Structural pattern and genetic diversity in blueberry (Vaccinium) clones and cultivars using EST-PCR and microsatellite markers

Abstract

The blueberry (Vaccinium L. section Cyanococcus Rydb.) is a health promoting and economically important small fruit crop. Structured genetic diversity and relatedness were studied in 63 blueberry wild clones and cultivars , using eleven EST-PCR and nine microsatellite markers. Markers were found to be polymorphic and detected 249 alleles with mean polymorphic information content of 0.80 for EST-PCR; and 164 alleles with mean polymorphic information content of 0.77 for microsatellite markers. The average resolving power was 4.6 for EST-PCR and 2.6 for microsatellite markers. The average values of expected and observed heterozygosity, inbreeding coefficient and Shannon’s index were higher for the EST-PCR markers than those of microsatellites. Multivariate clustering analyses using neighbor joining and principal coordinate analyses formed five groups and clustered the genotypes according to their place of origin that were also confirmed by STRUCTURE analysis and analysis of molecular variance. While 33% of variation was found among the geographic groups, the variation among the communities within the groups was 23% and among genotypes within the communities was 44%, in combined analysis. The availability of high genetic diversity among the wild clones will contribute significantly in germplasm management and their utilization in the current blueberry improvement program.

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

Fig. 1
Fig. 2
Fig. 3

References

  1. Aalders LE, Hall IV, Jackson LP (1977) Brunswick lowbush blueberry. Can J Plant Sci 57:301

    Article  Google Scholar 

  2. Adams RP, Rieseberg LH (1998) The effects of non-homology in RAPD bands on similarity and multivariate statistical ordination in Brassica and Helianthus. Theor Appl Genet 97:323–326

    CAS  Article  Google Scholar 

  3. Bell DJ, Rowland LJ, Polashock JJ, Drummond FA (2008) Suitability of EST-PCR markers developed in highbush blueberry for genetic fingerprinting and relationship studies in lowbush blueberry and related species. J Am Soc Hortic Sci 133:701–707

    Google Scholar 

  4. Bian Y, Ballington J, Raja A, Brouwer C, Reid R, Burke M, Wang X, Rowland LJ, Bassil N, Brown A (2014) Patterns of simple sequence repeats in cultivated blueberries (Vaccinium section Cyanococcus spp.) and their use in revealing genetic diversity and population structure. Mol Breed 34:675–689

    CAS  Article  Google Scholar 

  5. Boches PS, Bassil NV, Rowland LJ (2005) Microsatellite markers for Vaccinium from EST and genomic libraries. Mol Ecol Notes 5:657–660

    CAS  Article  Google Scholar 

  6. Boches P, Bassil NV, Rowland L (2006) Genetic diversity in the highbush blueberry evaluated with microsatellite markers. J Am Soc Hortic Sci 131:674–686

    CAS  Google Scholar 

  7. Chapman MA, Hvala J, Strever J, Matvienko M, Kozik A, Michelmore RW, Tang S, Knapp SJ, Burke JM (2009) Development, polymorphism, and cross-taxon utility of EST-SSR markers from safflower (Carthamus tinctorius L.). Theor Appl Genet 120:85–91

    CAS  Article  PubMed  Google Scholar 

  8. Debnath SC (2009) Development of ISSR markers for genetic diversity studies in Vaccinium angustifolium. Nord J Bot 27:141–148

    Article  Google Scholar 

  9. Debnath SC (2014) Structured diversity using EST-PCR and EST-SSR markers in a set of wild blueberry clones and cultivars. Biochem Syst Ecol 54:337–347

    CAS  Article  Google Scholar 

  10. Earl DA, Vonholdt BM (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Resour 4:359–361

    Article  Google Scholar 

  11. Esselink GD, Smulders MJM, Vosman B (2003) Identification of cut rose (Rosa hybrida) and rootstock varieties using robust sequence tagged microsatellite site markers. Theor Appl Genet 106:277–286

    CAS  Article  PubMed  Google Scholar 

  12. Esselink GD, Nybom H, Vosman B (2004) Assignment of allelic configuration in polyploids using the MAC-PR (microsatellite DNA allele counting-peak ratios) method. Theor Appl Genet 109:402–408

    CAS  Article  PubMed  Google Scholar 

  13. 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

    CAS  Article  PubMed  Google Scholar 

  14. Excoffier L, Laval G, Schneider S (2005) Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evol Bioinform 1:47–50

    CAS  Google Scholar 

  15. Finn C, Luny J, Wildung D (1990) Half-high blueberry cultivars. Fruit Var J 44:63–68

    Google Scholar 

  16. Galletta GJ, Ballington JR (1996) Blueberries, cranberries and lingonberries. In: Janick J, Moore JN (eds) Fruit breeding, volume II: vine and small fruit crops. Wiley, Prentice Hall, New York, pp 1–107

    Google Scholar 

  17. Halliwell B (2007) Dietary polyphenols: good, bad, or indifferent for your health? Cardiovasc Res 73:341–347

    CAS  Article  PubMed  Google Scholar 

  18. Hardy GH (1908) Mendelian proportions in a mixed population. Science 28:49–50

    CAS  Article  PubMed  Google Scholar 

  19. Hepler P, Draper A (1976) Patriot blueberry. HortScience 11:272

    Google Scholar 

  20. Horvath A, Sanchez-Sevilla JF, Punelli F, Richard L, Sesmero-Carrasco R, Leone A, Hoefer M, Chartier P, Balsemin E, Barreneche T, Denoyes B (2011) Structured diversity in octoploid strawberry cultivars: importance of the old European germplasm. Ann Appl Biol 159:358–371

    Article  Google Scholar 

  21. Joseph JA, Denisova NA, Arendash G, Gordon M, Diamond D, Shukitt-Hale B, Morgan D (2003) Blueberry supplementation enhances signaling and prevents behavioral deficits in an Alzheimer disease model. Nutr Neurosci 6:153–162

    CAS  Article  PubMed  Google Scholar 

  22. Kim CS, Lee CH, Shin JS, Chung YS, Hyung NI (1997) A simple and rapid method for isolation of high quality genomic DNA from fruit trees and conifers using PVP. Nucl Acids Res 25:1085–1086

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  23. Liu KJ, Muse SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21:2128–2129

    CAS  Article  PubMed  Google Scholar 

  24. Liu Y, Liu S, Liu D, Wei Y, Liu C, Yang Y, Tao C, Liu W (2014) Exploiting EST databases for the development and characterization of EST-SSR markers in blueberry (Vaccinium) and their cross-species transferability in Vaccinium spp. Sci Hort 176:319–329

    CAS  Article  Google Scholar 

  25. Lyrene P (2002) Blueberry. HortScience 37:252

    Google Scholar 

  26. Ojango JM, Malmfors B, Okeyo AM (2011) Module 4: quantitative methods to improve the understanding and utilisation of animal genetic resources. [Animal genetic training resources (AGTR). International Livestock Research Institute (ILRI)]. http://agtr.ilri.cgiar.org/index.php?option=com_content&view=article&id=28&Itemid=268

  27. Okie W (1997) Register of new fruit and nut varieties. Brooks and Olmo list 38. HortScience 32:785–805

    Google Scholar 

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

    CAS  Article  PubMed  PubMed Central  Google Scholar 

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

    CAS  PubMed  PubMed Central  Google Scholar 

  30. Rosenberg NA, Burke T, Elo K, Feldmann MW, Freidlin PJ, Groenen MAM, Hillel J, Maki-Tanila A, Tixier-Boichard M, Vignal A, Wimmers K, Weigend S (2001) Empirical evaluation of genetic clustering methods using multilocus genotypes from 20 chicken breeds. Genetics 159:699–713

    CAS  PubMed  PubMed Central  Google Scholar 

  31. Rowland LJ, Mehra S, Dhanaraj AL, Ogden EL, Slovin JP, Ehlenfeldt MK (2003) Development of EST-PCR markers for DNA fingerprinting and genetic relationship studies in blueberry (Vaccinium, section Cyanococcus). J Am Soc Hortic Sci 128:682–690

    CAS  Google Scholar 

  32. Rowland LJ, Ogden EL, Ehlenfeldt MK (2010) EST-PCR markers developed for highbush blueberry are also useful for genetic fingerprinting and relationship studies in rabbiteye blueberry. Sci Hortic 125:779–784

    CAS  Article  Google Scholar 

  33. Shannon CE, Weaver W (1949) The mathematical theory of communication. University of Illinois Press, Urbana

    Google Scholar 

  34. Templeton AR (1996) Translocation as conservation tool. In: Szaro RC, Johnston DW (eds) Biodiversity in managed landscapes: theory and practice. Oxford University Press, Oxford, pp 315–325

    Google Scholar 

  35. Vander Kloet SP (1988) The genus Vaccinium in North America. Agriculture Canada Research Branch, Ottawa

    Google Scholar 

  36. Vander Kloet SP, Dickinson TA (2009) A subgeneric classification of the genus Vaccinium and the metamorphosis of V. section Bracteata Nakai: more terrestrial and less epiphyticin habit, more continental and less insular in distribution. J Plant Res 122:253–268

    CAS  Article  PubMed  Google Scholar 

  37. Willis L, Bickford P, Zaman V, Moore A, Granholm AC (2005) Blueberry extract enhances survival of intraocular hippocampal transplants. Cell Transpl 14:213–223

    Article  Google Scholar 

Download references

Acknowledgements

The authors like to thank Darryl Martin, Glenn Chubbs, Sarah Leonard, Juran Goyali and Amrita Ghosh for their excellent technical help.

Author information

Affiliations

Authors

Corresponding author

Correspondence to Samir C. Debnath.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary Fig. 1

Neighbor joining (NJ) dendrogram of 63 blueberry genotypes based on the proportion of shared alleles distance for EST-PCR markers. Numbers refer to branch lengths (TIFF 379 kb)

Supplementary Fig 2

Neighbor joining (NJ) dendrogram of 63 blueberry genotypes based on the proportion of shared allele distance for microsatellite markers. Numbers refer to branch lengths (TIFF 404 kb)

Supplementary Fig. 3

Principle co-ordinate analysis of 63 blueberry genotypes using EST-PCR marker (TIFF 140 kb)

Supplementary Fig. 4

Principle co-ordinate analysis of 63 blueberry genotypes using microsatellite marker (TIFF 148 kb)

Supplementary Fig. 5

Q-plot showing Bayesian clustering of 63 genotypes, for K=6, based on analysis of EST-PCR using STRUCTURE software. Each genotype is represented by a vertical bar. The colored subsections within each vertical bar indicate membership coefficient (Q) of the accession to different clusters. Identified clusters are I, II, III, IV, V and VI (TIFF 409 kb)

Supplementary Fig. 6

Q-plot showing Bayesian clustering of 63 genotypes, for K=6, based on analysis of microsatellite using STRUCTURE software. Each genotype is represented by a vertical bar. The colored subsections within each vertical bar indicate membership coefficient (Q) of the accession to different clusters. Identified clusters are I, II, III, IV, V and VI (TIFF 325 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Tailor, S., Bykova, N.V., Igamberdiev, A.U. et al. Structural pattern and genetic diversity in blueberry (Vaccinium) clones and cultivars using EST-PCR and microsatellite markers. Genet Resour Crop Evol 64, 2071–2082 (2017). https://doi.org/10.1007/s10722-017-0497-1

Download citation

Keywords

  • Molecular markers
  • Structured diversity
  • Wild germplasm
  • Vaccinium spp.