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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

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Abstract

Amplified fragment length polymorphism (AFLP) analysis is a rapid and efficient method for producing DNA fingerprints and molecular characterization. Our objectives were to: estimate genetic similarities (GS), marker indices, and polymorphic information contents (PICs) for AFLP markers in almond cultivars; assess the genetic diversity of almond cultivars and wild species, using GS estimated from AFLP fingerprints and molecular characterization; and facilitate the use of markers in inter-specific introgression and cultivar improvement. The genetic diversity of 45 almond cultivars from Iran, Europe, and America, were studied assaying 19 primer combinations. In addition, several agronomic traits were evaluated, including flowering and maturity times, self-incompatibility, and kernel and fruit properties. Out of the 813 polymerase chain reaction fragments that were scored, 781 (96.23%) were polymorphic. GS ranged from 0.5 to 0.96, marker indices ranged from 51.37 to 78.79, and PICs ranged from 0.56 to 0.86. Results allowed the unique molecular identification of all assayed genotypes. However, the correlation between genetic similarity clustering as based on AFLP and clustering for agronomic traits was low. Cluster analysis based on AFLP data clearly differentiated the genotypes and wild species according to their origin and pedigree, whereas, cluster analysis based on agronomic data differentiated according the pomological characterization. Our results showed the great genetic diversity of the almond cultivars and their interest for almond breeding.

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References

  • Aranzana M, Pineda A, Cosson P, Dirlewanger E, Ascasibar J, Cipriani G, Ryder C, Testolin R, Abbott A, King G, Arus P (2003) A set of simple sequence repeat (SSR) markers covering most of the Prunus genome. Theor Appl Genet 106:819–825

    PubMed  CAS  Google Scholar 

  • Arulsekar S, Parfitt DE, Kester DE, (1986) Comparison of Isozyme variability in peach and almond cultivars. J Hered 77:272–274

    CAS  Google Scholar 

  • Bartolozzi F, Warburton ML, Arulsekar S, Gradziel TM (1998) Genetic characterization and relatedness among California almond cultivars and breeding line detected by randomly amplified polymorphic DNA (RAPD) analysis. J Am Sco Hort Sci 123:381–387

    CAS  Google Scholar 

  • Bassam BJ, Caetano-Anolles G (1993) Silver staining of DNA in polyacrylamide gels. Appl Biochem Biotech 42:181–188

    CAS  Google Scholar 

  • Berry ST, Allen RJ, Barnes SR, Caligari PDS (1994) Molecular marker analysis of Helianthus annus L. Restriction fragment length polymorphism between inbred lines of cultivated sunflower. Theor Appl Genet 89:435–441

    CAS  Google Scholar 

  • Bortiri PE, Oh S, Jiang J, Baggett S, Granger A, Weeks C, Potter D, Parfitt DE (2001) Phylogeny and systematics of Prunus (Rosaceae) as determined by sequence analysis of ITS and the chloroplast trnL-trnF spacer DNA. Syetematic Bot 26:797–807

    Google Scholar 

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

    Google Scholar 

  • Brown-Guedira GL, Thompson JA, Nelson RL, Warburton ML (2000) Evaluation of genetic diversity of soybean introductions and North American ancestors using RAPD and SSR markers. Crop Sci 40:815–823

    Article  CAS  Google Scholar 

  • Caicedo AL, Gaitan E, Duque MC, Chica OT, Tohma J (1999) AFLP fingerprinting of Phaseolus lunatus L. and related wild species from South America. Crop Sci 39:1497–1507

    Google Scholar 

  • Cerezo M, Socias I, Company R, Vargas F (1989) Identification of almond cultivars by pollen isoenzymes. J Am Soc Hort Sci 114:164–169

    CAS  Google Scholar 

  • Channuntapipat C, Wirthensohn M, Ramesh SA, Batlle I, Arus P, Sedgley M, Collins G (2003) Identification of incompatibility genotypes in almond (Prunus dulcis Mill.) using specific primers based on the introns of the S-alleles. Plant Breed 122:164–168

    Article  CAS  Google Scholar 

  • 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, characterization and cross-species amplification in prunus. Theor Appl Genet 100:713–722

    Google Scholar 

  • De Nettancourt D (1997) Incompatibility in angiosperms. Monographs on theoretical and applied genetics, vol 3. Springer, Berlin

    Google Scholar 

  • Denisov VP (1988) Almond genetics resources in the USSR and their use in production and breeding. Acta Hort 224:299–306

    Google Scholar 

  • Dicenta F (1991) Mejora Genética del Almondro (Prunus dulcis Miller) por Cruzamientos intervarietales: Herencia de caracters y Selectión. Thesis. University Murcia, Spain, p 313

  • Doweny LD, Iezzoni AF (2000) Polymorphic DNA markers in black cherry are identified using sequences from sweet cherry, peach and sour cherry. J Am Soci Hort Sci 125:76–80

    Google Scholar 

  • Evreinoff VA (1958) Contribution a letude de l’amandier. Fruits et Primeurs Afrique 28:99–104

    Google Scholar 

  • Excoffier L, Smouse P, Quattro J (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 

  • Gentzbittel L, Zhang Y-X, Vear F, Griveau B (1994) RFLP studies of genetics relationships among inbred lines of cultivated sunflower, Helianthus annus L. evidence for distinct restorer and maintainer germplasm pools. Theo Appl Genet 89:419–425

    CAS  Google Scholar 

  • Gradziel TM, Kester DE (1998) Breeding for self-fertility in California almond cultivars. Acta Hort 470:109–117

    Google Scholar 

  • Gradziel TM, Martínez-Gómez P, Dicenta F, Kester DE (2001) The utilization of Prunus species for almond variety improvement. J Am Pomol Soc 55:100–108

    Google Scholar 

  • Grasselly C (1976) Les espéces sauvages ďamandier (in French). Options Méditerr 32:28–44

    Google Scholar 

  • Hauagge R, Kester DE, Arulsekar S, Parfitt DE, Liu L (1987) Isozyme variation among California almond cultivars. II. Cultivar characterization and origins. J Am Sco Hort Sci 112:693–698

    CAS  Google Scholar 

  • Hesse CO (1975) Peaches. In: Janick J, Moore JN (eds) Advances in fruit breeding. Purdue Univ. Press, West Lafayette, Ind, pp 285–326

    Google Scholar 

  • Kester DE (1994) Almond cultivar and breeding programs in California. Acta Hort 373:13–28

    Google Scholar 

  • Kester DE, Gradziel TM (1996) Almonds In: Janick J, Moore JN (eds) Fruit breeding, Almond, vol. 1. Wiley, New York, pp 1–97

    Google Scholar 

  • Kester DE, Gradziel TM, Micke WC (1994) Identifying pollen incompatibility groups in California almond cultivars. J Am Sco Hort Sci 119:106–109

    Google Scholar 

  • Kovaleff NV, Kostina KF (1935) A contribution of the study of the genus prunus Focke. Leningrad

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

    Article  Google Scholar 

  • Mantel N (1967) The detection of disease clustering and generalized regression approach. Cancer Res 27:209–220

    PubMed  CAS  Google Scholar 

  • Martínez de Toda E, Saccha JC (1997) Ampelographical characterization of red Vitis vinifera L. cultivars preserved in Rioja. Bultten de tow, Mars-Avril, 70:220–234

    Google Scholar 

  • Martínez-Gómez P, Arulsekar S, Potter D, Gradziel TM (2003a) An extended inter-specific gene pool available to peach and almond breeding as characterized using simple sequence repeat (SSR) markers. Euphytica 131:313–322

    Article  Google Scholar 

  • Martínez-Gómez P, Arulsekar S, Potter D, Gradziel TM (2003b) Relationships among peach and almond and related species as detected by SSR markers. J Am Sco Hort Sci 128:667–671

    Google Scholar 

  • Martínez-Gómez P, Sánchez-Pérez R, Dicenta F, Howad W, Arus P, Gradziel TM (2007) Almonds. In: Kole CR (ed) Genome mapping and molecular breeding, vol. 4: Fruits & Nuts. Springer. Heidelberg, Berlin, New York, Tokio, pp 229–242

    Google Scholar 

  • Martins M, Farinha A, Ferreira E, Cordeiro V, Monterio A, Tenreiro R, Oliveira M (2001) Molecular analysis of the genetic variability of Portuguese almond collection. Act Hort 546:449–456

    CAS  Google Scholar 

  • Martins M, Tenreiro R, Oliveira M (2003) Genetic relatedness of Portuguese almond collection 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, 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 4:163–165

    Article  CAS  Google Scholar 

  • Mir Ali N, Nabulsi I (2003) Genetic diversity of almond (Prunus dulcis) using RAPD technique. Sci Hort 98:461–471

    Article  CAS  Google Scholar 

  • Murray HC, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acid Res 8:4321–4325

    Article  PubMed  CAS  Google Scholar 

  • Nei M (1973) Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci (USA) 70:3321–3323

    Article  CAS  Google Scholar 

  • Powell W, Morgante M, Andre C, Hanafey Mm Vogel J, Tingey S, Rafalski A (1996) The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Mol Breed 2:225–238

    Article  CAS  Google Scholar 

  • Reina A, Giorgio V, Godini A (1985) Autres types autocompatibles parmi la population ďamandiers des Pouilles (in Italian). Options Méditerr 85:25–29

    Google Scholar 

  • Resta P, Corona MG, Fanizza G, Palasciano M, Godini A (1998) Random amplified DNA polymorphism in Amygdalus communis L. and A. webbii Spach. Acta Hort 470:82–90

    Google Scholar 

  • Rohlf FJ (1998) NYSYS-pc. Numerical taxonomy and Multivariate Analysis System, Version 2.02 Exeter Software, Setauket, NY

  • Roland-Ruiz L, Vaneeuwijk FA, Gilliland TJ, Dubreil P, Dillman C, Lallemand J, De loost M, Barii CP (2001) A comparative study of molecular and morphological methods of describing relationships between perennial ryegrass (Lolium Perenne L.) varieties. Theor Appl Genet 103(8):1138–1150

    Article  Google Scholar 

  • Schneider S, Roessli D, Excoffier L (2001) Arlequin: a software for population genetics data analysis. Version 2.000. Genetics and Biometry Lab, Dep. of Athropology, University of Geneva, Geneva

  • Scorza R, Sherman WB (1996) Peaches, In: Janick J, Moore JN (eds) Fruit breeding, Wiely, New York, pp 285–326

    Google Scholar 

  • Shiran B, Ameirbakhtiar N, Kiani S, Mohamadi Sh, Tabatabaei BES, Moradi H (2007) Molecular characterization and genetic relationships among almond cultivars assessed by RAPD and SSR markers, Scientia Horticulturae 111:280–292

    Article  CAS  Google Scholar 

  • Socias i Company R, Felipe AJ (1988) Self-incompatibility in almond: transmission and recent advances in breeding. Acta Hort 224:307–317

    Google Scholar 

  • Van de Peer Y, De Wachter R (1994) TREECON for Windows: as software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment. Comput Appl Biosci 10:569–570

    PubMed  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: Proceeding of the IX International Horticultural Congress report and proceeding. London, pp 271–286

  • Vezvaei A (2003) Isozyme diversity in Iranian almond. Acta Hort 622:451–456

    CAS  Google Scholar 

  • Viruel MA, Messeguer R, de Vicente MC, Garcia-Mas J, Puigdomenaech P, Arus P (1995) A linkage map with RFLP and isozyme markers for almond. Thero Appl Genet 91:964–971

    CAS  Google Scholar 

  • Vos P, Hogers R, Bleeker M, Reijans M, Van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414

    Article  PubMed  CAS  Google Scholar 

  • Watkins R (1976) Cherry, Plum, Peach, apricot and almond. In: Simmonds NW (ed) Evolution of crop plants. Longman, London, pp 342–347

    Google Scholar 

  • Weising K, Nybon H, Wolff K, Meyer W (1995) DNA fingerprinting in plants and fungi. CRC Press, Boca Raton, USA

    Google Scholar 

  • Wishart D (1987) CLASTAN user manual, 3rd edn. Program Library Unit, Univ. of Edinburgh, Edinburgh

  • Wood MN (1925) Almond varieties in the United States. USDA Bul 1282:1–42

    Google Scholar 

  • Woolley FM, Collins GG, Sedgly M (2000) Application of DNA fingerprinting for the classification of selected almond [prunus dulcis (Miller) D. A. Webb] cultivars. Aust J Exp Agr 40:995–1001

    Article  CAS  Google Scholar 

  • Xie 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, Xie H, 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 

  • Zabeau M (1993) Selective restriction fragment amplification: a general method for DNA fingerprinting. European patent Application No.0–534-858-A1

Download references

Acknowledgement

The authors are grateful to Shahrekord University for financial assistance and Dr Ali Vezvaei for helpful suggestions. Thanks to the section of Horticulture, Agriculture and Natural Resources Research Center of Shahrekord for access to trees.

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Authors and Affiliations

  1. Department of Agronomy and Plant Breeding, Faculty of Agriculture, Shahrekord University, Shahrekord, P.O. Box 115, Iran

    Karim Sorkheh & Behrouz Shiran

  2. Department of Pomology, University of California, Davis, CA, 95616, USA

    T. M. Gradziel

  3. Department of Forestry, Michigan State University, 126 Natural Resources Building, East Lansing, MI, 48824, USA

    B. K. Epperson

  4. Department of Plant Breeding, CEBAS-CSIC, P.O. Box 164, 30100, Espinardo, Murcia, Spain

    Pedro Martínez-Gómez

  5. Department of Natural Resources, Faculty of Agriculture, Shahrekord University, Shahrekord, P.O. Box 115, Iran

    E. Asadi

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  1. Karim Sorkheh
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  2. Behrouz Shiran
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  3. T. M. Gradziel
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  4. B. K. Epperson
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  5. Pedro Martínez-Gómez
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Correspondence to Behrouz Shiran.

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Sorkheh, K., Shiran, B., Gradziel, T.M. et al. 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. Euphytica 156, 327–344 (2007). https://doi.org/10.1007/s10681-007-9382-x

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