MYB Transcription factors (TFs) are most imperative and largest gene family in plants, which participate in development, metabolism, defense, differentiation and stress response. The MYB TFs has been ...studied in various plant species. However, comprehensive studies of MYB gene family in the sweet cherry (Prunus avium L.) are still unknown.
In the current study, a total of 69 MYB genes were investigated from sweet cherry genome and classified into 28 subfamilies (C1-C28 based on phylogenetic and structural analysis). Microcollinearity analysis revealed that dispersed duplication (DSD) events might play an important role in the MYB genes family expansion. Chromosomal localization, the synonymous (Ks) and nonsynonymous (Ka) analysis, molecular characteristics (pI, weight and length of amino acids) and subcellular localization were accomplished using several bioinformatics tools. Furthermore, the members of distinct subfamilies have diverse cis-acting regions, conserved motifs, and intron-exon architectures, indicating functional heterogeneity in the MYB family. Moreover, the transcriptomic data exposed that MYB genes might play vital role in bud dormancy. The quantitative real-time qRT-PCR was carried out and the expression pattern indicated that MYB genes significantly expressed in floral bud as compared to flower and fruit.
Our comprehensive findings provide supportive insights into the evolutions, expansion complexity and functionality of PavMYB genes. These PavMYB genes should be further investigated as they seem to be brilliant candidates for dormancy manipulation in sweet cherry.
Stem growth and development has considerable effects on plant architecture and yield performance. Strigolactones (SLs) modulate shoot branching and root architecture in plants. However, the molecular ...mechanisms underlying SLs regulate cherry rootstocks stem growth and development remain unclear. Our studies showed that the synthetic SL analog rac-GR24 and the biosynthetic inhibitor TIS108 affected stem length and diameter, aboveground weight, and chlorophyll content. The stem length of cherry rootstocks following TIS108 treatment reached a maximum value of 6.97 cm, which was much higher than that following rac-GR24 treatments at 30 days after treatment. Stem paraffin section showed that SLs affected cell size. A total of 1936, 743, and 1656 differentially expressed genes (DEGs) were observed in stems treated with 10 μM rac-GR24, 0.1 μM rac-GR24, and 10 μM TIS108, respectively. RNA-seq results highlighted several DEGs, including
,
,
,
, and
, which play vital roles in stem growth and development. UPLC-3Q-MS analysis revealed that SL analogs and inhibitors affected the levels of several hormones in the stems. The endogenous GA
content of stems increased significantly with 0.1 μM rac-GR24 or 10 μM TIS108 treatment, which is consistent with changes in the stem length following the same treatments. This study demonstrated that SLs affected stem growth of cherry rootstocks by changing other endogenous hormone levels. These results provide a solid theoretical basis for using SLs to modulate plant height and achieve sweet cherry dwarfing and high-density cultivation.
The cytochrome P450 (CYP) monooxygenase superfamily, belonging to heme-thiolate protein products, plays a vital role in metabolizing physiologically valuable compounds in plants. To date, CYP ...superfamily genes have not yet been characterized in grapevine (
L.), and their functions remain unclear. In this study, a sum of 236
, divided into 46 families and clustered into nine clans, have been identified based on bioinformatics analyses in grapevine genome. The characteristics of both exon-intron organizations and motif structures further supported the close evolutionary relationships of
superfamily as well as the reliability of phylogenetic analysis. The gene number-based hierarchical cluster of CYP subfamilies of different plants demonstrated that the loss of CYP families seems to be limited to single species or single taxa. Promoter analysis elucidated various
-regulatory elements related to phytohormone signaling, plant growth and development, as well as abiotic/biotic stress responses. The tandem duplication mainly contributed to the expansion of the
superfamily, followed by singleton duplication in grapevine. Global RNA-sequencing data of grapevine showed functional divergence of
as diverse expression patterns of
in various organs, tissues, and developmental phases, which were confirmed by quantitative real-time reverse transcription PCR (qRT-PCR). Taken together, our results provided valuable inventory for understanding the classification and biological functions of the
and paved the way for further functional verification of these
and are helpful to grapevine molecular breeding.
The gibberellin-dioxygenase (GAox) gene family plays a crucial role in regulating plant growth and development. GAoxs, which are encoded by many gene subfamilies, are extremely critical in regulating ...bioactive GA levels by catalyzing the subsequent stages in the biosynthesis process. Moreover, GAoxs are important enzymes in the GA synthesis pathway, and the GAox gene family has not yet been identified in Rosaceae species (
Prunus avium
L.,
F. vesca
, and
P. mume
), especially in response to gibberellin and PCa (prohexadione calcium; reduce biologically active GAs). In the current investigation, 399 GAox members were identified in sweet cherry, Japanese apricot, and strawberry. Moreover, they were further classified into six (A-F) subgroups based on phylogeny. According to motif analysis and gene structure, the majority of the
PavGAox
genes have a remarkably well-maintained exon–intron and motif arrangement within the same subgroup, which may lead to functional divergence. In the systematic investigation,
PavGAox
genes have several duplication events, but segmental duplication occurs frequently. A calculative analysis of orthologous gene pairs in
Prunus avium
L.,
F. vesca
, and
P. mume
revealed that GAox genes are subjected to purifying selection during the evolutionary process, resulting in functional divergence. The analysis of
cis
-regulatory elements in the upstream region of the 140
PavGAox
members suggests a possible relationship between genes and specific functions of hormone response-related elements. Moreover, the
PavGAox
genes display a variety of tissue expression patterns in diverse tissues, with most of the
PavGAox
genes displaying tissue-specific expression patterns. Furthermore, most of the
PavGAox
genes express significant expression in buds under phytohormonal stresses. Phytohormones stress analysis demonstrated that some of
PavGAox
genes are responsible for maintaining the GA level in plant-like
Pav co4017001.1 g010.1.br
,
Pav sc0000024.1 g340.1.br
, and
Pav sc0000024.1 g270.1.mk
. The subcellular localization of
PavGAox
protein utilizing a tobacco transient transformation system into the tobacco epidermal cells predicted that GFP signals were mostly found in the cytoplasm. These findings will contribute to a better understanding of the GAox gene family’s interaction with prohexadione calcium and GA, as well as provide a strong framework for future functional characterization of GAox genes in sweet cherry.
Glutathione S-transferases (GSTs) in plants are multipurpose enzymes that are involved in growth and development and anthocyanins transportation. However, members of the GST gene family were not ...identified in sweet cherry (
Prunus avium
). To identify the GST genes in sweet cherry, a genome-wide analysis was conducted. In this study, we identified 67 GST genes in
P. avium
genome and nomenclature according to chromosomal distribution. Phylogenetic tree analysis revealed that
PavGST
genes were classified into seven chief subfamily: TCHQD, Theta, Phi, Zeta, Lambda, DHAR, and Tau. The majority of the
PavGST
genes had a relatively well-maintained exon–intron and motif arrangement within the same group, according to gene structure and motif analyses. Gene structure (introns-exons) and conserved motif analysis revealed that the majority of the
PavGST
genes showed a relatively well-maintained motif and exons–introns configuration within the same group. The chromosomal localization, GO enrichment annotation, subcellular localization, syntenic relationship, Ka/Ks analysis, and molecular characteristics were accomplished using various bioinformatics tools. Mode of gene duplication showed that dispersed duplication might play a key role in the expansion of
PavGST
gene family. Promoter regions of
PavGST
genes contain numerous
cis
-regulatory components, which are involved in multiple stress responses, such as abiotic stress and phytohormones responsive factors. Furthermore, the expression profile of sweet cherry
PavGSTs
showed significant results under LED treatment. Our findings provide the groundwork for future research into induced LED anthocyanin and antioxidants deposition in sweet cherries.
The basic leucine zippers (bZIPs) transcription factors play crucial roles in various vital biological processes and have been extensively studied across multiple species. However, their presence in ...the Rubus species has received limited attention. In this study, we identified 49 bZIP transcription factor genes in the genomes of black raspberry (R. occidentalis) and red raspberry (R. idaeus). Phylogenetic analysis successfully classified the bZIPs into 13 subfamilies. Comparative genomic analysis revealed a conservation of bZIP gene numbers among ten Rosaceae species, with gene duplications partially contributing to the expansion of this family in Rubus. Microsynteny analysis further supported the evolutionary conservation of this gene family among Rosaceae genomes. Tissue-specific expression of black raspberry bZIPs was observed, and gene ontology enrichment analyses revealed their involvement in various biological processes. Those members that respond to nitrogen were identified. Dimerization properties of bZIP proteins were predicted based on the amino acid composition of their coiled-coil domains. Protein interaction network analysis and yeast two-hybrid assays unveiled the formation of heterodimers between the S1/C groups in R. occidentalis. This comprehensive characterization of the bZIP transcription factor family provides valuable insights into the evolution and functions of bZIP genes in Rubus.
Abstract Prunus conradinae , a valuable flowering cherry belonging to the Rosaceae family subgenus Cerasus and endemic to China, has high economic and ornamental value. However, a high-quality P. ...conradinae genome is unavailable, which hinders our understanding of its genetic relationships and phylogenesis, and ultimately, the possibility of mining of key genes for important traits. Herein, we have successfully assembled a chromosome-scale P. conradinae genome, identifying 31,134 protein-coding genes, with 98.22% of them functionally annotated. Furthermore, we determined that repetitive sequences constitute 46.23% of the genome. Structural variation detection revealed some syntenic regions, inversions, translocations, and duplications, highlighting the genetic diversity and complexity of Cerasus . Phylogenetic analysis demonstrated that P. conradinae is most closely related to P. campanulata , from which it diverged ~ 19.1 million years ago (Mya). P. avium diverged earlier than P. cerasus and P. conradinae . Similar to the other Prunus species, P. conradinae underwent a common whole-genome duplication event at ~ 138.60 Mya. Furthermore, 79 MADS -box members were identified in P. conradinae , accompanied by the expansion of the SHORT VEGETATIVE PHASE subfamily. Our findings shed light on the complex genetic relationships, and genome evolution of P. conradinae and will facilitate research on the molecular breeding and functions of key genes related to important horticultural and economic characteristics of subgenus Cerasus .
•Nanoparticles (NPs) show promise in enhancing fruit tree growth, antioxidant defense, and productivity.•Nanoparticles have unique properties that positively impact plant growth, abiotic stress ...tolerance, and fruit quality, offering a potential tool for fruit crop improvement.•Nanoparticles have been found to enhance nutrient uptake, scavenge free radicals, and induce stress response pathways, resulting in improved fruit quality and yield.
Nanotechnology offers promising applications in agriculture and horticulture. Specifically, nanofertilizers (NFs) have been investigated for enhancing growth, antioxidant defense, and productivity in fruit-bearing plants. These crops are vital for supplying essential nutrients and minerals to humans. However, their production and quality often face challenges from various stresses. Using nanoparticles (NPs) can potentially mitigate these challenges, thereby improving the productivity and quality of horticulture crops. NPs possess unique chemical and physical properties that benefit plant growth, development, and stress tolerance, making them valuable for fruit crop enhancement. This review highlights recent advancements in employing nanoparticles to bolster fruit crop growth. Various nanoparticle types, such as metal oxide, metallic, carbon-based, and organic NPs have been demonstrated positive effects on plant abiotic stress tolerance growth and fruit quality. They have been found to boost nutrient absorption, neutralize free radicals, and activate plant stress response pathways, leading to enhanced quality and yield of fruit. This review aims to elucidate significant insights into the utilization of nanoparticles as a promising strategy for bolstering the resilience of horticultural plants and safeguarding food security in the face of environmental alterations. Notwithstanding the favorable outcomes observed in ameliorating plant performance under abiotic stresses, the molecular mechanisms underlying the beneficial effects of NPs remain a subject of ongoing investigation. Further research is imperative to delve into the enduring implications, safety considerations, and optimal techniques for the application of NPs in horticultural plants.
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Abstract
Waterlogging has occurred more frequently in recent years due to climate change, so it is a huge threat to crop yield and quality. Sweet cherry, a fruit tree with a high economic value, is ...sensitive to waterlogging stress. One of the most effective methods for enhancing the waterlogging tolerance of sweet cherries is to select waterlogging-tolerant rootstocks. However, the waterlogging tolerance of different cherry rootstocks, and the underlying mechanism remains uncharacterized. Thus, we first evaluated the waterlogging resistance of five sweet cherry rootstocks planted in China. The data showed that ‘Gisela 12’ and ‘Colt’ were the most waterlogging-sensitive and -tolerant among the five tested varieties, respectively. Oxygenation effectively alleviated the adverse impacts of waterlogging stress on cherry rootstocks. Moreover, we found that the waterlogging group had lower relative water content, Fv/Fm value, net photosynthetic rate, and higher antioxidant enzyme activities, whereas the oxygenated group performed better in all these parameters. RNA-Seq analysis revealed that numerous DEGs were involved in energy production, antioxidant metabolism, hormone metabolism pathways, and stress-related transcription factors. These findings will help provide management strategies to enhance the waterlogging tolerance of cherry rootstocks and thereby achieve higher yield and better quality of cherries.
Graphical Abstract
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