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.

Expression analysis of LIM gene family in poplar, toward an updated phylogenetic classification.

BACKGROUND: Plant LIM domain proteins may act as transcriptional activators of lignin biosynthesis and/or as actin binding and bundling proteins. Plant LIM genes have evolved in phylogenetic subgroups differing in their expression profiles: in the whole plant or specifically in pollen. However, several poplar PtLIM genes belong to uncharacterized monophyletic subgroups and the expression patterns of the LIM gene family in a woody plant have not been studied. FINDINGS: In this work, the expression pattern of the twelve duplicated poplar PtLIM genes has been investigated by semi quantitative RT-PCR in different vegetative and reproductive tissues. As in other plant species, poplar PtLIM genes were widely expressed in the tree or in particular tissues. Especially, PtXLIM1a, PtXLIM1b and PtWLIM1b genes were preferentially expressed in the secondary xylem, suggesting a specific function in wood formation. Moreover, the expression of these genes and of the PtPLIM2a gene was increased in tension wood. Western-blot analysis confirmed the preferential expression of PtXLIM1a protein during xylem differentiation and tension wood formation. Genes classified within the pollen specific PLIM2 and PLIM2-like subgroups were all strongly expressed in pollen but also in cottony hairs. Interestingly, pairs of duplicated PtLIM genes exhibited different expression patterns indicating subfunctionalisations in specific tissues. CONCLUSIONS: The strong expression of several LIM genes in cottony hairs and germinating pollen, as well as in xylem fibers suggests an involvement of plant LIM domain proteins in the control of cell expansion. Comparisons of expression profiles of poplar LIM genes with the published functions of closely related plant LIM genes suggest conserved functions in the areas of lignin biosynthesis, pollen tube growth and mechanical stress response. Based on these results, we propose a novel nomenclature of poplar LIM domain proteins.

Variations in bulk leaf carbon isotope discrimination, growth and related leaf traits among three Populus nigra L. populations.

The ongoing global change could be an additional threat to the establishment and the long-term survival of Populus nigra L., an emblematic European riparian species. With the general aim of gaining insights into the adaptive potential of this species, we (i) quantified variations within and among three French P. nigra populations for key physiological attributes, i.e., water-use efficiency (assessed from bulk leaf carbon isotope discrimination, Δ(13)C), growth performance and related leaf traits, (ii) examined genotype and population by environment interactions, and (iii) explored the relationship between Δ(13)C and growth. Thirty genotypes were sampled in each of three naturally established populations and grown in two different sites, Orléans (ORL) and Guémené-Penfao (GMN). In ORL, two similar plots were established and different watering regimes were applied in order to test for the drought response. Significant variations were observed for all traits within and among populations irrespective of site and watering. Trait variation was larger within than among populations. The effect of drought was neither genotype- nor population-dependent, contrary to the effect of site. The population ranking was maintained in all sites and watering regimes for the two most complex traits: Δ(13)C and growth. Moreover, these two traits were unrelated, which indicates that (i) water-use efficiency and growth are largely uncoupled in this species, and (ii) the environmental factors driving genetic structuration for Δ(13)C and growth act independently. The large variations found within populations combined with the consistent differences among populations suggest a large adaptive potential for P. nigra.

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.

Diversity of leaf traits related to productivity in 31 Populus deltoides x Populus nigra clones.

To test if some leaf parameters are predictors of productivity in a range of Populus deltoides (Bartr.) Marsh. x P. nigra L. clones, we assessed leaf traits and productivity in 2-month-old rooted cuttings from 31 clones growing in 4-l pots in a greenhouse, under conditions of controlled temperature and optimal irrigation. We evaluated four groups of variables describing (1) productivity (total biomass), (2) leaf growth (total leaf number increment and total leaf area increment rate), (3) leaf structure (specific leaf area and nitrogen and carbon contents) and (4) carbon isotope discrimination (delta), which is negatively correlated with time-integrated water-use efficiency. High-yielding clones did not necessarily display high leaf growth rates, but they displayed a larger total leaf area, lower specific leaf area and lower leaf nitrogen concentration than clones with low productivity. Total leaf area was mainly controlled by maximal individual leaf area and total leaf area increment rate (r = 0.51 and 0.56, respectively). Carbon isotope discrimination did not correlate with total biomass, but it was associated with total number of leaves and total leaf area increment rate (r = 0.39 and 0.45, respectively). Therefore, leaf area and specific leaf area were better indicators of productivity than leaf growth traits. The observed independence of delta from biomass production provides opportunities for selecting poplar clones combining high productivity and high water-use efficiency.