Skip to main content

Advent of genomics in blueberry

Molecular Breeding volume 32, pages 493–504 (2013)Cite this article

Abstract

Blueberry is a high-value crop with recognized nutritional characteristics that has led to an increase in consumer demand over the last several years. With its increasing agricultural and commercial importance, genetic and genomic tools have recently become available for use in characterizing its genetic diversity and in molecular breeding strategies. Here, we provide an overview of genomic research in blueberry, with a focus on expressed sequence tag/transcriptome sequencing efforts. These resources are already providing novel insights into various biological processes from large-scale expression studies, such as microarrays, elucidation of phylogenetic relationships, and development of molecular markers and genetic linkage maps. Future blueberry breeding programs should benefit greatly from these new genomic tools.

This is a preview of subscription content, access via your institution.

Access options

Buy single article

Instant access to the full article PDF.

USD 39.95

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Fig. 1

References

  • Albert V, Soltis D, Carlson J, Farmerie W, Wall PK et al (2005) Floral gene resources from basal angiosperms for comparative genomics research. BMC Plant Biol 5(1):5

    Article  PubMed  Google Scholar 

  • Alkharouf N, Dhanaraj A, Naik D, Overall C, Matthews B, Rowland L (2007) BBGD: an online database for blueberry genomic data. BMC Plant Biol 7(1):5

    Article  PubMed  Google Scholar 

  • Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408 (6814):796–815. Available at: http://www.nature.com/nature/journal/v408/n6814/suppinfo/408796a0_S1.html

  • Arús P, Verde I, Sosinski B, Zhebentyayeva T, Abbott A (2012) The peach genome. Tree Genetics Genomes 8(3):531–547. doi:10.1007/s11295-012-0493-8

    Article  Google Scholar 

  • Bañados M (2008) Expanding blueberry production into non-traditional production areas: northern Chile and Argentina, Mexico and Spain. Ninth Int Vaccin Symp, In, pp 439–445

    Google Scholar 

  • Bell DJ, Rowland LJ, Zhang D, Drummond FA (2009) Spatial genetic structure of lowbush blueberry, Vaccinium angustifolium, in four fields in Maine. Botany 87(10):932–946. doi:10.1139/b09-058

    Article  CAS  Google Scholar 

  • Bell DJ, Drummond FA, Rowland LJ (2012) Fine-scale spatial genetic structure associated with Vaccinium angustifolium Aiton (Ericaceae). Int J Modern Bot 2(4):72–82. doi:10.5923/j.ijmb.20120204.02

    Google Scholar 

  • Boches PS, Bassil NV, Rowland LJ (2005) Microsatellite markers for Vaccinium from EST and genomic libraries. Mol Ecol Notes 5(3):657–660. doi:10.1111/j.1471-8286.2005.01025.x

    Article  CAS  Google Scholar 

  • Boches PS, Bassil NV, Rowland LJ (2006) Genetic diversity in the highbush blueberry evaluated with microsatellite markers. J Am Soc Hortic Sci 131(5):674–686

    CAS  Google Scholar 

  • Buck EJ, Scalzo J, Wiedow C, Hurst R, Allan AC, McGhie TK, Bassil NV, Rowland LJ (2012) Progress in blueberry research in New Zealand. Int J Fruit Sci 12(1–3):304–315. doi:10.1080/15538362.2011.619444

    Article  Google Scholar 

  • Costich DE, Ortiz R, Meagher TR, Bruederle LP, Vorsa N (1993) Determination of ploidy level and nuclear DNA content in blueberry by flow cytometry. Theoret Appl Genetics 86(8):1001–1006

    Article  CAS  Google Scholar 

  • Dhanaraj AL, Slovin JP, Rowland LJ (2004) Analysis of gene expression associated with cold acclimation in blueberry floral buds using expressed sequence tags. Plant Sci 166(4):863–872. doi:10.1016/j.plantsci.2003.11.013

    Article  CAS  Google Scholar 

  • Dhanaraj A, Alkharouf N, Beard H, Chouikha I, Matthews B, Wei H, Arora R, Rowland L (2007) Major differences observed in transcript profiles of blueberry during cold acclimation under field and cold room conditions. Planta 225(3):735–751. doi:10.1007/s00425-006-0382-1

    Article  PubMed  CAS  Google Scholar 

  • Diatchenko L, Lukyanov S, Lau Y-FC, Siebert PD (1999) Suppression subtractive hybridization: a versatile method for identifying differentially expressed genes. In: Sherman MW (ed) Methods in enzymology, vol 303. Academic Press, New York, pp 349–380. doi:10.1016/S0076-6879(99)03022-0

  • Graham J, Jennings N (2009) Raspberry breeding. In: Breeding plantation tree crops: temperate species. Springer, New York, pp 233–248. doi:10.1007/978-0-387-71203-1_7

  • Gulyani V, Khurana P (2011) Identification and expression profiling of drought-regulated genes in mulberry (Morus sp.) by suppression subtractive hybridization of susceptible and tolerant cultivars. Tree Genet Genomes 7 (4):725–738. doi:10.1007/s11295-011-0369-3

  • Hou D (2003) Potential mechanisms of cancer chemoprevention by anthocyanins. Curr Mol Med 3(3):149–159

    Article  PubMed  CAS  Google Scholar 

  • Inostroza-Blancheteau C, Aquea F, Reyes-Díaz M, Alberdi M, Arce-Johnson P (2011) Identification of aluminum-regulated genes by cDNA-AFLP analysis of roots in two contrasting genotypes of highbush blueberry (Vaccinium corymbosum L.). Mol Biotechnol 49(1):32–41. doi:10.1007/s12033-010-9373-3

    Article  PubMed  CAS  Google Scholar 

  • Jaillon O, Aury J-M, Noel B, et al (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449 (7161):463–467. http://www.nature.com/nature/journal/v449/n7161/suppinfo/nature06148_S1.html

    Google Scholar 

  • Jain M (2012) Next-generation sequencing technologies for gene expression profiling in plants. Briefings Funct Genomics 11(1):63–70. doi:10.1093/bfgp/elr038

    Article  CAS  Google Scholar 

  • Kodama Y, Shumway M, Leinonen R (2012) The sequence read archive: explosive growth of sequencing data. Nucleic Acids Res 40 (D1):D54–D56. doi:10.1093/nar/gkr854

  • Legay G, Marouf E, Berger D, Neuhaus J-M, Mauch-Mani B, Slaughter A (2011) Identification of genes expressed during the compatible interaction of grapevine with Plasmopara viticola through suppression subtractive hybridization (SSH). Eur J Plant Pathol 129(2):281–301. doi:10.1007/s10658-010-9676-z

    Article  Google Scholar 

  • Leida C, Terol J, Martí G, Agustí M, Llácer G, Badenes ML, Ríos G (2010) Identification of genes associated with bud dormancy release in Prunus persica by suppression subtractive hybridization. Tree Physiol 30(5):655–666. doi:10.1093/treephys/tpq008

    Article  PubMed  CAS  Google Scholar 

  • Li X, Sun H, Pei J, Dong Y, Wang F, Chen H, Sun Y, Wang N, Li H, Li Y (2012) De novo sequencing and comparative analysis of the blueberry transcriptome to discover putative genes related to antioxidants. Gene 511 (1):54–61. doi:10.1016/j.gene.2012.09.021

    Google Scholar 

  • Mainland CMM (2012) Frederick V. Coville and the history of North American highbush blueberry culture. Int J Fruit Sci 12 (1–3):4–13. doi:10.1080/15538362.2011.619117

  • Miles TD, Day B, Schilder AC (2011) Identification of differentially expressed genes in a resistant versus a susceptible blueberry cultivar after infection by Colletotrichum acutatum. Mol Plant Pathol 12(5):463–477. doi:10.1111/j.1364-3703.2010.00687.x

    Article  PubMed  CAS  Google Scholar 

  • Milholland RD (1995) Anthracnose fruit rot (ripe rot). In: Caruso FL, Ramsdell DC (eds) Compendium of blueberry and cranberry diseases. APS Press, St Paul, p 17

    Google Scholar 

  • Naik D, Dhanaraj AL, Arora R, Rowland LJ (2007) Identification of genes associated with cold acclimation in blueberry (Vaccinium corymbosum L.) using a subtractive hybridization approach. Plant Sci 173 (2):213–222. doi:10.1016/j.plantsci.2007.05.003

    Google Scholar 

  • Oakenfull RJ, Baxter R, Knight MR (2013) A C-repeat binding factor transcriptional activator (CBF/DREB1) from European Bilberry (Vaccinium myrtillus) induces freezing tolerance when expressed in Arabidopsis thaliana. PLoS ONE 8(1):e54119. doi:10.1371/journal.pone.0054119

    Article  PubMed  CAS  Google Scholar 

  • Polashock JJ, Ehlenfeldt MK, Stretch AW, Kramer M (2005) Anthracnose fruit rot resistance in blueberry cultivars. Plant Dis 89(1):33–38. doi:10.1094/pd-89-0033

    Article  Google Scholar 

  • Polashock JJ, Arora R, Peng Y, Naik D, Rowland LJ (2010) Functional identification of a C-repeat binding factor transcriptional activator from blueberry associated with cold acclimation and rreezing tolerance. J Am Soc Hortic Sci 135(1):40–48

    Google Scholar 

  • Prior RL, Cao G, Martin A, Sofic E, McEwen J, O’Brien C, Lischner N, Ehlenfeldt M, Kalt W, Krewer G, Mainland CM (1998) Antioxidant capacity as influenced by total phenolic and anthocyanin content, maturity, and variety of Vaccinium species. J Agric Food Chem 46(7):2686–2693. doi:10.1021/jf980145d

    Article  CAS  Google Scholar 

  • Qu L, Hancock JF (1997) Randomly Amplified Polymorphic DNA- (RAPD-) based genetic linkage map of blueberry derived from an interspecific cross between diploid Vaccinium darrowi and tetraploid V. corymbosum. J Am Soc Hortic Sci 122(1):69–73

    CAS  Google Scholar 

  • 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(5):682–690

    CAS  Google Scholar 

  • Rowland LJ, Dhanaraj AL, Naik D, Alkharouf N, Matthews B, Arora R (2008) Study of cold tolerance in blueberry using EST libraries, cDNA microarrays, and subtractive hybridization. HortScience 43(7):1975–1981

    Google Scholar 

  • 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 (4):779–784. doi:10.1016/j.scienta.2010.05.008

    Google Scholar 

  • Rowland L, Alkharouf N, Darwish O, Ogden E, Polashock J, Bassil N, Main D (2012a) Generation and analysis of blueberry transcriptome sequences from leaves, developing fruit, and flower buds from cold acclimation through deacclimation. BMC Plant Biol 12(1):46

    Article  PubMed  CAS  Google Scholar 

  • Rowland LJ, Bell DJ, Alkharouf N, Bassil NV, Drummond FA, Beers L, Buck EJ, Finn CE, Graham J, McCallum S, Hancock JF, Polashock JJ, Olmstead JW, Main D (2012b) Generating genomic tools for blueberry improvement. Int J Fruit Sci 12(1–3):276–287. doi:10.1080/15538362.2011.619452

    Article  Google Scholar 

  • Şahin-Çevik M (2013) Identification and expression analysis of early cold-induced genes from cold-hardy Citrus relative Poncirus trifoliata (L.) Raf. Gene 512 (2):536–545. doi:10.1016/j.gene.2012.09.084

  • Schnable PS, Ware D, Fulton RS, Stein JC, Wei F et al (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326(5956):1112–1115. doi:10.1126/science.1178534

    Article  PubMed  CAS  Google Scholar 

  • USDA-NASS (2013) Noncitrus fruits and nuts 2012 preliminary summary. http://usda01.library.cornell.edu/usda/current/NoncFruiNu/NonFruiNu-01-25-2013.pdf. Accessed 3 Jan 2013

  • Verma N, MacDonald L, Punja ZK (2006) Inoculum prevalence, host infection and biological control of Colletotrichum acutatum: causal agent of blueberry anthracnose in British Columbia. Plant Pathol 55(3):442–450. doi:10.1111/j.1365-3059.2006.01401.x

    Article  Google Scholar 

  • Walworth A, Rowland L, Polashock J, Hancock J, Song G-q (2012) Overexpression of a blueberry-derived CBF gene enhances cold tolerance in a southern highbush blueberry cultivar. Mol Breed 30(3):1313–1323. doi:10.1007/s11032-012-9718-7

    Article  CAS  Google Scholar 

  • Wang H, Cao G, Prior RL (1996) Total antioxidant capacity of fruits. J Agric Food Chem 44(3):701–705. doi:10.1021/jf950579y

    Article  CAS  Google Scholar 

  • Wisnieswski M, Nassuth A, Teulières C, Marque C, Rowland LJ, Cao PB, Brown A (2013) Genomics of cold hardiness in woody plants. Crit Rev Plant Sci (in press)

  • Wu X, Beecher GR, Holden JM, Haytowitz DB, Gebhardt SE, Prior RL (2004) Lipophilic and hydrophilic antioxidant capacities of common toods in the United States. J Agric Food Chem 52(12):4026–4037. doi:10.1021/jf049696w

    Article  PubMed  CAS  Google Scholar 

  • Young ND, Debelle F, Oldroyd GED, Geurts R, Cannon SB et al (2011) The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature 480(7378):520–524

    PubMed  CAS  Google Scholar 

  • Zifkin M, Jin A, Ozga JA, Zaharia LI, Schernthaner JP, Gesell A, Abrams SR, Kennedy JA, Constabel CP (2012) Gene expression and metabolite profiling of developing highbush blueberry fruit indicates transcriptional regulation of flavonoid metabolism and activation of abscisic acid metabolism. Plant Physiol 158(1):200–224. doi:10.1104/pp.111.180950

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. U.S. Department of Agriculture, Agricultural Research Service, Beltsville, MD, USA

    Jose V. Die & Lisa J. Rowland

Authors
  1. Jose V. Die
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Lisa J. Rowland
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Lisa J. Rowland.

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Die, J.V., Rowland, L.J. Advent of genomics in blueberry. Mol Breeding 32, 493–504 (2013). https://doi.org/10.1007/s11032-013-9893-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11032-013-9893-1

Keywords

  • Bioinformatics
  • cDNA libraries
  • EST
  • NGS
  • Transcriptome