High-Resolution Genetic Maps of Eucalyptus Hybrids Improve E. grandis Genome Assembly and Give Insight into Genes Associated with Carbon Isotope Composition

Genetic maps constitute the key framework of many applications in genetics, such as quantitative trait loci (QTL) detection and the assembly of genome sequences. The linkage mapping accuracy is crucial for any of these applications. In this study we genotyped one thousand interspecific Eucalyptus urophylla x E. grandis hybrids with 5,175 SNPs evenly distributed along the first version of E. grandis genome. Two high-resolution genetic maps were obtained containing 1,832 and 1,773 markers with an average marker interval of 0.45 and 0.5 cM for E. grandis and E. urophylla, respectively. The comparison between high-resolution linkage maps and the reference genome suggested 85% collinear regions. A total of 43 non-collinear regions and 13 non-synthetic regions were detected and corrected in the version 2.0 of E. grandis genome. The total size of this improved version is 691.3 Mb (with 7.4% scaffold gaps) of which 88.6% were captured by 11 chromosomes. The phenotyping of the same interspecific crosses for carbon isotope composition (δ¹³C) enabled us to dissect the genetic architecture of this trait and its interplay with environment. High resolution genetic maps anchored on the reference genome allowed to target genomic regions underlying δ¹³C QTLs. Gene ontology term enrichment analysis suggested several candidate genes related to foliar δ¹³C including two involved in the regulation of stomatal movements. This study provides the most reliable linkage maps for Eucalyptus, the version 2.0 of E. grandis genome and the first report of the genetic architecture of δ¹³C in Eucalyptus.