Tree Genetics & Genomes

, Volume 8, Issue 2, pp 289–301

Discovery, validation, and in silico functional characterization of EST-SSR markers in Eucalyptus globulus

  • Cintia V. Acuña
  • Paula Fernandez
  • Pamela V. Villalba
  • Martín N. García
  • H. Esteban Hopp
  • Susana N. Marcucci Poltri
Original Paper

DOI: 10.1007/s11295-011-0440-0

Cite this article as:
Acuña, C.V., Fernandez, P., Villalba, P.V. et al. Tree Genetics & Genomes (2012) 8: 289. doi:10.1007/s11295-011-0440-0
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Abstract

Eucalyptus globulus is the most commonly planted hardwood species for pulpwood in temperate regions. We aimed to develop and characterize functional molecular markers for population genetic analyses and molecular breeding in this model tree species. Public expressed sequence tag (EST) databases were screened for nonredundant sequences to predict putative gene functions and to discover simple sequence repeats (EST-SSRs), which were then validated in E. globulus and six other Eucalyptus species. A total of 4,924 nonredundant sequences were identified from 12,690 updated E. globulus ESTs. Approximately 19.3% (952) were unigenes and contained 1,140 EST-SSR markers, which were mainly trimeric (58.6%). A set of 979 primers for putative SSR markers was designed after bioinformatic analysis. The predicted functions of these ESTs containing SSR were classified according to their gene ontology (GO) categories (biological process, molecular function, and cellular component). GO categories were assigned to 226 ESTs (30.2%). Most ESTs containing SSR (78.7%) had significant matches (E ≤ 10−5) with the nonredundant protein database using BLASTX. From a set of 56 random primer pairs, 37 could be validated in eight E. globulus genotypes and were also tested for cross-transferability to other six Eucalyptus species (Eucalyptus grandis, Eucalyptus saligna, Eucalyptus dunnii, Eucalyptus viminalis, Eucalyptus camaldulensis, Eucalyptus tereticornis). Seventeen polymorphic EST-SSR markers for E. globulus were evaluated in 60 unrelated trees, being representative of the species’ natural distribution. As a result, six highly informative markers were proposed for genetic diversity analyses, fingerprinting, and comparative population studies, between different species of E. globulus.

Keywords

Eucalyptus globulusEST-SSRFunctional diversityPolymorphismTransferability

Supplementary material

11295_2011_440_MOESM1_ESM.xls (1.3 mb)
Online Resource 1In silico EST-SSRs derived from curated public E. globulus libraries. The data describe the 1,140 EST-SSRs: unigenes names, similarity matches, E value, similarity mean, GO term, sequence length, SSR description, primers description (sequence of forward and reverse primers, annealing temperature (°C)), expected product size (bp), and unigene sequences (XLS 1295 kb)
11295_2011_440_MOESM2_ESM.xls (112 kb)
Online Resource 2Gene ontology annotation. This table provides the detailed information of sequence distribution in graph levels, GO term, number of sequences and parents for biological process, molecular function, and component categories (XLS 112 kb)
11295_2011_440_MOESM3_ESM.xls (54 kb)
Online Resource 3Pathways maps. This table provides information on the enzymes putatively encoded by the ESTs containing SSR, based on homology prediction and their associated pathways. This includes KEGG maps, enzyme names, and sequences (XLS 54 kb)

Copyright information

© Springer-Verlag 2011

Authors and Affiliations

  • Cintia V. Acuña
    • 1
  • Paula Fernandez
    • 1
  • Pamela V. Villalba
    • 1
  • Martín N. García
    • 1
  • H. Esteban Hopp
    • 1
    • 2
  • Susana N. Marcucci Poltri
    • 1
  1. 1.Instituto de Biotecnología, CICVyAInstituto Nacional de Tecnología Agropecuaria (INTA Castelar)CastelarArgentina
  2. 2.Facultad de Ciencias Exactas y NaturalesUniversidad de Buenos AiresBuenos AiresArgentina