A draft genome of sweet cherry (Prunus avium L.) reveals genome‐wide and local effects of domestication

Sweet cherry (Prunus avium L.) trees are both economically important fruit crops but also important components of natural forest ecosystems in Europe, Asia and Africa. Wild and domesticated trees currently coexist in the same geographic areas with important questions arising on their historical relationships. Little is known about the effects of the domestication process on the evolution of the sweet cherry genome. We assembled and annotated the genome of the cultivated variety “Big Star*” and assessed the genetic diversity among 97 sweet cherry accessions representing three different stages in the domestication and breeding process (wild trees, landraces and modern varieties). The genetic diversity analysis revealed significant genome‐wide losses of variation among the three stages and supports a clear distinction between wild and domesticated trees, with only limited gene flow being detected between wild trees and domesticated landraces. We identified 11 domestication sweeps and five breeding sweeps covering, respectively, 11.0 and 2.4 Mb of the P. avium genome. A considerable fraction of the domestication sweeps overlaps with those detected in the related species, Prunus persica (peach), indicating that artificial selection during domestication may have acted independently on the same regions and genes in the two species. We detected 104 candidate genes in sweep regions involved in different processes, such as the determination of fruit texture, the regulation of flowering and fruit ripening and the resistance to pathogens. The signatures of selection identified will enable future evolutionary studies and provide a valuable resource for genetic improvement and conservation programs in sweet cherry.     

A rangewide herbarium‐derived dataset indicates high levels of gene flow in black cherry (Prunus serotina)

Isolation by Distance (IBD) is a genetic pattern in which populations geographically closer to one another are more genetically similar to each other than populations which are farther apart. Black cherry (Prunus serotina Ehrh.) (Rosaceae) is a forest tree species widespread in eastern North America, and found sporadically in the southwestern United States, Mexico, and Guatemala. IBD has been studied in relatively few North American plant taxa, and no study has rigorously sampled across the range of such a widespread species. In this study, IBD and overall genetic structure were assessed in eastern black cherry (P. serotina Ehrh. var. serotina), the widespread variety of eastern North America. Eastern North America. Prunus serotina Ehrh. var. serotina (Rosaceae). Dense sampling across the entire range of eastern black cherry was made possible by genotyping 15 microsatellite loci in 439 herbarium samples from all portions of the range. Mantel tests and STRUCTURE analyses were performed to evaluate the hypothesis of IBD and genetic structure. Mantel tests demonstrated significant but weak IBD, while STRUCTURE analyses revealed no clear geographic pattern of genetic groups. The modest geographic/genetic structure across the eastern black cherry range suggests widespread gene flow in this taxon. This is consistent with P. serotina's status as a disturbance‐associated species. Further studies should similarly evaluate IBD in species characteristic of low‐disturbance forests.     

Clarifying springtime temperature reconstructions of the medieval period by gap-filling the cherry blossom phenological data series at Kyoto, Japan

We investigated documents and diaries from the ninth to the fourteenth centuries to supplement the phenological data series of the flowering of Japanese cherry (Prunus jamasakura) in Kyoto, Japan, to improve and fill gaps in temperature estimates based on previously reported phenological data. We then reconstructed a nearly continuous series of March mean temperatures based on 224 years of cherry flowering data, including 51 years of previously unused data, to clarify springtime climate changes. We also attempted to estimate cherry full-flowering dates from phenological records of other deciduous species, adding further data for 6 years in the tenth and eleventh centuries by using the flowering phenology of Japanese wisteria (Wisteria floribunda). The reconstructed tenth century March mean temperatures were around 7°C, indicating warmer conditions than at present. Temperatures then fell until the 1180s, recovered gradually until the 1310s, and then declined again in the mid-fourteenth century.     

Reproductive phenology of two Mimusops species in relation to climate,tree diameter and canopy position in Benin (West Africa)

Assessing species phenology provides useful understanding about their autecology, to contribute to management strategies. We monitored reproductive phenology of Mimusops andongensis and Mimusops kummel, and its relationship with climate, tree diameter and canopy position. We sampled trees in six diameter classes and noted their canopy position. For both species flowering began in the dry season through to the rainy season, but peaked in the dry season, whilst fruiting occurred in the rainy season and peaked during the most humid period. Flowering was positively correlated with temperature. Conversely, fruiting was negatively correlated with temperature and positively with rainfall, only in the Guineo‐Sudanian zone. For M. andongensis, flowering and fruiting prevalences were positively linked to stem diameter, while only flowering was significantly related to canopy position. For M. kummel, the relationship with stem diameter was significant for flowering prevalence only and in the Guineo‐Sudanian zone. Results suggest that phylogenetic membership is an important factor restricting Mimusops species phenology. Flowering and fruiting of both species are influenced by climate, and consequently climate change might shift their phenological patterns. Long‐term investigations, considering flowering and fruiting abortion, will help to better understand the species phenology and perhaps predict demographic dynamics.     

Phenological match drives pollen‐mediated gene flow in a temporally dimorphic tree

• Variation in flowering phenology is common in natural populations, and is expected to be, together with inter‐mate distance, an important driver of effective pollen dispersal. In populations composed of plants with temporally separated sexual phases (i.e. dichogamous or heterodichogamous populations), pollen‐mediated gene flow is assumed to reflect phenological overlap between complementary sexual phases. In this study, we conducted paternity analyses to test this hypothesis in the temporally dimorphic tree Acer opalus.
• We performed spatially explicit analyses based on categorical and fractional paternity assignment, and included tree size, pair‐wise genetic relatedness and morph type as additional predictors. Because differences between morphs in flowering phenology may also influence pollination distances, we modelled separate pollen dispersal kernels for the two morphs.
• Extended phenological overlap between male and female phases (mainly associated with inter‐morph crosses) resulted in higher siring success after accounting for the effects of genetic relatedness, morph type and tree size, while reduced phenological overlap (mainly associated with intra‐morph crosses) resulted in longer pollination distances achieved. Siring success also increased in larger trees.
• Mating patterns could not be predicted by phenology alone. However, as heterogeneity in flowering phenology was the single morph‐specific predictor of siring success, it is expected to be key in maintaining the temporal dimorphism in A. opalus, by promoting not only a prevalent pattern of inter‐morph mating, but also long‐distance pollination resulting from intra‐morph mating events.

     

Using remote sensing to model tree species distribution in Peruvian lowland Amazonia

Species distribution models for Amazonian trees have mostly been produced at scales and resolutions that are too broad and coarse for practical use in either conservation or forestry. On the other hand, several studies have shown that elevation and the medium‐resolution remote sensing data available via Landsat imagery can be successfully used to detect differences in plant species composition in Amazonia. Therefore, it seems likely that the same data can also be used to predict geographical distributions of individual taxa. Here we use remotely sensed data and a maximum entropy algorithm (MaxEnt) to generate landscape‐scale distribution models at 30‐m‐resolution for five economically important timber tree genera (Apuleia, Amburana, Crepidospermum, Dipteryx, and Manilkara). Individual Landsat Thematic Mapper bands and normalized difference vegetation index yielded acceptable model performance, and the use of averaging filters (3 × 3 and 5 × 5 pixel low‐pass filters) improved model performance further. Including elevation as a predictor also improved model performance for all the genera. Our results suggest that it is possible to use Landsat bands and elevation as predictors for modeling the potential distribution of tree species in lowland Amazonia at a fine enough resolution to facilitate the practical management of forest resources.     

“Candidatus Phytoplasma asteris” and “Candidatus Phytoplasma mali” strains infecting sweet and sour cherry in the Czech Republic

A survey for phytoplasma diseases was conducted in a sweet and sour cherry germplasm collection and in cherry orchards within the Czech Republic during 2014–2015. Phytoplasmas were detected in 21 symptomatic trees. Multiple infections of cherry trees by diverse phytoplasmas of 16SrI and 16SrX groups and 16SrI‐A, 16SrI‐B, 16SrI‐L, 16SrX‐A subgroups were detected by restriction fragment length polymorphism (RFLP). Nevertheless, phylogenetic analysis placed subgroups 16SrI‐B and 16SrI‐L inseparable together onto one branch of phylogenetic tree. This is the first report of subgroups 16SrI‐A and 16SrI‐L in Prunus spp., and subgroup 16SrX‐A in sour cherry trees. Additionally, novel RFLP profiles for 16SrI‐A and 16SrI‐B‐related phytoplasmas were found in cherry samples. Phytoplasmas with these novel profiles belong, however, to their respective 16SrI‐A or 16SrI‐B phylogenetic clades.     

Glacier melting and stoichiometric implications for lake community structure: zooplankton species distributions across a natural light gradient

Glaciers around the globe are melting rapidly, threatening the receiving environments of the world's fresh water reservoirs with significant changes. The meltwater, carried by rivers, contains large amounts of suspended sediment particles, producing longitudinal gradients in the receiving lakes. These gradients may result in changes in the light : nutrient ratio that affect grazer performance by altering elemental food quality. Thus, glacial melting may induce a shift in the phytoplankton carbon : nutrient ratio and hence influence the dominance of herbivorous zooplankton through stoichiometric mechanisms. To test this hypothesis, we combined field and experimental data, taking advantage of a natural light intensity gradient caused by glacial clay input in a deep oligotrophic Patagonian lake. Across this gradient, we evaluated the abundances of two consumer taxa with different phosphorus requirements, the copepod Boeckella gracilipes and the cladoceran Daphnia commutata, using a six‐station transect along the lake. We found significant differences in light : nutrient ratio and stoichiometric food quality of the seston, together with a switch from dominance of P‐rich Daphnia in low carbon : nutrient stations to dominance of low‐P copepods in high carbon : nutrient stations. The laboratory experiments confirmed that the difference in the carbon : nutrient ratio across the gradient is sufficient to impair Daphnia growth. The overall patterns are consistent with our prediction that shifts in the environmental light : nutrient ratio as a result of glacial melting would contribute to shifts in the dominance of stoichiometrically contrasting taxa in consumer guilds.     

Can phenological models predict tree phenology accurately in the future? The unrevealed hurdle of endodormancy break

The onset of the growing season of trees has been earlier by 2.3 days per decade during the last 40 years in temperate Europe because of global warming. The effect of temperature on plant phenology is, however, not linear because temperature has a dual effect on bud development. On one hand, low temperatures are necessary to break bud endodormancy, and, on the other hand, higher temperatures are necessary to promote bud cell growth afterward. Different process‐based models have been developed in the last decades to predict the date of budbreak of woody species. They predict that global warming should delay or compromise endodormancy break at the species equatorward range limits leading to a delay or even impossibility to flower or set new leaves. These models are classically parameterized with flowering or budbreak dates only, with no information on the endodormancy break date because this information is very scarce. Here, we evaluated the efficiency of a set of phenological models to accurately predict the endodormancy break dates of three fruit trees. Our results show that models calibrated solely with budbreak dates usually do not accurately predict the endodormancy break date. Providing endodormancy break date for the model parameterization results in much more accurate prediction of this latter, with, however, a higher error than that on budbreak dates. Most importantly, we show that models not calibrated with endodormancy break dates can generate large discrepancies in forecasted budbreak dates when using climate scenarios as compared to models calibrated with endodormancy break dates. This discrepancy increases with mean annual temperature and is therefore the strongest after 2050 in the southernmost regions. Our results claim for the urgent need of massive measurements of endodormancy break dates in forest and fruit trees to yield more robust projections of phenological changes in a near future.     

Commercial Yellow Sticky Strips more attractive than yellow boards to western cherry fruit fly (Dipt., Tephritidae)

Bright yellow sticky rectangles made of paper boards were previously identified as the most effective traps for capturing western cherry fruit fly, Rhagoletis indifferens Curran (Dipt., Tephritidae). However, no data on the effectiveness of commercial sticky yellow plastic traps against R. indifferens have been reported. In tests conducted in sweet cherry trees [Prunus avium (L.) L.] in Washington state (USA) using ammonium carbonate as the chemical lure, commercial plastic ‘Yellow Sticky Strips’ made of translucent high‐impact polystyrene captured ~two or three times more flies than commercial sticky yellow‐folded Pherocon^® AM and Alpha Scents boards. Yellow Sticky Strips also minimized captures of non‐target flies and bees per surface area compared with Pherocon^®AM and/or Alpha Scents boards. Trap size and adhesive type were not factors for greater catches of R. indifferens. However, more flies were caught on the shade‐facing side of Yellow Sticky Strips, which was brightly illuminated, than on the shade‐facing side of boards, which was darker, suggesting differential light passage was a factor. The Yellow Sticky Strips could be very useful for monitoring R. indifferens in detection programmes and based on the results of this study can replace yellow boards. They are also useful because they are relatively unattractive to non‐target insects.     

Association between blooming time and climatic adaptation in Prunus mume

Prunus mume Sieb. et Zucc. is an important fruit crop of the subtropical region, originating in China. It blooms earlier than other deciduous fruit trees, but different regions have different blooming periods. The time of anthesis is related to the dormancy period, and a certain amount of chilling promotes bud break and blooming. To identify the relationship between blooming time and the climatic adaptation of P. mume cultivars in China, the nuclear and chloroplast genomes of 19 cultivars from the main cultivation areas of P. mume in China were resequenced. The average depth of coverage was 34X–76X, and a total of 388,134 single nucleotide polymorphisms were located within the coding regions of the gene (CDs). Additionally, the 19 cultivar accessions were divided into three groups based on their blooming time: early, mid, and late. Associated with the blooming time groups, 21 selective sweep regions were identified, which could provide evidence supporting the possible model of P. mume domestication originating due to natural selection. Furthermore, we identified a flowering gene, FRIGIDA‐LIKE 3 (FRL3), seems to affect the blooming time and the climatic adaptation of P. mume cultivars. This study is a major step toward understanding the climatic adaptation of P. mume cultivars in China.     

Nitrogen as a key regulator of flowering in Fagus crenata: understanding the physiological mechanism of masting by gene expression analysis

The role of resource availability in determining the incidence of masting has been widely studied, but how floral transition and initiation are regulated by the resource level is unclear. We tested the hypothesis that floral transition is stimulated by high resource availabiltiy in Fagus crenata based on a new technique, the expression analyses of flowering genes. We isolated F. crenata orthologues of FLOWERING LOCUS T, LEAFY and APETALA1, and confirmed their functions using transgenic Arabidopsis thaliana. We monitored the gene expression levels for 5 years and detected a cycle of on and off years, which was correlated with fluctuations of the shoot‐nitrogen concentration. Nitrogen fertilisation resulted in the significantly higher expression of flowering genes than the control, where all of the fertilised trees flowered, whereas the control did not. Our findings identified nitrogen as a key regulator of mast flowering, thereby providing new empirical evidence to support the resource budget model.     

Estimating the first flowering and full blossom dates of Yoshino cherry (Cerasus × yedoensis ‘Somei-yoshino’) in Japan using machine learning algorithms

Climate change alters the phenology of various plants. For example, increasing temperatures shift the first flowering and full blossom days of Yoshino cherry trees and affect cultural events related to cherry blossoms. We developed models to estimate the first flowering and full blossom dates of Yoshino cherry in Japan based on temperature and phenological data observed at 82 stations in Japan for 68 years (1953–2020). Three machine learning algorithms, namely, the random forest (RF), artificial neural network (ANN), and gradient boosting decision tree (GBDT) algorithms, were utilized, and the hyperparameters were optimized using Optuna. The GBDT models produced the best estimation accuracy, with an overall root mean square error (RMSE) = 1.53 and 1.48 days for the first flowering date and full blossom date, respectively. Furthermore, our analysis using Shapley Additive Explanations (SHAP) revealed that in the RF and GBDT models, the low temperature in winter and high temperature in spring would advance the estimated first flowering and full blossom dates.     

A root chicory MADS box sequence and the Arabidopsis flowering repressor FLC share common features that suggest conserved function in vernalization and de‐vernalization responses

Root chicory (Cichorium intybus var. sativum) is a biennial crop, but is harvested to obtain root inulin at the end of the first growing season before flowering. However, cold temperatures may vernalize seeds or plantlets, leading to incidental early flowering, and hence understanding the molecular basis of vernalization is important. A MADS box sequence was isolated by RT‐PCR and named FLC‐LIKE1 (CiFL1) because of its phylogenetic positioning within the same clade as the floral repressor Arabidopsis FLOWERING LOCUS C (AtFLC). Moreover, over‐expression of CiFL1 in Arabidopsis caused late flowering and prevented up‐regulation of the AtFLC target FLOWERING LOCUS T by photoperiod, suggesting functional conservation between root chicory and Arabidopsis. Like AtFLC in Arabidopsis, CiFL1 was repressed during vernalization of seeds or plantlets of chicory, but repression of CiFL1 was unstable when the post‐vernalization temperature was favorable to flowering and when it de‐vernalized the plants. This instability of CiFL1 repression may be linked to the bienniality of root chicory compared with the annual lifecycle of Arabidopsis. However, re‐activation of AtFLC was also observed in Arabidopsis when a high temperature treatment was used straight after seed vernalization, eliminating the promotive effect of cold on flowering. Cold‐induced down‐regulation of a MADS box floral repressor and its re‐activation by high temperature thus appear to be conserved features of the vernalization and de‐vernalization responses in distant species.     

Structural diversity and regeneration of the endangered Prunus africana (Rosaceae) in Zimbabwe

Prunus africana is endemic to Africa and was included in Appendix II of the Convention on International Trade in Endangered Species (CITES) in 1995. In Zimbabwe, the species was reported to be rare and confined to the Eastern Highlands. The objective of this study was to assess size–class distribution and regeneration levels and to characterize structural diversity of P. africana. Given the clustered nature of the species, adaptive cluster sampling was used based on the assumption that there were more P. africana trees in the neighbourhood of reference trees. Each cluster was terminated when there were no more P. africana trees within a distance of 500 m. Data on diameter and height were collected in each cluster using standard forestry procedures. Regeneration was determined by counting seedlings and saplings within a radial distance of 14 m from the mother tree. Structural indices, that ie, diameter and height differentiation and mingling were determined for a structural group of four trees. Findings from this study indicated poor regeneration, fewer P. africana trees in small and large size classes, dominance of positive height and diameter differentiation and high mingling. These findings have implications on management and conservation of P. africana in Zimbabwe.     

Molecular Phylogeny,Diversity, and Bioprospecting of Endophytic Fungi Associated with wild Ethnomedicinal North American Plant Echinacea purpurea (Asteraceae)

The endophytic fungal community associated with the ethnomedicinal plant Echinacea purpurea was investigated as well as its potential for providing antifungal compounds against plant pathogenic fungi. A total of 233 endophytic fungal isolates were obtained and classified into 42 different taxa of 16 genera, of which Alternaria alternata, Colletotrichum dematium, and Stagonosporopsis sp. 2 are the most frequent colonizers. The extracts of 29 endophytic fungi displayed activities against important phytopathogenic fungi. Eight antifungal extracts were selected for chemical analysis. Forty fatty acids were identified by gas chromatography‐flame‐ionization detection (GC‐FID) analysis. The compounds (–)‐5‐methylmellein and (–)‐(3R)‐8‐hydroxy‐6‐methoxy‐3,5‐dimethyl‐3,4‐dihydroisocoumarin were isolated from Biscogniauxia mediterraneaEPU38CA crude extract. (–)‐5‐Methylmellein showed weak activity against Phomopsis obscurans, P. viticola, and Fusarium oxysporum, and caused growth stimulation of C. fragariae, C. acutatum, C. gloeosporioides, and Botrytis cinerea. (–)‐(3R)‐8‐Hydroxy‐6‐methoxy‐3,5‐dimethyl‐3,4‐dihydroisocoumarin appeared slightly more active in the microtiter environment than 5‐methylmellein. Our results indicate that E. purpurea lives symbiotically with different endophytic fungi, which are able to produce bioactive fatty acids and aromatic compounds active against important phytopathogenic fungi. The detection of the different fatty acids and aromatic compounds produced by the endophytic community associated with wild E. purpurea suggests that it may have intrinsic mutualistic resistance against phytopathogen attacks in its natural environment.     

Altered expression of CmNRRa changes flowering time of Chrysanthemum morifolium

Flowering time is an important ornamental trait for chrysanthemum (Chrysanthemum morifolium, Dendranthema x grandiflorum) floricultural production. In this study, CmNRRa, an orthologous gene of OsNRRa that regulates root growth in response to nutrient stress in rice, was identified from Chrysanthemum and its role in flowering time was studied. The entire CmNRRa cDNA sequence was determined using a combinatorial PCR approach along with 5′ and 3′ RACE methods. CmNRRa expression levels in various tissues were monitored by real‐time RT‐PCR. CmNRRa was strongly expressed in flower buds and peduncles, suggesting that CmNRRa plays a regulatory role in floral development. To investigate the biological function of CmNRRa in chrysanthemums, overexpression and knockdown of CmNRRa were carried out using transgenic Chrysanthemum plants generated through Agrobacterium‐mediated transformation. CmNRRa expression levels in the transgenic plants were assayed by real‐time RT‐PCR and Northern blot analysis. The transgenic plants showed altered flowering times compared with nontransgenic plants. CmNRRa‐RNAi transgenic plants flowered 40–64 days earlier, while CmNRRa‐overexpressing plants exhibited a delayed flowering phenotype. These results revealed a negative effect of CmNRRa on flowering time modulation. Alteration of CmNRRa expression levels might be an effective means of controlling flowering time in Chrysanthemum. These results possess potential application in molecular breeding of chrysanthemums that production year‐round, and may improve commercial chrysanthemum production in the flower industry.     

FT overexpression induces precocious flowering and normal reproductive development in Eucalyptus

Eucalyptus trees are among the most important species for industrial forestry worldwide. However, as with most forest trees, flowering does not begin for one to several years after planting which can limit the rate of conventional and molecular breeding. To speed flowering, we transformed a Eucalyptus grandis × urophylla hybrid (SP7) with a variety of constructs that enable overexpression of FLOWERING LOCUS T (FT). We found that FT expression led to very early flowering, with events showing floral buds within 1–5 months of transplanting to the glasshouse. The most rapid flowering was observed when the cauliflower mosaic virus 35S promoter was used to drive the Arabidopsis thaliana FT gene (AtFT). Early flowering was also observed with AtFT overexpression from a 409S ubiquitin promoter and under heat induction conditions with Populus trichocarpa FT1 (PtFT1) under control of a heat‐shock promoter. Early flowering trees grew robustly, but exhibited a highly branched phenotype compared to the strong apical dominance of nonflowering transgenic and control trees. AtFT‐induced flowers were morphologically normal and produced viable pollen grains and viable self‐ and cross‐pollinated seeds. Many self‐seedlings inherited AtFT and flowered early. FT overexpression‐induced flowering in Eucalyptus may be a valuable means for accelerating breeding and genetic studies as the transgene can be easily segregated away in progeny, restoring normal growth and form.