RNAseq based variant dataset in a black poplar association panel.

OBJECTIVE: Black poplar (Populus nigra L.) is a species native to Eurasia with a wide distribution area. It is an ecologically important species from riparian ecosystems, that is used as a parent of interspecific (P. deltoides x P. nigra) cultivated poplar hybrids. Variant detection from transcriptomics sequences of 241 P. nigra individuals, sampled in natural populations from 11 river catchments (in four European countries) is described here. These data provide new valuable resources for population structure analysis, population genomics and genome-wide association studies. DATA DESCRIPTION: We generated transcriptomics data from a mixture of young differentiating xylem and cambium tissues of 480 Populus nigra trees sampled in a common garden experiment located at Orléans (France), corresponding to 241 genotypes (2 clonal replicates per genotype, at maximum) by using RNAseq technology. We launched on the resulting sequences an in-silico pipeline that allowed us to obtain 878,957 biallelic polymorphisms without missing data. More than 99% of these positions are annotated and 98.8% are located on the 19 chromosomes of the P. trichocarpa reference genome. The raw RNAseq sequences are available at the NCBI Sequence Read Archive SPR188754 and the variant dataset at the Recherche Data Gouv repository under https://doi.org/10.15454/8DQXK5 .

Use of near-infrared spectroscopy to estimate physical, anatomical and hydraulic properties of Eucalyptus wood.

Tree breeding programs and wood industries require simple, time- and cost-effective techniques to process large volumes of samples. In recent decades, near-infrared spectroscopy (NIRS) has been acknowledged as one of the most powerful techniques for wood analysis, making it the most used tool for high-throughput phenotyping. Previous studies have shown that a significant number of anatomical, physical, chemical and mechanical wood properties can be estimated through NIRS, both for angiosperm and gymnosperm species. However, the ability of this technique to predict functional traits related to drought resistance has been poorly explored, especially in angiosperm species. This is particularly relevant since determining xylem hydraulic properties by conventional techniques is complex and time-consuming, clearly limiting its use in studies and applications that demand large amounts of samples. In this study, we measured several wood anatomical and hydraulic traits and collected NIR spectra in branches of two Eucalyptus L'Hér species. We developed NIRS calibration models and discussed their ability to accurately predict the studied traits. The models generated allowed us to adequately calibrate the reference traits, with high R2 (≥0.75) for traits such as P12, P88, the slope of the vulnerability curves to xylem embolism or the fiber wall fraction, and with lower R2 (0.39-0.52) for P50, maximum hydraulic conductivity or frequency of ray parenchyma. We found that certain wavenumbers improve models' calibration, with those in the range of 4000-5500 cm-1 predicting the highest number of both anatomical and functional traits. We concluded that the use of NIRS allows calibrating models with potential predictive value not only for wood structural and chemical variables but also for anatomical and functional traits related to drought resistance in wood types with complex structure as eucalypts. These results are promising in light of the required knowledge about species and genotypes adaptability to global climatic change.

Author Correction: The GenTree Dendroecological Collection, tree-ring and wood density data from seven tree species across Europe.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

The GenTree Dendroecological Collection, tree-ring and wood density data from seven tree species across Europe.

The dataset presented here was collected by the GenTree project (EU-Horizon 2020), which aims to improve the use of forest genetic resources across Europe by better understanding how trees adapt to their local environment. This dataset of individual tree-core characteristics including ring-width series and whole-core wood density was collected for seven ecologically and economically important European tree species: silver birch (Betula pendula), European beech (Fagus sylvatica), Norway spruce (Picea abies), European black poplar (Populus nigra), maritime pine (Pinus pinaster), Scots pine (Pinus sylvestris), and sessile oak (Quercus petraea). Tree-ring width measurements were obtained from 3600 trees in 142 populations and whole-core wood density was measured for 3098 trees in 125 populations. This dataset covers most of the geographical and climatic range occupied by the selected species. The potential use of it will be highly valuable for assessing ecological and evolutionary responses to environmental conditions as well as for model development and parameterization, to predict adaptability under climate change scenarios.

Phenomic Selection Is a Low-Cost and High-Throughput Method Based on Indirect Predictions: Proof of Concept on Wheat and Poplar.

Genomic selection - the prediction of breeding values using DNA polymorphisms - is a disruptive method that has widely been adopted by animal and plant breeders to increase productivity. It was recently shown that other sources of molecular variations such as those resulting from transcripts or metabolites could be used to accurately predict complex traits. These endophenotypes have the advantage of capturing the expressed genotypes and consequently the complex regulatory networks that occur in the different layers between the genome and the phenotype. However, obtaining such omics data at very large scales, such as those typically experienced in breeding, remains challenging. As an alternative, we proposed using near-infrared spectroscopy (NIRS) as a high-throughput, low cost and non-destructive tool to indirectly capture endophenotypic variants and compute relationship matrices for predicting complex traits, and coined this new approach "phenomic selection" (PS). We tested PS on two species of economic interest (Triticum aestivum L. and Populus nigra L.) using NIRS on various tissues (grains, leaves, wood). We showed that one could reach predictions as accurate as with molecular markers, for developmental, tolerance and productivity traits, even in environments radically different from the one in which NIRS were collected. Our work constitutes a proof of concept and provides new perspectives for the breeding community, as PS is theoretically applicable to any organism at low cost and does not require any molecular information.

Saccharification Performances of Miscanthus at the Pilot and Miniaturized Assay Scales: Genotype and Year Variabilities According to the Biomass Composition.

HIGHLIGHTS Biomass production and cell wall composition are differentially impacted by harvesting year and genotypes, influencing then cellulose conversion in miniaturized assay.Using a high-throughput miniaturized and semi-automated method for performing the pretreatment and saccharification steps at laboratory scale allows for the assessment of these factors on the biomass potential for producing bioethanol before moving to the industrial scale. The large genetic diversity of the perennial grass miscanthus makes it suitable for producing cellulosic ethanol in biorefineries. The saccharification potential and year variability of five genotypes belonging to Miscanthus × giganteus and Miscanthus sinensis were explored using a miniaturized and semi-automated method, allowing the application of a hot water treatment followed by an enzymatic hydrolysis. The studied genotypes highlighted distinct cellulose conversion yields due to their distinct cell wall compositions. An inter-year comparison revealed significant variations in the biomass productivity and cell wall compositions. Compared to the recalcitrant genotypes, more digestible genotypes contained higher amounts of hemicellulosic carbohydrates and lower amounts of cellulose and lignin. In contrast to hemicellulosic carbohydrates, the relationships analysis between the biomass traits and cellulose conversion clearly showed the same negative effect of cellulose and lignin on cellulose digestion. The miniaturized and semi-automated method we developed was usable at the laboratory scale and was reliable for mimicking the saccharification at the pilot scale using a steam explosion pretreatment and enzymatic hydrolysis. Therefore, this miniaturized method will allow the reliable screening of many genotypes for saccharification potential. These findings provide valuable information and tools for breeders to create genotypes combining high yield, suitable biomass composition, and high saccharification yields.

Effect of light conditions on anatomical and biochemical aspects of somatic and zygotic embryos of hybrid larch (Larix × marschlinsii).

BACKGROUND AND AIMS: In conifers, mature somatic embryos and zygotic embryos appear to resemble one another physiologically and morphologically. However, phenotypes of cloned conifer embryos can be strongly influenced by a number of in vitro factors and in some instances clonal variation can exceed that found in nature. This study examines whether zygotic embryos that develop within light-opaque cones differ from somatic embryos developing in dark/light conditions in vitro. Embryogenesis in larch is well understood both in situ and in vitro and thus provides a suitable system for addressing this question. METHODS: Features of somatic and zygotic embryos of hybrid larch, Larix × marschlinsii, were quantified, including cotyledon numbers, protein concentration and phenol chemistry. Somatic embryos were placed either in light or darkness for the entire maturation period. Embryos at different developmental stages were embedded and sectioned for histological analysis. KEY RESULTS: Light, and to a lesser degree abscisic acid (ABA), influenced accumulation of protein and phenolic compounds in somatic and zygotic embryos. Dark-grown mature somatic embryos had more protein (91·77 ± 11·26 µg protein mg(-1) f.wt) than either dark-grown zygotic embryos (62·40 ± 5·58) or light-grown somatic embryos (58·15 ± 10·02). Zygotic embryos never accumulated phenolic compounds at any stage, whereas somatic embryos stored phenolic compounds in the embryonal root caps and suspensors. Light induced the production of quercetrin (261·13 ± 9·2 µg g(-1) d.wt) in somatic embryos. Mature zygotic embryos that were removed from seeds and placed on medium in light rapidly accumulated phenolics in the embryonal root cap and hypocotyl. Delaying germination with ABA delayed phenolic compound accumulation, restricting it to the embryonal root cap. CONCLUSIONS: In larch embryos, light has a negative effect on protein accumulation, but a positive effect on phenol accumulation. Light did not affect morphogenesis, e.g. cotyledon number. Somatic embryos produced different amounts of phenolics, such as quercetrin, depending on light conditions. The greatest difference was seen in the embryonal root cap in all embryo types and conditions.

Comprehensive genetic dissection of wood properties in a widely-grown tropical tree: Eucalyptus.

BACKGROUND: Eucalyptus is an important genus in industrial plantations throughout the world and is grown for use as timber, pulp, paper and charcoal. Several breeding programmes have been launched worldwide to concomitantly improve growth performance and wood properties (WPs). In this study, an interspecific cross between Eucalyptus urophylla and E. grandis was used to identify major genomic regions (Quantitative Trait Loci, QTL) controlling the variability of WPs. RESULTS: Linkage maps were generated for both parent species. A total of 117 QTLs were detected for a series of wood and end-use related traits, including chemical, technological, physical, mechanical and anatomical properties. The QTLs were mainly clustered into five linkage groups. In terms of distribution of QTL effects, our result agrees with the typical L-shape reported in most QTL studies, i.e. most WP QTLs had limited effects and only a few (13) had major effects (phenotypic variance explained > 15%). The co-locations of QTLs for different WPs as well as QTLs and candidate genes are discussed in terms of phenotypic correlations between traits, and of the function of the candidate genes. The major wood property QTL harbours a gene encoding a Cinnamoyl CoA reductase (CCR), a structural enzyme of the monolignol-specific biosynthesis pathway. CONCLUSIONS: Given the number of traits analysed, this study provides a comprehensive understanding of the genetic architecture of wood properties in this Eucalyptus full-sib pedigree. At the dawn of Eucalyptus genome sequence, it will provide a framework to identify the nature of genes underlying these important quantitative traits.

Durability of five native Argentine wood species of the genera Prosopis and Acacia decayed by rot fungi and its relationship with extractive content.

The natural durability of four Argentinean species of Prosopis and one of Acacia was evaluated in laboratory tests, according to European standards, using three brown rot and one white rot fungi. These tests were complemented by assessing the wood chemical composition. All the species were from moderately slightly durable to very durable (classes 4-1), and in all cases the heartwood was the most resistant to fungal attack. Chemical extractives content (organic, aqueous, tannic and phenolic) was higher in the heartwood. However, species durability was not related to extractive contents nor with wood density. Instead, it is possible that extractives could contribute to natural durability in different ways, including the effects related to the antioxidant properties of some of them.

Expression of genes encoding chalcone synthase, flavanone 3-hydroxylase and dihydroflavonol 4-reductase correlates with flavanol accumulation during heartwood formation in Juglans nigra.

Heartwood formation is generally characterized by the accumulation of phenolic substances that increase the natural color and durability of wood. Although there is evidence that these substances are synthesized in aging sapwood cells, little is known about heartwood formation at the molecular level. We monitored seasonal changes in flavanol concentration across the stems of 23-year-old Juglans nigra L. trees by sampling growth rings extending from the differentiating xylem to the heartwood. We also analyzed expression of phenylpropanoid and flavonoid structural genes in these samples. In the sapwood-heartwood transition zone, flavanol accumulation was correlated with the transcription levels of the chalcone synthase (CHS) and flavanone 3-hydroxylase (F3H) genes. We also observed correlations between flavanol accumulation and the amount of dihydroflavonol 4-reductase (DFR) gene transcript in October, January and May. Although transcription of phenylalanine ammonia-lyase (PAL) and 4-coumarate:CoA ligase (4CL) genes did not correlate with flavanol accumulation, PAL genes were strongly expressed in the transition zone of samples collected in autumn, suggesting that their transcription in these tissues contributes to phenolic biosynthesis. Western immunoblotting showed that accumulation of CHS protein correlated with the amount of CHS gene transcript, whereas accumulation of PAL protein did not correlate with the the transcription levels PAL genes. Preliminary analyses revealed that PAL and CHS activities were higher in the transition zone than in the inner sapwood in autumn, winter, and spring. Thus, CHS activity could be regulated mainly at the transcriptional level, whereas post-translational modifications could modulate PAL activity. We conclude that flavanols are synthesized de novo in J. nigra sapwood cells that are undergoing transformation to heartwood.

Cuttings of the non-rooting rac tobacco mutant overaccumulate phenolic compounds.

The auxin and phenolic contents, as well as phenylalanine ammonia-lyase (PAL) activity, were determined in in vitro cultured shoots of the recalcitrant-to-root rac mutant of tobacco, and compared with wild-type shoots. The mutant and wild-type shoots showed similar auxin changes during the culture cycle, but with higher contents for the mutant. A transient peak of auxin (corresponding to the achievement of the rooting inductive phase) occurred at day 14 in both types of shoots, but earlier in the basal parts of the wild-type stems. The rac shoots contained more phenolics, corresponding with an increased PAL activity. The most abundant phenolic compound found in the two types of tobacco was chlorogenic acid, which was more abundant in the rac shoots. Rutin was also detected at a higher concentration in the mutant shoots. Basal parts of wild-type shoots treated with 10-3 M chlorogenic acid reacted by accumulating auxins and, unlike untreated controls, did not form adventitious roots. The relationships between these biochemical analyses in relation to the growth limitation of the rac mutant, and the inhibition of its root development, are discussed.