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A novel genome-wide microsatellite resource for species of Eucalyptus with linkage-to-physical correspondence on the reference genome sequence.
Mol Ecol Resour. 2015 Mar; 15(2):437-48.ME

Abstract

Keystone species in their native ranges, eucalypts, are ecologically and genetically very diverse, growing naturally along extensive latitudinal and altitudinal ranges and variable environments. Besides their ecological importance, eucalypts are also the most widely planted trees for sustainable forestry in the world. We report the development of a novel collection of 535 microsatellites for species of Eucalyptus, 494 designed from ESTs and 41 from genomic libraries. A selected subset of 223 was evaluated for individual identification, parentage testing, and ancestral information content in the two most extensively studied species, Eucalyptus grandis and Eucalyptus globulus. Microsatellites showed high transferability and overlapping allele size range, suggesting they have arisen still in their common ancestor and confirming the extensive genome conservation between these two species. A consensus linkage map with 437 microsatellites, the most comprehensive microsatellite-only genetic map for Eucalyptus, was built by assembling segregation data from three mapping populations and anchored to the Eucalyptus genome. An overall colinearity between recombination-based and physical positioning of 84% of the mapped microsatellites was observed, with some ordering discrepancies and sporadic locus duplications, consistent with the recently described whole genome duplication events in Eucalyptus. The linkage map covered 95.2% of the 605.8-Mbp assembled genome sequence, placing one microsatellite every 1.55 Mbp on average, and an overall estimate of physical to recombination distance of 618 kbp/cM. The genetic parameters estimates together with linkage and physical position data for this large set of microsatellites should assist marker choice for genome-wide population genetics and comparative mapping in Eucalyptus.

Authors+Show Affiliations

Laboratório de Genética Vegetal, EMBRAPA Recursos Genéticos e Biotecnologia, PqEB, Brasilia, DF, 70770-970, Brazil.No affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

25146326

Citation

Grattapaglia, Dario, et al. "A Novel Genome-wide Microsatellite Resource for Species of Eucalyptus With Linkage-to-physical Correspondence On the Reference Genome Sequence." Molecular Ecology Resources, vol. 15, no. 2, 2015, pp. 437-48.
Grattapaglia D, Mamani EM, Silva-Junior OB, et al. A novel genome-wide microsatellite resource for species of Eucalyptus with linkage-to-physical correspondence on the reference genome sequence. Mol Ecol Resour. 2015;15(2):437-48.
Grattapaglia, D., Mamani, E. M., Silva-Junior, O. B., & Faria, D. A. (2015). A novel genome-wide microsatellite resource for species of Eucalyptus with linkage-to-physical correspondence on the reference genome sequence. Molecular Ecology Resources, 15(2), 437-48. https://doi.org/10.1111/1755-0998.12317
Grattapaglia D, et al. A Novel Genome-wide Microsatellite Resource for Species of Eucalyptus With Linkage-to-physical Correspondence On the Reference Genome Sequence. Mol Ecol Resour. 2015;15(2):437-48. PubMed PMID: 25146326.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - A novel genome-wide microsatellite resource for species of Eucalyptus with linkage-to-physical correspondence on the reference genome sequence. AU - Grattapaglia,Dario, AU - Mamani,Eva M C, AU - Silva-Junior,Orzenil B, AU - Faria,Danielle A, Y1 - 2014/09/06/ PY - 2014/06/05/received PY - 2014/08/05/revised PY - 2014/08/13/accepted PY - 2014/8/23/entrez PY - 2014/8/26/pubmed PY - 2015/10/22/medline KW - Eucalyptus globulus KW - Eucalyptus grandis KW - ancestry informative markers KW - microsatellites KW - simple sequence repeats SP - 437 EP - 48 JF - Molecular ecology resources JO - Mol Ecol Resour VL - 15 IS - 2 N2 - Keystone species in their native ranges, eucalypts, are ecologically and genetically very diverse, growing naturally along extensive latitudinal and altitudinal ranges and variable environments. Besides their ecological importance, eucalypts are also the most widely planted trees for sustainable forestry in the world. We report the development of a novel collection of 535 microsatellites for species of Eucalyptus, 494 designed from ESTs and 41 from genomic libraries. A selected subset of 223 was evaluated for individual identification, parentage testing, and ancestral information content in the two most extensively studied species, Eucalyptus grandis and Eucalyptus globulus. Microsatellites showed high transferability and overlapping allele size range, suggesting they have arisen still in their common ancestor and confirming the extensive genome conservation between these two species. A consensus linkage map with 437 microsatellites, the most comprehensive microsatellite-only genetic map for Eucalyptus, was built by assembling segregation data from three mapping populations and anchored to the Eucalyptus genome. An overall colinearity between recombination-based and physical positioning of 84% of the mapped microsatellites was observed, with some ordering discrepancies and sporadic locus duplications, consistent with the recently described whole genome duplication events in Eucalyptus. The linkage map covered 95.2% of the 605.8-Mbp assembled genome sequence, placing one microsatellite every 1.55 Mbp on average, and an overall estimate of physical to recombination distance of 618 kbp/cM. The genetic parameters estimates together with linkage and physical position data for this large set of microsatellites should assist marker choice for genome-wide population genetics and comparative mapping in Eucalyptus. SN - 1755-0998 UR - https://www.unboundmedicine.com/medline/citation/25146326/A_novel_genome_wide_microsatellite_resource_for_species_of_Eucalyptus_with_linkage_to_physical_correspondence_on_the_reference_genome_sequence_ L2 - https://doi.org/10.1111/1755-0998.12317 DB - PRIME DP - Unbound Medicine ER -