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Genetic Diversity and Characterization of a Core Collection of Malus Germplasm Using Simple Sequence Repeats (SSRs)

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Abstract

Simple sequence repeats (SSRs) were used to assess genetic diversity and study genetic relatedness in a large collection of Malus germplasm. A total of 164 accessions from the Malus core collection, maintained at the University of Illinois, were genotyped using apple SSR markers. Each of the accessions was genotyped using a single robust SSR marker from each of the 17 different linkage groups in Malus. Data were subjected to principal component analysis, and a dendrogram was constructed to establish genetic relatedness. As expected, this diverse core collection showed high allelic diversity; moreover, this allelic diversity was higher than that previously reported. Cluster analysis revealed the presence of four distinct clusters of accessions in this collection.

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References

  • Baraket G, Chatti K, Saddoud O, Ben Abdelkarim A, Mars M, Trifi M, Hannachi A (2011) Comparative assessment of SSR and AFLP markers for evaluation of genetic diversity and conservation of fig, Ficus carica L., genetic resources in Tunisia. Plant Mol Biol Rep 29:171–184

    Article  Google Scholar 

  • Bengtsson B, Weibull P, Ghatnekar L (1995) The loss of alleles by sampling: a study of the common outbreeding grass Festuca ovina over three geographical scales. Hereditas 122:221–238

    Article  Google Scholar 

  • Benson L, Lamboy W, Zimmerman R (2001) Molecular identification of Malus hupehensis (tea crabapple) accessions using simple sequence repeats. HortScience 36:961–966

    Google Scholar 

  • Botstein D, White R, Skolnick M, Davis R (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Human Genet 32:314–331

    CAS  Google Scholar 

  • Brown A (1989) The case for core collections. In: Brown AHD, Frankel OH, Marshall DR, Williams JT (eds) The use of plant genetic resources. Cambridge University Press, Cambridge, pp 136–156

    Google Scholar 

  • Brown A (1995) The core collection at the crossroads. In: Hodgkin T, Brown AHD, Hintum TJL, Morales EAV (eds) Core collections of plant genetic resources. Wiley, Chichester, pp 3–19

    Google Scholar 

  • Chen X, Xia Z, Fu Y, Lu C, Wang W (2010) Constructing a genetic linkage map using an F1 population of non-inbred parents in Cassava (Manihot esculenta Crantz). Plant Mol Biol Rep 28:676–683

    Article  CAS  Google Scholar 

  • Clarke J, Tobutt K (2009) A standard set of accessions, microsatellites and genotypes for harmonising the fingerprinting of cherry collections for the ECPGR. Acta Hort 814:615–618

    Google Scholar 

  • Dávila J, Sánchez de la Hoz M, Loarce Y, Ferrer E (1998) The use of random amplified microsatellite polymorphic DNA and coefficients of parentage to determine genetic relationships in barley. Genome 41:477–486

    Article  Google Scholar 

  • Dunemann F, Kahnau R, Schmidt H (1994) Genetic relationships in Malus evaluated by RAPD ‘fingerprinting’ of cultivars and wild species. Plant Breed 113:150–159

    Article  Google Scholar 

  • Evans K, Fernández F, Laurens F, Feugey L, Van de Weg E (2007) Harmonizing fingerprinting protocols to allow comparisons between germplasm collections. Eucarpia XII Fruit Selection Symposium, September 16–20, 2007, Zaragoza, Spain, pp 57–58

  • Evans K, Fernández F, Govan C (2009) Harmonising fingerprinting protocols to allow comparisons between germplasm collections—Pyrus. Acta Hort 814:103–106

    Google Scholar 

  • Forsline P (1996) Core subsets in the USDA/NPGS with Apple as an example. Proceedings of the 2nd Workshop on Clonal Genetic Resources, Ottawa, Ontario, January 23–24, 1996. pp 172–175

  • Frankel O (1984) Genetic perspectives of germplasm conservation. In: Arber WK, Llimensee K, Peacock WJ, Starlinger P (eds) Genetic manipulation: Impact on man and society. Cambridge University Press, Cambridge, pp 161–170

    Google Scholar 

  • Garkava-Gustavsson L, 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

    Article  PubMed  CAS  Google Scholar 

  • Gasic K, Han Y, Kertbundit S, Shulaev V, Iezzoni A, Stover E, Bell R, Wisniewski M, Korban SS (2009) Characteristics and transferability of new apple EST-derived SSRs to other Rosaceae species. Mol Breed 23:397–411

    Article  CAS  Google Scholar 

  • Goulão L, Cabrita L, Oliveira C, Leitao J (2001) Comparing RAPD and AFLPTM analysis in discrimination and estimation of genetic similarities among apple (Malus domestica Borkh.) cultivars—RAPD and AFLP analysis of apples. Euphytica 119:259–270

    Article  Google Scholar 

  • Govan C, Simpson D, Johnson A, Tobutt K, Sargent D (2008) A reliable multiplexed microsatellite set for genotyping Fragaria and its use in a survey of 60 F. × ananassa cultivars. Mol Breed 22:649–661

    Article  CAS  Google Scholar 

  • Guilford P, Prakash S, Zhu J, Rikkerink E, Gardiner S, Bassett H (1997) Microsatellites in Malus xdomestica (apple): abundance, polymorphism and cultivar identification. Theor Appl Genet 94:249–254

    Article  CAS  Google Scholar 

  • Han Y, Korban SS (2010) Strategies for map-based cloning in apple. Crit Rev Plant Sci 29:265–284

    Article  CAS  Google Scholar 

  • Hearne C, Ghosh S, Todd J (1992) Microsatellites for linkage analysis of genetic traits. Trends Genet 8:288–294

    PubMed  CAS  Google Scholar 

  • Hokanson S, Szewc-McFadden A, Lamboy W, McFerson J (1998) Microsatellite (SSR) markers reveal genetic identities, genetic diversity and relationships in a Malus xdomestica Borkh. core subset collection. Theor Appl Genet 97:671–683

    Article  CAS  Google Scholar 

  • Hokanson S, Lamboy W, Szewc-McFadden A, McFerson J (2001) Microsatellite (SSR) variation in a collection of Malus (apple) species and hybrids. Euphytica 118:281–294

    Article  CAS  Google Scholar 

  • Johnson D (1998) Principal component analysis, and cluster analysis. In: Johnson DE (ed) Applied multivariate methods for data analysts. Brooks/Cole, Pacific Grove, pp 319–396

    Google Scholar 

  • Kalinowski S, Taper M, Marshall T (2007) Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Mol Ecol 16:1099–1106

    Article  PubMed  Google Scholar 

  • Király I, Tóth M, Pedryc A, Halász J, Deák T (2009) Parent identification of Hungarian apple cultivars using SSR markers. Acta Hort 839:471–477

    Google Scholar 

  • Kitahara K, Matsumoto S, Yamamoto T, Soejima J, Kimura T, Komatsu H (2005) Molecular characterization of apple cultivars in Japan by S-RNase analysis and SSR markers. J Amer Soc Hort Sci 130:885–892

    CAS  Google Scholar 

  • Kobayashi N, Horikoshi T, Katsuyama H, Handa T, Takayanagi K (1998) A simple and efficient DNA extraction method for plants, especially woody plants. Plant Tiss Cult Biotech 4:76–80

    Google Scholar 

  • Kouassi A, Durel C, Costa F, Tartarini S, van de Weg E, Evans K (2009) Estimation of genetic parameters and prediction of breeding values for apple fruit-quality traits using pedigreed plant material in Europe. Tree Genet Genomes 5:659–672

    Article  Google Scholar 

  • Kresovich S, McFerson J (1992) Assessment and management of plant genetic diversity: considerations of intra- and inter-specific variation. In: Kresovich S (ed.) The impact of progress in genetics on plant resources (germplasm) conservation and utilization. Field Crops Res 29:185–204

  • Lamboy W, Alpha C (1998) Using simple sequence repeats (SSRs) for DNA fingerprinting germplasm accessions of grape (Vitis L.) species. J Amer Soc Hort Sci 123:182–188

    CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Marshall D (1990) Crop genetic resources: current and emerging issues. In: Brown AHD, Clegg MH, Kahler AL, Weir BS (eds) Plant population genetics, breeding, and genetic resources. Wiley, Chichester, pp 367–388

    Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Naik S, Hampson C, Gasic K, Bakkeren G, Korban S (2006) Development and linkage mapping of E-STS and RGA markers for functional gene homologues in apple. Genome 49:959–968

    Article  PubMed  CAS  Google Scholar 

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

    Google Scholar 

  • Raymond M, Rousset F (1995) GENEPOP (version 1.2): population genetics software for exact tests and ecumenicism. J Heredity 86:248–249

    Google Scholar 

  • Richards C (2009) Genetic diversity and population structure in Malus sieversii, a wild progenitor species of domesticated apple. Tree Genet Genomes 5:339–347

    Article  Google Scholar 

  • Richter T, Soltis P, Soltis D (1994) Genetic variation within and among populations of the narrow endemic, Delphinium viridescens (Ranunculaceae). Amer J Bot 81:1070–1076

    Article  Google Scholar 

  • Rousset F (2008) Genepop'007: a complete reimplementation of the Genepop software for Windows and Linux. Mol Ecol Res 8:103–106

    Article  Google Scholar 

  • Russell J, Fuller J, Macaulay M, Hatz B, Jahoor A, Powell W, Waugh R (1997) Direct comparison of levels of genetic variation among barley accessions detected by RFLPs, AFLPs, SSRs and RAPDs. Theor Appl Genet 95:714–722

    Article  CAS  Google Scholar 

  • Wang Y, Zhang J, Sun H, Ning N, Yang L (2011) Construction and evaluation of a primary core collection of apricot germplasm in China. Scient Hort 128:311–319

    Article  Google Scholar 

  • Zhang Q, Li L, Zhao Y, Korban S, Han Y (2011) Evaluation of genetic diversity in Chinese wild apple species along with apple cultivars using SSR markers. Plant Mol Biol Rep. doi:10.1007/s11105-011-0366-6

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Acknowledgments

This research was supported by Pioneer Hi-Bred International, Inc., Illinois Plant Breeding Center, USDA-NIFA-SCRI grant AG 2009-51181-06023, University of Illinois Office of Research Project 875-325, and University of Illinois Office of Research Project 875-922.

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Authors and Affiliations

  1. Department of Crop Sciences, University of Illinois at Urbana–Champaign, Urbana, IL, 61801, USA

    Sarah M. Potts, Mosbah M. Kushad, A. Lane Rayburn & Schuyler S. Korban

  2. Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Moshan, Wuhan, 430074, People’s Republic of China

    Yuepeng Han

  3. Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana–Champaign, Urbana, IL, 61801, USA

    M. Awais Khan & Schuyler S. Korban

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  1. Sarah M. Potts
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  2. Yuepeng Han
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  3. M. Awais Khan
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  4. Mosbah M. Kushad
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  5. A. Lane Rayburn
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  6. Schuyler S. Korban
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Correspondence to Schuyler S. Korban.

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Potts, S.M., Han, Y., Khan, M.A. et al. Genetic Diversity and Characterization of a Core Collection of Malus Germplasm Using Simple Sequence Repeats (SSRs). Plant Mol Biol Rep 30, 827–837 (2012). https://doi.org/10.1007/s11105-011-0399-x

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