Tree Genetics & Genomes

, Volume 6, Issue 5, pp 689–700 | Cite as

Prunus microsatellite marker transferability across rosaceous crops

  • Mourad Mnejja
  • Jordi Garcia-Mas
  • Jean-Marc Audergon
  • Pere Arús
Original Paper


A total of 145 microsatellite primer pairs from Prunus DNA sequences were studied for transferability in a set of eight cultivars from nine rosaceous species (almond, peach, apricot, Japanese plum, European plum, cherry, apple, pear, and strawberry), 25 each of almond genomic, peach genomic, peach expressed sequence tags (EST), and Japanese plum genomic, 22 of almond EST, and 23 of apricot (13 EST and 10 genomic), all known to produce single-locus and polymorphic simple-sequence repeats in the species where they were developed. Most primer pairs (83.6%) amplified bands of the expected size range in other Prunus. Transferability, i.e., the proportion of microsatellites that amplified and were polymorphic, was also high in Prunus (63.9%). Almond and Japanese plum were the most variable among the diploid species (all but the hexaploid European plum) and peach the least polymorphic. Thirty-one microsatellites amplified and were polymorphic in all Prunus species studied, 12 of which, covering its whole genome, are proposed as the “universal Prunus set”. In contrast, only 16.3% were transferable in species of other Rosaceae genera (apple, pear, and strawberry). Polymorphic Prunus microsatellites also detected lower levels of variability in the non-congeneric species. No significant differences were detected in transferability and the ability to detect variability between microsatellites of EST and genomic origin.


Transferability Rosaceae Universal Prunus SSR set 



This research was partly funded by a project of the Spanish Ministry of Education (AGL2006-07767/AGR). The group of IRTA is a member of the CONSOLIDER Center for Basic Genomics and Agro-food Orientation (CSD2007-00036).

Supplementary material

11295_2010_284_MOESM1_ESM.doc (62 kb)
Table 1S EST-derived almond microsatellites (DOC 62 kb)
11295_2010_284_MOESM2_ESM.doc (63 kb)
Table 2S EST-derived peach microsatellites (DOC 63 kb)
11295_2010_284_MOESM3_ESM.doc (812 kb)
Table 3S Variability of 145 Prunus SSRs in nine rosaceous species (DOC 811 kb)


  1. Aranzana MJ, Garcia-Mas J, Carbó J, Arús P (2002) Development and variability analysis of microsatellite markers in peach. Plant Breed 121:87–92CrossRefGoogle Scholar
  2. Aranzana MJ, Pineda A, Cosson P, Dirlewanger E, Ascasibar J, Cipriani G, Ryder CD, Testolin R, Abbott A, King GJ, Iezzoni AF, Arús P (2003a) A set of simple-sequence repeat (SSR) markers covering the Prunus genome. Theor Appl Genet 106:819–825PubMedGoogle Scholar
  3. Aranzana MJ, Carbó J, Arús P (2003b) Microsatellite variability in peach [Prunus persica (L) Batsch.]: cultivar identification, marker mutation, pedigree inferences and population structure. Theor Appl Genet 106:1341–1352PubMedGoogle Scholar
  4. Arulsekar S, Parfitt DE, Kester DE (1986) Comparison of isozyme variability in peach and almond cultivars. J Heredity 77:272–274Google Scholar
  5. Arús P, Yamamoto T, Dirlewanger E, Abbott AG (2005) Synteny in the Rosaceae. In: Janick J (ed) Plant Breeding Reviews 27:175–211Google Scholar
  6. Byrne DH (1990) Isozyme variability in four diploid stone fruits compared with other woody perennial plants. J Heredity 81:68–71Google Scholar
  7. Cipriani G, Lot G, Huang WG, Marrazzo MT, Peterlunger E, Testolin R (1999) AC/GT and AG/CT microsatellite repeats in peach (Prunus persica (L.) Batsch): isolation, characterisation and cross-species amplification in Prunus. Theor Appl Genet 99:65–72CrossRefGoogle Scholar
  8. Decroocq V, Favé 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 MJ, Poizat C, Zanetto A, Arús 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 105:127–138CrossRefPubMedGoogle Scholar
  10. Dirlewanger E, Graziano E, Joobeur T, Garriga-Calderé F, Cosson P, Howad W, Arús P (2004a) Comparative mapping and marker-assisted selection in Rosaceae fruit crops. Proc Natl Acad Sci U S A 101:9891–9896CrossRefPubMedGoogle Scholar
  11. Dirlewanger E, Cosson P, Howad W, Capdeville G, Bosselut N, Claverie M, Voisin R, Poizat C, Lafargue B, Baron O, Laigret F, Kleinhentz M, Arús P, Esmenjaud D (2004b) Microsatellite genetic linkage maps of myrobalan plum and an almond–peach hybrid—location of root-knot nematode resistance genes. Theor Appl Genet 109:827–838CrossRefPubMedGoogle Scholar
  12. Dondini L, Lain O, Geuna F, Banfi R, Gaiotti F, Tartarini S, Bassi D, Testolin R (2007) Development of a new SSR-based linkage map in apricot and analysis of synteny with existing Prunus maps. Tree Genet Genomes 3:239–249CrossRefGoogle Scholar
  13. Doyle JJ, Doyle JL (1990) Isolation of plant DNA from fresh tissue. Focus 12:13–15Google Scholar
  14. Garcia-Mas J, Monforte AJ, Arús P (2004) Phylogenetic relationships among Cucumis species based on the ribosomal internal transcribed spacer sequence and microsatellite markers. Plant Syst Evol 248:191–203CrossRefGoogle Scholar
  15. Graham J, Smith K, Woodhead M, Russell J (2002) Development and use of simple sequence repeat SSR markers in Rubus species. Mol Ecol Notes 2:250–252CrossRefGoogle Scholar
  16. Granger AR, Clarke GR, Jackson JF (1993) Sweet cherry cultivar identification by leaf isozyme polymorphism. Theor Appl Genet 86:458–464CrossRefGoogle Scholar
  17. Hagen LS, Chaib J, Fady B, Decroocq V, Bouchet JP, Lambert P, Audergon JM (2004) Genomic and cDNA microsatellites from apricot (Prunus armeniaca L.). Mol Ecol Notes 4:742–745CrossRefGoogle Scholar
  18. Hendre PS, Phanindranath R, Annapurna V, Lalremruata A, Aggarwal RK (2008) Development of new genomic microsatellite markers from robusta coffee (Coffea canephora Pierre ex A. Froehner) showing broad cross-species transferability and utility in genetic studies. BMC Plant Biol 8:51CrossRefPubMedGoogle Scholar
  19. Hesse C (1975) Peaches. In: Janick J, Moore J (eds) Advances in fruit breeding. Purdue University Press, West Lafayette, pp 285–335Google Scholar
  20. Hormaza JI (2002) Molecular characterization and similarity relationships among apricot (Prunus armeniaca L.) genotypes using simple sequence repeats. Theor Appl Genet 104:321–328CrossRefPubMedGoogle Scholar
  21. Horn R, Lecouls AC, Callahan A, Dandekar A, Garay L et al (2005) Candidate gene database and transcript map for peach, a model species for fruit trees. Theor Appl Genet 110:1419–1428CrossRefPubMedGoogle Scholar
  22. Howad W, Yamamoto T, Dirlewanger E, Testolin R, Cosson P, Cipriani G, Monforte AJ, Georgi L, Abbott AG, Arús P (2005) Mapping with a few plants: using selective mapping for microsatellite saturation of the Prunus reference map. Genetics 171:1305–1309CrossRefPubMedGoogle Scholar
  23. Kimura T, Nishitani C, Iketani H, Ban Y, Yamamoto T (2006) Development of microsatellite markers in rose. Mol Ecol Notes 2:250–252Google Scholar
  24. Liebhard R, Gianfranceschi L, Koller B, Ruder CD, Tarchini R, Weg EVD, Gessler C (2002) Development and characterisation of 140 new microsatellites in apple (Malus x domestica Borkh.). Mol Breed 10:217–241CrossRefGoogle Scholar
  25. Luro FL, Constantino G, Terol J, Argout X, Allario T, Wincker P, Talón M, Ollitraut P, Morillon R (2008) Transferability of the ESR-SSRs developed on Nules clementine (Citrus clementina Hort ex Tan) to other Citrus species and their effectiveness for genetic mapping. BMC Genomics 9:287CrossRefPubMedGoogle Scholar
  26. Miller PJ, Parfitt DE, Weinbaum SA (1989) Outcrossing in peach. HortScience 24:359–360Google Scholar
  27. Mnejja M, Garcia-Mas J, Howad W, Badenes ML, Arús P (2004) Simple-sequence repeat (SSR) markers of Japanese plum (Prunus salicina Lindl.) are highly polymorphic and transferable to peach and almond. Mol Ecol Notes 4:163–166CrossRefGoogle Scholar
  28. Mnejja M, Garcia-Mas J, Howad W, Arús P (2005) Development and transportability across Prunus species of forty-two polymorphic almond microsatellites. Mol Ecol Notes 5:531–535CrossRefGoogle Scholar
  29. Monfort A, Vilanova S, Davis TM, Arús P (2006) A new set of polymorphic simple sequence repeat (SSR) markers from a wild strawberry (Fragaria vesca) are transferable to other diploid Fragaria species and to Fragaria × ananassa. Mol Ecol Notes 6:197–200CrossRefGoogle Scholar
  30. Morgante M, Olivieri AM (1993) PCR-amplified microsatellites as markers in plant genetics. Plant J 3(1):175–182CrossRefPubMedGoogle Scholar
  31. Morgante M, Hanafey M, Powell W (2002) Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat Genet 30:194–200CrossRefPubMedGoogle Scholar
  32. Palop M, Palacios C, González-Candelas F (2000) Development and across-species transferability of microsatellite markers in the genus Limonium (Plumbaginaceae). Conservat Genet 1:177–179CrossRefGoogle Scholar
  33. Peakall R, Gilmore S, Keys W, Morgante M, Rafalski A (1998) Cross-species amplification of soybean (Glycine max) simple-sequence repeats (SSRs) within the genus and other legume genera: implications for the transferability of SSRs in plants. Mol Biol Evol 15:1275–1287PubMedGoogle Scholar
  34. Pierantoni L, Cho KH, Shin IS, Chiodini R, Tartarini S, Dondini L, Kang SJ, Sansavini S (2004) Characterisation and transferability of apple SSRs to two European pear F1 populations. Theor Appl Genet 109:1519–1524CrossRefPubMedGoogle Scholar
  35. Potter D, Eriksson T, Evans RC, Oh S, Smedmark JEE, Morgan DR, Kerr M, Robertson KR, Arsenault M, Dickinson TA, Campbell CS (2007) Phylogeny and classification of Rosaceae. Plant Syst Evol 266:5–43CrossRefGoogle Scholar
  36. Rousseau-Gueutin M, Lerceteau-Köhler E, Barrot L, Sargent DJ, Monfort A, Simpson D, Arús P, Guérin G, Denoyes-Rothan B (2008) Comparative genetic mapping between octoploid and diploid Fragaria species reveals a high level of colinearity between their genomes and the essentially disomic behavior of the cultivated octoploid strawberry. Genetics 179:2045–2060CrossRefPubMedGoogle Scholar
  37. Sánchez-Pérez R, Howad W, Dicenta F, Arús P, Martínez-Gómez P (2007) Mapping major genes and quantitative trait loci controlling agronomic traits in almond. Plant Breed 126:310–318CrossRefGoogle Scholar
  38. Sargent DJ, Cipriani G, Vilanova S, Gil-Ariza D, Arús P, Simpson DW, Tobutt KR, Monfort A (2008) The development of a bin mapping population and the selective mapping of 103 markers in the diploid Fragaria reference map. Genome 51:120–127CrossRefPubMedGoogle Scholar
  39. Scorza R, Sherman WB (1996) Peaches. In: Janick J, Moore JN (eds) Fruit breeding: tree and tropic fruits. Wiley, New York, pp 325–440Google Scholar
  40. Shulaev V, Korban SS, Sosinski B et al (2008) Multiple models for Rosaceae genomics. Plant Physiol 147:985–1003CrossRefPubMedGoogle Scholar
  41. Silfverberg-Dilworth E, Matasci CL, van de Weg WE, van Kaauwen MPW, Walser M, Kodde LP, Soglio V, Gianfranceschi L, Durel C-E, Costa F, Yamamoto T, Koller B, Gessler C, Patocchi A (2006) Microsatellite markers spanning the apple (Malus x domestica Borkh.) genome. Tree Genet Genomes 2:202–224CrossRefGoogle Scholar
  42. Smulders MJM, Bredemeijer G, Rus-Kortekaas W, Arens P, Vosman B (1997) Use of short microsatellites from database sequences to generate polymorphisms among Lycopersicon esculentum cultivars and accessions of other Lycopersicon species. Theor Appl Genet 94:264–272CrossRefGoogle Scholar
  43. Soriano JM, Romero C, Vilanova S, Llácer G, Badenes ML (2005) Genetic diversity of loquat germplasm (Eriobotrya japonica (Thunb) Lindl) assessed by SSR markers. Genome 48:108–114CrossRefPubMedGoogle Scholar
  44. Soriano JM, Vera-Ruiz EM, Vilanova S, Martínez-Calvo J, Llácer G, Badenes ML, Romero C (2008) Identification and mapping of a locus conferring plum pox virus resistance in two apricot-improved linkage maps. Tree Genet Genomes 4:391–402CrossRefGoogle Scholar
  45. Squirrell J, Hollingsworth PM, Woodhead M, Russell J, Lowe AJ, Gibby M, Powell W (2003) How much effort is required to isolate nuclear microsatellites from plants? Mol Ecol 12:1339–1348CrossRefPubMedGoogle Scholar
  46. Tavaud M (2002) Diversité génétique du cerisier doux (Prunus avium L.) sur son aire de répartition : Comparaison avec ses espèces apparentées (P. cerasus et P. gondouinii) et son compartiment sauvage. Ph.D. thesis. École Nationale Superieure Agronomique de Montpellier (France)Google Scholar
  47. Terakami S, Shoda M, Adach Y, Gonai T, Kasumi M, Sawamura Y, Iketani H, Kotobuki K, Patocchi A, Gessler C, Hayashi T, Yamamoto T (2006) Genetic mapping of the pear scab resistance gene Vnk of Japanese pear cultivar Kinchaku. Theor Appl Genet 113:743–752CrossRefPubMedGoogle Scholar
  48. Varshney RK, Graner A, Sorrels M (2005) Genic microsatellite markers in plants: features and applications. Trends Biotech 23:48–55CrossRefGoogle Scholar
  49. Vaughan SP, Russell K (2004) Characterization of novel microsatellites and development of multiplex PCR for large-scale population studies in wild cherry, Prunus avium. Mol Ecol Notes 4:429–431CrossRefGoogle Scholar
  50. Vilanova S, Romero C, Abbott AG, Llacer G, Badenes ML (2003) An apricot (Prunus armeniaca L.) F2 progeny linkage map based on SSR and AFLP markers, mapping plum pox virus resistance and self-incompatibility traits. Theor Appl Genet 107:239–247CrossRefPubMedGoogle Scholar
  51. Vilanova S, Sargent DJ, Arús P, Monfort A (2008) Synteny conservation between two distantly-related Rosaceae genomes: Prunus (the stone fruits) and Fragaria (the strawberry). BMC Plant Biol 8:67CrossRefPubMedGoogle Scholar
  52. Viruel MA, Sánchez D, Aranzana MJ, Garcia-Mas J, Arús P (2002) Aislamiento, caracterización y herencia de loci microsatélites en fresón (Fragaria x ananassa Dutch.). Acta Hortic 34:615–620Google Scholar
  53. Watkins R (1995) Cherry, plum, peach apricot and almond. In: Smartt J, Simmonds NW (eds) Evolution of crop plants, 2nd edn. Longman Scientific and Technical, Burnt MillGoogle Scholar
  54. Weeden NF, Lamb RC (1985) Identification of apple cultivars by isozyme phenotypes. J Am Soc Hortic Sci 110:509–515Google Scholar
  55. Wen J, Berggren ST, Lee CH, Ickert-Bond S, Yi TS, Yoo KO, Xie L, Shaw J, Potter D (2008) Phylogenetic inferences in Prunus (Rosaceae) using chloroplast ndhF and nuclear ribosomal ITS sequences. J Syst Evol 46:322–332Google Scholar
  56. Wünsch A (2009) Cross-transferable polymorphic SSR loci in Prunus species. Sci Hortic 120:348–352CrossRefGoogle Scholar
  57. Wünsch A, Hormaza JI (2002) Molecular characterisation of sweet cherry (Prunus avium L.) genotypes using peach (Prunus persica (L.) Batsch) SSR sequences. Heredity 89:56–63CrossRefPubMedGoogle Scholar
  58. Yamamoto T, Kimura T, Sawamura Y, Kotobuki K, Ban Y, Hayashi T, Matsuta N (2001) SSRs isolated from apple can identify polymorphism and genetic diversity in pear. Theor Appl Genet 102:865–870CrossRefGoogle Scholar
  59. Yamamoto T, Kimura T, Shoda M, Ban Y, Hayashi T, Matsuta N (2002) Development of microsatellite markers in Japanese pear (Pyrus pyrifolia Nakai). Mol Ecol Notes 2:14–16CrossRefGoogle Scholar
  60. Yamamoto T, Kimura T, Soejima J, Sanada T, Ban Y, Hayashi T (2004) Identification of quince varieties using SSR markers developed from pear and apple. Breed Sci 54:239–244CrossRefGoogle Scholar
  61. Zhang LY, Bernard M, Leroy P, Feuillet C (2005) High transferability of bread wheat EST-derived SSRs to other cereals. Theor Appl Genet 111:677–687CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag 2010

Authors and Affiliations

  • Mourad Mnejja
    • 1
  • Jordi Garcia-Mas
    • 1
  • Jean-Marc Audergon
    • 2
  • Pere Arús
    • 1
  1. 1.IRTACentre de Recerca en Agrigenòmica CSIC–IRTA–UAB08348Cabrils (Barcelona)Spain
  2. 2.INRAUnité de Génétique et Amélioration des Fruits et LégumesMontfavetFrance

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