Skip to main content
SpringerLink
Log in

Development of genic molecular markers linked to a rust resistance gene in cultivated groundnut (Arachis hypogaea L.)

  • Published:
Euphytica Aims and scope Submit manuscript

Abstract

Development of molecular markers for different economically important traits in cultivated groundnut has progressed at slow pace. Although many genomic SSR markers were developed in both the wild and cultivated groundnut, the genetic linkage map in the species is still not saturated. Availability of a large number of ESTs in GenBank opened up the possibility of integrating new markers and to identify markers closely linked to agronomic traits. EST-SSR markers are also considered as genic molecular markers. In this study, 259 EST-SSR markers were developed by mining 5,184 Arachis hypogaea ESTs from NCBI database. These EST-SSRs and 34 resistance gene candidate markers were used for association and genetic mapping of rust resistance in cultivated groundnut. From these, Cer2, SSR_GO340445, SSR_HO115759, SSR_GO341324 and RGC 2 had a significant association with rust resistance based on locus-by-locus AMOVA and/or Kruskal–Wallis ANOVA. Some of these associated markers also had protein activity related to biotic stress responses. Through genetic mapping, EST-SSR markers SSR_GO340445 and SSR_HO115759 were found closely linked to a rust resistance gene at 1.9 and 3.8 cM distances, respectively. These markers are thus suitable candidates for marker assisted selection in groundnut. The tight linkage of SSR_GO340445 would be helpful to screen BAC clones and to isolate rust resistance gene in groundnut.

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
Fig. 5

Similar content being viewed by others

References

  • Aggarwal RK, Hendre PS, Varshney RK, Bhat PR, Krishnakumar V, Singh L (2007) Identification, characterization and utilization of EST-derived genic microsatellite markers for genome analyses of coffee and related species. Theor Appl Genet 114:359–372

    Article  PubMed  CAS  Google Scholar 

  • Bertioli DJ, Leal-Bertioli SCM, Lion MB, Santos VL, Pappas JG, Cannon SB, Guimarães PM (2003) A large scale analysis of resistance gene homologues in Arachis. Mol Genet Genomics 270:34–45

    Article  PubMed  CAS  Google Scholar 

  • Cuc LM, Mace ES, Crouch JH, Quang VD, Long TD, Varshney RK (2008) Isolation and characterization of novel microsatellite markers and their application for diversity assessment in cultivated groundnut (Arachis hypogaea). BMC Plant Biol 8:55

    Article  PubMed  Google Scholar 

  • Excoffier L, Smouse PE, Quattro JM (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction sites. Genetics 131:479–491

    PubMed  CAS  Google Scholar 

  • Ferguson ME, Burow MD, Schulze SR, Bramel PJ, Paterson AH, Kresovich S, Mitchell S (2004) Microsatellite identification and characterization in peanut (A. hypogaea L.). Theor Appl Genet 108:1064–1070

    Article  PubMed  CAS  Google Scholar 

  • Galiana E, Bonnet P, Conrod S, Keller H, Panabieres F, Ponchet M, Poupet A, Ricci P (1997) Rnase activity prevents the growth of a fungal pathogen in tobacco leaves and increases upon induction of systemic acquired resistance with elicitin. Plant Physiol 115:1557–1567

    Article  PubMed  CAS  Google Scholar 

  • Hammer O, Harper DAT, Ryan PD (2008) PAST-Palaeontological statistics, ver 1.81. http://folk.uio.no/ohammer/past. Accessed 25 Apr 2008

  • Hardham AR, Jones DA, Takemoto D (2007) Cytoskeleton and cell wall function in penetration resistance. Curr Opin Plant Biol 10:342–348

    Article  PubMed  CAS  Google Scholar 

  • He G, Meng R, Newman M, Gao G, Pittman RN, Prakash CS (2003) Microsatellite as DNA markers in cultivated peanut (Arachis hypogaea L.). BMC Plant Biol 3:3

    Article  PubMed  Google Scholar 

  • Hopkins MS, Casa AM, Wang T, Mitchell SE, Dean RE, Kochert GD, Kresovich S (1999) Discovery and characterization of polymorphic simple sequence repeats (SSRs) in peanut. Crop Sci 39:1243–1247

    Article  CAS  Google Scholar 

  • Khedikar YP, Gowda MVC, Sarvamangala C, Patgar KV, Upadhyaya HD, Varshney RK (2010) A QTL study on late leaf spot and rust revealed one major QTL for molecular breeding for rust resistance in groundnut (Arachis hypogaea L.). Theor Appl Genet 121:971–984

    Article  PubMed  CAS  Google Scholar 

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

    Google Scholar 

  • Liang X, Chen X, Hong Y, Liu H, Zhou G, Li S, Guo B (2009) Utility of EST-derived SSR in cultivated peanut (Arachis hypogaea L.) and Arachis wild species. BMC Plant Biol 9:35

    Article  PubMed  Google Scholar 

  • Lincoln SE, Daly MJ, Lander ES (1993) Constructing genetic linkage maps with MAPMAKER EXP V3.0: a tutorial and reference manual. A Whitehead Institute of Biomedical research technical report. http://www.broad.mit.edu/ftp/distribution/software/mapmaker3. Accessed 20 July 2011

  • Luo M, Dang P, Guo B, He G, Holbrook CC, Bausher MG, Lee RD (2005) Generation of expressed sequence tags (ESTs) for gene discovery and marker development in cultivated peanut. Crop Sci 45:346–353

    Article  CAS  Google Scholar 

  • Mace ES, Phong DT, Upadhyaya HD, Chandra S, Crouch JH (2006) SSR analysis of cultivated groundnut (Arachis hypogaea L.) gremplasm resistant to rust and late leaf spot diseases. Euphytica 152:317–330

    Google Scholar 

  • Martins W, de Souza D, Proite K, Guimarães P, Moretzsohn M, Bertioli D (2006) New software for automated microsatellite marker development. Nucleic Acids Res 34:e31

    Article  PubMed  Google Scholar 

  • Martins WS, Lucas DCS, de Souza Neves KF, Bertioli DJ (2009) Websat—a web software for microsatellite marker development. Bioinformation 3(6):282–283

    Article  PubMed  Google Scholar 

  • Mondal S, Badigannavar AM (2010) Molecular diversity and association of SSR markers to rust and late leaf spot resistance in cultivated groundnut (Arachis hypogaea L.). Plant Breed 129:68–71

    Article  CAS  Google Scholar 

  • Mondal S, Ghosh S, Badigannavar AM (2005) RAPD polymorphism among groundnut genotypes differing in disease reaction to late leaf spot and rust. Int Arachis Newsl 25:27–30

    Google Scholar 

  • Mondal S, Badigannavar AM, Murty GSS (2007) RAPD markers linked to a rust resistance gene in groundnut (Arachis hypogaea L.). Euphytica 159:233–239

    Article  Google Scholar 

  • Mondal S, Badigannavar AM, D’Souza SF (2011) Molecular tagging of a rust resistance gene in cultivated groundnut (Arachis hypogaea L.) introgressed from Arachis cardenasii. Mol Breed. doi:10.1007/s11032-011-9564-z

  • Moretzsohn MC, Leoi L, Proite K, Guimaraes PM, Leal-Bertioli SCM, Gimenes MA, Martins WS, Valls JFM, Grattapaglia D, Bertioli DJ (2005) Microsatellite based, gene-rich linkage map for the AA genome of Arachis (Fabaceae). Theor Appl Genet 111:1060–1071

    Article  PubMed  CAS  Google Scholar 

  • Moretzsohn MC, Barbosa AVG, Alves-Freitas DMT, Teixeira C, Leal-Bertioli SCM, Guimarães PM, Pereira RW, Lopes CR, Cavallari MM, Valls JFM, Bertioli DJ, Gimenes MA (2009) A linkage map for the B genome of Arachis (Fabaceae) and its synteny to the A-genome. BMC Plant Biol 9:40

    Article  PubMed  Google Scholar 

  • Nicot N, Chiquet V, Gandon B, Amilhat L, legeai F, Leroy P, Bernard M, Sourdille P (2004) Study of simple sequence repeat (SSR) markers from wheat expressed sequence tags (ESTs). Theor Appl Genet 109:800–805

    Article  PubMed  CAS  Google Scholar 

  • Nobile PM, Lopes CR, Barsalobres-Cavallari C, Quecini V, Coutinho LL, Hoshino AA, Gimenes MA (2008) Peanut genes identified during initial phase of Cercosporidium personatum infection. Plant Sci 174:78–87

    Article  CAS  Google Scholar 

  • Oliveira KM, Pinto LR, Marconi TG, Mollinari M, Ulian EC, Chabregas SM, Falco MC, Burnquist W, Garcia AAF, Souza AP (2009) Characterization of new polymorphic functional markers for sugarcane. Genome 52:191–209

    Article  PubMed  CAS  Google Scholar 

  • Pande S, Rao NJ (2001) Resistance of wild Arachis species to late leaf spot and rust in greenhouse trials. Plant Dis 85:851–855

    Article  Google Scholar 

  • Paterson AH, Stalker HT, Gallo-Meagher M, Burow MD, Dwivedi SL, Crouch JH, Mace ES (2004) Genomics and genetic enhancement of peanut. In: Wilson RF, Stalker HT, Brummer CE (eds) Genomic for legume crops. American Oil Chemical Society Press, Champaign, pp 97–109

    Google Scholar 

  • Patil SH, Kale DM, Deshmukh SN, Fulzele GR, Weginwar BG (1995) Semi-dwarf, early maturing and high yielding new groundnut variety, TAG 24. J Oilseed Res 12:254–257

    Google Scholar 

  • Peakall R, Smouse PE (2006) GenALEx 6: Genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6:288–295

    Article  Google Scholar 

  • Proite K, Leal-Bertioli SC, Bertioli DJ, Moretzsohn MC, da Silva FR, Martins NF, Guimarães PM (2008) ESTs from a wild Arachis species for gene discovery and marker development. BMC Plant Biol 7:7

    Article  Google Scholar 

  • Radwan OE, Ahmed TA, Knapp SJ (2010) Phylogenetic analyses of peanut resistance gene candidates and screening of different genotypes for polymorphic markers. Saudi J Biol Sci 17:43–49

    Article  CAS  Google Scholar 

  • Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. Methods in Mol Biol 132:365–386

    CAS  Google Scholar 

  • Schmelzer E (2002) Cell proliferation, a crucial process in fungal defence. Trends Plant Sci 7:411–415

    Article  PubMed  CAS  Google Scholar 

  • Singh AK, Nigam SN (1997) Groundnut. In: Fuccilo D, Sears L, Stapleton P (eds) Biodiversity in trust, conversation and use of plant genetic resources in CGIAR centers. Cambridge University press, Cambridge, pp 114–127

    Google Scholar 

  • Song GQ, Li MJ, Xiao H, Wang XJ, Tang RH, Xia H, Zhao CZ, Bi YP (2010) EST sequencing and SSR marker development from cultivated peanut (Arachis hypogaea L.). Electron J Biotechnol 13:1

    Article  Google Scholar 

  • Subrahmanyam P, McDonald D, Waliyar F, Reddy LJ, Nigam SN, Gibbons RW, Rao VR, Singh AK, Pande S, Reddy PM, Subba Rao PV (1995) Screening methods and sources of resistance to rust and late leaf spot of groundnut. In: Information Bulletin No 47. International Crops Research Institute for the Semi-Arid Tropics, Patancheru

  • Thiel T, Michalek W, Varshney RK, Graner A (2003) Exploiting EST databases for the development and characterization of gene-derived SSR markers in barley (Hordeum vulgare L.). Theor Appl Genet 106:411–422

    PubMed  CAS  Google Scholar 

  • Varman PV (1999) A foliar disease resistant line developed through interspecific hybridization in groundnut (Arachis hypogaea L.). Indian J Agric Sci 69:67–68

    Google Scholar 

  • Varshney RK, Thiel T, Stein N, Langridge P, Graner A (2002) In silico analysis on frequency and distribution of microsatellites in ESTs of some cereal species. Cell Mol Biol Lett 7:537–546

    PubMed  CAS  Google Scholar 

  • Varshney RK, Mahender T, Aggarwal RK, Börner A (2007) Genic molecular markers in plants: development and applications. In: Varshney RK, Tuberosa R (eds) Genomic-assisted crop improvement: Vol. 1: genomic approaches and platforms. Springer, Dordrecht, pp 13–29

    Chapter  Google Scholar 

  • Voorrips RE (2002) Mapchart: software for the graphical presentation of linkage map and QTL. J Hered 93:77–78

    Article  PubMed  CAS  Google Scholar 

  • Weir SB (1996) Genetic data analysis II. Sinauer Publishers, Sunderland, p 445

    Google Scholar 

  • Whan V, Hobbs M, McWilliam S, Lynn DJ, Lutzow YS, Khatkar M, Barendse W, Raadsma H, Tellam R (2010) Bovine proteins containing poly-glutamine repeats are often polymorphic and enriched for components of transcriptional regulatory complexes. BMC Genomics 11:654

    Article  PubMed  Google Scholar 

  • Wynne JC, Beute MK, Nigam SN (1991) Breeding for disease resistance in peanut (Arachis hypogaea L.). Annu Rev Phytopathol 29:279–303

    Article  Google Scholar 

  • Yuksel B, Estill JC, Schulze SR, Paterson AH (2005) Organization and evolution of resistance gene analogs in peanut. Mol Genet Genomics 274:248–263

    Article  PubMed  CAS  Google Scholar 

  • Zar JH (2003) Biostatistical analysis, 4th edn. Pearson Education Inc., New Delhi

    Google Scholar 

Download references

Acknowledgments

The authors are thankful to International Atomic Energy Agency for partial financial support (IND 12818). The technical help rendered by Shakthi, Anantha, R. K. Sachan and T. Chalapathi during laboratory and field experimentations is duly acknowledged.

Author information

Authors and Affiliations

  1. Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India

    Suvendu Mondal, A. M. Badigannavar & S. F. D’Souza

Authors
  1. Suvendu Mondal
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. A. M. Badigannavar
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. S. F. D’Souza
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Suvendu Mondal.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (XLSX 44 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Mondal, S., Badigannavar, A.M. & D’Souza, S.F. Development of genic molecular markers linked to a rust resistance gene in cultivated groundnut (Arachis hypogaea L.). Euphytica 188, 163–173 (2012). https://doi.org/10.1007/s10681-011-0619-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10681-011-0619-3

Keywords

Search

Navigation