Advertisement

Molecular Genetics and Genomics

, Volume 276, Issue 5, pp 436–449 | Cite as

SSR mining in coffee tree EST databases: potential use of EST–SSRs as markers for the Coffea genus

  • Valérie PoncetEmail author
  • Myriam Rondeau
  • Christine Tranchant
  • Anne Cayrel
  • Serge Hamon
  • Alexandre de Kochko
  • Perla Hamon
Original Paper

Abstract

Expressed sequence tags (ESTs) from Coffea canephora leaves and fruits were used to search for types and frequencies of simple sequence repeats (EST–SSRs) with a motif length of 1–6 bp. From a non-redundant (NR) EST set of 5,534 potential unigenes, 6.8% SSR-containing sequences were identified, with an average density of one SSR every 7.73 kb of EST sequences. Trinucleotide repeats were found to be the most abundant (34.34%), followed by di- (25.75%) and hexa-nucleotide (22.04%) motifs. The development of unique genic SSR markers was optimized by a computational approach which allowed us to eliminate redundancy in the original EST set and also to test the specificity of each pair of designed primers. Twenty-five EST–SSRs were developed and used to evaluate cross-species transferability in the Coffea genus. The orthology was supported by the amplicon sequence similarity and the amplification patterns. The >94% identity of flanking sequences revealed high sequence conservation across the Coffea genus. A high level of polymorphic loci was obtained regardless of the species considered (from 75% for C. liberica to 86% for C. canephora). Moreover, the polymorphism revealed by EST–SSR was similar to that exposed by genomic SSR. It is concluded that Coffea ESTs are a valuable resource for microsatellite mining. EST-SSR markers developed from C. canephora sequences can be easily transferred to other Coffea species for which very little molecular information is available. They constitute a set of conserved orthologous markers, which would be ideal for assessing genetic diversity in coffee trees as well as for cross-referencing transcribed sequences in comparative genomics studies.

Keywords

SSR mining EST–SSR Coffea Transferability Genetic variation 

Notes

Acknowledgments

This work was partly supported by EU grant No. ICA4-CT-2001-10068. The authors wish to thank I. Mougenot, C. Fizames, B. Piegu, A. Wissocq, F. Lechauve, F. Moreews, X. Argout, F. Chevalier, and many Genetrop researchers for their involvement in the development of ESTdb, and M. Lorieux for his help in developing the SSR script (http://www.mpl.ird.fr/bioinfo/). Thank to Dr. Santiago C.González-Martínez for his valuable comments on the manuscript.

References

  1. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402PubMedCrossRefGoogle Scholar
  2. Baruah A, Naik P, Hendre S, Rajkumar R, Rajendrakumar P, Aggarwal RK (2003) Isolation and characterization of nine microsatellite markers from Coffea arabica L., showing wide cross-species amplifications. Mol Ecol Notes 3:647–650CrossRefGoogle Scholar
  3. Bhat PR, Krishnakumar V, Hendre PS, Rajendrakumar P, Varshney RK, Aggarwal RK (2005) Identification and characterization of expressed sequence tags-derived simple sequence repeats, markers from robusta coffee variety ‘CxR’ (an interspecific hybrid of Coffea canephora × Coffea congensis). Mol Ecol Notes 5:80–83CrossRefGoogle Scholar
  4. Brown GR, Kadel EE III, Bassoni DL, Kiehne KL, Temesgen B, van Buijtenen JP, Sewell MM, Marshall KA, Neale DB (2001) Anchored reference loci in loblolly pine (Pinus taeda L.) for integrating pine genomics. Genetics 159:799–809PubMedGoogle Scholar
  5. Cato SA, Gardner RC, Kent J, Richardson TE (2001) A rapid PCR-based method for genetically mapping ESTs. Theor Appl Genet 102:296–306CrossRefGoogle Scholar
  6. Cho YG, Ishii T, Temnykh S, Chen X, Lipovich L, McCouch SR, Park WD, Ayres N, Cartinhour S (2000) Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativa L.). Theor Appl Genet 100:713–722CrossRefGoogle Scholar
  7. Coulibaly I, Revol B, Noirot M, Poncet V, Lorieux M, Carasco-Lacombe C, Minier J, Dufour M, Hamon P (2003) AFLP and SSR polymorphism in a Coffea interspecific backcross progeny [(C. heterocalyx × C. canephora) × C. canephora]. Theor Appl Genet 107:1148–1155PubMedCrossRefGoogle Scholar
  8. Decroocq V, Fave MG, Hagen L, Bordenave L, Decroocq S (2003) Development and transferability of apricot and grape EST microsatellite markers across taxa. Theor Appl Genet 106:912–922PubMedGoogle Scholar
  9. Dirlewanger E, Cosson P, Tavaud M, Aranzana J, Poizat C, Zanetto A, Arus P, Laigret F (2002) Development of microsatellite markers in peach [Prunus persica (L.) Batsch] and their use in genetic diversity analysis in peach and sweet cherry (Prunus avium L.). Theor Appl Genet 105:127–138PubMedCrossRefGoogle Scholar
  10. Dufour M, Hamon P, Noirot M, Ristrerucci AM, Brottier P, Vico V, Leroy T (2001) Potential use of SSR markers for Coffea spp. genetic mapping. In: ASIC (ed) 19th international science colloquium on coffee, Trieste, ItalyGoogle Scholar
  11. Ellegren H (2004) Microsatellites: simple sequences with complex evolution. Nat Rev Genet 5:435–445PubMedCrossRefGoogle Scholar
  12. Eujayl I, Sledge MK, Wang L, May GD, Chekhovskiy K, Zwonitzer JC, Mian MA (2004) Medicago truncatula EST-SSRs reveal cross-species genetic markers for Medicago spp. Theor Appl Genet 108:414–422PubMedCrossRefGoogle Scholar
  13. Eujayl I, Sorrells M, Baum M, Wolters P, Powell W (2001) Assessment of genotypic variation among cultivated durum wheat based on EST-SSRS and genomic SSRS. Euphytica 119:39–43CrossRefGoogle Scholar
  14. Fernandez D, Santos P, Agostini C, Bon MC, Petitot AS, Silva MC, Guerra Guimaraes L, Ribeiro A, Argout X, Nicole M (2004) Coffee (Coffea arabica L.) genes early expressed during infection by the rust fungus (Hemileia vastatrix). Mol Plant Pathol 5:527–536CrossRefGoogle Scholar
  15. Fraser LG, Harvey CF, Crowhurst RN, De Silva HN (2004) EST-derived microsatellites from Actinidia species and their potential for mapping. Theor Appl Genet 108:1010–1016PubMedCrossRefGoogle Scholar
  16. Gao LF, Tang JF, Li HW, Jia JZ (2003) Analysis of microsatellites in major crops assessed by computational and experimental approaches. Mol Breed 12:245–261CrossRefGoogle Scholar
  17. Gonzalez-Martinez SC, Robledo-Arnuncio JJ, Collada C, Diaz A, Williams CG, Alia R, Cervera MT (2004) Cross-amplification and sequence variation of microsatellite loci in Eurasian hard pines. Theor Appl Genet 109:103–111PubMedCrossRefGoogle Scholar
  18. Gonzalo MJ, Oliver M, Garcia Mas J, Monfort A, Dolcet Sanjuan R, Katzir N, Arus P, Monforte A (2005) Simple-sequence repeat markers used in merging linkage maps of melon (Cucumis melo L.). Theor Appl Genet 110:802–811PubMedCrossRefGoogle Scholar
  19. Gupta PK, Rustgi S, Sharma S, Singh R, Kumar N, Balyan HS (2003) Transferable EST-SSR markers for the study of polymorphism and genetic diversity in bread wheat. Mol Genet Genomics 270:315–323PubMedCrossRefGoogle Scholar
  20. Kantety RV, La Rota M, Matthews DE, Sorrells ME (2002) Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat. Plant Mol Biol 48:501–510PubMedCrossRefGoogle Scholar
  21. Kumpatla SP, Mukhopadhyay S (2005) Mining and survey of simple sequence repeats in expressed sequence tags of dicotyledonous species. Genome 48:985–998PubMedCrossRefGoogle Scholar
  22. Ky CL, Barre P, Lorieux M, Trouslot P, Akaffou S, Louarn J, Charrier A, Hamon S, Noirot M (2000) Interspecific genetic linkage map, segregation distortion and genetic conversion in coffee (Coffea sp.). Theor Appl Genet 101:669–676CrossRefGoogle Scholar
  23. La Rota M, Kantety RV, Yu JK, Sorrells ME (2005) Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat, and barley. BMC Genomics 6:23PubMedCrossRefGoogle Scholar
  24. Lashermes P, Combes MC, Prakash NS, Trouslot P, Lorieux M, Charrier A (2001) Genetic linkage map of Coffea canephora: effect of segregation distortion and analysis of recombination rate in male and female meioses. Genome 44:589–596PubMedCrossRefGoogle Scholar
  25. Lashermes P, Combes MC, Trouslot P, Charrier A (1997) Phylogenetic relationships of coffee-tree species (Coffea L.) as inferred from ITS sequences of nuclear ribosomal DNA. Theor Appl Genet 94:947–955CrossRefGoogle Scholar
  26. Lem P, Lallemand J (2003) Grass consensus STS markers: an efficient approach for detecting polymorphism in Lolium. Theor Appl Genet 107:1113–1122PubMedCrossRefGoogle Scholar
  27. Liewlaksaneeyanawin C, Ritland CE, El-Kassaby YA, Ritland K (2004) Single-copy, species-transferable microsatellite markers developed from loblolly pine ESTs. Theor Appl Genet 109:361–369PubMedCrossRefGoogle Scholar
  28. Lin C, Mueller LA, Carthy JM, Crouzillat D, Petiard V, Tanksley SD (2005) Coffee and tomato share common gene repertoires as revealed by deep sequencing of seed and cherry transcripts. Theor Appl Genet 112:114–130PubMedCrossRefGoogle Scholar
  29. Liu K, Muse SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21:2128–2129PubMedCrossRefGoogle Scholar
  30. Metzgar D, Bytof J, Wills C (2000) Selection against frameshift mutations limits microsatellite expansion in coding DNA. Genome Res 10:72–80PubMedGoogle Scholar
  31. Moncada P, McCouch S (2004) Simple sequence repeat diversity in diploid and tetraploid Coffea species. Genome 47:501–509PubMedCrossRefGoogle Scholar
  32. Morgante M, Hanafey M, Powell W (2002) Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat Genet 30:194–200PubMedCrossRefGoogle Scholar
  33. N’Diaye A, Noirot M, Hamon S, Poncet V (2006) Genetic basis of species differentiation between Coffea liberica Hiern and C. canephora Pierre: analysis of an interspecific cross. Genet Resour Crop Evol (in press)Google Scholar
  34. N’Diaye A, Poncet V, Louarn J, Hamon S, Noirot M (2005) Genetic differentiation between Coffea liberica var. liberica and C. liberica var Dewevrei and comparison with C. canephora. Plant Syst Evol 253:95–104CrossRefGoogle Scholar
  35. Park YH, Alabady MS, Ulloa M, Sickler B, Wilkins TA, Yu J, Stelly DM, Kohel RJ, el-Shihy OM, Cantrell RG (2005) Genetic mapping of new cotton fiber loci using EST-derived microsatellites in an interspecific recombinant inbred line cotton population. Mol Genet Genomics 274:428–441PubMedCrossRefGoogle Scholar
  36. Pinto LR, Oliveira KM, Ulian EC, Garcia AA, de Souza AP (2004) Survey in the sugarcane expressed sequence tag database (SUCEST) for simple sequence repeats. Genome 47:795–804PubMedCrossRefGoogle Scholar
  37. Poncet V, Hamon P, Minier J, Carasco-Lacombe C, Hamon S, Noirot M (2004) SSR cross-amplification and variation within coffee trees (Coffea spp.). Genome 47:1071–1081PubMedCrossRefGoogle Scholar
  38. Rallo P, Tenzer I, Gessler C, Baldoni L, Dorado G, Martin A (2003) Transferability of olive microsatellite loci across the genus Olea. Theor Appl Genet 107:940–946PubMedCrossRefGoogle Scholar
  39. Rovelli P, Mettulio R, Anthony F, Anzueto F, Lashermes P, Graziosi G (2000) Microsatellites in Coffea arabica L. In: Sera T, Soccol CR, Pandey A, Roussos S (eds) Coffee biotechnology and quality. Kluwer, Netherlands, pp 123–133Google Scholar
  40. Rozen S, Skaletsky HJ (2000) Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds) Bioinformatics methods and protocols: methods in molecular biology. Humana Press, Totowa, pp 365–386Google Scholar
  41. Saha MC, Mian MA, Eujayl I, Zwonitzer JC, Wang L, May GD (2004) Tall fescue EST-SSR markers with transferability across several grass species. Theor Appl Genet 109:783–791PubMedCrossRefGoogle Scholar
  42. Saha MC, Mian R, Zwonitzer JC, Chekhovskiy K, Hopkins AA (2005) An SSR- and AFLP-based genetic linkage map of tall fescue (Festuca arundinacea Schreb.). Theor Appl Genet 110:323–336PubMedCrossRefGoogle Scholar
  43. Sambrook J, Fristch EF, Maniatis T (1989) Molecular cloning–a laboratory manual. Cold Spring Harbor Laboratory edn. Cold Spring HarborGoogle Scholar
  44. Scott KD, Eggler P, Seaton G, Rossetto M, Ablett EM, Lee LS, Henry RJ (2000) Analysis of SSRs derived from grape ESTs. Theor Appl Genet 100:723–726CrossRefGoogle Scholar
  45. Sethy NK, Choudhary S, Shokeen B, Bhatia S (2006) Identification of microsatellite markers from Cicer reticulatum: molecular variation and phylogenetic analysis. Theor Appl Genet 112:347–357PubMedCrossRefGoogle Scholar
  46. 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 106:411–422PubMedGoogle Scholar
  47. Varshney RK, Graner A, Sorrells ME (2005a) Genic microsatellite markers in plants: features and applications. Trends Biotechnol 23:48–55CrossRefGoogle Scholar
  48. Varshney RK, Sigmund R, Borner A, Korzun V, Stein N, Sorrells ME, Langridge P, Graner A (2005b) Interspecific transferability and comparative mapping of barley EST-SSR markers in wheat, rye and rice. Plant Sci 168:195–202CrossRefGoogle Scholar
  49. Vigouroux Y, Mitchell S, Matsuoka Y, Hamblin M, Kresovich S, Smith JS, Jaqueth J, Smith OS, Doebley J (2005) An analysis of genetic diversity across the maize genome using microsatellites. Genetics 169:1617–1630PubMedCrossRefGoogle Scholar
  50. Wu KS, Tanksley SD (1993) Abundance, polymorphism and genetic mapping of microsatellites in rice. Mol Gen Genet 241:225–235PubMedCrossRefGoogle Scholar
  51. Yu JK, La Rota M, Kantety RV, Sorrells ME (2004) EST derived SSR markers for comparative mapping in wheat and rice. Mol Genet Genomics 271:742–751PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2006

Authors and Affiliations

  • Valérie Poncet
    • 1
    Email author
  • Myriam Rondeau
    • 1
  • Christine Tranchant
    • 1
  • Anne Cayrel
    • 1
  • Serge Hamon
    • 1
  • Alexandre de Kochko
    • 1
  • Perla Hamon
    • 1
  1. 1.UMR 1097 Diversité et Génomes des Plantes Cultivées (DGPC)IRD, Institut de Recherche pour le DéveloppementMontpellier Cedex 5France

Personalised recommendations