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A reference linkage map for Eucalyptus.
BMC Genomics. 2012 Jun 15; 13:240.BG

Abstract

BACKGROUND

Genetic linkage maps are invaluable resources in plant research. They provide a key tool for many genetic applications including: mapping quantitative trait loci (QTL); comparative mapping; identifying unlinked (i.e. independent) DNA markers for fingerprinting, population genetics and phylogenetics; assisting genome sequence assembly; relating physical and recombination distances along the genome and map-based cloning of genes. Eucalypts are the dominant tree species in most Australian ecosystems and of economic importance globally as plantation trees. The genome sequence of E. grandis has recently been released providing unprecedented opportunities for genetic and genomic research in the genus. A robust reference linkage map containing sequence-based molecular markers is needed to capitalise on this resource. Several high density linkage maps have recently been constructed for the main commercial forestry species in the genus (E. grandis, E. urophylla and E. globulus) using sequenced Diversity Arrays Technology (DArT) and microsatellite markers. To provide a single reference linkage map for eucalypts a composite map was produced through the integration of data from seven independent mapping experiments (1950 individuals) using a marker-merging method.

RESULTS

The composite map totalled 1107 cM and contained 4101 markers; comprising 3880 DArT, 213 microsatellite and eight candidate genes. Eighty-one DArT markers were mapped to two or more linkage groups, resulting in the 4101 markers being mapped to 4191 map positions. Approximately 13% of DArT markers mapped to identical map positions, thus the composite map contained 3634 unique loci at an average interval of 0.31 cM.

CONCLUSION

The composite map represents the most saturated linkage map yet produced in Eucalyptus. As the majority of DArT markers contained on the map have been sequenced, the map provides a direct link to the E. grandis genome sequence and will serve as an important reference for progressing eucalypt research.

Authors+Show Affiliations

School of Plant Science and CRC for Forestry, University of Tasmania, Private Bag 55 Hobart, Tasmania, 7001, Australia. cjhudson@utas.edu.auNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo 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

22702473

Citation

Hudson, Corey J., et al. "A Reference Linkage Map for Eucalyptus." BMC Genomics, vol. 13, 2012, p. 240.
Hudson CJ, Freeman JS, Kullan AR, et al. A reference linkage map for Eucalyptus. BMC Genomics. 2012;13:240.
Hudson, C. J., Freeman, J. S., Kullan, A. R., Petroli, C. D., Sansaloni, C. P., Kilian, A., Detering, F., Grattapaglia, D., Potts, B. M., Myburg, A. A., & Vaillancourt, R. E. (2012). A reference linkage map for Eucalyptus. BMC Genomics, 13, 240. https://doi.org/10.1186/1471-2164-13-240
Hudson CJ, et al. A Reference Linkage Map for Eucalyptus. BMC Genomics. 2012 Jun 15;13:240. PubMed PMID: 22702473.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - A reference linkage map for Eucalyptus. AU - Hudson,Corey J, AU - Freeman,Jules S, AU - Kullan,Anand R K, AU - Petroli,César D, AU - Sansaloni,Carolina P, AU - Kilian,Andrzej, AU - Detering,Frank, AU - Grattapaglia,Dario, AU - Potts,Brad M, AU - Myburg,Alexander A, AU - Vaillancourt,René E, Y1 - 2012/06/15/ PY - 2012/03/23/received PY - 2012/06/04/accepted PY - 2012/6/19/entrez PY - 2012/6/19/pubmed PY - 2012/12/20/medline SP - 240 EP - 240 JF - BMC genomics JO - BMC Genomics VL - 13 N2 - BACKGROUND: Genetic linkage maps are invaluable resources in plant research. They provide a key tool for many genetic applications including: mapping quantitative trait loci (QTL); comparative mapping; identifying unlinked (i.e. independent) DNA markers for fingerprinting, population genetics and phylogenetics; assisting genome sequence assembly; relating physical and recombination distances along the genome and map-based cloning of genes. Eucalypts are the dominant tree species in most Australian ecosystems and of economic importance globally as plantation trees. The genome sequence of E. grandis has recently been released providing unprecedented opportunities for genetic and genomic research in the genus. A robust reference linkage map containing sequence-based molecular markers is needed to capitalise on this resource. Several high density linkage maps have recently been constructed for the main commercial forestry species in the genus (E. grandis, E. urophylla and E. globulus) using sequenced Diversity Arrays Technology (DArT) and microsatellite markers. To provide a single reference linkage map for eucalypts a composite map was produced through the integration of data from seven independent mapping experiments (1950 individuals) using a marker-merging method. RESULTS: The composite map totalled 1107 cM and contained 4101 markers; comprising 3880 DArT, 213 microsatellite and eight candidate genes. Eighty-one DArT markers were mapped to two or more linkage groups, resulting in the 4101 markers being mapped to 4191 map positions. Approximately 13% of DArT markers mapped to identical map positions, thus the composite map contained 3634 unique loci at an average interval of 0.31 cM. CONCLUSION: The composite map represents the most saturated linkage map yet produced in Eucalyptus. As the majority of DArT markers contained on the map have been sequenced, the map provides a direct link to the E. grandis genome sequence and will serve as an important reference for progressing eucalypt research. SN - 1471-2164 UR - https://www.unboundmedicine.com/medline/citation/22702473/A_reference_linkage_map_for_Eucalyptus_ L2 - https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-13-240 DB - PRIME DP - Unbound Medicine ER -