Advertisement

Springer Nature is making SARS-CoV-2 and COVID-19 research free. View research | View latest news | Sign up for updates

Genetic diversity and structure of local apple cultivars from Northeastern Spain assessed by microsatellite markers

Abstract

A set of 493 old and local Spanish accessions of apple (Malus x domestica Borkh) maintained at three collections in Northeastern Spain was studied using 16 simple sequence repeats in order to estimate their genetic diversity and to identify the genetic structure and relationships among their accessions. An additional diverse set of 45 apple cultivars, including old Spanish and international cultivars, was added as reference. Genetic analyses performed by Bayesian model-based clustering revealed a very strong differentiation of two major groups. The first one clustered 159 individuals (52 % of unique genotypes) including local accessions and six old Spanish cultivars. The second major group was formed by 145 individuals, including 38 international reference cultivars and one old Spanish cultivar. Nested Bayesian clustering was applied to those two groups and two and four sub-groups were found at each one, respectively. The identification of private and unique alleles, and the remarkable differences in allelic richness among groups and sub-groups constitute further evidence of a clear genetic structure. The results obtained through the factorial correspondence and analyses of molecular variance confirmed those obtained by Bayesian analyses, revealing moderate but significant differentiation among the two major groups (F ST = 0.076) and the six sub-groups (F ST = 0.111). Our results highlight that the genetic diversity encompassed by currently cultivated apple accounts only for a small fraction of that existing within the species, and that an important part (≈60 %) of the local material analyzed constitutes a good example of genetic distinctness with respect to the main cultivars used in European orchards.

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

Fig. 1
Fig. 2
Fig. 3

References

  1. Bassil N, Postdam K, Dolan S, Lawliss L (2008) Molecular fingerprints identify historic pear trees in two U.S. National Parks. Acta Hortic 800:417–422

  2. Belkhir K, Borsa P, Chikhi L, Raufaste N, Bonhomme F (1996–2004) GENETIX 4.05, logiciel sous Windows TM pour la génétique des populations. Laboratoire Génome, Populations, Interactions, Université de Montpellier II, Montpellier, France

  3. Berg EE, Hamrick JL (1997) Quantification of genetic diversity at allozyme loci. Can J For Res 27:415–424

  4. Boccacci P, Akkak A, Botta R (2006) DNA typing and genetic relations among European hazelnut (Corylus avellana L.) cultivars using microsatellite markers. Genome 49:598–611

  5. Breton C, Pinatel C, Médail F, Bonhomme F, Bervillé A (2008) Comparison between classical and Bayesian methods to investigate the history of olive cultivars using SSR-polymorphisms. Plant Sci 175:524–532

  6. Brooks RM, Olmo HP (1991) Register of new fruit and nut varieties list 35. HortScience 26:951–978

  7. Brooks RM, Olmo HP (1994) Register of new fruit and nut varieties list 36. HortScience 29:942–969

  8. Bruford MW, Ciofi C, Funk SM (1998) Characteristics of microsatellites. In: Karp A, Isaac PG, Ingram SI (eds) Molecular tools for screening biodiversity. Chapman and Hall, London, pp 202–205

  9. Coart E, Vekemans X, Smulders MJM, Wagner I, van Huylenbroeck J, van Bockstaele E, Roldan-Ruiz I (2003) Genetic variation in the endangered wild apple (Malus sylvestris (L.) Mill.) in Belgium as revealed by amplified fragment length polymorphism and microsatellite markers. Mol Ecol 12:845–857

  10. Dayton DF, Mowry JB, Hough LF, Bailey CH, Williams EB, Janick J, Emerson FH (1970) Prima an early fall red apple with resistance to apple scab. Fruit Var Hort Dig 24:20–22

  11. Earl DA (2011) Structure harvester v0.6.1. Available at http://taylor0.biology.ucla.edu/structureHarvester/

  12. Einset J (1948) The ocurrence of spontaneous triploids and tetraploids in apples. Proc Am Soc Hortic Sci 51:61–63

  13. Einset J (1952) Spontaneous polyploidy in cultivated apples. Proc Am Soc Hortic Sci 59:291–302

  14. El Mousadik A, Petit RH (1996) High level of genetic differentiation for allelic richness among populations of the argan tree [Argania spinosa (L.) Skeels] endemic of Morocco. Theor Appl Genet 92:832–839

  15. Ellstrand NC, Roose ML (1987) Patterns of genotypic diversity in clonal plants species. Am J Bot 74:123–131

  16. Erre P, Chessa I, Muñoz-Diez C, Belaj A, Rallo L, Trujillo I (2010) Genetic diversity and relationships between wild and cultivated olives (Olea europaea L.) in Sardinia as assessed by SSR markers. Genet Resour Crop Evol 57:41–54

  17. 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

  18. Evans KM, Fernández F, Laurens F, Feugey L, van de Weg WE (2007) Harmonising fingerprinting protocols to allow camparisons between germplasm collections. Eucarpia XII Fruit Section Symposium, Zaragoza (Spain), pp 16–20

  19. Falush D, Stephens M, Pritchard JK (2007) Inference of population structure using multilocus genotype data: dominant markers and null alleles. Mol Ecol Notes 7:574–578

  20. Ferreira dos Santos AR, Ramos-Cabrer AM, Díaz-Hernández MB, Pereira-Lorenzo S (2011) Genetic variability and diversification process in local pear cultivars from Northwestern Spain using microsatellites. Tree Genet Genomes 7:1041–1056

  21. Food and Agriculture Organization of the United Nations (2011) FAO statistics database on the World Wide Web http://faostat.fao.org/site/567/DesktopDefault.aspx?PageID=567#ancor. Accessed 25 September 2011

  22. Food and Agriculture Organization of the United Nations/International Plant Genetic Resources Institute (2001) Multi-crop passport descriptors. FAO/IPGRI, Rome, Italy

  23. Garkava-Gustavsson L, Brantestam AK, Sehic J, Nybom H (2008) Molecular characterisation of indigenous Swedish apple cultivars based on SSR and S-allele analysis. Hereditas 145:99–112

  24. Gasi F, Simon S, Pojskic N, Kurtovic M, Pejic I (2010) Genetic assessment of apple germplasm in Bosnia and Herzegovina using microsatellite and morphologic markers. Sci Hortic 126:164–171

  25. Gharghani A, Zamani Z, Talaie A, Oraguzie NC, Fatahi R, Hajnajari H, Wiedow C, Gardiner SE (2009) Genetic identity and relationships of Iranian apple (Malus x domestica Borkh.) cultivars and landraces, wild Malus species and representative old apple cultivars based on simple sequence repeat (SSR) marker analysis. Genet Resour Crop Evol 56:829–842

  26. Gianfranceschi L, Seglias N, Tarchini R, Komjanc M, Gessler C (1998) Simple sequence repeats for the genetic analysis of apple. Theor Appl Genet 96:1069–1076

  27. Goudet J (1995) FSTAT, a program for INM PC compatibles to calculate Weir and Cockerham’s (1984) estimators of F-statistics. J Hered 86:485–486

  28. Guarino C, Santoro S, De Simone L, Lain O, Cipriani G, Testolin R (2006) Genetic diversity in a collection of ancient cultivars of apple (Malus x domestica Borkh.) as revealed by SSR-based fingerprinting. J Hortic Sci Biotechnol 81:39–44

  29. Guilford P, Prakash S, Zhu JM, Rikkerink E, Gardiner S, Bassett H, Forster R (1997) Microsatellites in Malus x domestica (apple): abundance, polymorphism and cultivar identification. Theor Appl Genet 94:249–254

  30. Hardy OJ, Vekemans X (2002) SPAGEDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Mol Ecol Notes 2:618–620

  31. Hokanson SC, Szewc-McFadden AK, Lamboy WF, McFerson JR (1998) Microsatellite (SSR) markers reveal genetic identities, genetic diversity and relationships in a Malus x domestica Borkh. core subset collection. Theor Appl Genet 97:671–683

  32. Hokanson SC, Lamboy WF, Szewc-McFadden AK, McFerson JR (2001) Microsatellite (SSR) variation in a collection of Malus (apple) species and hybrids. Euphytica 118:281–294

  33. Horvath A, Balsemin E, Barbot JC, Christmann H, Manzano G, Reynet P, Laigret F, Mariette S (2011) Phenotypic variability and genetic structure in plum (Prunus domestica L.), cherry plum (P. Cerasifera Ehrh.) and sloe (P. Spinosa L.). Sci Hortic 129:283–293

  34. Iketani H, Yamamoto T, Katayama H, Uematsu C, Mase N, Sato Y (2010) Introgression between native and prehistorically naturalized (archaeophytic) wild pear (Pyrus spp.) populations in Northern Tohoku, Northeast Japan. Cons Genet 11:115–126

  35. INIA (2011) Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria. Inventario Nacional de Recursos Fitogenéticos. http://wwwx.inia.es/webcrf/CRFesp/Paginaprincipal.asp. Accessed 26 September 2011

  36. Itoiz R (2000) Caracterización de la colección de manzanos (Malus x domestica Borkh) del banco de germoplasma de la Universidad Pública de Navarra. Evaluación de su variabilidad. Dissertation, Universidad Pública de Navarra

  37. Jacobs MMJ, Smulders MJM, van den Berg RG, Vosman B (2011) What’s in a name; genetic structure in Solanum section Petota studied using population-genetic tools. BMC Evol Biol 11:42

  38. Janick J, Moore JN (1996) Fruit breeding. Wiley, Chichester

  39. Jing RC, Vershinin A, Grzebyta J, Shaw P, Smykal P, Marshall D, Ambrose MJ, Ellis THN, Flavell AJ (2010) The genetic diversity and evolution of field pea (Pisum) studied by high throughput retrotransposon based insertion polymorphism (RBIP) marker analysis. BMC Evol Biol 10:44

  40. Kenis K, Keulemans J (2005) Genetic linkage maps of two apple cultivars (Malus x domestica Borkh.) based on AFLP and microsatellite markers. Mol Breed 15:205–219

  41. Larsen AS, Asmussen CB, Coart E, Olrik DC, Kjaer ED (2006) Hybridization and genetic variation in Danish populations of European crab apple (Malus sylvestris). Tree Genet Genomes 2:86–97

  42. Laurens F, Durel CE, Lascostes M (2004) Molecular characterization of French local apple cultivars using SSRs. Proc XIth Eucarpia Symp Fruit Breed Genet 1 and 2:639–642

  43. Liebhard R, Gianfranceschi L, Koller B, Ryder CD, Tarchini R, van de Weg E, Gessler C (2002) Development and characterisation of 140 new microsatellites in apple (Malus x domestica Borkh.). Mol Breed 10:217–241

  44. Mariette S, Tavaud M, Arunyawat U, Capdeville G, Millan M, Salin F (2010) Population structure and genetic bottleneck in sweet cherry estimated with SSRs and the gametophytic self-incompatibility locus. BMC Genet 11:77

  45. 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

  46. Miranda C, Urrestarazu J, Santesteban LG, Royo JB, Urbina V (2010) Genetic diversity and structure in a collection of ancient Spanish pear cultivars assessed by microsatellite markers. J Am Soc Hortic Sci 135:428–437

  47. Morgante M, Rafalski A, Biddle P, Tingey S, Olivieri AM (1994) Genetic-mapping and variability of seven soybean simple sequence repeat loci. Genome 37:763–769

  48. Noiton DAM, Alspach PA (1996) Founding clones, inbreeding, coancestry, and status number of modern apple cultivars. J Am Soc Hortic Sci 121:773–782

  49. Pereira-Lorenzo S, Ramos-Cabrer AM, Díaz-Hernández MB (2007) Evaluation of genetic identity and variation of local apple cultivars (Malus x domestica Borkh.) from Spain using microsatellite markers. Genet Resour Crop Evol 54:405–429

  50. Pereira-Lorenzo S, Ramos-Cabrer AM, Gonzalez-Diaz AJ, Diaz-Hernandez MB (2008) Genetic assessment of local apple cultivars from La Palma, Spain, using simple sequence repeats (SSRs). Sci Hortic 117:160–166

  51. Pereira-Lorenzo S, Costa RML, Ramos-Cabrer AM, Ribeiro CAM, da Silva MFS, Manzano G, Barreneche T (2010) Variation in grafted European chestnut and hybrids by microsatellites reveals two main origins in the Iberian Peninsula. Tree Genet Genomes 6:701–715

  52. Pereira-Lorenzo S, Costa RML, Ramos-Cabrer AM, Ciordia-Ara M, Ribeiro CAM, Borges O, Barreneche T (2011) Chestnut cultivar diversification process in the Iberian Peninsula, Canary Islands, and Azores. Genome 54:301–315

  53. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959

  54. Ramos-Cabrer AM, Pereira-Lorenzo S, Diaz-Hernandez MB (2007) Morphology and microsatellites in Spanish apple collections. J Hortic Sci Biotechnol 82:257–265

  55. Richards CM, Volk GM, Reilley AA, Henk AD, Lockwood DR, Reeves PA, Forsline PL (2009) Genetic diversity and population structure in Malus sieversii, a wild progenitor species of domesticated apple. Tree Genet Genomes 5:339–347

  56. Rosenberg NA (2004) DISTRUCT: a program for the graphical display of population structure. Mol Ecol Notes 4:137–138

  57. Santesteban LG, Miranda C, Royo JB (2009) Assessment of the genetic and phenotypic diversity maintained in apple core collections constructed by using either agro-morphologic or molecular marker data. Span J Agr Res 7:572–584

  58. Schlötterer C (2004) The evolution of molecular markers: just a matter or fashion? Nat Rev Genet 5:63–69

  59. Silfverberg-Dilworth E, Matasci CL, van de Weg WE, van Kaauwen MPW, Walser M, Kodde LP, Soglio V, Gianfranceschi L, Durel CE, Costa F, Yamamoto T, Koller B, Gessler C, Patocchi A (2006) Microsatellite markers spanning the apple (Malus x domestica Borkh.) genome. Tree Genet Genomes 2:202–224

  60. Stöck M, Ustinova J, Lamatsch DK, Schartl M, Perrin N, Moritz C (2010) A vertebrate reproductive system involving three ploidy levels: hybrid origin of triploids in a contact zone of diploid and tetraploid palearctic green toads (Bufo viridis subgroup). Evolution 64:944–959

  61. Tessier R, David J, This P, Boursiquot JM, Charrier A (1999) Optimization of the choice of molecular markers for varietal identification in Vitis vinifera L. Theor Appl Genet 98:171–177

  62. Urrestarazu J, Miranda C, Santesteban LG, Royo JB (2010) Análisis comparativo de la diversidad genética retenida en las colecciones nucleares de los bancos de germoplasma de manzano del Noreste español. Actas de Horticultura 55:263–264

  63. Urrestarazu J, Laquidáin MJ, Miranda C, Santesteban LG, Royo JB (2011) Comparative analysis of the genetic diversity maintained in Apple germplasm Banks from Northeastern Spain. Acta Hortic 918:655–660

  64. van Oosterhout C, Hutchinson WF, Wills DPM, Shipley P (2004) Micro-Checker: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Notes 4:535–538

  65. van Treuren R, Kemp H, Ernsting G, Jongejans B, Houtman H, Visser L (2010) Microsatellite genotyping of apple (Malus x domestica Borkh.) genetic resources in the Netherlands: application in collection management and variety identification. Genet Resour Crop Evol 57:853–865

  66. Velasco R, Zharkikh A, Affourtit J, Dhingra A, Cestaro A, Kalyanaraman A, Fontana P, Bhatnagar SK, Troggio M et al (2010) The genome of the domesticated apple (Malus x domestica Borkh.). Nature Genet 42:833–839

  67. Volk GM, Richards CM, Henk AD, Reilley AA, Bassil NV, Postman JD (2006) Diversity of wild Pyrus communis based on microsatellite analyses. J Am Soc Hortic Sci 131:408–417

  68. Volk GM, Richards CM, Henk AD, Reilley AA, Reeves PA, Forsline PL, Aldwinckle HS (2009) Capturing the diversity of wild Malus orientalis from Georgia, Armenia, Russia, and Turkey. J Am Soc Hortic Sci 134:453–459

  69. Weissinger AK (1985) Technologies for germplasm conservation Ex Situ. In: Orians G, Brown G, Kunin W, Swierzbinski J (eds) The preservation and valuation of biological resources. University of Washington Press, Seattle, pp 3–32

  70. World Apple and Pear Association (2010) European apple and pear crop forecast. World Apple and Pear Assn, Brussels, Belgium

Download references

Acknowledgments

This study was partially funded by INIA, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (project grant no RF2004-008-C03-00). The authors want to thank Dr. Valero Urbina, director of the UdL Germplasm Bank and Dr. Alvaro Blanco, director of the EEAD-CSIC Germplasm Bank for their support.

Author information

Correspondence to Jorge Urrestarazu.

Additional information

Communicated by E. Dirlewanger

Electronic supplementary material

Below is the link to the electronic supplementary material.

Online resource 1

Apple accessions maintained by the Universidad Pública de Navarra (UPNA), Escuela Técnica Superior de Ingeniería Agraria de la Universidad de Lleida (ETSIA-UDL) and Estación Experimental Aula Dei-CSIC (EEAD-CSIC) Germplasm Banks. Collection information includes accession name and bank code, site of collection, specific latitude and longitude, approximate elevation and collecting source code according to Food and Agriculture Organization of the United Nations/International Plant Genetic Resources Institute (FAO/IPGRI, 2001) multicrop passport descriptors (PDF 58 kb)

Online resource 2

Number of accessions evaluated in this study according to their origin, indicated by latitude (°N) and altitude (meter above sea level; PDF 5 kb)

Online resource 3

Groups of genotypes that shared alleles (in bold and italics) at each of the 16 SSR loci analyzed. Underline indicates reference cultivars (PDF 15 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Urrestarazu, J., Miranda, C., Santesteban, L.G. et al. Genetic diversity and structure of local apple cultivars from Northeastern Spain assessed by microsatellite markers. Tree Genetics & Genomes 8, 1163–1180 (2012). https://doi.org/10.1007/s11295-012-0502-y

Download citation

Keywords

  • Malus x domestica
  • SSR
  • diversity
  • genetic structure
  • Northeastern Spain