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Development of a reliable Corylus sp. reference database through the implementation of a DNA fingerprinting test

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Abstract

Main conclusion

This DNA fingerprinting test confirmed 195 unique Corylus sp. accessions that were used to build a reference database for identity verification of unknown hazelnut trees from three locations in Ontario.

Abstract

Hazelnut is one of the most profitable tree nuts worldwide. Development of a hazelnut industry in Ontario is urgently required, but economically important cultivars must be genetically verified first in order to meet industry standards. Traditional methods for cultivar identification are largely trait-based and unreliable. In this study, a multiplexed fingerprinting test was modified to allow for hazelnut cultivar discrimination at the DNA level. Fourteen highly polymorphic SSR markers covering the 11 linkage groups of Corylus genome were PCR amplified in multiplex using fluorescent-labelled primers. PCR conditions and primer physical properties were optimized to generate a clear signal for each locus. The 14 SSRs were used to fingerprint 195 unique Corylus accessions collected from the USDA-NCGR. Fragment sizes were subjected to a UPGMA clustering analysis which separated Corylus accessions based on species and geographic origin. For validation purposes, hazelnut leaves from three locations in Ontario were collected for identity verification using this DNA fingerprinting test. As a result, 33.3% of the unknown trees were duplicates of seven distinct genotypes and a small percentage (8.3%) of these were identical to reference Corylus hybrids. These results reflect common mislabelling issues and genotype duplications that can prevent a uniform plant propagation system. Implementation of this test together with the addition of more unique accessions to the reference database will help verification of trueness-to-type of economically important cultivars for the hazelnut industry.

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Abbreviations

EFB:

Eastern filbert blight

PIC:

Polymorphism information content

SSR:

Simple sequence repeat

UPGMA:

Unweighted pair group method with arithmetic mean

References

  • Akin M, Nyberg A, Postman J, Mehlenbacher S, Bassil NV (2016) A multiplexed microsatellite fingerprinting set for hazelnut cultivar identification. Eur J Hortic Sci 81(6):327–338

    Article  Google Scholar 

  • Bassil NV, Azarenko AN (2001) Random amplified polymorphic DNA (RAPD) markers for self-incompatibility in Corylus avellana. Acta Hort 556:537–543

    Article  CAS  Google Scholar 

  • Bassil NV, Botta R, Mehlenbacher SA (2005) Microsatellite markers in hazelnut: isolation, characterization, and cross-species amplification. J Am Soc Hortic Sci 130(4):543–549

    Article  CAS  Google Scholar 

  • Bassil N, Boccacci P, Botta R, Postman J, Mehlenbacher S (2013) Nuclear and chloroplast microsatellite markers to assess genetic diversity and evolution in hazelnut species, hybrids and cultivars. Genet Resour Crop Evol 60(2):543–568

    Article  CAS  Google Scholar 

  • Bhattarai G (2015) Microsatellite marker development, characterization and mapping in European hazelnut (Corylus avellana L.), and investigation of novel sources of eastern filbert blight resistance in Corylus. Dissertation, Oregon State University

  • Boccacci P, Botta R (2009) Investigating the origin of hazelnut (Corylus avellana L.) cultivars using chloroplast microsatellites. Genet Resour Crop Evol 56(6):851–859

    Article  CAS  Google Scholar 

  • Boccacci P, Botta R (2010) Microsatellite variability and genetic structure in hazelnut (Corylus avellana L.) cultivars from different growing regions. Sci Hort 124:128–133

    Article  CAS  Google Scholar 

  • Boccacci P, Akkak A, Botta R (2006) DNA typing and genetic relations among European hazelnut (Corylus avellana L.) cultivars using microsatellite markers. Genome 49(6):598–611

    Article  CAS  PubMed  Google Scholar 

  • Boccacci P, Botta R, Rovira M (2008) Genetic diversity of hazelnut (Corylus avellana L.) germplasm in northeastern Spain. HortScience 43(3):667–672

    Article  Google Scholar 

  • Boccacci P, Aramini M, Valentini N, Bacchetta L, Rovira M, Drogoudi P, Silva AP, Solar A, Calizzano F, Erdoğan V, Cristofori V (2013) Molecular and morphological diversity of on-farm hazelnut (Corylus avellana L.) landraces from southern Europe and their role in the origin and diffusion of cultivated germplasm. Tree Genet Genomes 9(6):1465–1480

    Article  Google Scholar 

  • Brownstein MJ, Carpten JD, Smith JR (1996) Modulation of non-templated nucleotide addition by Taq DNA polymerase: primer modifications that facilitate genotyping. Biotechniques 20(6):1004–1010

    Article  CAS  PubMed  Google Scholar 

  • Cameron HR (1976) Eastern filbert blight established in the Pacific Northwest. Plant Dis Rep 60:737–740

    Google Scholar 

  • Capik JM, Molnar TJ (2014) Flowering phenology of eastern filbert blight-resistant hazelnut accessions in New Jersey. HortTechnol 24(2):196–208

    Article  Google Scholar 

  • Chapuis MP, Estoup A (2006) Microsatellite null alleles and estimation of population differentiation. Mol Biol Evol 24(3):621–631

    Article  CAS  Google Scholar 

  • Coyne CJ, Mehlenbacher SA, Smith DC (1998) Sources of resistance to eastern filbert blight in hazelnut. J Am Soc Hortic Sci 123(2):253–257

    Article  Google Scholar 

  • Dale A, Galic D, Leuty T, Filotas M, Currie E (2012) Hazelnuts in Ontario—biology and potential varieties. OMAFRA FactSheet. http://www.omafra.gov.on.ca/english/crops/facts/12-007.htm. Accessed 13 Sep 2018

  • Davison AD, Davidson RM (1973) Apioporthe and Monochaetia cankers reported in western Washington. Plant Dis Rep 57:522–523

    Google Scholar 

  • Erdogan V (1999) Genetic relationships among hazelnut (Corylus) species. Dissertation, Oregon State University

  • Erdogan V, Mehlenbacher SA (2000a) Interspecific hybridization in hazelnut (Corylus). J Am Soc Hortic Sci 125(4):489–497

    Article  Google Scholar 

  • Erdogan V, Mehlenbacher SA (2000b) Phylogenetic relationships of Corylus species (Betulaceae) based on nuclear ribosomal DNA ITS region and chloroplast matK gene sequences. Syst Bot 25(4):727–737

    Article  Google Scholar 

  • FAOSTAT database (2013) Food and Agriculture Organization of the United Nations, Statistics Division. http://fenix.fao.org/faostat/beta/en/#home. Accessed 22 Nov 2018

  • Ferrari M, Gori M, Monnanni R, Biuatti M, Scarascia Mugnozza GT, De Pace C (2004) DNA fingerprinting of Corylus avellana L. accessions revealed by AFLP molecular markers. Acta Hort 686:125–134

    Google Scholar 

  • Gökirmak T, Mehlenbacher SA, Bassil NV (2009) Characterization of European hazelnut (Corylus avellana) cultivars using SSR markers. Genet Resour Crop Evol 56(2):147–172

    Article  CAS  Google Scholar 

  • Gottwald TR, Cameron HR (1979) Studies in the morphology and life history of Anisogramma anomala. Mycologia 71(6):1107–1126

    Article  Google Scholar 

  • Gürcan K, Mehlenbacher SA, Erdoğan V (2010) Genetic diversity in hazelnut (Corylus avellana L.) cultivars from Black Sea countries assessed using SSR markers. Plant Breed 129(4):422–434

    Google Scholar 

  • Huang K, Ritland K, Dunn DW, Qi X, Guo S, Li B (2016) Estimating relatedness in the presence of null alleles. Genetics 202(1):247–260

    Article  CAS  PubMed  Google Scholar 

  • Jaceldo-Siegl K, Haddad E, Oda K, Fraser GE, Sabaté J (2014) Tree nuts are inversely associated with metabolic syndrome and obesity: the Adventist health study-2. PLoS One 9(1):e85133

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Julian J, Seavert C, Olsen JL (2009) An economic evaluation of the impact of eastern filbert blight resistant cultivars in Oregon, USA. Acta Hort 845:725–732

    Article  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(5):1099–1106

    Article  PubMed  Google Scholar 

  • Korir NK, Han J, Shangguan L, Wang C, Kayesh E, Zhang Y, Fang J (2013) Plant variety and cultivar identification: advances and prospects. Crit Rev Biotechnol 33(2):111–125

    Article  PubMed  Google Scholar 

  • Lagerstedt HB (1975) Filberts. In: Janick J, Moore JN (eds) Advances in fruit breeding. Purdue University Press, West Lafayette, pp 456–489

    Google Scholar 

  • Leuty T, Galic D, Bailey P, Dale A, Currie E, Filotas M (2012) Hazelnuts in Ontario—growing, harvesting and food safety. OMAFRA FactSheet. http://www.omafra.gov.on.ca/english/crops/facts/12-011.htm. Accessed 25 Oct 2018

  • Lunde CF, Mehlenbacher SA, Smith DC (2000) Survey of hazelnut cultivars for response to eastern filbert blight inoculation. HortScience 35(4):729–731

    Article  Google Scholar 

  • Markoulatos P, Siafakas N, Moncany M (2002) Multiplex polymerase chain reaction: a practical approach. J Clin Lab Anal 16:47–51

    Article  CAS  PubMed  Google Scholar 

  • Marshall TC, Slate JBKE, Kruuk LEB, Pemberton JM (1998) Statistical confidence for likelihood-based paternity inference in natural populations. Mol Ecol 7(5):639–655

    Article  CAS  PubMed  Google Scholar 

  • Mehlenbacher SA, Thompson MM, Cameron HR (1991) Occurrence and inheritance of resistance to eastern filbert blight in ‘Gasaway’ hazelnut. HortScience 26(4):410–411

    Article  Google Scholar 

  • Mehlenbacher SA, Smith DC, McCluskey RL, Thompson MM (2011) ‘Tonda Pacifica’ hazelnut. HortScience 46(3):505–508

    Article  Google Scholar 

  • Molnar TJ (2011) Corylus. In: Kole C (ed) Wild crop relatives: Genomic and breeding resources, forest trees. Springer, Berlin, pp 15–48

    Chapter  Google Scholar 

  • Molnar TJ, Goffreda JC, Funk CR (2005) Developing hazelnuts for the Eastern United States. Acta Hort 686:609–618

    Article  Google Scholar 

  • Nei M (1972) Genetic distance between populations. Am Nat 106:283–292

    Article  Google Scholar 

  • Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89:583–590

    CAS  PubMed  PubMed Central  Google Scholar 

  • Peakall ROD, Smouse PE (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6(1):288–295

    Article  Google Scholar 

  • Peakall R, Smouse PE (2012) GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research—an update. Bioinformatics 28(19):2537–2539

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Peterschmidt B (2013) DNA markers and characterization of novel sources of eastern filbert blight resistance in European hazelnut (Corylus avellana L.). Dissertation, Oregon State University

  • Pomper KW, Azarenko AN, Bassil N, Davis JW, Mehlenbacher SA (1998) Identification of random amplified polymorphic DNA (RAPD) markers for self-incompatibility alleles in Corylus avellana L. Theor Appl Genet 97:479–487

    Article  CAS  Google Scholar 

  • Powell W, Morgante M, Andre C, Hanafey M, Vogel J, Tingey S, Rafalski A (1996) The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Mol Breed 2(3):225–238

    Article  CAS  Google Scholar 

  • R Core Team (2013) R: a language and environment for statistical computing. R Foundation for Statistical Computing. http://www.Rproject.org/. Accessed 28 Sep 2018

  • Sathuvalli VR, Mehlenbacher SA (2013) De novo sequencing of hazelnut bacterial artificial chromosomes (BACs) using multiplex Illumina sequencing and targeted marker development for eastern filbert blight resistance. Tree Genet Genom 9:1109–1118

    Article  Google Scholar 

  • Sathuvalli VR, Mehlenbacher SA, Smith DC (2012) Identification and mapping of DNA markers linked to eastern filbert blight resistance from OSU 408.040 hazelnut. HortScience 47(5):570–573

    Article  CAS  Google Scholar 

  • Solar A, Stampar F (2011) Characterisation of selected hazelnut cultivars: phenology, growing and yielding capacity, market quality and nutraceutical value. J Sci Food Agric 91(7):1205–1212

    Article  CAS  PubMed  Google Scholar 

  • Tekin E (2016) The politics of market relations in a nutshell. PGDT 15(4):419–448

    Article  Google Scholar 

  • Thompson MM, Romisondo P, Germain E, Vidal-Barraquer R, Valls JT (1978) An evaluation system for filberts (Corylus avellana L.). HortScience 13:514–517

    Google Scholar 

  • Thompson MM, Lagerstedt HB, Mehlenbacher SA (1996) Hazelnuts. In: Janick J, Moore N (eds) Fruit breeding, vol III. N uts. Wiley, New York, pp 125–184

    Google Scholar 

  • Tulum O (2008) Political economy, productivity and profitability of Turkish hazelnut production. Dissertation, University of Massachusetts Lowell

  • Venkatachalam M, Sathe SK (2006) Chemical composition of selected edible nut seeds. J Agric Food Chem 54(13):4705–4714

    Article  CAS  PubMed  Google Scholar 

  • Waples RS (2014) Testing for Hardy-Weinberg proportions: have we lost the plot? J Hered 106(1):1–19

    Article  PubMed  Google Scholar 

  • Weissensteiner T, Lanchbury JS (1996) Strategy for controlling preferential amplification and avoiding false negatives in PCR typing. Biotechniques 21(6):1102–1109

    Article  CAS  PubMed  Google Scholar 

  • Whitcher IN, Wen J (2001) Phylogeny and biogeography of Corylus (Betulaceae): inferences from ITS sequences. Syst Bot 26(2):283–298

    Google Scholar 

  • Yang Z, Zhao T, Ma Q, Liang L, Wang G (2018) Comparative genomics and phylogenetic analysis revealed the chloroplast genome variation and interspecific relationships of Corylus (Betulaceae) species. Front Plant Sci 9:927

    Article  PubMed  PubMed Central  Google Scholar 

  • Zohary D, Hopf M, Weiss E (2012) Domestication of plants in the old world, 4th edn. Oxford University Press, Oxford, p 151

    Book  Google Scholar 

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Acknowledgements

We thank Dr. Murali Mohan Ayyanath (GRIPP, University of Guelph) for assistance with hazelnut tree sampling at the local farms. We also thank Linda Grimo and Martin Hodgson for allowing us to fingerprint hazelnut trees from their nursery and farm, respectively. We are grateful to Dr. Shawn Mehlenbacher (Oregon State University) and April Nyberg (NCGR-USDA) for providing support with the multiplex PCR technique and germplasm collection. Technical assistance with sample preparation and operation of the ABI 3500 Genetic Analyzer from Christopher Grainger at the Plant Genomics Laboratory (Department of Plant Agriculture, University of Guelph) is gratefully acknowledged.

Funding

This study was funded by Ontario Center of Excellence and Ferrero Canada.

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Authors and Affiliations

  1. Gosling Research Institute for Plant Preservation (GRIPP), University of Guelph, 50 Stone Rd E, Guelph, ON, N1G 2W1, Canada

    Jose A. Freixas-Coutin, Shengyu An, Mukund Shukla & Praveen K. Saxena

  2. USDA-ARS, National Clonal Germplasm Repository, 33447 Peoria Rd, Corvallis, OR, 97333, USA

    Joseph Postman & Nahla V. Bassil

  3. Ferrero Canada Ltd., 1 Ferrero Blvd, Brantford, ON, N3V 1G3, Canada

    Barbara Yates

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  1. Jose A. Freixas-Coutin
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  2. Shengyu An
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  4. Nahla V. Bassil
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Correspondence to Praveen K. Saxena.

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Freixas-Coutin, J.A., An, S., Postman, J. et al. Development of a reliable Corylus sp. reference database through the implementation of a DNA fingerprinting test. Planta 249, 1863–1874 (2019). https://doi.org/10.1007/s00425-019-03131-4

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