Integrating genome annotation and QTL position to identify candidate genes for productivity, architecture and water-use efficiency in Populus spp

Four leaf traits and 7 growth traits were measured on 330 F1 P. deltoides x P. trichocarpa progeny. A total of 77 QTLs controlling 11 traits were identified explaining from 1.8 to 17.2% of the variation of traits. For 58 QTLs, confidence intervals could be projected on the genome. An extended functional annotation was built based on data retrieved from the plant genome database Phytozome and from an inference of function using homology between Populus and the model plant Arabidopsis. Genes located within QTL confidence intervals were retrieved and enrichments in gene ontology (GO) terms were determined using different methods. Significant enrichments were found for all traits. Particularly relevant biological processes GO terms were identified for QTLs controlling number of sylleptic branches: intervals were enriched in GO terms of biological process like ‘ripening’ and ‘adventitious roots development’.Beyond the simple identification of QTLs, this study is the first to use a global approach of GO terms enrichment analysis to fully explore gene function under QTLs confidence intervals in plants. This global approach may lead to identification of new candidate genes for traits of interest.Dissection of genetic architecture of complex trait such as growth and yield in plants has been achieved by Quantitative Trait Loci (QTL) detection approaches. Dissecting loci to find the causative genes can be considered as the Holy Grail for geneticists. The ultimate road to find the genes, positional cloning, has been achieved in main crop plants [1] but it is slow and labour intensive especially because large segregating populations have to be developed. The advent of plant whole genome sequences has opened the possibility of anchoring genetic maps and positioning QTL on a physical map. Nevertheless, QTL intervals correspond to several hundreds of genes [1]. Despite of some successful positional cloning stories in plants, there is room for complementary approaches, like associat