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Using SNP/INDEL diversity patterns to identify a core group of genotypes from FVC11, a superior hybrid family of Fragaria virginiana Miller and F. chiloensis (L.) Miller

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Abstract

A diverse strawberry family (FVC11) was created by intercrossing elite native clones of the progenitor species of F. × ananassa Duchesne in Lamarck [F. virginiana Miller × F. chiloensis (L.) Miller]. The impressive performance of FVC11 led us to identify a core subset within the family for conservation and breeding purposes. Cluster procedures were conducted on the phenotypic data of 16 traits and 29,251 SNP data generated using the genome wide SNP array, Affymetrix Axiom IStraw90TW. To select a core group, the best performing individuals were identified in each of the major clades shown in the phenographs derived from the genotypic and phenotypic data. A subgroup of 10 individuals was selected that represents most of the genetic diversity in FVC11.

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References

  • Bassil NV, Davis TM, Zhang H, Ficklin S, Mittmann M, Webster T, Mahoney L, Wood D, Alperin ES, Rosyara UR, Putten HKV, Monfort A, Sargent DJ, Amaya I, Denoyes B, Bianco L, van Dijk T, Pirani A, Iezzoni A, Main D, Peace C, Yang Y, Whitaker V, Verma S, Bellon L, Brew F, Herrera R, van de Weg E (2015) Development and preliminary evaluation of a 90 K Axiom® SNP array for the allo-octoploid cultivated strawberry Fragaria × ananassa. BMC Genom 16:155. https://doi.org/10.1186/s12864-015-1310-1

    Article  Google Scholar 

  • Brown AHD (1989) Core collections: a practical approach to genetic resources management. Genome 31:818–824. https://doi.org/10.1139/g89-144

    Article  Google Scholar 

  • Brown AHD, Marshall DR (1995) A basic sampling strategy: theory and practice. In: Guarino L, Rao VR, Reid R (eds) Collecting genetic diversity. CABI Publishing, Wallingford

    Google Scholar 

  • Dale A, Sjulin TM (1990) Few cytoplasm contribute to North American strawberry cultivars. HortScience 25:1341–1342

    Article  Google Scholar 

  • Goodman MM (1990) Genetic and germplasm stocks worth saving. J Hered 81(1):11–16. https://doi.org/10.1093/oxfordjournals.jhered.a110919

    Article  CAS  PubMed  Google Scholar 

  • Hancock JF (1999) Strawberries. CABI Publishing, Wallingford

    Google Scholar 

  • Hancock J, Luby J, Dale A (1992) Should we reconstitute the strawberry? Acta Hortic 348:86–93. https://doi.org/10.17660/ActaHortic.1993.348.8

    Article  Google Scholar 

  • Hancock JF, Hokanson SC, Finn CE, Hummer KE (2000) Introducing a supercore collection of wild octoploid strawberries. Acta Hortic 567:77–79. https://doi.org/10.17660/ActaHortic.2002.567.6

    Article  Google Scholar 

  • Hancock JF, Finn CA, Hokanson SC, Luby JJ, Goulart BL, Demchak K, Callow PW, Serce S, Schilder AMC, Hummer KE (2001) A multistate comparison of native octoploid strawberries from North and South America. J Am Soc Hortic Sci 126:579–586. https://doi.org/10.21273/JASHS.126.5.579

    Article  Google Scholar 

  • Hancock JF, Finn CE, Luby JJ, Dale A, Callow PW, Serçe S (2010) Reconstruction of the strawberry, Fragaria × ananassa, using genotypes of F. virginiana and F. chiloensis. HortScience 45:1006–1013. https://doi.org/10.21273/Hortsci.45.7.1006

    Article  Google Scholar 

  • Hancock JF, Sooriyapathirana SS, Bassil NV, Stegmeir T, Cai L, Finn CE, Van de Weg E, Weebadde CK (2016) Public availability of a genotyped segregating population may foster marker assisted breeding (MAB) and quantitative trait loci (QTL) discovery: an example using strawberry. Front Plant Sci 7:619. https://doi.org/10.3389/fpls.2016.00619

    Article  PubMed  PubMed Central  Google Scholar 

  • Iezzoni A, Weebadde C, Luby J, Yue C, van de Weg E, Fazio G, Main D, Peace CP, Bassil NV, McFerson J (2010) RosBREED: enabling marker-assisted breeding in Rosaceae. Acta Hortic 859:389–394

    Article  Google Scholar 

  • Kennedy C (2013) Genetic resistance to powdery mildew in strawberry: Response to selection and wild species characterization. Thesis—University of Florida

  • Lewers KS, Turechek WW, Hokanson SC, Maas JL, Hancock JF, Serce S, Smith BJ (2007) Evaluation of elite native strawberry germplasm for resistance to anthracnose crown rot disease caused by Colletotrichum species. J Am Soc Hortic Sci 132:842–849. https://doi.org/10.21273/JASHS.132.6.842

    Article  Google Scholar 

  • Mangandi J, Peres NA, Whitaker VM (2015) Identifying resistance to crown rot caused by Colletotrichum gloeosporioides in strawberry. Plant Dis 99:954–961. https://doi.org/10.1094/PDIS-09-14-0907-RE

    Article  PubMed  Google Scholar 

  • Mathey MM, Mookerjee S, Gündüz K, Hancock JF, Iezzoni AF, Mahoney LL, Davis TM, Bassil NV, Hummer KE, Stewart PJ, Whitaker VM, Sargent DJ, Denoyes B, Amaya I, van de Weg E, Finn CE (2013) Large-scale standardized phenotyping of strawberry in RosBREED. J Am Pomol Soc 67:205–216

    Google Scholar 

  • Pinkerton J, Finn CE (2005) Responses of strawberry species and cultivars to the root-lesion and northern root-knot nematodes. HortScience 40:33–38

    Article  Google Scholar 

  • Sjulin TM, Dale A (1987) Genetic diversity of North American strawberry cultivars. J Am Soc Hortic Sci 112:375–385

    Google Scholar 

  • Stegmeir TL, Finn CE, Warner RM, Hancock JF (2010) Performance of an elite strawberry population derived from wild germplasm of Fragaria chiloensis and F. virginiana. HortScience 451:140–1145. https://doi.org/10.21273/HORTSCI.45.8.1140

    Article  Google Scholar 

  • Torun AA, Erdem N, Kacar YA, Serçe S (2013) Screening of wild strawberry genotypes against iron deficiency under greenhouse conditions. Not Bot Horti Agrobo 41:560–566. https://doi.org/10.15835/nbha4129111

    Article  CAS  Google Scholar 

  • Verma S, Zurn JD, Salinas N, Mathey MM, Denoyes B, Hancock JF, Finn CE, Bassil NV, Whitaker VM (2017) Clarifying sub-genomic positions of QTLs for flowering habit and fruit quality in US strawberry (Fragaria × ananassa) breeding populations using pedigree-based QTL analysis. Hort Res 4:17062

    Article  Google Scholar 

  • Vining KJ, Davis TM, Jamieson AR, Mahoney LL (2015) Germplasm resources for verticillium wilt resistance breeding and genetics in strawberry (Fragaria). J Berry Res 5:183–195. https://doi.org/10.3233/JBR-150096

    Article  CAS  Google Scholar 

  • Wang SY, Lewers KS (2007) Antioxidant capacity and flavonoid content in wild strawberries. J Am Soc Hortic Sci 132:629–637. https://doi.org/10.21273/JASHS.132.5.629

    Article  CAS  Google Scholar 

  • Wang SY, Lewers KS, Bowman L, Ding M (2007) Antioxidant activities and anticancer cell proliferation properties of wild strawberries. J Am Soc Hortic Sci 132:647–658

    Article  CAS  Google Scholar 

  • Zurn JD, Ivors KL, Knapp SJ, Whitaker VM, Hummer KE, Hancock JF, Finn CE, Bassil NV (2019) Exploring cultivated strawberries and the Fragaria supercore for resistance to soilborne pathogens. J Amer Pom Soc (in press)

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Funding

This grant was supported by the USDA-National Institute of Food and Agriculture “Specialty Crop Research Initiative Project”, “RosBREED: Enabling marker-assisted breeding in Rosaceae” (2009-51181-05808), AgBio Research, Michigan State University, East Lansing, MI, USA, the Oregon and Washington Strawberry Commissions.

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Authors and Affiliations

  1. Department of Molecular Biology and Biotechnology, Faculty of Science, University of Peradeniya, Peradeniya, 20400, Sri Lanka

    S. D. S. S. Sooriyapathirana, L. T. Ranaweera & H. A. C. R. Perera

  2. Postgraduate Institute of Science, University of Peradeniya, Peradeniya, 20400, Sri Lanka

    S. D. S. S. Sooriyapathirana & H. A. C. R. Perera

  3. Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA

    C. K. Weebadde

  4. USDA-ARS, Horticultural Crops Research Unit, Corvallis, OR, USA

    C. E. Finn

  5. USDA-ARS, National Clonal Germplasm Repository, Corvallis, OR, USA

    N. V. Bassil

  6. Department of Horticulture, Michigan State University, East Lansing, MI, USA

    J. F. Hancock

  7. Berry Blue LLC, Grand Junction, MI, USA

    J. F. Hancock

Authors
  1. S. D. S. S. Sooriyapathirana
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  2. L. T. Ranaweera
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  3. H. A. C. R. Perera
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  4. C. K. Weebadde
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  5. C. E. Finn
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  6. N. V. Bassil
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  7. J. F. Hancock
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Correspondence to J. F. Hancock.

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Sooriyapathirana, S.D.S.S., Ranaweera, L.T., Perera, H.A.C.R. et al. Using SNP/INDEL diversity patterns to identify a core group of genotypes from FVC11, a superior hybrid family of Fragaria virginiana Miller and F. chiloensis (L.) Miller. Genet Resour Crop Evol 66, 1691–1698 (2019). https://doi.org/10.1007/s10722-019-00819-0

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