SpringerLink
Log in

Genetic diversity of some wild almonds and related Prunus species revealed by SSR and EST-SSR molecular markers

  • Original Article
  • Published:
Plant Systematics and Evolution Aims and scope Submit manuscript

Abstract

Almond and its related wild species, which are widely distributed in Central and West Asia, have high genetic variation. This is an important source of genetic diversity for crop improvement. In this study a set of 32 SSR and 12 EST-SSR primer pairs were used to determine genetic diversity in 89 accessions of almond and other Prunus species. Most of the accessions (68) were collected from natural habitats of Iran. SSR primers amplified higher numbers of alleles than EST-SSR markers and discriminated genotypes more effectively. Results indicated high diversity among accessions. Observed heterozygosity (Ho) was 0.581. Nei’s index of diversity (He) and average number of alleles per locus (na) were 0.885 and 34, respectively. The mean value of polymorphism information content (PIC) was 0.874. The average Fst (F-statistics index) was 0.271 and the fixation index (Fis) was 0.151. Estimated variance among putative populations (AP) and individuals (AI) and within individuals (WI) were 5, 35, and 60%, respectively, which revealed that most of the variation was distributed among individuals rather than groups. Cultivated almonds were highly similar to P. fenzeliana, which is native to West Asia, supporting the importance of these regions in almond domestication. In the dendrogram of groups, minimum genetic distance was observed between Amygdalus and Orientalis groups from the Euamygdalus section. The Leptopus and Chameamygdalus sections were more distant from almonds than plums. The results also showed Dodecandra (Lycioides) series should be taxonomically classified closer to the section Euamygdalus.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or Ebook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

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

Similar content being viewed by others

References

  • Amirbakhtiar N, Shiran B, Moradi H, Sayed-Tabatabaei BE (2006) Molecular characterization of almond cultivars using microsatellite markers. Acta Hort 726:51–56

    CAS  Google Scholar 

  • Aranza MJ, Garcia-Mas J, Carbo J, Arus P (2002) Development and variability analysis of microsatellite markers in peach. Plant Breed 121:87–92

    Article  Google Scholar 

  • Botstein D, White RL, Skolmick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphism. Am J Hum Genet 32:314–332

    PubMed  CAS  Google Scholar 

  • Browicz K (1974) The genus Amygdalus in Turkey. In: Proc. Int. Symposium on Turkish Flora. Istanbul Univ. Orman Facult. Yainlari No. 209: 239–255

  • Browicz K, Zohary D (1996) The genus Amygdalus L (Rosaceae): species relationships, distribution and evolution under domestication. Genet Resour Crop Evol 43:229–247

    Article  Google Scholar 

  • Bruford MW, Wayne RK (1993) Microsatellites and their application to population genetic studies. Curr Opin Genet Develop 3:939–943

    Article  CAS  Google Scholar 

  • Cantini C, Iezzoni AF, Lamboy WF, Boritzki M, Struss D (2001) DNA fingerprinting of tetraploid cherry germplasm using SSR. J Am Soc Hort Sci 126:205–209

    CAS  Google Scholar 

  • Cipriani G, Lot G, Huang WG, Marrazzo MT, Peterlunger E, Testolin R (1999) AG/GT and AG/CT microsatellite repeats in peach [Prunus persica (L.) Batsch]: isolation, characterization and cross-species amplification in Prunus. Theor Appl Genet 99:65–72

    Article  CAS  Google Scholar 

  • Cociu V (1967) Pomology of the Socialist Republic of Romania. Bucarest Acad. De la Repub. Socialistic de Roumanic

  • Crossa-Raynaud P, Grasselly CH (1985) Existence de groupes d’intersterilte chez l’amandier. Options Mediterr 1:43–45

    Google Scholar 

  • Dirlewanger E, Cosson P, Tavaud M, Aranza MJ, 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 105:127–138

    Article  PubMed  CAS  Google Scholar 

  • Dirlewanger E, Graziano E, Joobeur T, Garriga-Caldere F, Cosson P, Howad W, Arus P (2004) Comparative map** and marker-assisted selection in Rosaceae fruit crops. PNAS 101(26):9891–9896

    Article  PubMed  CAS  Google Scholar 

  • Duke JA (2000) Handbook of nuts. CRC Press, Inc., FL

    Google Scholar 

  • Evreinov VA (1952) Quelques obsevations biologiques sur l'amandier. Rev Int Bot App D’Agr Trop 32:442–459

    Google Scholar 

  • Evreinov VA (1958) Contribution a l’etude de l’amandier. Fruit et Primers Afrique 28:99–104

    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 data. Genetics 131:479–491

    PubMed  CAS  Google Scholar 

  • Fathi A, Ghareyazi B, Haghnazari A, Ghaffari MR, Pirseyedi SM, Kadkhodaei S, Naghavi MR, Mardi M (2008) Assessment of the genetic diversity of almond (Prunus dulcis) using microsatellite markers and morphological traits. Iran J Biotechnol 6(2):98–106

    CAS  Google Scholar 

  • Fellipe AJ (2000) El Almendro, EL Manterial vegetale. INTEGRUM

  • Focke WO (1894) Rosaceae. In: Engler A, Prantl K (eds) Die natürlichen pflanzenfamilien. III, 3, 1–61. Engelmann, Leipzig

  • Grasselly CH (1976) Origine et evolution de lespece cultivee. Options Mediterraneennes (L’Amandier) 32:45–50

  • Grasselly CH, Duval H (1997) L’Amandier (monographie). Ctifl, Prix: 180F

  • Hartl DL, Clark AG (1989) Principles of population genetics, 2nd edn. Sinauer Associates, Sunderland

    Google Scholar 

  • Jung S, Abbott A, Jesudurai C, Tomkins J, Main D (2005) Frequency, type, distribution and annotation of simple sequence repeats in Rosaceae ESTs. Funct Integr Genomics 5:136–143

    Article  PubMed  CAS  Google Scholar 

  • Kadkhodaei SR, Aghdaei T, Grigorian V, Moghadam M, Hashemi SMM (2006) A study on genetic variation among some wild almond species using RAPD markers. Acta Hort 726:93–98

    CAS  Google Scholar 

  • Kester DE, Assay RA (1975) Almond breeding. In: Janick J, Moore JN (eds) Advances in fruit breeding. Purdue Univ. Press, West Lafayette, pp 382–419

    Google Scholar 

  • Kester DE, Gradziel TM (1996) Almonds. In: Janick J, Moore JN (eds) Fruit breeding, vol III: Nuts: 1–97. John Wiley and Sons, New York

  • Kester DE, Gradziel TM, Grasselly CH (1991) Almonds (Prunus). In: Moore JN, Ballington JR (eds) Genetic resources of temperate fruit and nut crops. Acta Hort 290:701–758

  • Khatamsaz M (1992) Flora of Iran. No. 6: Rosaceae, Research Institute of Forest and rangelands

  • Kiani S, Shiran B, Mohammadi S, Moradi H (2006) Molecular characterization of variability and relationships among almond cultivars (Prunus dulcis) and selected wild species of Amygdalus using RAPD. Acta Hort 726:113–122

    CAS  Google Scholar 

  • Kovalev NV, Kostina KF (1935) A contribution of the study of the genus Prunus, Leningerad

  • Ladizinsky G (1999) On the origin of almond. Genet Resour Crop Evol 46:143–147

    Article  Google Scholar 

  • Lee S, Wen J (2001) A phylogenetic analysis of Prunus and the Amygdaloideae (Rosaceae) using ITS sequences of nuclear ribosomal DNA. Am J Bot 88:150–160

    Article  PubMed  CAS  Google Scholar 

  • Levene H (1949) On a matching problem in genetics. Ann Math Stat 20:91–94

    Article  Google Scholar 

  • Ma RC, Yong X, Yan M, Hua X, Yuan-Qing J, Ming Qing C, Chun-Hui G, Xue-Shi H, Yo-**ang L, Jian-Ting L, Tian ** Z (2003) Molecular analysis of almond germplasm in China. Options Mediterr 63:281–290

    Google Scholar 

  • Martinez-Gomez P, Arulsekar S, Pother D, Gradziel TM (2003a) An extended interspecific gene pool available to peach and almond breeding as characterized using simple sequence repeate (SSR) markers. Euphytica 131:313–322

    Article  CAS  Google Scholar 

  • Martinez-Gomez P, Arulsekar S, Pother D, Gradziel TM (2003b) Relationships among peach and almond and related species as detected by SSR markers. J Ame Soc Hort Sci 128:667–671

    Google Scholar 

  • Martinez-Gomez P, Sanchez-Perez R, Rubio M, Dicenta F, Gradziel TM, Sozzi GO (2005) Application of recent biotechnologies to Prunus tree crop genetic improvement. Cien Inv Agr 32(2):73–96

    Google Scholar 

  • Martinez-Gomez P, Sanchez-Perez R, Dicenta F, Howad W, Arus P, Gradziel TM (2007) Almond. In: Genome map** and molecular breeding in plants, vol 4, pp 229–242, Fruits and Nuts, Chapter 11, Springer

  • Martins M, Tenreiro R, Oliveira MM (2003) Genetic relatedness of Portuguese almond cultivars assessed by RAPD and ISSR markers. Plant Cell Rep 22:71–78

    Article  PubMed  CAS  Google Scholar 

  • Mnejja M, Garcia-Mas J, Howad W, Badenes ML, Arus P (2004) Simple-sequence repeat (SSR) markers of Japanese plum (Prunus salicina Lindl.) are highly polymorphic and transferable to peach and almond. Molecular ecology notes, pp 163–166

  • Mnejja M, Garcia-Mas J, Howad W, Arus P (2005) Development and transportability across Prunus species of 42 polymorphic almond microsatellites. Mol Ecol Notes 5(3):531–535

    Article  CAS  Google Scholar 

  • Nei M, Takezaki N (1983) Estimation of genetic distances and phylogenetic trees from DNA analysis. Proc 5th World Cong Genet Appl Livestock Prod 21:405–412

    Google Scholar 

  • Ortega E, Dicenta F (2003) Inheritance of self-compatibility in almond: breeding strategies to assure self-compatibility in the progeny. Theor Appl Genet 106:904–911

    PubMed  CAS  Google Scholar 

  • Rahemi A, Yadollahi A (2006) Rainfed almond orchards in Iran, ancient and new methods and the value of water harvesting techniques. Acta Hort 726:449–453

    Google Scholar 

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

    Google Scholar 

  • Rickler AA (1972) L’amandier. Academie des Sciences Agricoles. Jardin Botanique de Nikils. Yalla

  • Schueler S, Tusch A, Schuster M, Ziegenhagen B (2003) Characterization of microsatellites in wild and sweet cherry (Prunus avium L.) markers for individual identification and reproductive processes. Genome 46:95–102

    Article  PubMed  CAS  Google Scholar 

  • Serafimov S (1975) L’amandier in Bulgaria, II Coll. GREMPA, CIHEAM, Montpelier, France

  • Shannon CE, Weaver W (1949) The mathematical theory of communication. University of Illinois Press, Urbana

    Google Scholar 

  • Shaw J, Small RL (2004) Addressing the ‘‘hardest puzzle in American pomology:’’ phylogeny of Prunus sect. Prunocerasus (Rosaceae) based on seven noncoding chloroplast dna regions1. Am J Bot 91(6):985–996

    Article  PubMed  CAS  Google Scholar 

  • Shiran B, Amirbakhtiar N, Kiani S, Mohammmadi Sh, Sayed-Tabatabaei BE, Moradi H (2007) Molecular characterization and genetic relationship among almond cultivars assessed by RAPD and SSR markers. Scientia Hortic 111:280–292

    Article  CAS  Google Scholar 

  • Siami A, Heidari R, Mohseni M (2002) Comparative study of amygdalin, fat and total protein of 7 species of wild almond in west Azarbaijan. Acta Hort 591:181–187

    CAS  Google Scholar 

  • Slatkin M, Barton NH (1989) A comparison of three indirect methods for estimating average levels of gene flow. Evolution 43:1349–1368

    Article  Google Scholar 

  • Socias i Company R (1998) La taxonomie de l’amandier. Cahiers. Options Mediterr 33:91–93

  • Sorkheh K, Shiran B, Gradziel TM, Epperson BK, Martinez-Gomez P, Asadi E (2007) Amplified fragment length polymorphism as a tool for molecular characterization of almond germplasm: genetic diversity among cultivated genotypes and related wild species of almond, and its relationships with agronomic traits. Euphetica 156:327–344

    Article  CAS  Google Scholar 

  • Sosinski B, Gannavarapu M, Hager LD, Beck LE, King GJ, Ryder CD, Rajapakse S, Baird WV, Ballard RE, Abbott AG (2000) Characterization of microsatellite markers in peach [Prunus persica (L.) Batsch]. Theor Appl Genet 101:421–428

    Article  CAS  Google Scholar 

  • Spach E (1843) Monographia, generis Amygdalus. Annu Sci Natur Ser 2(19):106–128

    Google Scholar 

  • Takhtajan A (1997) Diversity and classification of flowering plants. Columbia University Press, New York

    Google Scholar 

  • Testolin R, Marrazzo T, Cipriani G, Quarta R, Verde I, Dettori MT, Pancaldi M, Sansavini S (2000) Microsatellite DNA in peach (Prunus persica L Batsch) and its use in fingerprinting and testing the genetic origin of cultivars. Genome 43:512–520

    PubMed  CAS  Google Scholar 

  • Vavilov NI (1930) Wild progenitors of the fruit trees of Turkistan and Caucasus and the problem of the origin of fruit trees. In: IX International Horticultural Congress report and Proceedings, London, pp 271–286

  • Vendramin E, Dettori MT, Giovinazzi J, Micali S, Quarta R, Verde I (2007) A set of EST-SSRs isolated from peach fruit transcriptome and their transportability across Prunus species. Mol Ecol Notes 7:307–310

    Article  CAS  Google Scholar 

  • Vezvaei A (2003) Izosyme diversity in Iranian almond, XXVI International Horticulture Congress: genetics and breeding of tree fruits and nuts. Acta Hort 622:451–456

    CAS  Google Scholar 

  • Vilanova S, Sargent DJ, Arus P, Monfort A (2008) Synteny conservation between two distantly-related Rosaceae genomes: Prunus (the stone fruits) and Fragaria (the strawberry). BMC Plant Biol 8:67

    Article  PubMed  Google Scholar 

  • Warren CM (1996) Almond production manual. University of California, California

    Google Scholar 

  • Watkins R (1995) Cherry, plum, peach, apricot and almond. In: Smartt J, Simonds NW (eds) Evolution of crop plants, 2nd edn. Burnt Mill: Longman Scientific and Technical Longman, London, pp 326–332

    Google Scholar 

  • Wunsch A (2008) Cross transferable polymorphic SSR loci in Prunus species. Scientia Hortic 120(3):348–352

    Article  Google Scholar 

  • **e H, Sui Y, Chang FQ, Xu Y, Ma RC (2006) SSR allelic variation in almond (Prunus dulcis Mill.). Theor Appl Genet 112:366–372

    Article  PubMed  CAS  Google Scholar 

  • Xu Y, Ma RC, **e H, Liu JT, Cao MQ (2004) Development of SSR markers for the phylogenetic analysis of almond trees from china and the mediterranean region. Genome 47:1091–1104

    Article  PubMed  CAS  Google Scholar 

  • Yeh FC, Yang RC, Boyle T (1997) POPGENE 1.21. (URL http://www.ualberta.ca/~fyeh)

  • Zeinalabedini M, Majourhat K, Khayam-Nekoui M, Grigorian V, Torchi M, Dicenta F, Martinez-Gomez P (2007a) Molecular characterization of almond cultivars and related wild species using nuclear and chloroplast DNA markers. J Food Agric Environ 5(3–4):242–247

    CAS  Google Scholar 

  • Zeinalabedini M, Majourhat K, Khayam-Nekoui M, Grigorian V, Torchi M, Dicenta F, Martinez-Gomez P (2007b) Comparison of the use of morphological, protein and DNA markers in the genetic characterization of Iranian wild Prunus species. Scientia Hortic 116(1):80–88

    Article  Google Scholar 

  • Zhebentyayeva T, Reighard G, Gorina V, Abbott A (2003) Simple sequence repeat (SSR) analysis for assessment of genetic variability in apricot germplasm. Theor Appl Genet 106:435–444

    PubMed  CAS  Google Scholar 

  • Zohary M (1973) Geobotanical foundations of the Middle East. Gustav Fisher, Stuttgart

    Google Scholar 

  • Zohary D (1998) Taxonomy of the almonds. FAO, CIHEAM, Nucis (Information Bulletin of the FAO Research Network on Nuts 7:5–6

  • Zohary D, Hopf M (2000) Domestication of plants in the old world, 3rd edn. Oxford University Press, NY

    Google Scholar 

Download references

Acknowledgments

This work was financed by and performed in the Stone Fruit Genetic Laboratory in the Department of Horticultural Science, University of Florida (UF), USA. We are grateful to Valerie Jones, the laboratory manager, for her assistance in this research. The authors also thank the Ministry of Agriculture and National Plant Gene Bank of Iran (NPGBI) for supporting germplasm sampling. We are also grateful for plant materials provided by the United States Department of Agriculture, Davis, California (USDA), University of California, Davis (UC Davis), University of Florida, Gainesville, and University of Georgia (UGA).

Author information

Authors and Affiliations

  1. Department of Horticultural Science, Islamic Azad University (Science and Research Branch), Hesarak, Ashrafi Isfahani Blvd, Tehran, Iran

    Alireza Rahemi

  2. Department of Horticultural Science, University of Tehran, Karaj, Iran

    Reza Fatahi, Ali Ebadi & Toktam Taghavi

  3. Department of Horticulture, Seed and Plant Improvement Institute, Karaj, Iran

    Darab Hassani

  4. Department of Plant Sciences, University of California, Davis, USA

    Thom Gradziel

  5. Department of Horticultural Science, University of Florida, Gainesville, USA

    Kevin Folta & José Chaparro

Authors
  1. Alireza Rahemi
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Reza Fatahi
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Ali Ebadi
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Toktam Taghavi
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Darab Hassani
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Thom Gradziel
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Kevin Folta
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. José Chaparro
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Alireza Rahemi.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOC 1173 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Rahemi, A., Fatahi, R., Ebadi, A. et al. Genetic diversity of some wild almonds and related Prunus species revealed by SSR and EST-SSR molecular markers. Plant Syst Evol 298, 173–192 (2012). https://doi.org/10.1007/s00606-011-0536-x

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00606-011-0536-x

Keywords

Search

Navigation