High-resolution genetic maps of Eucalyptus improve Eucalyptus grandis genome assembly.
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.
CIRAD, UMR AGAP, F-33612, Cestas, France.|INRA, UMR1202 BIOGECO, F-33610, Cestas, France.|BIOGECO, UMR 1202, Univ. Bordeaux, F-33600, Pessac, France.
Jérôme
J
Bartholomé
INRA, UMR1202 BIOGECO, F-33610, Cestas, France.|BIOGECO, UMR 1202, Univ. Bordeaux, F-33600, Pessac, France.|Plate-forme Bio-informatique Genotoul, INRA, Biométrie et Intelligence Artificielle, BP 52627, 31326, Castanet-Tolosan Cedex, France.
Eric
E
Mandrou
CRDPI, BP 1291, Pointe Noire, Republic of Congo.
André
A
Mabiala
HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35801, USA.
Jerry
J
Jenkins
Plate-forme Bio-informatique Genotoul, INRA, Biométrie et Intelligence Artificielle, BP 52627, 31326, Castanet-Tolosan Cedex, France.
Ibouniyamine
I
Nabihoudine
Plate-forme Bio-informatique Genotoul, INRA, Biométrie et Intelligence Artificielle, BP 52627, 31326, Castanet-Tolosan Cedex, France.
Christophe
C
Klopp
HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35801, USA.|US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA.
Jeremy
J
Schmutz
INRA, UMR1202 BIOGECO, F-33610, Cestas, France.|BIOGECO, UMR 1202, Univ. Bordeaux, F-33600, Pessac, France.
Christophe
C
Plomion
CIRAD, UMR AGAP, F-33612, Cestas, France.|INRA, UMR1202 BIOGECO, F-33610, Cestas, France.|BIOGECO, UMR 1202, Univ. Bordeaux, F-33600, Pessac, France.
Jean-Marc
JM
Gion
D002874:Chromosome Mapping; D005052:Eucalyptus / Q000235:genetics*; D005819:Genetic Markers; D018745:Genome, Plant; D005838:Genotype; D020161:Physical Chromosome Mapping; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D018401:Sample Size; D017422:Sequence Analysis, DNA; D026801:Synteny / Q000235:genetics
D005819:Genetic Markers
Eucalyptus; genetic mapping; genome assembly; segregation distortion; single nucleotide polymorphism (SNP) array