Theoretical and Applied Genetics

, Volume 121, Issue 3, pp 599–610 | Cite as

Fine mapping of the soybean aphid-resistance gene Rag2 in soybean PI 200538

  • Ki-Seung Kim
  • Curtis B. Hill
  • Glen L. Hartman
  • David L. Hyten
  • Matthew E. Hudson
  • Brian W. Diers
Original Paper


The discovery of biotype diversity of soybean aphid (SA: Aphis glycines Matsumura) in North America emphasizes the necessity to identify new aphid-resistance genes. The soybean [Glycine max (L.) Merr.] plant introduction (PI) 200538 is a promising source of SA resistance because it shows a high level of resistance to a SA biotype that can overcome the SA-resistance gene Rag1 from ‘Dowling’. The SA-resistance gene Rag2 was previously mapped from PI 200538 to a 10-cM marker interval on soybean chromosome 13 [formerly linkage group (LG) F]. The objective of this study was to fine map Rag2. This fine mapping was carried out using lines derived from 5,783 F2 plants at different levels of backcrossing that were screened with flanking genetic markers for the presence of recombination in the Rag2 interval. Fifteen single nucleotide polymorphism (SNP) markers and two dominant polymerase chain reaction-based markers near Rag2 were developed by re-sequencing target intervals and sequence-tagged sites. These efforts resulted in the mapping of Rag2 to a 54-kb interval on the Williams 82 8× assembly (Glyma1). This Williams 82 interval contains seven predicted genes, which includes one nucleotide-binding site-leucine-rich repeat gene. SNP marker and candidate gene information identified in this study will be an important resource in marker-assisted selection for aphid resistance and for cloning the gene.



Insertion and deletion


Kilobase pair


Marker-assisted selection


Melting curve assay


Nucleotide-binding site-leucine-rich repeat


Single nucleotide polymorphism


Sequence-tagged site



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.


  1. Ashfield T, Bocian A, Held D, Henk AD, Marek LF, Danesh D, Penuela S, Meksem K, Lightfoot DA, Young ND, Shoemaker RC, Innes RW (2003) Genetic and physical localization of the soybean Rpg1-b disease resistance gene reveals a complex locus containing several tightly linked families of NBS–LRR genes. Mol Plant Microbe Interact 16:817–826CrossRefPubMedGoogle Scholar
  2. 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 25:115–117Google Scholar
  3. Brotman Y, Silberstein L, Kovalski I, Perin C, Dogimont C, Pitrat M, Klingler J, Thompson GA, Perl-Treves R (2002) Resistance gene homologous in melon are linked to genetic loci conferring disease and pest resistance. Theor Appl Genet 104:1055–1063CrossRefPubMedGoogle Scholar
  4. 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 176:685–696CrossRefPubMedGoogle Scholar
  5. 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 173–185Google Scholar
  6. 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 2009Google Scholar
  7. Hayes AJ, Yue YG, Saghai Maroof MA (2000) Expression of two soybean resistance gene candidates shows divergence of paralogous single-copy genes. Theor Appl Genet 101:789–795CrossRefGoogle Scholar
  8. Hill CB, Li Y, Hartman GL (2004a) Resistance to the soybean aphid in soybean germplasm. Crop Sci 44:98–106CrossRefGoogle Scholar
  9. Hill CB, Li Y, Hartman GL (2004b) Resistance to Glycine species and various cultivated legumes to the soybean aphid (Homoptera: Aphididae). J Econ Entomol 97:1071–1077CrossRefPubMedGoogle Scholar
  10. Hill CB, Li Y, Hartman GL (2006a) A single dominant gene for resistance to the soybean aphid in the soybean cultivar Dowling. Crop Sci 46:1601–1605CrossRefGoogle Scholar
  11. Hill CB, Li Y, Hartman GL (2006b) Soybean aphid resistance in soybean Jackson is controlled by a single dominant gene. Crop Sci 46:1606–1608CrossRefGoogle Scholar
  12. Hill CB, Kim KS, Crull L, Diers BW, Hartman GL (2009) Inheritance of resistance to the soybean aphid in soybean PI 200538. Crop Sci 49:1193–1200CrossRefGoogle Scholar
  13. Hill CB, Crull L, Herman T, Voegtlin DJ, Hartman GL (2010) A new soybean aphid (Hemiptera: Aphididae) biotype identified. J Econ Entomol 103:509–515CrossRefPubMedGoogle Scholar
  14. Honeycutt RJ, Sobral BWS, Keim P, Irvine JE (1992) A rapid DNA extraction method for sugarcane and its relatives. Plant Mol Biol Rep 10:66–72CrossRefGoogle Scholar
  15. Hulbert SH, Bennetzen JL (1991) Recombination at the RP1 locus of maize. Mol Gen Genet 226:377–382CrossRefPubMedGoogle Scholar
  16. Hyten DL, Choi I-Y, Song Q, Specht JE, Carter TE, Shoemaker RC, Hwang E-Y, Matukumalli LK, Cregan PB (2010) 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)Google Scholar
  17. 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 1:89–98CrossRefGoogle Scholar
  18. Kang ST, Mian MAR, Hammond RB (2008) Soybean aphid resistance in PI 243540 is controlled by a single dominant gene. Crop Sci 48:1744–1788CrossRefGoogle Scholar
  19. Kim KS, Hill CB, Hartman GL, Mian MAR, Diers BW (2008) Discovery of soybean aphid biotypes. Crop Sci 48:923–928CrossRefGoogle Scholar
  20. Kim KS, Bellendir S, Hudson KA, Hill CB, Hartman GL, Hyten D, Hudson ME, Diers BW (2010) Fine mapping the soybean aphid resistance gene Rag1 in soybean. Theor Appl Genet 120:1063–1071CrossRefPubMedGoogle Scholar
  21. 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 137:1445–1455CrossRefPubMedGoogle Scholar
  22. Li Y, Hill CB, Hartman GL (2004) Effect of three resistant soybean genotypes on the fecundity, mortality, and maturation of soybean aphid (Homoptera: Aphididae). J Econ Entomol 97:1106–1111CrossRefPubMedGoogle Scholar
  23. 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 19:25–34CrossRefGoogle Scholar
  24. Li Y, Zou J, Li M, Bilgin DD, Vodkin LO, Hartman GL, Clough SJ (2008) Soybean defense responses to the soybean aphid. New Phytol 179:185–195CrossRefPubMedGoogle Scholar
  25. Martin GB, Bogdenove AJ, Sessa G (2003) Understanding the functions of plant disease resistance proteins. Annu Rev Plant Biol 54:23–61CrossRefPubMedGoogle Scholar
  26. Mensah C, DiFonzo C, Wang D (2008) Inheritance of soybean aphid resistance in PI 567541B and PI 567598B. Crop Sci 48:1759–1763CrossRefGoogle Scholar
  27. Mian MAR, Hammond RB, St Martin SK (2008a) New plant introductions with resistance to the soybean aphid. Crop Sci 48:1055–1061CrossRefGoogle Scholar
  28. Mian MAR, Kang ST, Beil SE, Hammond RB (2008b) Genetic linkage mapping of the soybean aphid resistance gene in PI 243540. Theor Appl Genet 117:955–962CrossRefGoogle Scholar
  29. Michel AP, Zhang W, Jung JK, Kang ST, Mian MAR (2009) Population genetic structure of Aphis glycines. Environ Entomol 38:1301–1311CrossRefPubMedGoogle Scholar
  30. 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 10:1307–1320CrossRefPubMedGoogle Scholar
  31. Nickell CD, Noel GR, Cary TR, Thomas DJ, Leitz RA (1999) Registration of ‘Ina’ Soybean. Crop Sci 39:1533Google Scholar
  32. 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 95:9750–9754CrossRefPubMedGoogle Scholar
  33. SAS Institute (2002) The SAS system for Windows. Release 9.00. SAS Institute, CaryGoogle Scholar
  34. Schmutz J, Cannon S, Schlueter J, Ma J, Mitros T, Nelson W, Hyten D, Song Q, Thelen J, Cheng J, Xu D, Hellsten U, May G, Yu Y, Sakurai T, Umezawa T, Bhattacharyya M, Sandhu D, Valliyodan B, Lindquist E, Peto M, Grant D, Shu S, Goodstein D, Barry K, Futrell-Griggs M, Du J, Tian Z, Zhu L, Gill N, Joshi T, Libault M, Sethuraman A, Zhang X-C, Shinozaki K, Nguyen H, Wing R, Cregan P, Specht J, Grimwood J, Rokhsar D, Stacey G, Shoemaker R, Jackson S (2010) Genome sequence of the paleopolyploid soybean. Nature 463:178–183CrossRefPubMedGoogle Scholar
  35. Shoemaker RC, Polzin K, Labate J, Specht J, Brummer EC, Olson T, Young N, Concibido V, Wilcox J, Tamulonis JP (1996) Genome duplication in soybean (Glycine subgenus soja). Genetics 144:329–338PubMedGoogle Scholar
  36. 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 109:122–128CrossRefPubMedGoogle Scholar
  37. Tamulonis JP, Luzzi BM, Hussey RS, Parrott WA, Boerma HR (1997) DNA marker analysis of loci conferring resistance to peanut root-knot nematode in soybean. Theor Appl Genet 95:664–670CrossRefGoogle Scholar
  38. Van Ooijen JW, Voorrips RE (2001) JoinMap 3.0 software for the calculation of genetic linkage maps. Plant Research International, WageningenGoogle Scholar
  39. Voegtlin DJ (2008) United States soybean aphid commentary (online). Accessed 18 Jun 2009
  40. Wang Z, Dai L, Jiang Z, Peng W, Zhang L, Wang G, Xie D (2005) GmCOI1, a soybean F-box protein gene, shows ability to mediate jasmonate-regulated plant defense and fertility in Arabidopsis. Mol Plant Microbe Interact 18:1285–1295CrossRefPubMedGoogle Scholar
  41. Wei F, Gobelman-Werner K, Morroll SM, Kurth J, Mao L, Wing R, Leister D, Schulze-Lefert P, Wis RP (1999) The Mla (powdery mildew) resistance cluster is associated with three NBS-LRR gene families and suppressed recombination within a 240-kb DNA interval on chromosome 5S (1HS) of barley. Genetics 153:1929–1948PubMedGoogle Scholar
  42. Witsenboer H, Kesseli RV, Fortin MG, Stanghellini M, Michelmore RW (1995) Sources and genetic structure of a cluster of genes for resistance to three pathogens in lettuce. Theor Appl Genet 91:178–188CrossRefGoogle Scholar
  43. Zhang G, Gu C, Wang D (2009) Molecular mapping of soybean aphid resistance genes in PI 567541B. Theor Appl Genet 118:473–482CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag 2010

Authors and Affiliations

  • Ki-Seung Kim
    • 1
  • Curtis B. Hill
    • 1
  • Glen L. Hartman
    • 2
  • David L. Hyten
    • 3
  • Matthew E. Hudson
    • 1
  • Brian W. Diers
    • 1
  1. 1.Department of Crop SciencesUniversity of IllinoisUrbanaUSA
  2. 2.USDA-ARS and Department of Crop SciencesUniversity of IllinoisUrbanaUSA
  3. 3.Soybean Genomics and Improvement LaboratoryUSDA-ARSBeltsvilleUSA

Personalised recommendations