Skip to main content
SpringerLink
Log in

Genetic Diversity, Population Structure, Parentage Analysis, and Construction of Core Collections in the French Apple Germplasm Based on SSR Markers

  • Original Paper
  • Published:
Plant Molecular Biology Reporter Aims and scope Submit manuscript

Abstract

In-depth characterization of apple genetic resources is a prerequisite for genetic improvement and for germplasm management. In this study, we fingerprinted a very large French collection of 2163 accessions with 24 SSR markers in order to evaluate its genetic diversity, population structure, and genetic relationships, to link these features with cultivar selection date or usage (old or modern, dessert or cider cultivars), and to construct core collections. Most markers were highly discriminating and powerful for varietal identification, with a probability of identity P (ID) over the 21 retained SSR loci close to 10−28. Pairwise comparisons revealed 34 % redundancy and 18.5 % putative triploids. The results showed that the germplasm is highly diverse with an expected heterozygosity H e of 0.82 and observed heterozygosity H o of 0.83. A Bayesian model-based clustering approach revealed a weak but significant structure in three subgroups (FST = 0.014–0.048) corresponding, albeit approximately, to the three subpopulations defined beforehand (Old Dessert, Old Cider, and Modern Cultivars). Parentage analyses established already known and yet unknown relationships, notably between old cultivars, with the frequent occurrence of cultivars such as “King of Pippin” and “Calville Rouge d’Hiver” as founders. Finally, core collections based on allelic diversity were constructed. A large dessert core collection of 278 cultivars contained 90 % of the total dessert allelic diversity, whereas a dessert subcore collection of 48 cultivars contained 71 % of diversity. For cider apples, a 48-cultivar core collection contained 83 % of the total cider allelic diversity.

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

Similar content being viewed by others

References

  • Aldrich J, Cullis C (1993) RAPD analysis in flax: optimization of yield and reproducibility using klenTaq 1 DNA polymerase, chelex 100, and gel purification of genomic DNA. Plant Mol Biol Rep 11:128–141. doi:10.1007/BF02670471

    Article  CAS  Google Scholar 

  • Aranzana M, Abbassi E-K, Howad W, Arus P (2010) Genetic variation, population structure and linkage disequilibrium in peach commercial varieties. BMC Genet 11:69

    Article  PubMed  PubMed Central  Google Scholar 

  • Belkhir K, Borsa P, Chikhi L (2004) GENETIX 4.05.02, logiciel sous WindowsTM pour la genetique des populations. Laboratoire Genome, Populations, Interactions CNRS UMR 5000, Montpellier

    Google Scholar 

  • Blazek J, Kloutvor J, Paprstein F, Vondracek J (1995) New apple cultivar ‘Nabella’. Vědecké práce ovocnářské 14:119–125

    Google Scholar 

  • Botstein D, White R, Skolnick M, Davis R (1980) Construction of a genetic linkage map in man using RFLP. Am J H um G enet 32:314–331

  • Cipriani G, Spadotto A, Jurman I, Di Gaspero G, Crespan M, Meneghetti S, Frare E, Vignani R, Cresti M, Morgante M, Pezzotti M, Pe E, Policriti A, Testolin R (2010) The SSR-based molecular profile of 1005 grapevine (Vitis vinifera L.) accessions uncovers new synonymy and parentages, and reveals a large admixture amongst varieties of different geographic origin. Theor Appl Genet 121:1569–1585. doi:10.1007/s00122-010-1411-9

  • Coart E, Vekemans X, Smulders MJM, Wagner I, Van Huylenbroeck J, Van Bockstaele E, Roldán-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. doi:10.1046/j.1365-294X.2003.01778.x

  • Cornille A, Gladieux P, Smulders MJM, Roldán-Ruiz I, Laurens F, Le Cam B, Nerseyan A, Clavel J, Olonova M, Feugey L, Gabrielyan I, Zhang XG, Tenaillon MI, Giraud T (2012) New insight into the history of domesticated apple: secondary contribution of the European wild apple to the genome of cultivated varieties. PLoS Genet 8:e1002703

  • Dakin EE, Avise JC (2004) Microsatellite null alleles in parentage analysis. Heredity 93:504–509

    Article  CAS  PubMed  Google Scholar 

  • Earl D, VonHoldt B (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method Conservation. Genet Resour 4:359–361. doi:10.1007/s12686-011-9548-7

    Article  Google Scholar 

  • Emanuelli F, Lorenzi S, Grzeskowiak L, Catalano V, Stefanini M, Troggio M, Myles S, Martinez-Zapater JM, Zyprian E, Moreira FM, Grando MS (2013) Genetic diversity and population structure assessed by SSR and SNP markers in a large germplasm collection of grape. BMC Plant Biol 13:39

  • 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 

  • Evett I, Weir B (1998) Interpreting DNA evidence: statistical genetics for forensic scientists. Sinauer Associates Inc., USA

    Google Scholar 

  • Faivre-Rampant O, Bruschi G, Abbruscato P, Cavigiolo S, Picco AM, Borgo L, Lupotto E, Piffanelli P (2011) Assessment of genetic diversity in Italian rice germplasm related to agronomic traits and blast resistance (Magnaporthe oryzae). Mol Breeding 27:233–246. doi:10.1007/s11032-010-9426-0

  • Fischer C, Richter K, Blazek J (2004) Testing of Czech cultivars and advanced selections of apples for fire blight (Erwinia amylovora) resistance. Hortic Sci 31:8–11

  • Frankel O, Brown A (1984) Plant genetic resources today: a critical appraisal. In: Holden J, Williams J (eds) Crop genetic resources: conservation and evaluation. George Allen and Unwin, London, pp 249–257

    Google Scholar 

  • Garkava-Gustavsson L, Kolodinska Brantestam A, Sehic J, Nybom H (2008) Molecular characterisation of indigenous Swedish apple cultivars based on SSR and S-allele analysis. Hereditas 145:99–112. doi:10.1111/j.0018-0661.2008.02042.x

    Article  CAS  PubMed  Google Scholar 

  • 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. doi:10.1016/j.scienta.2010.07.002

    Article  Google Scholar 

  • 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 × 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. doi:10.1007/s10722-008-9404-0

  • 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. doi:10.1007/s001220050841

    Article  CAS  Google Scholar 

  • Gross BL, Henk AD, Richards CM, Fazio G, Volk GM (2014) Genetic diversity in Malus × domestica (Rosaceae) through time in response to domestication. Am J Bot 101:1770–1779. doi:10.3732/ajb.1400297

  • Gross BL, Volk GM, Richards CM, Forsline PL, Fazio G, Chao CT (2012) Identification of “duplicate” accessions within the USDA-ARS National Plant Germplasm System Malus collection. J Am Soc Hortic Sci 137:333–342

    Google Scholar 

  • 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. doi:10.1007/s001220050407

    Article  CAS  Google Scholar 

  • Gulsen O, Roose ML (2001) Chloroplast and nuclear genome analysis of the parentage of lemons. J Am Soc Hortic Sci 126:210–215

    CAS  Google Scholar 

  • 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. doi:10.1023/A:1017591202215

    Article  CAS  Google Scholar 

  • Hokanson SC, Szewc-McFadden AK, Lamboy WF, McFerson JR (1998) Microsatellite (SSR) markers reveal genetic identities, genetic diversity and relationships in a Malus × domestica borkh. core subset collection. Theor Appl Genet 97:671–683. doi:10.1007/s001220050943

  • Jakobsson M, Rosenberg NA (2007) CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23:1801–1806. doi:10.1093/bioinformatics/btm233

    Article  CAS  PubMed  Google Scholar 

  • Kalinowski ST, Taper ML, Marshall TC (2007) Revising how the computer program cervus accommodates genotyping error increases success in paternity assignment. Mol Ecol 16:1099–1106. doi:10.1111/j.1365-294X.2007.03089.x

    Article  PubMed  Google Scholar 

  • Kloosterman A, Budowle B, Daselaar P (1993) PCR-amplification and detection of the human D1S80 VNTR locus. Int J Leg Med 105:257–264. doi:10.1007/BF01370382

    Article  CAS  Google Scholar 

  • Lacombe T, Boursiquot JM, Laucou V, Di Vecchi-Staraz M, Peros JP, This P (2013) Large-scale parentage analysis in an extended set of grapevine cultivars (Vitis vinifera L.). Theor Appl Genet 126:401–414. doi:10.1007/s00122-012-1988-2

    Article  PubMed  Google Scholar 

  • Larsen A, Asmussen C, Coart E, Olrik D, Kjær E (2006) Hybridization and genetic variation in Danish populations of European crab apple (Malus sylvestris). Tree Genet Genomes 2:86–97. doi:10.1007/s11295-005-0030-0

    Article  Google Scholar 

  • Laurens F, Durel CE, Patocchi A, Peil A, Salvi S, Tartarini S, Velasco R, Van de Weg WE (2010) Review on apple genetics and breeding programs and presentation of a new initiative of a news European initiative to increase fruit breeding efficiency. Journal of fruit science 27:102–107

  • Leforestier D, Ravon E, Muranty H, Lemaire C, Giraud T, Durel C, Branca A (2015) Genomic basis of the differences between cider and dessert apple varieties. Evol Appl 8:650–661

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liang W, Dondini L, De Franceschi P, Paris R, Sansavini S, Tartarini S (2015) Genetic diversity, population structure and construction of a core collection of apple cultivars from Italian germplasm. Plant Mol Biol Rep 33:458–473

    Article  CAS  Google Scholar 

  • 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 Breeding 10:217–241. doi:10.1023/A:1020525906332

    Article  CAS  Google Scholar 

  • 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

    Article  PubMed  PubMed Central  Google Scholar 

  • Marshall TC, Slate J, Kruuk LEB, Pemberton JM (1998) Statistical confidence for likelihood-based paternity inference in natural populations. Mol Ecol 7:639–655. doi:10.1046/j.1365-294x.1998.00374.x

    Article  CAS  PubMed  Google Scholar 

  • Moriya S, Iwanami H, Okada K, Yamamoto T, Abe K (2011) A practical method for apple cultivar identification and parent-offspring analysis using simple sequence repeat markers. Euphytica 177:135–150. doi:10.1007/s10681-010-0295-8

    Article  Google Scholar 

  • Motilal L, Zhang D, Umaharan P, Mischke S, Boccara M, Pinney S (2009) Increasing Accuracy and Throughput in Large-Scale Microsatellite Fingerprinting of Cacao Field Germplasm Collections. Tropical Plant Biol 2:23–37. doi:10.1007/s12042-008-9016-z

    CAS  Google Scholar 

  • Nicolaï M, Cantet M, Lefebvre V, Sage-Palloix A-M, Palloix A (2013) Genotyping a large collection of pepper (Capsicum spp.) with SSR loci brings new evidence for the wild origin of cultivated C. annuum and the structuring of genetic diversity by human selection of cultivar types. Genet Resour Crop Evol 60:2375–2390. doi:10.1007/s10722-013-0006-0

    Article  Google Scholar 

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

    Google Scholar 

  • Pereira-Lorenzo S, Ramos-Cabrer A, Díaz-Hernández M (2007) Evaluation of genetic identity and variation of local apple cultivars (Malus × domestica Borkh.) from Spain using microsatellite markers. Genet Resou Crop Ev 54:405–420. doi:10.1007/s10722-006-0003-7

    Article  CAS  Google Scholar 

  • Pereira-Lorenzo S, Ramos-Cabrer AM, González-Díaz AJ, Díaz-Hernández MB (2008) Genetic assessment of local apple cultivars from La Palma, Spain, using simple sequence repeats (SSRs) Sci Hortic 117:160–166 doi:http://dx.doi.org/10.1016/j.scienta.2008.03.033

  • Perrier X, Flori A, Bonnot F (2003) Data analysis methods Genetic diversity of cultivated tropical plants., pp 43–76

    Google Scholar 

  • Perrier X, Jacquemoud-Collet J (2006) DARwin software. http://darwin.cirad.fr/darwin

  • Pina A, Urrestarazu J, Errea P (2014) Analysis of the genetic diversity of local apple cultivars from mountainous areas from Aragon (Northeastern Spain) Sci Hortic 174:1–9 doi:http://dx.doi.org/10.1016/j.scienta.2014.04.037

  • Prat D, Faivre-Rampant P, Prado E (2006) Analyse du génome et gestion des ressources génétiques forestières. INRA (eds), Savoir Faire, 484p

  • Pritchard J, Stephens M, Donnelly P (2000) Inference of Population Structure Using Multilocus Genotype Data. Genetics 155:945–959

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ramos-Cabrer AM, Diaz-Hernandez M, Pereira-Lorenzo S (2007) Morphology and microsatelittes in spanish apple collections. J Hortic Sci Biotech 82:257–265

    Article  CAS  Google Scholar 

  • Richards C, Volk G, Reilley A, Henk A, Lockwood D, Reeves P, Forsline P (2009) Genetic diversity and population structure in Malus sieversii, a wild progenitor species of domesticated apple. Tree Genet Genomes 5:339–347. doi:10.1007/s11295-008-0190-9

    Article  Google Scholar 

  • Rosenberg NA (2004) Distruct: a program for the graphical display of population structure. Mol Ecol Notes 4:137–138. doi:10.1046/j.1471-8286.2003.00566.x

    Article  Google Scholar 

  • Salvi S, Micheletti D, Magnago P, Fontanari M, Viola R, Pindo M, Velasco R (2014) One-step reconstruction of multi-generation pedigree networks in apple (Malus × domestica Borkh.) and the parentage of Golden Delicious. Mol Breeding 34:511–524. doi:10.1007/s11032-014-0054-y

  • 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. doi:10.1007/s11295-006-0045-1

  • Song Y, Zhai H, Yao Y-x, Li M, Du Y-p (2006) Analysis of Genetic Diversity of Processing Apple Varieties. Agr Sci China 5:745–750 doi:http://dx.doi.org/10.1016/S1671-2927(06)60119-3

  • Szpiech ZA, Jakobsson M, Rosenberg NA (2008) ADZE: a rarefaction approach for counting alleles private to combinations of populations. Bioinformatics 24:2498–2504. doi:10.1093/bioinformatics/btn478

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Upadhyaya HD, Yadav D, Dronavalli N, Gowda CLL, Singh S (2010) Mini core germplasm collections for infusing genetic diversity in plant breeding programs. Electronic Journal of Plant Breeding 1:1294–1309

    Google Scholar 

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

    Article  Google Scholar 

  • van Treuren R, Kemp H, Ernsting G, Jongejans B, Houtman H, Visser L (2010) Microsatellite genotyping of apple (Malus × domestica Borkh.) genetic resources in the Netherlands: application in collection management and variety identification. Genet Resour Crop Evol 57:853–865 doi:10.1007/s10722-009-9525-0

  • Velasco R et al. (2010) The genome of the domesticated apple (Malus × domestica Borkh.) Nat Genet 42:833–839 doi:http://www.nature.com/ng/journal/v42/n10/abs/ng.654.html#supplementary-information

  • Vinatzer BA, Patocchi A, Tartarini S, Gianfranceschi L, Sansavini S, Gessler C (2004) Isolation of two microsatellite markers from BAC clones of the Vf scab resistance region and molecular characterization of scab-resistant accessions in Malus germplasm. Plant Breeding 123:321–326. doi:10.1111/j.1439-0523.2004.00973.x

  • Waits LP, Luikart G, Taberlet P (2001) Estimating the probability of identity among genotypes in natural populations: cautions and guidelines. Mol Ecol 10:249–256

    Article  CAS  PubMed  Google Scholar 

  • Way R et al. (1990) Apples. In: Moore J, Ballington J (eds) Genetic resources of temperate fruit and nut crops. International society for horticultural science, Wageningen, Netherlands, pp 1–62

  • Zeigler RS (2013) Food security, climate change and genetic resources. In: Jackson M, Ford-Lloyd B, Parry M (eds) Plant Genetic Resources and Climate Change. CAB International, UK, pp 1–15

    Chapter  Google Scholar 

  • Zhen Y, Li Z, Huang H, Wang Y (2004) Molecular Characterization of Kiwifruit (Actinidia) Cultivars and Selections Using SSR Markers. J Am So Hortic Sci 129:374–382

Download references

Acknowledgments

The authors thank the Fondation pour la Recherche sur la Biodiversité (FRB), which contributed to the funding of this study (entitled “CorePom” AAP-IN-2009-14), and the French “Pays de la Loire” region for the post-doctoral grant of L. Lassois.

They greatly thank all of the following amateur groups, associations, governmental and non-governmental organizations for their kind contribution of apple leaf material for this study, in addition to their general support and collaboration:

• Association Nationale des Amateurs Bénévoles pour la Sauvegarde des Variétés Fruitières Régionales en voie de Disparition, dite “Les Croqueurs de Pommes®” (especially J. Lefèvre, J. Marchand, J.C. Hénin, H. Fourrey, C. Scribe)

• Association “Les Mordus de la Pomme” (especially J.F. Aubert)

• Association pour la Sauvegarde des Variétés Fruitières du Terroir, dite “I z’on creuqué eun’pomm” (especially E. Verbrugghe)

• Association “Fruits Oubliés Réseau” (especially C. Sunt)

• Confédération des Producteurs de Fruits d’Alsace (especially P. Heitzler, D. Siegel)

• Conseil Général du Tarn - Service Biodiversité Végétale/Conservatoire des Espèces Fruitières et de Vignes Anciennes (CREFAV) (especially I. Calvière)

• Conservatoire Végétal Régional d’Aquitaine (CVRA) (especially E. Leterme)

• Espaces Naturels Régionaux/Centre Régional de Ressources Génétiques du Nord-Pas-de-Calais (CRRG) (especially J.B. Rey, R. Stievenard)

• Jardin du Luxembourg (especially G. Bachelier)

• Parc Naturel Régional du Luberon (especially J.P. Talichet)

• Société Pomologique du Berry (especially F. Moyse, D. Labouret)

• Verger Conservatoire de Pétré (especially S. Guérin)

• Union Pomologique de France (UPF) (especially D. Retournard)

The staffs of the ANAN genotyping platform of the SFR 149 QUASAV (Angers, France), the GENTYANE genotyping platform (INRA, Clermont-Ferrand, France) and the Unité Expérimentale Horticole (INRA, Angers, France) are warmly acknowledged, for their help in producing the genotyping data and for maintaining the apple germplasm collection in experimental plots, respectively.

Thanks are also due to Xavier Perrier, working at the CIRAD, Montpellier, France, for his valuable assistance in data analysis using DARwin software, to Tristan Marshall for his assistance in using CERVUS software, and to Laurana Serres-Giardi for her help with structure and duplicate analyses.

Author information

Authors and Affiliations

  1. Institut de Recherche en Horticulture et Semences – UMR 1345, INRA, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex, France

    Ludivine Lassois, Caroline Denancé, Elisa Ravon, Arnaud Guyader, Rémi Guisnel, Laurence Hibrand-Saint-Oyant, Pauline Lasserre-Zuber, Laurence Feugey & Charles-Eric Durel

  2. Plateforme Gentyane, INRA UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 63100 Clermont-Ferrand, France

    Charles Poncet

  3. INRA, UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, 63100, Clermont-Ferrand, France

    Pauline Lasserre-Zuber

  4. UBP, UMR 1095 Genetics, Diversity and Ecophysiology of Cereals, 63100, Clermont-Ferrand, France

    Pauline Lasserre-Zuber

  5. BIOSystem Engineering (BIOSE) Department, University of Liege, Gembloux Agro-Bio Tech, Forest Resources Management, Passage des Déportés 2, 5030, Gembloux, Belgium

    Ludivine Lassois

Authors
  1. Ludivine Lassois
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Caroline Denancé
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Elisa Ravon
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Arnaud Guyader
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Rémi Guisnel
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Laurence Hibrand-Saint-Oyant
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Charles Poncet
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Pauline Lasserre-Zuber
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Laurence Feugey
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Charles-Eric Durel
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Charles-Eric Durel.

Electronic supplementary material

Below is the link to the electronic supplementary material.

ESM 1

List of the 2163 accessions considered in the present study with their accession code (AcceNumber), name (AcceName), the name of the partner who furnished the leaf sample, their usage (mainly Dessert or Cider apple) and cultivar selection date (Old or Modern = before or after 1950), their ploidy level determined according to the occurrences of three alleles per locus (see text), their duplicate code according to the SSR profile (see text), their subgroup assignment inferred by the STRUCTURE analysis with the highest membership probability (qI), their group prior to the STRUCTURE analysis (subpopulation: 1: Modern cultivars, 2: Old Cider cultivars, 3: Old Dessert cultivars), their involvement in statistical analyses, and their selection in the dessert and cider core collections (see text).

In the “Cultivar Usage” column, the asterisk (*) indicates an accession initially classified as Cider (resp. Dessert) that has finally been considered as Dessert (resp. Cider) in the statistical analyses because of more consistent information derived from its duplicate(s). In addition, seven accessions of the Dessert core collection (“CC-dessert-278” in the column “Core Collection”) identified by “Cider!” were initially considered as Dessert cultivars but finally corrected as Cider cultivars thanks to additional information from partners; since the core collection was already vegetatively propagated and genotyped for further association studies, they were maintained in the Dessert core collection for contingency reasons.

In the “Old/Modern” column, the asterisk (*) indicates an accession initially classified as Old (resp. Modern) that has finally been considered as Modern (resp. Old) in the statistical analyses because of more consistent information derived from its duplicate(s).

In the “Subgroup” column, a bold number indicates that the highest subgroup membership probability (qI) is greater than 0.8.

In the “Analyzed/Excluded” column:

– A indicates an accession that has been considered in the statistical analyses.

– E indicates an accession that has been excluded from the statistical analyses (mostly because another duplicated accession has been retained; in that case, the subgroup membership and the qI probability has been imputed according to the analyzed duplicate accession).

– E (SSR) indicates an accession that has been excluded from the statistical analyses because of an exceedingly low number of SSR marker data (<17 SSR).

– E (Ext.) indicates an accession that has been excluded from the statistical analyses because of its extreme situation in a preliminary FCA.

– E (Rs) indicates an accession that has been excluded from the statistical analyses because of its rootstock status identified using the SSR profile (generally MM106 instead of the expected accession). (XLS 476 kb).

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Lassois, L., Denancé, C., Ravon, E. et al. Genetic Diversity, Population Structure, Parentage Analysis, and Construction of Core Collections in the French Apple Germplasm Based on SSR Markers. Plant Mol Biol Rep 34, 827–844 (2016). https://doi.org/10.1007/s11105-015-0966-7

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11105-015-0966-7

Keywords

Search

Navigation