Transcriptome sequencing of the apricot (Prunus armeniaca L.) and identification of differentially expressed genes involved in drought stress

Integrated transcriptome and physiological analysis revealed core transcription factors that promote flavonoid biosynthesis in apricot in response to pathogenic fungal infection

MAIN CONCLUSION

Integrated transcriptome and physiological analysis of apricot leaves after Fusarium solani treatment. In addition, we identified core transcription factors and flavonoid-related synthase genes which may function in apricot disease resistance. Apricot (Prunus armeniaca) is an important economic fruit species, whose yield and quality of fruit are limited owing to its susceptibility to diseases. However, the molecular mechanisms underlying the response of P. armeniaca to diseases is still unknown. In this study, we used physiology and transcriptome analysis to characterize responses of P. armeniaca subjected to Fusarium solani. The results showed increasing malondialdehyde (MDA) content, enhanced peroxidase (POD) and catalase (CAT) activity during F. solani infestation. A large number of differentially expressed genes (DEGs), which included 4281 upregulated DEGs and 3305 downregulated DEGs, were detected in P. armeniaca leaves exposed to F. solani infestation. Changes in expression of transcription factors (TFs), including bHLH, AP2/ERF, and WRKY indicated their role in triggering pathogen-responsive genes in P. armeniaca. During the P. armeniaca response to F. solani infestation, the content of total flavonoid was changed, and we identified enzyme genes associated with flavonoid biosynthesis. Ectopic overexpression of PabHLH15 and PabHLH102 in Nicotiana benthamiana conferred elevated resistance to Fspa_1. Moreover, PabHLH15 and PabHLH102 positively interact with the promoter of flavonoid biosynthesis-related genes. A regulatory network of TFs regulating enzyme genes related to flavonoid synthesis affecting apricot disease resistance was constructed. These results reveal the potential underlying mechanisms of the F. solani response of P. armeniaca, which would help improve the disease resistance of P. armeniaca and may cultivate high-quality disease-resistant varieties in the future.

Transcriptomic Analysis on the Peel of UV-B-Exposed Peach Fruit Reveals an Upregulation of Phenolic- and UVR8-Related Pathways

UV-B treatment deeply influences plant physiology and biochemistry, especially by activating the expression of responsive genes involved in UV-B acclimation through a UV-B-specific perception mechanism. Although the UV-B-related molecular responses have been widely studied in Arabidopsis, relatively few research reports deepen the knowledge on the influence of post-harvest UV-B treatment on fruit. In this work, a transcriptomic approach is adopted to investigate the transcriptional modifications occurring in the peel of UV-B-treated peach (Prunus persica L., cv Fairtime) fruit after harvest. Our analysis reveals a higher gene regulation after 1 h from the irradiation (88% of the differentially expressed genes-DEGs), compared to 3 h recovery. The overexpression of genes encoding phenylalanine ammonia-lyase (PAL), chalcone syntase (CHS), chalcone isomerase (CHI), and flavonol synthase (FLS) revealed a strong activation of the phenylpropanoid pathway, resulting in the later increase in the concentration of specific flavonoid classes, e.g., anthocyanins, flavones, dihydroflavonols, and flavanones, 36 h after the treatment. Upregulation of UVR8-related genes (HY5, COP1, and RUP) suggests that UV-B-triggered activation of the UVR8 pathway occurs also in post-harvest peach fruit. In addition, a regulation of genes involved in the cell-wall dismantling process (PME) is observed. In conclusion, post-harvest UV-B exposure deeply affects the transcriptome of the peach peel, promoting the activation of genes implicated in the biosynthesis of phenolics, likely via UVR8. Thus, our results might pave the way to a possible use of post-harvest UV-B treatments to enhance the content of health-promoting compounds in peach fruits and extending the knowledge of the UVR8 gene network.

Identification of QTL and candidate genes associated with biomass yield and Feed Quality in response to water deficit in alfalfa (Medicago sativa L.) using linkage mapping and RNA-Seq

Biomass yield and Feed Quality are the most important traits in alfalfa (Medicago sativa L.), which directly affect its economic value. Drought stress is one of the main limiting factors affecting alfalfa production worldwide. However, the genetic and especially the molecular mechanisms for drought tolerance in alfalfa are poorly understood. In this study, linkage mapping was performed in an F1 population by combining 12 phenotypic data (biomass yield, plant height, and 10 Feed Quality-related traits). A total of 48 significant QTLs were identified on the high-density genetic linkage maps that were constructed in our previous study. Among them, nine main QTLs, which explained more than 10% phenotypic variance, were detected for biomass yield (one), plant height (one), CP (two), ASH (one), P (two), K(one), and Mg (one). A total of 31 candidate genes were identified in the nine main QTL intervals based on the RNA-seq analysis under the drought condition. Blast-P was further performed to screen candidate genes controlling drought tolerance, and 22 functional protein candidates were finally identified. The results of the present study will be useful for improving drought tolerance of alfalfa varieties by marker-assisted selection (MAS), and provide promising candidates for further gene cloning and mechanism study.

Effect of Chitosan Nanoparticles as Edible Coating on the Storability and Quality of Apricot Fruits

Apricots are a fragile fruit that rots quickly after harvest. Therefore, they have a short shelf-life. The purpose of this work is to determine the effect of coatings containing chitosan (CH) as well as its nanoparticles (CHNPs) as thin films on the quality and shelf-life of apricots stored at room (25 ± 3 °C) and cold (5 ± 1 °C) temperatures. The physical, chemical, and sensorial changes that occurred during storage were assessed, and the shelf-life was estimated. Transmission electron microscopy was used to examine the size and shape of the nanoparticle. The nanoparticles had a spherical shape with an average diameter of 16.4 nm. During the storage of the apricots, those treated with CHNPs showed an obvious decrease in weight loss, decay percent, total soluble solids, and lipid peroxidation, whereas total acidity, ascorbic acid, and carotenoid content were higher than those in the fruits treated with CH and the untreated fruits (control). The findings of the sensory evaluation revealed a significant difference in the overall acceptability scores between the samples treated with CHNPs and the other samples. Finally, it was found that CHNP coatings improved the qualitative features of the apricots and extended their shelf-life for up to 9 days at room temperature storage and for 30 days in cold storage.

Japanese plums behavior under water stress: impact on yield and biochemical traits

This work investigates response to drought of nine local cultivars alongside two exotic varieties of Japanese plum (Prunus salicina L.) through their yield and fruit quality components. It was carried out at Sais plain, northern Morocco, over two consecutive years (2019–2020). Water stress was imposed by a deficit irrigation (DI) treatment of 50% ETc during the whole fruit growth period, compared to full irrigation of 100% ETc (CI). At their full ripening stage, the cultivars were assessed for their yield, fruit weight and fruit quality attributes, namely total soluble solids (TSS), pH, titratable acidity (TA), maturity index (MI), soluble sugars content (SSC), amino acids content (AAC), total phenolic compounds (TPC) and total antioxidant capacity (TAC). Results displayed significant decrease in yield and fruit weight since the first year of DI application. Owing to calculated stability indexes of the aforementioned traits along with water use efficiency, the local cultivar ‘Fortu-43’ was the most insensitive to drought, whereas ‘Timhdit’ and ‘Black-D35’ showed the lowest drought tolerability. The effects of water stress on fruit chemical and biochemical traits varied significantly among cultivars, exhibiting an overall significant improvement in fruit quality. Two-dimensional clustered heatmap analysis subdivided the cultivars into two distinct clusters, mainly discriminated based on stability indexes of SSC, MI, TPC and TAC. Among the latter, SSC stability index was probably the most significant drought tolerance marker for Japanese plum.

Transcriptome Characterization of the Roles of Abscisic Acid and Calcium Signaling during Water Deficit in Garlic

Garlic (Allium sativum L.) is one of the most important vegetable crops, and breeding drought-tolerant varieties is a vital research goal. However, the underlying molecular mechanisms in response to drought stress in garlic are still limited. In this study, garlic seedlings were subjected to 15% PEG6000 for 0, 1, 4, and 12 h, respectively, to simulate drought stress. Changes of transcriptomes as a result of drought stress in garlic leaves were determined by de novo assembly using the Illumina platform. In total, 96,712 unigenes and 11,936 differentially expressed genes (DEGs) were identified in the presence of drought conditions. Transcriptome profiling revealed that the DEGs were mainly enriched in the biosynthesis of secondary metabolites, MAPK signaling pathway, starch and sucrose metabolism, phenylpropanoid biosynthesis, and plant hormone signal transduction. Genes involved in abscisic acid and calcium signaling were further investigated and discussed. Our results indicated that a coordinated interplay between abscisic acid and calcium is required for drought-induced response in garlic.

Physiological, Biochemical and Transcriptomic Analysis of the Aerial Parts (Leaf-Blade and Petiole) of Asarum sieboldii Responding to Drought Stress

Asarum sieboldii Miq. is a leading economic crop and a traditional medicinal herb in China. Leaf-blade and petiole are the only aerial tissues of A. sieboldii during the vegetative growth, playing a vital role in the accumulation and transportation of biomass energy. They also act as critical indicators of drought in agricultural management, especially for crops having underground stems. During drought, variations in the morphology and gene expression of the leaves and petioles are used to control agricultural irrigation and production. Besides, such stress can also alter the differential gene expression in these tissues. However, little is known about the drought-tolerant character of the aerial parts of A. sieboldii. In this study, we examined the physiological, biochemical and transcriptomic responses to the drought stress in the leaf blades and petioles of A. sieboldii. The molecular mechanism, involving in drought stress response, was elucidated by constructing the cDNA libraries and performing transcriptomic sequencing. Under drought stress, a total of 2912 and 2887 unigenes were differentially expressed in the leaf blade and petiole, respectively. The detection of many transcription factors and functional genes demonstrated that multiple regulatory pathways were involved in drought tolerance. In response to drought, the leaf blade and petiole displayed a general physiological character, a higher SOD and POD activity, a higher MDA content and lower chlorophyll content. Three unigenes encoding POD were up-regulated, which can improve POD activity. Essential oil in petiole was extracted. The relative contents of methyleugenol and safrole in essential oil were increased from 0.01% to 0.05%, and 3.89% to 16.97%, respectively, while myristicin slightly reduced from 24.87% to 21.52%. Additionally, an IGS unigene, involved in eugenol biobiosynthesis, was found up-regulated under drought stress, which was predicated to be responsible for the accumulation of methyleugenol and safrole. Simple sequence repeats (SSRs) were characterized in of A. sieboldii, and a total of 5466 SSRs were identified. Among them, mono-nucleotides were the most abundant repeat units, accounting for 44.09% followed by tri-, tetra-, penta and hexa-nucleotide repeats. Overall, the present work provides a valuable resource for the population genetics studies of A. sieboldii. Besides, it provides much genomic information for the functional dissection of the drought-resistance in A. sieboldii, which will be useful to understand the bio-regulatory mechanisms linked with drought-tolerance to enhance its yield.

Yield, Fruit Quality, and Storability of 'Canino' Apricot in Response to Aminoethoxyvinylglycine, Salicylic Acid, and Chitosan

Ethylene plays a pivotal role in the climacteric fruit ripening and senescence process. The effect of three ethylene inhibitors on the yield, quality, and storability of ‘Canino’ apricot fruit was studied. Foliar sprays of distilled water (control), aminoethoxyvinylglycine (AVG) (150 and 100 mg·L⁻¹), salicylic acid (SA) (4 and 2 mM), and chitosan (2.5% and 1.5%) were applied 30 and 15 days before harvest. Results indicated that the high concentrations of AVG and SA recorded the lowest percentage of preharvest fruit drop and, hence, the highest yield. Trees receiving either concentration of AVG showed the highest fruit firmness. High concentrations of all three ethylene inhibitors reduced fruit weight loss, total carotenoids, and soluble solid content (SSC), but increased total acidity (TA) during cold storage (2 °C). A high score of overall taste acceptability was observed with a higher concentration of SA, which was also recorded the lowest fruit malondialdehyde content (MDA) at harvest and during storage. The highest concentrations of SA and chitosan recorded no decay for 28 days of storage. Gene expression analysis reflected higher expression of PaACS1 gene with the highest concentrations of ethylene inhibitors, suggesting that SA (4 mM) is recommended for optimal yield, quality, and storability of ‘Canino’ apricot fruit grown under Egyptian conditions.

Transcriptome divergence between developmental senescence and premature senescence in Nicotiana tabacum L

Senescence is a degenerative process triggered by intricate and coordinated regulatory networks, and the mechanisms of age-dependent senescence and stress-induced premature senescence still remain largely elusive. Thus we selected leaf samples of developmental senescence (DS) and premature senescence (PS) to reveal the regulatory divergence. Senescent leaves were confirmed by yellowing symptom and physiological measurement. A total of 1171 and 309 genes (DEGs) were significantly expressed respectively in the whole process of DS and PS. Up-regulated DEGs in PS were mostly related to ion transport, while the down-regulated DEGs were mainly associated with oxidoreductase activity and sesquiterpenoid and triterpenoid biosynthesis. In DS, photosynthesis, precursor metabolites and energy, protein processing in endoplasmic reticulum, flavonoid biosynthesis were notable. Moreover, we found the vital pathways shared by DS and PS, of which the DEGs were analyzed further via protein-protein interaction (PPI) network analysis to explore the alteration responding to two types of senescence. In addition, plant hormone transduction pathway was mapped by related DEGs, suggesting that ABA and ethylene signaling played pivotal roles in formulating the distinction of DS and PS. Finally, we conducted a model containing oxidative stress and ABA signaling as two hub points, which highlighted the major difference and predicted the possible mechanism under DS and PS. This work gained new insight into molecular divergence of developmental senescence and premature senescence and would provide reference on potential mechanism initiating and motivating senescence for further study.