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

BACKGROUND: Hybrid poplars species are candidates for biomass production but breeding efforts are needed to combine productivity and water use efficiency in improved cultivars. The understanding of the genetic architecture of growth in poplar by a Quantitative Trait Loci (QTL) approach can help us to elucidate the molecular basis of such integrative traits but identifying candidate genes underlying these QTLs remains difficult. Nevertheless, the increase of genomic information together with the accessibility to a reference genome sequence (Populus trichocarpa Nisqually-1) allow to bridge QTL information on genetic maps and physical location of candidate genes on the genome. The objective of the study is to identify QTLs controlling productivity, architecture and leaf traits in a P. deltoides x P. trichocarpa F1 progeny and to identify candidate genes underlying QTLs based on the anchoring of genetic maps on the genome and the gene ontology information linked to genome annotation. The strategy to explore genome annotation was to use Gene Ontology enrichment tools to test if some functional categories are statistically over-represented in QTL regions. RESULTS: 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'. CONCLUSION: 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.

Xylem anatomy correlates with gas exchange, water-use efficiency and growth performance under contrasting water regimes: evidence from Populus deltoides x Populus nigra hybrids.

Six Populus deltoides Bartr. ex Marsh. x P. nigra L. genotypes were selected to investigate whether stem xylem anatomy correlated with gas exchange rates, water-use efficiency (WUE) and growth performance. Clonal copies of the genotypes were grown in a two-plot common garden test under contrasting water regimes, with one plot maintained irrigated and the other one subjected to moderate summer water deficit. The six genotypes displayed a large range of xylem anatomy, mean vessel and fibre diameter varying from about 40 to 60 microm and from 7.5 to 10.5 microm, respectively. Decreased water availability resulted in a reduced cell size and an important rise in vessel density, but the extent of xylem plasticity was both genotype and trait dependent. Vessel diameter and theoretical xylem-specific hydraulic conductivity correlated positively with stomatal conductance, carbon isotope discrimination and growth performance-related traits and negatively with intrinsic WUE, especially under water deficit conditions. Vessel diameter and vessel density measured under water deficit conditions correlated with the relative losses in biomass production in response to water deprivation; this resulted from the fact that a more plastic xylem structure was generally accompanied by a larger loss in biomass production.

Leaf proteome analysis of eight Populus xeuramericana genotypes: genetic variation in drought response and in water-use efficiency involves photosynthesis-related proteins.

Genetic variation of leaf proteome in drought response was investigated among eight Populus xeuramericana genotypes contrasting for their leaf carbon isotope discrimination (Delta), an estimate of intrinsic water-use efficiency. Plants were grown in open field on two similar plots. Drought was induced by an 86-day irrigation cessation on one plot, whereas a second plot remained regularly irrigated. Using 2-DE, 863 reproducible spots were detected; about 60% presented at least one significant effect i.e. treatment, genotype and/or genotype by treatment interaction effect. A significant genotype by treatment interaction was detected for 62 reliably identified proteins among which, about 65% consisted in chloroplast-associated proteins either involved in the Calvin cycle or in the electron-transport chains. The other proteins were involved in oxidative stress, amino acid or protein metabolisms. Correlations between protein abundance and Delta variations were found for 45 reliably identified proteins. The abundance of ribulose-1,5-bisphosphate carboxylase/oxygenase activase isoforms scaled negatively with Delta regardless of the treatment, suggesting that a large intrinsic water-use efficiency could be due to higher abundance of ribulose-1,5-bisphosphate carboxylase/oxygenase activase. Under control condition, abundance of enzymes involved in carbon fixation was also negatively correlated with Delta, whereas abundance of enzymes involved in photorespiration or respiration was positively correlated with Delta.

Genetic variation and drought response in two Populus x euramericana genotypes through 2-DE proteomic analysis of leaves from field and glasshouse cultivated plants.

Genotype and water deficit effects on leaf 2-DE protein profiles of two Populus deltoides x Populus nigra, cv. 'Agathe_F' and 'Cima', were analysed over a short-term period of 18 days in glasshouse using 4-month-old rooted cuttings and over a long-lasting period of 86 days in open field using 4-year-old rooted cuttings. Leaf proteomes were analyzed using two-dimensional gel electrophoresis, and proteins were identified after database searching from MS peptide spectra. A reliable genotype effect was observed in the leaf proteome over experiment locations, water regimes and sampling dates. Quantitative differences between genotypes were found. Most of them corresponded to proteins matching isoforms or post-translational modification variants. However, 'Cima' displayed the highest abundance of antioxidant enzymes. In response to water deficit, about 10% of the reproducible spots significantly varied regardless of the experiment location, among which about 25% also displayed genotype-dependent variations. As a whole, while 'Cima' differed from 'Agathe_F' by increased abundance of enzymes involved in photorespiration and in oxidative stress, 'Agathe_F' was mainly differentiated by increased abundance of enzymes involved in photosynthesis.

Impact of drought on productivity and water use efficiency in 29 genotypes of Populus deltoides x Populus nigra.

We examined the relationships among productivity, water use efficiency (WUE) and drought tolerance in 29 genotypes of Populus x euramericana (Populus deltoides x Populus nigra), and investigated whether some leaf traits could be used as predictors for productivity, WUE and drought tolerance. At Orléans, France, drought was induced on one field plot by withholding water, while a second plot remained irrigated and was used as a control. Recorded variables included stem traits (e.g. biomass) and leaf structural (e.g. leaf area) and functional traits [e.g. intrinsic water use efficiency (Wi) and carbon isotope discrimination (Delta)]. Productivity and Delta displayed large genotypic variability and were not correlated. Delta scaled negatively with Wi and positively with stomatal conductance under moderate drought, suggesting that the diversity for Delta was mainly driven by stomatal conductance. Most of the productive genotypes displayed a low level of drought tolerance (i.e. a large reduction of biomass), while the less productive genotypes presented a large range of drought tolerance. The ability to increase WUE in response to water deficit was necessary but not sufficient to explain the genotypic diversity of drought tolerance.

Productivity, leaf traits and carbon isotope discrimination in 29 Populus deltoides x P. nigra clones.

Here we tested whether some leaf traits could be used as predictors for productivity in a range of Populus deltoides x P. nigra clones. These traits were assessed in 3-yr-old rooted cuttings from 29 clones growing in an open field trial, in a five randomized complete block design, under optimal irrigation. Variables were assigned to four groups describing productivity (above-ground biomass, total leaf area), leaf growth (total number of leaves increment rate), leaf structure (area of the largest leaf, specific leaf area, carbon and nitrogen contents), and carbon isotope discrimination in the leaves (Delta). High-yielding clones displayed larger total leaf area and individual leaf area, while no correlation could be detected between productivity and either leaf structure or Delta. By contrast, Delta was negatively correlated with number of leaves increment rate and leaf N content. Our study shows that there is a potential to improve water-use efficiency in poplar without necessarily reducing the overall productivity.