Skip to main content
SpringerLink
Log in

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

  • Research Article
  • Published:
Genetic Resources and Crop Evolution Aims and scope Submit manuscript

Abstract

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.

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
Fig. 6
Fig. 7

Similar content being viewed by others

References

  • Arunyawat U, Capdeville G, Decroocq V, Mariette S (2012) Linkage disequilibrium in French wild cherry germplasm and worldwide sweet cherry germplasm. Tree Genet Genomes 8:737–755

    Article  Google Scholar 

  • 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 52–60

    Google Scholar 

  • Barnaud A, Laucou V, This P, Lacombe T, Doligez A (2010) Linkage disequilibrium in wild French grapevine Vitis vinifera L. subsp. silvestris. Heredity 104:431–437

    Article  CAS  PubMed  Google Scholar 

  • Brookfield JFY (1996) A simple new method for estimating null allele frequency from heterozygote deficiency. Mol Ecol 5:453–455

    Article  CAS  PubMed  Google Scholar 

  • 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 15:2171–2182

    Article  CAS  PubMed  Google Scholar 

  • 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 119:175–187

    Article  CAS  PubMed  Google Scholar 

  • 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 3:1294–1303

    Article  Google Scholar 

  • Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620

    Article  CAS  PubMed  Google Scholar 

  • Felber F, Kozlowski G, Arrigo N, Guadagnuolo R (2007) Genetic and ecological consequences of transgene flow to the wild flora. Adv Biochem Eng Biotechnol 107:173–205

    CAS  PubMed  Google Scholar 

  • 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, 203–204

  • Felsenstein J (2005) PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle

  • 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 

  • 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 134:535–542

    Google Scholar 

  • Flint-Garcia SA, Thornsberry JM, Buckler ES (2003) Structure of linkage disequilibrium in plants. Ann Rev Plant Biol 54:357–374

    Article  CAS  Google Scholar 

  • 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 9:331–349

    Article  Google Scholar 

  • Gradziel TM (2011) Origin and dissemination of almond. Hort Rev 38:23–81

    Google Scholar 

  • Grasselly C, Crossa-Raynaud P (1980) L’amandier. G.P. Maisonneuve et Larose. Maisonneuve et Larose, Paris

    Google Scholar 

  • 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 24:1506–1517

    Article  CAS  PubMed  Google Scholar 

  • Kester DE, Gradziel TM, Grasselly C (1990) Almonds (Prunus). Acta Hortic 290:699–758

    Google Scholar 

  • 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, 1–76

  • Kuleung C, Baenzinger PS, Dweikat I (2004) Transferability of SSR markers among wheat, rye and triticale. Theor Appl Genet 108:1147–1150

    Article  CAS  PubMed  Google Scholar 

  • Ledig FT (1992) Human impacts on genetic diversity in forest ecosystems. Oikos 63:87–108

    Article  Google Scholar 

  • 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 131:313–322

    Article  Google Scholar 

  • Mather KA, Caicedo AL, Polato NR, Olsen KM, McCouch S, Purugganan MD (2007) The extent of linkage disequilibrium in rice (Oryza sativa L.). Genetics 177:2223–2232

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Meirmans PG, van Tienderen PH (2004) GENOTYPE and GENODIVE: two programs for the analysis of genetic diversity of asexual organisms. Mol Ecol Notes 4:792–794

    Article  Google Scholar 

  • Mnejja M, Garcia-Mas J, Audergon JM, Arús P (2010) Prunus microsatellite marker transferability across rosaceous crops. Tree Genet Genomes 6:689–700

    Article  Google Scholar 

  • Nei M, Li WH (1979) Mathematical model for studying genetic variation interms of restriction endonucleases. Proc Natl Acad Sci USA 76:5269–5273

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Nordborg M, Tabaré S (2002) Linkage disequilibrium: what history has to tell us. Trends Genet 18:83–90

    Article  CAS  PubMed  Google Scholar 

  • 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 15:1507–1517

    Article  CAS  PubMed  Google Scholar 

  • Popov MG, Kostina KF, Poyarkova AI (1929) Wild trees and shrubs in Central Asia (in Russian). Trudy po Prikladnoj Botanike Genetike i Selektsii 2:241–483

    Google Scholar 

  • Pritchard JK, Stephens M, Rosenberg NA, Donnelly P (2000) Association mapping in structured populations. Am J Hum Genet 67:170–181

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Quinn G (1905) Some notes on almonds. Department of Agriculture of South Australia, Bulletin 5

  • Rehder A (1940) Manual of cultivated trees and shrubs. MacMillan, New York

    Google Scholar 

  • 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 98:11479–11484

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Rikhter AA (1972) Biological basis for the creation of almond cultivars and commercial orchards (in Russian). Akademiya Nauk SSSR Glavnyj Botanicheskij Sad, Moscow

    Google Scholar 

  • Saitou N, Nei M (1987) The neighbour-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    CAS  PubMed  Google Scholar 

  • 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 148–150

    Google Scholar 

  • Socias i Company R (2004) The contribution of Prunus webbii to almond evolution. Plant Genet Resour News 14:9–13

    Google Scholar 

  • Socias i Company R, Felipe AJ (1992) Almond: a diverse germplasm. HortScience 27:717–718

    Google Scholar 

  • Socias i Company R R (1990) Breeding self-compatible almonds. Plant Breed Rev 8:313–338

    Google Scholar 

  • 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 697–728

    Google Scholar 

  • 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 108:1088–1092

    Article  PubMed Central  PubMed  Google Scholar 

  • Wirthensohn M, Sedgley M (2003) Australian almond cultivars: where are they? Australian Nutgrower 17:16

    Google Scholar 

Download references

Acknowledgments

Research conducted under the Spanish projects AGL2010-22197-C02-01 and INIA RF2011-00020-C02-01, and the Research Group A12 of Aragón.

Author information

Authors and Affiliations

  1. Unidad de Fruticultura, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Av. Montañana 930, 50059, Zaragoza, Spain

    Angel Fernández i Martí, Carolina Font i Forcada, María J. Rubio-Cabetas & Rafel Socias i Company

  2. Department of Horticulture, University of Ardakan, Yazd, Iran

    Kazem Kamali

  3. School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Glen Osmond, SA, 5064, Australia

    Michelle Wirthensohn

Authors
  1. Angel Fernández i Martí
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Carolina Font i Forcada
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Kazem Kamali
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. María J. Rubio-Cabetas
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Michelle Wirthensohn
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Rafel Socias i Company
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Rafel Socias i Company.

Additional information

Angel Fernández i Martí and Carolina Font i Forcada have contributed equally to this work.

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Fernández i Martí, A., Font i Forcada, C., Kamali, K. et al. 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. Genet Resour Crop Evol 62, 205–219 (2015). https://doi.org/10.1007/s10722-014-0146-x

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10722-014-0146-x

Keywords

Search

Navigation