Genetic Resources and Crop Evolution

, Volume 62, Issue 2, pp 205–219 | Cite as

Molecular analyses of evolution and population structure in a worldwide almond [Prunus dulcis (Mill.) D.A. Webb syn. P. amygdalus Batsch] pool assessed by microsatellite markers

  • Angel Fernández i Martí
  • Carolina Font i Forcada
  • Kazem Kamali
  • María J. Rubio-Cabetas
  • Michelle Wirthensohn
  • Rafel Socias i Company
Research Article


A total of 158 almond accessions representative of the diversity of almond across the five continents were included for analysis using 17 microsatellite polymorphic markers. Genetic relationships among genotypes were estimated using cluster analysis, allowing their differentiation in two main groups, one with the domesticated almond cultivars and selections and the other with all wild Prunus species close to almond. The unweighted pair group method average tree drawn from this analysis classified the genotypes according to their geographical origin, confirming the particular evolution of different almond ecotypes. Structure analysis showed a strong subpopulation structure and linkage disequilibrium decaying with increasing genetic linkage distance. Analysis of molecular variance confirmed that most of the genetic variability was within populations. Therefore the connection structure between the different populations and the possible bottlenecks in the expansion of almond cultivars could be established.


Almond Germplasm Gene flow Genetic diversity Linkage disequilibrium Phylogeography Prunus amygdalus Batsch Prunus dulcis (Mill.) D.A. Webb 

Supplementary material

10722_2014_146_MOESM1_ESM.docx (22 kb)
Supplementary material 1 (DOCX 23 kb)
10722_2014_146_MOESM2_ESM.docx (13 kb)
Supplementary material 2 (DOCX 14 kb)
10722_2014_146_MOESM3_ESM.tif (683 kb)
Supplementary material 3 (TIFF 682 kb)
10722_2014_146_MOESM4_ESM.tif (677 kb)
Supplementary material 4 (TIFF 677 kb)
10722_2014_146_MOESM5_ESM.tif (645 kb)
Supplementary material 5 (TIFF 644 kb)
10722_2014_146_MOESM6_ESM.tif (467 kb)
Supplementary material 6 (TIFF 466 kb)
10722_2014_146_MOESM7_ESM.tif (90 kb)
Supplementary material 7 (TIFF 90 kb)


  1. Arunyawat U, Capdeville G, Decroocq V, Mariette S (2012) Linkage disequilibrium in French wild cherry germplasm and worldwide sweet cherry germplasm. Tree Genet Genomes 8:737–755CrossRefGoogle Scholar
  2. Asai WK, Micke WC, Kester DE, Rough D (1996) The evaluation and selection of current varieties. In: Micke WC (ed) Almond production manual, vol 3364. University of California Publication, California, pp 52–60Google Scholar
  3. Barnaud A, Laucou V, This P, Lacombe T, Doligez A (2010) Linkage disequilibrium in wild French grapevine Vitis vinifera L. subsp. silvestris. Heredity 104:431–437PubMedCrossRefGoogle Scholar
  4. Brookfield JFY (1996) A simple new method for estimating null allele frequency from heterozygote deficiency. Mol Ecol 5:453–455PubMedCrossRefGoogle Scholar
  5. Coart E, Van Glabeke S, De Loose M, Larsen AS, Roldan-Ruiz I (2006) Chloroplast diversity in the genus Malus: new insights into the relationship between the European wild apple [Malus sylvestris (L.) Mill.] and the domesticated apple (Malus domestica Borkh.). Mol Ecol 15:2171–2182PubMedCrossRefGoogle Scholar
  6. Comadran J, Thomas WTB, van Eeuwijk FA, Ceccarelli S, Grando S, Stanca AM, Pecchioni N, Akar T, Al-Yassin A, Benbelkacem A, Ouabbou H, Bort J, Romagosa I, Hackett CA, Russell JR (2009) Patterns of genetic diversity and linkage disequilibrium in a highly structured Hordeum vulgare association-mapping population for the Mediterranean basin. Theor Appl Genet 119:175–187PubMedCrossRefGoogle Scholar
  7. Elhamzaoui A, Ouklabi A, Charafi J, Moumni M (2012) Assessment of genetic diversity of Moroccan cultivated almond (Prunus dulcis Mill. DA Webb) in its area of extreme diffusion, using SSR markers. Am J Plant Sci 3:1294–1303CrossRefGoogle Scholar
  8. Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620PubMedCrossRefGoogle Scholar
  9. Felber F, Kozlowski G, Arrigo N, Guadagnuolo R (2007) Genetic and ecological consequences of transgene flow to the wild flora. Adv Biochem Eng Biotechnol 107:173–205PubMedGoogle Scholar
  10. Felipe AJ (1984) État de l’arboretum des espèces sauvages à Saragosse. Considérations sur l’utilisation de ce matériel botanique. Options Méditerranéennes CIHEAM/IAMZ 84/II, 203–204Google Scholar
  11. Felsenstein J (2005) PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the author. Department of Genome Sciences, University of Washington, SeattleGoogle Scholar
  12. Fernandez i Marti A, Athanson B, Koepke T, Font i Forcada C, Dhingra A, Oraguzie N (2012) Genetic diversity and relatedness of sweet cherry cultivars based on SNP markers. Front Plant Sci. doi:10.3389/fpls.2012.00116 Google Scholar
  13. Fernández i Martí A, Alonso JM, Espiau MT, Rubio-Cabetas MJ, Socias i Company R (2009) Genetic diversity in Spanish and foreign almond germplasm assessed by molecular characterization with simple sequence repeats. J Am Soc Hort Sci 134:535–542Google Scholar
  14. Flint-Garcia SA, Thornsberry JM, Buckler ES (2003) Structure of linkage disequilibrium in plants. Ann Rev Plant Biol 54:357–374CrossRefGoogle Scholar
  15. Font i Forcada C, Oraguzie N, Igartua E, Moreno MA, Gogorcena Y (2013) Population structure and marker-trait associations for pomological traits in peach and nectarine cultivars. Tree Genet Genomes 9:331–349CrossRefGoogle Scholar
  16. Gradziel TM (2011) Origin and dissemination of almond. Hort Rev 38:23–81Google Scholar
  17. Grasselly C, Crossa-Raynaud P (1980) L’amandier. G.P. Maisonneuve et Larose. Maisonneuve et Larose, ParisGoogle Scholar
  18. Haudry A, Cenci A, Ravel C, Bataillon T, Brunel D, Poncet C, Hochu I, Poirier S, Santoni S, Glemin S, David J (2007) Grinding up wheat: a massive loss of nucleotide diversity since domestication. Mol Biol Evol 24:1506–1517PubMedCrossRefGoogle Scholar
  19. Kester DE, Gradziel TM, Grasselly C (1990) Almonds (Prunus). Acta Hortic 290:699–758Google Scholar
  20. Kovalyov NV, Kostina KF (1935) A contribution to the study of the genus Prunus Focke. Questions of taxonomy and plant breeding (in Russian). Trudy po Prikladnoj Botanike Genetike i Selektsii, Serie 8, 4, 1–76Google Scholar
  21. Kuleung C, Baenzinger PS, Dweikat I (2004) Transferability of SSR markers among wheat, rye and triticale. Theor Appl Genet 108:1147–1150PubMedCrossRefGoogle Scholar
  22. Ledig FT (1992) Human impacts on genetic diversity in forest ecosystems. Oikos 63:87–108CrossRefGoogle Scholar
  23. Martínez-Gómez P, Arulsekar S, Potter D, Gradziel TM (2003) An extended interspecific gene pool available to peach and almond breeding as characterized using simple sequence repeat (SSR) markers. Euphytica 131:313–322CrossRefGoogle Scholar
  24. Mather KA, Caicedo AL, Polato NR, Olsen KM, McCouch S, Purugganan MD (2007) The extent of linkage disequilibrium in rice (Oryza sativa L.). Genetics 177:2223–2232PubMedCentralPubMedCrossRefGoogle Scholar
  25. Meirmans PG, van Tienderen PH (2004) GENOTYPE and GENODIVE: two programs for the analysis of genetic diversity of asexual organisms. Mol Ecol Notes 4:792–794CrossRefGoogle Scholar
  26. Mnejja M, Garcia-Mas J, Audergon JM, Arús P (2010) Prunus microsatellite marker transferability across rosaceous crops. Tree Genet Genomes 6:689–700CrossRefGoogle Scholar
  27. Nei M, Li WH (1979) Mathematical model for studying genetic variation interms of restriction endonucleases. Proc Natl Acad Sci USA 76:5269–5273PubMedCentralPubMedCrossRefGoogle Scholar
  28. Nordborg M, Tabaré S (2002) Linkage disequilibrium: what history has to tell us. Trends Genet 18:83–90PubMedCrossRefGoogle Scholar
  29. Ostrowski MF, David J, Santoni S, McKhann H, Reboud X, Le Corre V, Camilleri C, Brunel D, Bouchez D, Faure B, Bataillon T (2006) Evidence for a large-scale population structure among accessions of Arabidopsis thaliana: possible causes and consequences for the distribution of linkage disequilibrium. Mol Ecol 15:1507–1517PubMedCrossRefGoogle Scholar
  30. Popov MG, Kostina KF, Poyarkova AI (1929) Wild trees and shrubs in Central Asia (in Russian). Trudy po Prikladnoj Botanike Genetike i Selektsii 2:241–483Google Scholar
  31. Pritchard JK, Stephens M, Rosenberg NA, Donnelly P (2000) Association mapping in structured populations. Am J Hum Genet 67:170–181PubMedCentralPubMedCrossRefGoogle Scholar
  32. Quinn G (1905) Some notes on almonds. Department of Agriculture of South Australia, Bulletin 5Google Scholar
  33. Rehder A (1940) Manual of cultivated trees and shrubs. MacMillan, New YorkGoogle Scholar
  34. Remington DL, Thornsberry JM, Matsuoka Y, Wilson LM, Whitt SR, Doebley J, Kresovich S, Goodman MM, Buckler ES (2001) Structure of linkage disequilibrium and phenotypic associations in the maize genome. Proc Natl Acad Sci USA 98:11479–11484PubMedCentralPubMedCrossRefGoogle Scholar
  35. Rikhter AA (1972) Biological basis for the creation of almond cultivars and commercial orchards (in Russian). Akademiya Nauk SSSR Glavnyj Botanicheskij Sad, MoscowGoogle Scholar
  36. Saitou N, Nei M (1987) The neighbour-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425PubMedGoogle Scholar
  37. Shepherd T (1841) Lecture on the horticulture of Australia. In: Allen J (ed) The South Australia magazine, vol 1., July 1841—September 1842, South Australia, Adelaide, pp 148–150Google Scholar
  38. Socias i Company R (2004) The contribution of Prunus webbii to almond evolution. Plant Genet Resour News 14:9–13Google Scholar
  39. Socias i Company R, Felipe AJ (1992) Almond: a diverse germplasm. HortScience 27:717–718Google Scholar
  40. Socias i Company R R (1990) Breeding self-compatible almonds. Plant Breed Rev 8:313–338Google Scholar
  41. Socias i Company R, Alonso JM, Kodad O, Gradziel TM (2012) Almond. In: Badenes ML, Byrne D (eds) Fruit breeding, handbook of plant breeding 8. Springer, Heidelberg, pp 697–728Google Scholar
  42. van Heerwaarden J, Doebley J, Briggs WH, Glaubitz JC, Goodman MM, Sánchez González JJ, Ross-Ibarra J (2011) Genetic signals of origin, spread, and introgression in a large sample of maize landraces. Proc Natl Acad Sci USA 108:1088–1092PubMedCentralPubMedCrossRefGoogle Scholar
  43. Wirthensohn M, Sedgley M (2003) Australian almond cultivars: where are they? Australian Nutgrower 17:16Google Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2014

Authors and Affiliations

  • Angel Fernández i Martí
    • 1
  • Carolina Font i Forcada
    • 1
  • Kazem Kamali
    • 2
  • María J. Rubio-Cabetas
    • 1
  • Michelle Wirthensohn
    • 3
  • Rafel Socias i Company
    • 1
  1. 1.Unidad de FruticulturaCentro de Investigación y Tecnología Agroalimentaria de Aragón (CITA)ZaragozaSpain
  2. 2.Department of HorticultureUniversity of ArdakanYazdIran
  3. 3.School of Agriculture, Food and Wine, Waite Research InstituteUniversity of AdelaideGlen OsmondAustralia

Personalised recommendations