Synergistic approach of PCR-based fragment length analysis and amplicon deep sequencing reveals rich diversity of S-alleles in sweet cherries from the Caucasian region of origin.

Introduction: The self-incompatibility system in sweet cherry (Prunus avium L.) prevents fertilization with own or genetically related pollen, and is genetically determined by the multi-allelic S-locus. Therefore, determining S-alleles is crucial for plant breeding and fruit production, as it enables the selection of compatible combinations of S-genotypes for successful pollination. Methods: In this study, S-alleles were identified in a total of 260 genotypes from the Caucasian region, the species' center of origin. S-allele genotyping was conducted using PCR fragment length analysis with the standard marker PaConsI-F/R2 and reference genotypes, complemented by sequence analysis through amplicon deep sequencing. Results and discussion: The genotypes collected from Azerbaijan and Turkey exhibit a high allelic richness at the S-locus, particularly compared to modern sweet cherry cultivars worldwide. Nine previously undescribed S-alleles were identified and designated as S45, S46, S47, S48, S49, S50, S51, S52 and S53. Given the expected high diversity for other traits, this plant material represents a valuable resource for further breeding research and introgression of new traits in future breeding programs. Furthermore, our results underscore that fragment length alone may not be sufficient for unambiguous assignment of S-alleles due to minimal length differences between different alleles. To address this issue, an S-allele reference ladder was developed using the rich diversity for precise assignment of the S-alleles. This tool can be applied in future experiments as a robust and cost-effective method for accurate S-genotyping across different runs and laboratories. Additionally, several selected S-genotypes were planted in a trial field and will be maintained as an S-allele reference collection.

Genotype-by-environment and QTL-by-environment interactions in sweet cherry (Prunus avium L.) for flowering date.

In sweet cherry (Prunus avium L.), flowering date is strongly dependent on the environment conditions and, therefore, is a trait of major interest for adaptation to climate change. Such trait can be influenced by genotype-by-environment interaction (G×E), that refers to differences in the response of genotypes to different environments. If not taken into account, G×E can reduce selection accuracy and overall genetic gain. However, little is known about G×E in fruit tree species. Flowering date is a highly heritable and polygenic trait for which many quantitative trait loci (QTLs) have been identified. As for the overall genetic performance, differential expression of QTLs in response to environment (QTL-by-environment interaction, QTL×E) can occur. The present study is based on the analysis of a multi-environment trial (MET) suitable for the study of G×E and QTL×E in sweet cherry. It consists of a sweet cherry F1 full-sib family (n = 121) derived from the cross between cultivars 'Regina' and 'Lapins' and planted in two copies in five locations across four European countries (France, Italy, Slovenia and Spain) covering a large range of climatic conditions. The aim of this work was to study the effect of the environment on flowering date and estimate G×E, to carry QTL detection in different environments in order to study the QTL stability across environments and to estimate QTL×E. A strong effect of the environment on flowering date and its genetic control was highlighted. Two large-effect and environment-specific QTLs with significant QTL×E were identified on linkage groups (LGs) 1 and 4. This work gives new insights into the effect of the environment on a trait of main importance in one of the most economically important fruit crops in temperate regions. Moreover, molecular markers were developed for flowering date and a strategy consisting in using specific markers for warm or cold regions was proposed to optimize marker-assisted selection (MAS) in sweet cherry breeding programs.

Are commercial sweet cherry rootstocks adapted to climate change? Short-term waterlogging and CO2 effects on sweet cherry cv. 'Burlat'.

High CO2 is able to ameliorate some negative effects due to climate change and intensify others. This study involves the sweet cherry (Prunus avium) cultivar 'Burlat' grafted on the 'Mariana 2624', 'Adara' and 'LC 52' rootstocks. In a climate chamber at two CO2 concentrations, ambient (400 µmol mol-1 ) and elevated (800 µmol mol-1 ), the plants were submitted to waterlogging for 7 d, followed by 7 d of recovery after drainage. Waterlogging drastically decreased the rate of photosynthesis, significantly endangering plant survival, particularly for the 'LC 52' and 'Adara' rootstocks. 'Mariana 2624' was also clearly affected by waterlogging that increased lipid peroxidation and the Cl- and SO42- concentrations in all the studied plants. Nevertheless, CO2 was able to overcome this reduction in photosynthesis, augmenting growth, increasing soluble sugars and starch, raising turgor and regulating the concentrations of Cl- and SO42- , while lowering the NO3- concentration in leaves of all the studied rootstocks. In concordance with these results, the proline levels indicated a more intense stress at control CO2 than at high CO2 for waterlogged plants. 'Mariana 2624' was more resistant to waterlogging than 'Adara', and both were more resistant than 'LC 52' in control CO2 conditions; this clearly enhanced the chance of survival under hypoxia.

Transcriptome and Metabolite Changes during Hydrogen Cyanamide-Induced Floral Bud Break in Sweet Cherry.

Release of bud dormancy in perennial woody plants is a temperature-dependent process and thus flowering in these species is heavily affected by climate change. The lack of cold winters in temperate growing regions often results in reduced flowering and low fruit yields. This is likely to decrease the availability of fruits and nuts of the Prunus spp. in the near future. In order to maintain high yields, it is crucial to gain detailed knowledge on the molecular mechanisms controlling the release of bud dormancy. Here, we studied these mechanisms using sweet cherry (Prunus avium L.), a crop where the agrochemical hydrogen cyanamide (HC) is routinely used to compensate for the lack of cold winter temperatures and to induce flower opening. In this work, dormant flower buds were sprayed with hydrogen cyanamide followed by deep RNA sequencing, identifying three main expression patterns in response to HC. These transcript level results were validated by quantitative real time polymerase chain reaction and supported further by phytohormone profiling (ABA, SA, IAA, CK, ethylene, JA). Using these approaches, we identified the most up-regulated pathways: the cytokinin pathway, as well as the jasmonate and the hydrogen cyanide pathway. Our results strongly suggest an inductive effect of these metabolites in bud dormancy release and provide a stepping stone for the characterization of key genes in bud dormancy release.

Two minuses can make a plus: waterlogging and elevated CO2 interactions in sweet cherry (Prunus avium) cultivars.

The increase in the ambient concentration of CO2 and other greenhouse gases is producing climate events that can compromise crop survival. However, high CO2 concentrations are sometimes able to mitigate certain stresses such as salinity or drought. In this experiment, the effects of waterlogging and CO2 are studied in combination to elucidate the eventual response in sweet cherry trees. For this purpose, four sweet cherry cultivars ('Burlat', 'Cashmere', 'Lapins and 'New Star') were grafted on a typically hypoxia-tolerant rootstock (Mariana 2624) and submitted to waterlogging for 7 days at either ambient CO2 concentration (400 µmol mol-1 ) or at elevated CO2 (800 µmol mol-1 ). Waterlogging affected plants drastically, by decreasing photosynthesis, stomatal conductance, transpiration, chlorophyll fluorescence and growth. It also brought about the accumulation of proline, chloride and sulfate. Nonetheless, raising the CO2 supply not only mitigated all these effects but also induced the accumulation of soluble sugars and starch in the leaf. Therefore, sweet cherry plants submitted to waterlogging were able to overcome this stress when grown in a CO2 -enriched environment.

CO2 effects on the waterlogging response of 'Gisela 5' and 'Gisela 6' (Prunus cerasusxPrunus canescens) sweet cherry (Prunus avium) rootstocks.

Climate change is submitting countries of the Mediterranean arc to periods of drought alternating with heavy rain and waterlogging. Eventual floods along with the rising CO2 in the atmosphere present an unpredictable scenario that affects crop survival. The effect of both stresses combined has been studied in sweet cherry plants. 'Gisela 5' and 'Gisela 6' were evaluated as rootstocks of the sweet cherry cultivar 'Burlat'. Plants were placed in a controlled-climate chamber for 7days, then they were submitted to waterlogging for another 7days and the response to this stress and the subsequent recovery were studied (7 more days). The experiment was carried out at 400µmolmol-1 CO2 (ambient CO2) and 800µmolmol-1 CO2, at 26°C, and plant water status and growth, net CO2 assimilation, transpiration, stomatal conductance, water potential, chlorophyll fluorescence, relative water content, anions content, proline, lipid peroxidation, soluble sugars, and starch were measured. Differences in the response and in its intensity were detected in both rootstocks. Some parameters - such as photosynthesis, soluble sugars, starch, TBARS, and NO3- - varied depending on the CO2 conditions and the waterlogging effect. Elevated CO2 was able to increase photosynthesis and thereby help plants to overcome waterlogging.

A collection of European sweet cherry phenology data for assessing climate change.

Professional and scientific networks built around the production of sweet cherry (Prunus avium L.) led to the collection of phenology data for a wide range of cultivars grown in experimental sites characterized by highly contrasted climatic conditions. We present a dataset of flowering and maturity dates, recorded each year for one tree when available, or the average of several trees for each cultivar, over a period of 37 years (1978-2015). Such a dataset is extremely valuable for characterizing the phenological response to climate change, and the plasticity of the different cultivars' behaviour under different environmental conditions. In addition, this dataset will support the development of predictive models for sweet cherry phenology exploitable at the continental scale, and will help anticipate breeding strategies in order to maintain and improve sweet cherry production in Europe.