
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  8. Brian W. Diers
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Corresponding author

Correspondence to Brian W. Diers.

Additional information

Communicated by A. Schulman.

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Kim, KS., Bellendir, S., Hudson, K.A. et al. Fine mapping the soybean aphid resistance gene Rag1 in soybean. Theor Appl Genet 120, 1063–1071 (2010). https://doi.org/10.1007/s00122-009-1234-8

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  • DOI: https://doi.org/10.1007/s00122-009-1234-8

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