Single-cell analysis resolves the genetic program of primary vascular system formation in hybrid poplar

Despite the enormous potential of novel approaches to explore gene expression at a single-cell level, we lack a high-resolution and cell type-specific gene expression map of the shoot apex in woody perennials. We use single-nuclei RNA sequencing to determine the cell type-specific transcriptome of the Populus vegetative shoot apex. We identified highly heterogeneous cell populations clustered into seven broad groups represented by 18 transcriptionally distinct cell clusters. Next, we established the developmental trajectories of epidermal cells, leaf mesophyll, and vascular tissue. Motivated by the high similarities between Populus and Arabidopsis cell population in the vegetative apex, we created and applied a pipeline for interspecific single-cell expression data integration. We contrasted the developmental trajectories of primary phloem and xylem formation in both species, establishing the first comparison of primary vascular development between a model annual herbaceous and a woody perennial plant species. Our results offer a valuable resource for investigating the basic principles underlying cell division and differentiation conserved between herbaceous and perennial species, which also allows the evaluation of the divergencies at single-cell resolution.

Mögliche künftige Trends der Lufttemperatur und des Blattaustriebs der Schwarzerle (Alnus glutinosa) in Deutschland

<p>Eine direkte Auswirkung des rezenten Klimawandels auf die Vegetation ist die Verfrühung phänologischer Stadien, besonders im Frühjahr (WALDAU & CHMIELEWSKI, 2018; CHMIELEWSKI et al., 2004; WOLFE et al., 2005). Diese Trends wurden weltweit beobachtet und sind hauptsächlich auf den Anstieg der Lufttemperatur zurückzuführen, was den engen Zusammenhang zwischen Pflanzenentwicklung und Temperatur belegt. Dieser stetige Temperaturanstieg wird sich in Zukunft fortsetzen und zu zeitlichen und räumlichen Verschiebungen in der Vegetationsentwicklung führen. Um diese Veränderungen abschätzen zu können, sind plausible phänologische Modelle erforderlich, wobei das Kältebedürfnis, das für die Überwindung der Dormanz erforderlich ist, hierbei eine der Schlüsselgrößen ist. <br />Ziel dieser Studie war es die zukünftigen Auswirkungen des Klimawandels auf die natürliche Vegetation in Deutschland abzuschätzen. In einer dreijährigen Studie (Winter 2015/16 – 2017/18) wurde der Zeitpunkt der Dormanzbrechung für verschiedene Baumarten experimentell in Klimakammerversuchen bestimmt. Im Rahmen dieses Vortrages sollen die Ergebnisse für die Schwarzerle (Alnus glutinosa) dargestellt werden. Nach der Ermittlung des für den Blattaustrieb der Schwarzerle notwendigen Kältereizes wurde ein Chilling/Forcing Modell parametrisiert und anschließend an den phänologischen Beobachtungdaten des Deutschen Wetterdienstes (1951-2015) validiert. Für die Abschätzung der künftigen klimatischen Entwicklung wurde ein Klimaensemble aus sieben verschieden Klimamodellrechnungen für zwei Klimaszenarien (RCP 2.6 & 8.5) verwendet. Für den Zeitraum 2010-2100 werden neben den zeitlichen Trends der Lufttemperatur und der Phänologie zusätzlich die regionalen Unterschiede in Deutschland (Nord-Ost/Nord-West/Süd-Ost/Süd-West) aufgezeigt.</p> <p> </p> <p>Literatur:</p> <p>CHMIELEWSKI, F. M., MÜLLER, A. & BRUNS, E. (2004): Climate changes and trends in phenology of fruit trees and field crops in Germany, 1961–2000. Agricultural and Forest Meteorology 121 (1), 69-DOI: https://doi.org/10.1016/S0168-1923(03)00161-8.</p> <p>WALDAU, T. & CHMIELEWSKI, F. M. (2018): Spatial and temporal changes of spring temperature, thermal growing season and spring phenology in Germany 1951–2015. Meteorol. Z. 27 (4), 335-342.DOI: https://doi.org/10.1127/metz/2018/0923.</p> <p>WOLFE, D. W., SCHWARTZ, M. D., LAKSO, A. N., OTSUKI, Y., POOL, R. M. & SHAULIS, N. J. (2005): Climate change and shifts in spring phenology of three horticultural woody perennials in northeastern USA. International Journal of Biometeorology 49 (5), 303-309. DOI: https://doi.org/10.1007/s00484-004-0248-9.</p>

Microtensiometers Accurately Measure Stem Water Potential in Woody Perennials

Stem water potential (Ψstem) is considered to be the standard measure of plant water status. However, it is measured with the pressure chamber (PC), an equipment that can neither provide continuous information nor be automated, limiting its use. Recent developments of microtensiometers (MT; FloraPulse sensors), which can continuously measure water tension in woody tissue of the trunk of the tree, can potentially highlight the dynamic nature of plant water relations. Thus, this study aimed to validate and assess the usefulness of the MT by comparing the Ψstem provided by MT with those same measurements from the PC. Here, two irrigation treatments (a control and a deficit treatment) were applied in a pear (Pyrus communis L.) orchard in Washington State (USA) to capture the full range of water potentials in this environment. Discrete measurements of leaf gas exchange, canopy temperature and Ψstem measured with PC and MT were made every two hours for four days from dawn to sunset. There were strong linear relationships between the Ψstem-MT and Ψstem-PC (R2 > 0.8) and with vapor pressure deficit (R2 > 0.7). However, Ψstem-MT was more variable and lower than Ψstem-PC when Ψstem-MT was below −1.5 MPa, especially during the evening. Minimum Ψstem-MT occurred later in the afternoon compared to Ψstem-PC. Ψstem showed similar sensitivity and coefficients of variation for both PC and MT acquired data. Overall, the promising results achieved indicated the potential for MT to be used to continuously assess tree water status.

Putative biotic drivers of plant phenology :with special reference to pathogens and deciduousness

Plant phenology is manifested in the seasonal timing of vegetative and reproductive processes, but also has ontogenetic aspects. The adaptive basis of seasonal phenology has been considered mainly in terms of climatic drivers. However, some biotic factors as likely evolutionary influences on plants’ phenology appear to have been under-researched. Several specific cases of putative biotic factors driving plant phenology are outlined, involving both herbivores and pathogens. These illustrate the diversity of likely interactions rather than any systematic coverage or review. Emphasis is on woody perennials, in which phenology is often most multi-faceted and complicated by the ontogenetic aspect. The complete seasonal leaf fall that characterises deciduous plants may be a very important defence against some pathogens. Whether biotic influences drive acquisition or long-term persistence of deciduousness is considered. In one case; of leaf rusts in poplars, countervailing influences of the rusts and climate suggest persistence. Often, however, biotic and environmental influences likely reinforce each other. The timing and duration of shoot flushing may in at least some cases contribute to defences against herbivores, largely through brief periods of ‘predator satiation’ when plant tissues have highest food value. Wide re-examination of plant phenology, accommodating the roles of biotic factors and their interplays with environments as additional adaptive drivers, is advocated, towards developing and applying hypotheses that are observationally or experimentally testable.

New Technologies and Strategies for Grapevine Breeding Through Genetic Transformation

Grapevine, as other woody perennials, has been considered a recalcitrant crop to produce transgenic plants. Since the production of transgenic and/or edited plants requires the ability to regenerate plants from transformed tissues, this step is often the biggest bottleneck in the process. The objective of this work is to review the state of the art technologies and strategies for the improvement of grapevine transformation and regeneration, focusing on three aspects: (i) problems associated with grapevine transformation; (ii) genes that promote grapevine regeneration; and (iii) vehicles for gene delivery. Concerning the first aspect, it is well documented that one of the main factors explaining the low success rate in obtaining transgenic plants is the regeneration process. After transgenic integration into receptor cells, tissue culture is required to regenerate transgenic seedlings from transformed cells. This process is time consuming and often requires the addition of environmentally damaging reagents (antibiotics and herbicides) to the culture medium to select transgenic plants. On the other hand, the expression of genes such as the so-called developmental regulators (DR), which induce specific development programs, can be used to avoid traditional tissue culture methods. The ectopic expression of specific combinations of DR in somatic cells has the potential to induce de novo meristems in diverse crops, including grapevine. Successful genome editing by de novo reprogramming of plant meristems in somatic tissues has been reported. Moreover, it has been shown that the expression of certain transcription factors can increase the regeneration efficiency in wheat, citrus, and rice. Finally, recent reports showed the use of nanoparticles, such as carbon dots (CDs), as an attractive alternative to Agrobacterium- and biolistic-mediated plant genetic transformation. In this way, the use of antibiotics in culture media is avoided, overcoming the loss of viability of plant tissues and accelerating the regeneration processes. It has been shown that CDs can act as a vehicle to transport plasmids to plant cells in transient transformation in several crops without negative impacts on photosynthesis or growth. Based on these advances, it is possible to combine these new available strategies and technologies to overcome the regeneration problems of species such as grapevine and other crops considered as recalcitrant.

Virtual pruning of 3D trees as a tool for managing shading effects in agroforestry systems

Light is a limiting resource for crops within integrated land use systems especially those including woody perennials. The amount of available light at ground level can be modified by artificially pruning the overstory. Aiming to increase the understanding of light management strategies, we simulated the pruning of wild cherry trees and compared the shading effects of the resulting tree structures over a complete growing season, with fine spatiotemporal resolution. Original 3D-tree structures were retrieved employing terrestrial laser scanning and quantitative structure models, and subjected to two pruning treatments at low and high intensities. By using the ‘shadow model’, the analogous tree structures created diverse shaded scenarios varying in size and intensity of insolation reduction. Conventional pruning treatments reduced the crown structure to the uppermost portion of the tree bole, reducing the shading effects, and thus, shrinking the shaded area on the ground by up to 38%, together with the shading intensity. As an alternative, the selective removal of branches reduced the shading effects, while keeping a more similar spatial distribution compared to the unpruned tree. Hence, the virtual pruning of tree structures can support designing and selecting adequate tending operations for the management of light distribution in agroforestry systems. The evidence assembled in this study is highly relevant for agroecosystems and can be strategically used for maintaining, planning and designing integrated tree-crop agricultural systems.

Changes in Reactive Oxygen Species, Antioxidants and Carbohydrate Metabolism in Relation to Dormancy Transition and Bud Break in Apple (Malus × domestica Borkh) Cultivars

Understanding the biochemical mechanisms underlying bud dormancy and bloom time regulation in deciduous woody perennials is critical for devising effective strategies to protect these species from spring frost damage. This study investigated the accumulation profiles of carbohydrates, ROS and antioxidants during dormancy in ‘Cripps Pink’ and ‘Honeycrisp’, two apple cultivars representing the early and late bloom cultivars, respectively. Our data showed that starch levels generally declined during dormancy, whereas soluble sugars increased. However, the present study did not record significant alternations in the carbohydrate accumulation profiles between the two cultivars that could account for the differences in their bloom dates. On the other hand, H2O2 accumulation patterns revealed an apparent correlation with the dormancy stage and bloom dates in both cultivars; peaking early in the early-blooming cultivar, sustaining high levels for a longer time in the late-blooming cultivars, and fading by the time of bud burst in both cultivars. Also, the redox balance during dormancy appeared to be maintained mainly by catalase and, to a lesser extent, by glutathione (GSH). Overall, the present study concludes that differences in ROS and the bud redox balance could, at least partially, explain the differences in dormancy duration and bloom date among apple cultivars.

The Siberian wild apple, Malus baccata (L.) Borkh., is an additional contributor to the genomes of cultivated European and Chinese apples

It is crucial to understand domestication to unravel the evolutionary processes that shape the divergence of populations. Differences in life-history traits have probably led to marked differences in the mode and speed of evolution between trees and annuals, particularly the extent of crop-wild gene flow during domestication. Apple is an iconic tree and major fruit crop grown worldwide. The contribution of wild apple species to the genetic makeup of the cultivated apple genome remains a topic of intense investigations. We used population genomics in combination with SNPs to investigate the contributions of the two known wild apple relatives, Malus sylvestris and Malus sieversii, and a supposed contributor, Malus baccata, to European and Chinese rootstock and dessert genomes, with a focus on the extent of wild-crop gene flow during apple domestication. We showed that the European dessert and rootstock apples form a specific gene pool, whereas the Chinese dessert and rootstock apples were a mixture of three wild gene pools. Coalescent-based inferences and gene flow estimates indicated that M. baccata is an additional contributor to the genome of both European and Chinese cultivated apples through wild-to-crop introgressions. We also confirmed previous results on the contribution of M. sylvestris to the cultivated apple genome, and provided insights into the origin of the apple rootstock. This study further demonstrates the role of gene flow during apple domestication, as seen in other woody perennials, and show that domestication of the apple tree involved several wild apple species.

Efficiency of graft-transmitted JcFT for floral induction in woody perennial species of the Jatropha genus depends on transport distance

Flowering Locus T (FT) promotes flowering by integrating six genetic pathways. In Arabidopsis, the FT protein is transported from leaves to shoot apices and induces flowering. However, contradictory conclusions about floral induction via graft-transmitted FT in trees were reported in previous studies. We obtained extremely early-flowering transgenic woody Jatropha curcas by overexpression of J. curcas FT using Arabidopsis thaliana SUC2 promoter (SUC2:JcFT) and non-flowering transgenic J. curcas by RNA interference (RNAi), which were used to investigate the function of graft-transmitted JcFT in floral induction in woody perennials. Scions from five wild-type species of the Jatropha genus and from JcFT-RNAi transgenic J. curcas were grafted onto SUC2:JcFT rootstocks. Most grafted plants produced flowers in 1–2 months, and the flowering percentage and frequency of various grafted plants decreased with increasing scion length. Consistently, FT protein abundance in scions also decreased with increasing distance from graft junctions to the buds. These findings suggest that FT proteins can be transmitted by grafting and can induce the floral transition in woody perennials, and the efficiency of graft-transmitted JcFT for floral induction depends on the scion length, which may help explain previous seemingly contradictory observations regarding floral induction via graft-transmitted FT in trees.

Integrating Genome-Wide Association Analysis With Transcriptome Sequencing to Identify Candidate Genes Related to Blooming Time in Prunus mume

Prunus mume is one of the most important woody perennials for edible and ornamental use. Despite a substantial variation in the flowering phenology among the P. mume germplasm resources, the genetic control for flowering time remains to be elucidated. In this study, we examined five blooming time-related traits of 235 P. mume landraces for 2 years. Based on the phenotypic data, we performed genome-wide association studies, which included a combination of marker- and gene-based association tests, and identified 1,445 candidate genes that are consistently linked with flowering time across multiple years. Furthermore, we assessed the global transcriptome change of floral buds from the two P. mume cultivars exhibiting contrasting bloom dates and detected 617 associated genes that were differentially expressed during the flowering process. By integrating a co-expression network analysis, we screened out 191 gene candidates of conserved transcriptional pattern during blooming across cultivars. Finally, we validated the temporal expression profiles of these candidates and highlighted their putative roles in regulating floral bud break and blooming time in P. mume. Our findings are important to expand the understanding of flowering time control in woody perennials and will boost the molecular breeding of novel varieties in P. mume.