High-resolution genetic maps of Eucalyptus improve Eucalyptus&nbsp;grandis genome assembly

Bartholomé, Jérôme; Mandrou, Eric; Mabiala, André; Jenkins, Jerry; Nabihoudine, Ibouniyamine; Klopp, Christophe; Schmutz, Jeremy; Plomion, Christophe; Gion, Jean-Marc

doi:10.1111/nph.13150

High-resolution genetic maps of Eucalyptus improve Eucalyptus grandis genome assembly

Journal Article · Mon Nov 10 00:00:00 EST 2014 · New Phytologist

DOI:https://doi.org/10.1111/nph.13150· OSTI ID:1616039

Bartholomé, Jérôme ^[1]; Mandrou, Eric ^[2]; Mabiala, André ^[3]; Jenkins, Jerry ^[4]; Nabihoudine, Ibouniyamine ^[5]; Klopp, Christophe ^[5]; Schmutz, Jeremy ^[6]; Plomion, Christophe ^[2]; Gion, Jean-Marc ^[1]

Agricultural Research for Development (CIRAD), Cestas (France); National Research Institute for Agriculture, Food and Environment (INRA), Cestas (France); BIOGEO, Pessac (France)
National Research Institute for Agriculture, Food and Environment (INRA), Cestas (France); BIOGEO, Pessac (France)
CRDPI, Pointe Noire (Republic of Congo)
HudsonAlpha Inst. for Biotechnology, Huntsville, AL (United States)
National Research Institute for Agriculture, Food and Environment (INRA), Cestas (France)
HudsonAlpha Inst. for Biotechnology, Huntsville, AL (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)

Genetic maps are key tools in genetic research as they constitute the framework for many applications, such as quantitative trait locus analysis, and support the assembly of genome sequences. The resequencing of the two parents of a cross between Eucalyptus urophylla and Eucalyptus grandis was used to design a single nucleotide polymorphism (SNP) array of 6000 markers evenly distributed along the E. grandis genome. The genotyping of 1025 offspring enabled the construction of two high-resolution genetic maps containing 1832 and 1773 markers with an average marker interval of 0.45 and 0.5 cM for E. grandis and E. urophylla, respectively. The comparison between genetic maps and the reference genome highlighted 85% of collinear regions. A total of 43 noncollinear regions and 13 nonsynthetic regions were detected and corrected in the new genome assembly. This improved version contains 4943 scaffolds totalling 691.3 Mb of which 88.6% were captured by the 11 chromosomes. The mapping data were also used to investigate the effect of population size and number of markers on linkage mapping accuracy. This study provides the most reliable linkage maps for Eucalyptus and version 2.0 of the E. grandis genome.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: ERANET; FEDER; USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1616039

Journal Information:: New Phytologist, Journal Name: New Phytologist Journal Issue: 4 Vol. 206; ISSN 0028-646X

Publisher:: WileyCopyright Statement

Country of Publication:: United States

Language:: English

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Additional file 2 of E. urophylla × E. grandis high-quality genome and comparative genomics provide insights on evolution and diversification of eucalyptus Shen, Chao; Li, Limei; Ouyang, Lejun figshare https://doi.org/10.6084/m9.figshare.22721408.v1	dataset	January 2023
Additional file 3 of E. urophylla × E. grandis high-quality genome and comparative genomics provide insights on evolution and diversification of eucalyptus Shen, Chao; Li, Limei; Ouyang, Lejun figshare https://doi.org/10.6084/m9.figshare.22721411.v1	dataset	January 2023
Additional file 4 of E. urophylla × E. grandis high-quality genome and comparative genomics provide insights on evolution and diversification of eucalyptus Shen, Chao; Li, Limei; Ouyang, Lejun figshare https://doi.org/10.6084/m9.figshare.22721414	dataset	January 2023
Additional file 5 of E. urophylla × E. grandis high-quality genome and comparative genomics provide insights on evolution and diversification of eucalyptus Shen, Chao; Li, Limei; Ouyang, Lejun figshare https://doi.org/10.6084/m9.figshare.22721417	dataset	January 2023
Additional file 6 of E. urophylla × E. grandis high-quality genome and comparative genomics provide insights on evolution and diversification of eucalyptus Shen, Chao; Li, Limei; Ouyang, Lejun figshare https://doi.org/10.6084/m9.figshare.22721420	dataset	January 2023
Additional file 7 of E. urophylla × E. grandis high-quality genome and comparative genomics provide insights on evolution and diversification of eucalyptus Shen, Chao; Li, Limei; Ouyang, Lejun figshare https://doi.org/10.6084/m9.figshare.22721423	dataset	January 2023
Additional file 8 of E. urophylla × E. grandis high-quality genome and comparative genomics provide insights on evolution and diversification of eucalyptus Shen, Chao; Li, Limei; Ouyang, Lejun figshare https://doi.org/10.6084/m9.figshare.22721426	dataset	January 2023
Additional file 9 of E. urophylla × E. grandis high-quality genome and comparative genomics provide insights on evolution and diversification of eucalyptus Shen, Chao; Li, Limei; Ouyang, Lejun figshare https://doi.org/10.6084/m9.figshare.22721429	dataset	January 2023
Additional file 10 of E. urophylla × E. grandis high-quality genome and comparative genomics provide insights on evolution and diversification of eucalyptus Shen, Chao; Li, Limei; Ouyang, Lejun figshare https://doi.org/10.6084/m9.figshare.22721432	dataset	January 2023

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