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High‐resolution genetic maps of E ucalyptus improve Eucalyptus grandis genome assembly
Author(s) -
Bartholomé Jérôme,
Mandrou Eric,
Mabiala André,
Jenkins Jerry,
Nabihoudine Ibouniyamine,
Klopp Christophe,
Schmutz Jeremy,
Plomion Christophe,
Gion JeanMarc
Publication year - 2015
Publication title -
new phytologist
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.742
H-Index - 244
eISSN - 1469-8137
pISSN - 0028-646X
DOI - 10.1111/nph.13150
Subject(s) - genome , biology , eucalyptus , genetics , locus (genetics) , quantitative trait locus , single nucleotide polymorphism , population , gene mapping , genetic linkage , computational biology , botany , gene , genotype , chromosome , demography , sociology
Summary 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 E ucalyptus urophylla and E ucalyptus 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 E ucalyptus and version 2.0 of the E . grandis genome.