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

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...

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Autores principales:	Acuña, Cintia Vanesa, Fernández, Paula Virginia, Hopp, Horacio Esteban, Marcucci Poltri, Susana N.
Publicado:	2012
Materias:	EST-SSR Eucalyptus globulus Functional diversity Polymorphism Transferability Eucalyptus Eucalyptus camaldulensis Eucalyptus dunnii Eucalyptus grandis Eucalyptus saligna Eucalyptus tereticornis Eucalyptus viminalis
Acceso en línea:	https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_16142942_v8_n2_p289_Acuna http://hdl.handle.net/20.500.12110/paper_16142942_v8_n2_p289_Acuna
Aporte de:	Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) de Universidad de Buenos Aires

id	paper:paper_16142942_v8_n2_p289_Acuna
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spelling	paper:paper_16142942_v8_n2_p289_Acuna2023-06-08T16:25:19Z Discovery, validation, and in silico functional characterization of EST-SSR markers in Eucalyptus globulus Acuña, Cintia Vanesa Fernández, Paula Virginia Hopp, Horacio Esteban Marcucci Poltri, Susana N. EST-SSR Eucalyptus globulus Functional diversity Polymorphism Transferability Eucalyptus Eucalyptus camaldulensis Eucalyptus dunnii Eucalyptus globulus Eucalyptus grandis Eucalyptus saligna Eucalyptus tereticornis Eucalyptus viminalis 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. © 2011 Springer-Verlag. Fil:Acuña, C.V. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Fernandez, P. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Hopp, H.E. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Marcucci Poltri, S.N. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. 2012 https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_16142942_v8_n2_p289_Acuna http://hdl.handle.net/20.500.12110/paper_16142942_v8_n2_p289_Acuna
institution	Universidad de Buenos Aires
institution_str	I-28
repository_str	R-134
collection	Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA)
topic	EST-SSR Eucalyptus globulus Functional diversity Polymorphism Transferability Eucalyptus Eucalyptus camaldulensis Eucalyptus dunnii Eucalyptus globulus Eucalyptus grandis Eucalyptus saligna Eucalyptus tereticornis Eucalyptus viminalis
spellingShingle	EST-SSR Eucalyptus globulus Functional diversity Polymorphism Transferability Eucalyptus Eucalyptus camaldulensis Eucalyptus dunnii Eucalyptus globulus Eucalyptus grandis Eucalyptus saligna Eucalyptus tereticornis Eucalyptus viminalis Acuña, Cintia Vanesa Fernández, Paula Virginia Hopp, Horacio Esteban Marcucci Poltri, Susana N. Discovery, validation, and in silico functional characterization of EST-SSR markers in Eucalyptus globulus
topic_facet	EST-SSR Eucalyptus globulus Functional diversity Polymorphism Transferability Eucalyptus Eucalyptus camaldulensis Eucalyptus dunnii Eucalyptus globulus Eucalyptus grandis Eucalyptus saligna Eucalyptus tereticornis Eucalyptus viminalis
description	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. © 2011 Springer-Verlag.
author	Acuña, Cintia Vanesa Fernández, Paula Virginia Hopp, Horacio Esteban Marcucci Poltri, Susana N.
author_facet	Acuña, Cintia Vanesa Fernández, Paula Virginia Hopp, Horacio Esteban Marcucci Poltri, Susana N.
author_sort	Acuña, Cintia Vanesa
title	Discovery, validation, and in silico functional characterization of EST-SSR markers in Eucalyptus globulus
title_short	Discovery, validation, and in silico functional characterization of EST-SSR markers in Eucalyptus globulus
title_full	Discovery, validation, and in silico functional characterization of EST-SSR markers in Eucalyptus globulus
title_fullStr	Discovery, validation, and in silico functional characterization of EST-SSR markers in Eucalyptus globulus
title_full_unstemmed	Discovery, validation, and in silico functional characterization of EST-SSR markers in Eucalyptus globulus
title_sort	discovery, validation, and in silico functional characterization of est-ssr markers in eucalyptus globulus
publishDate	2012
url	https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_16142942_v8_n2_p289_Acuna http://hdl.handle.net/20.500.12110/paper_16142942_v8_n2_p289_Acuna
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Discovery, validation, and in silico functional characterization of EST-SSR markers in Eucalyptus globulus

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