Regulation Of Fruit Development Research Articles

26S Proteasome Subunit SlPBB2 Regulates Fruit Development and Ripening in Tomato.

Proteasomes are protein complexes responsible for degrading unneeded or damaged proteins through proteolysis and play critical roles in regulating plant development and response to environmental stresses. However, it is still unclear whether proteasomes regulate fruit development and ripening. In this study, we investigated the function of a core proteasome subunit, SlPBB2, in tomato fruit. We found that silencing the SlPPB2 gene through virus-induced gene silencing resulted in tomato seedling death, while SlPPB2 RNA interference (RNAi-SlPBB2) plants driven by a fruit-specific promoter PP2C present normal development. Further observation reveals that silencing SlPBB2 in fruits impaired the chloroplast development and chlorophyll metabolism of fruits, increased the fruit size, and delayed fruit ripening. These findings provide novel insights into the role of proteasomes in regulating fruit development and ripening.

Tomato CONSTANS-LIKE SlCOL1 regulates the content of chlorophyll in fruit by stabilizing the GOLDEN2-LIKE protein

CONSTANS (CO) and CONSTANS-LIKE (COL) transcription factors have been known to regulate a series of cellular processes, including the transition from vegetative growth to flower development in plants. However, their role in regulating the content of chlorophyll in fruit is poorly understood. In this study, SlCOL1, the tomato (Solanum lycopersicum) ortholog of Arabidopsis CONSTANS, was shown to play key roles in the control of fruit chlorophyll. The suppression of SlCOL1 expression was found to lead to a reduction in the content of chlorophyll in the immature green fruit. In contrast, the overexpression of SlCOL1 increased the content of chlorophyll in the immature green fruit. An analysis of protein-protein interactions indicated that SlCOL1 forms a complex with GOLDEN2-LIKE (GLK2), which promotes the stability of its protein. The overexpression of SlCOL1 in the glk2 null mutation background of tomato failed to promote the accumulation of chlorophyll in the immature green fruit, which suggests that GLK2 is required for the function of SlCOL1 in the regulation of the content of chlorophyll. These results shed new light into the mechanisms used by COL1 and GLK2 to regulate fruit development and the accumulation of chlorophyll in tomato.

Characterization of Superoxide Dismutase (SOD) Gene Family and Their Responses to Salinity Stress and Fruit Development in Octoploid Strawberry

Superoxide dismutases (SODs), as the first line of defense against reactive oxygen species (ROS), play an essential role in protecting plants from adverse elicitors during plant growth and development. However, little is known about the SOD gene family and their response to salinity stress and fruit development in cultivated strawberries (Fragaria × ananassa). In this study, 32 SOD genes consisting of 16 Cu/ZnSODs, 11 FeSODs, and 5 MnSOD were identified, which presented three well-resolved clades in the phylogenetic tree. Each clade had similar motifs, and exon–intron structures, which in turn supported the evolutionary classification. Cis-acting element analysis suggested that FaSOD genes might be involved in the plant response to abiotic and biotic stresses, hormones, and light. The analysis of previously published transcriptome data revealed that FaSOD genes are expressed variably under salt stress. Among these SODs, FaMSD5 was expressed at relatively high levels in strawberry root and leaf, and its transcript abundance significantly increased after salt treatment. Some transcription factors related to photomorphogenesis, hormone signaling pathways, and hyperosmotic salinity response were predicted to bind to the FaMSD5 promoter. These outcomes implied that FaMSD5 might play an important role in protection against salt stress. In addition, the comprehensive transcriptome analysis of FaSOD genes in strawberry fruit showed that almost all FaCSDs and FaMSDs were more highly expressed than FaFSDs at different developmental stages, and the expression patterns of FaCSD1, FaCSD2, FaCSD7, FaCSD8, and FaCSD10 suggested that they were likely to be involved in fruit development and ripening. This study provides a basis for further exploration of the function of the FaSOD gene family in strawberry and provides candidate FaSOD genes for enhancing salinity tolerance and regulating fruit development and ripening.

PbbHLH137 interacts with PbGIF1 to regulate pear fruit development by promoting cell expansion to increase fruit size.

The regulation of fruit development is a complex process and a core issue in the fruit tree industry. To investigate the role of PbGIF1 in pear fruit development, we identified a transcription factor PbbHLH137 that regulates pear (Pyrus bretschneideri) fruit development by screening a yeast library constructed from fruit cDNA. Yeast two-hybrid (Y2H), bimolecular fluorescence complementation (BiFC), and split luciferase complementation (split-LUC) assays were performed to confirm the PbbHLH137-PbGIF1 interaction. By tracing the complete fruit development process, we found that PbbHLH137 expression was closely related to fruit size and highly involved at the late pear fruit development stage. Transgenic experiments showed that heterologous expression of PbbHLH137 or PbGIF1 promoted fruit enlargement. PbbHLH137 promoted mainly the expansion of fruit cell volume, whereas PbGIF1 mainly increased the number of cells. Further LUC experiments demonstrated that PbGIF1 promoted the transcriptional activation ability of PbbHLH137. Our work identified PbbHLH137 as a transcription factor that regulates fruit development, and showed that PbGIF1 played an ongoing role during fruit development, making it a candidate gene for genetic improvement of pear fruit development.

Genome-wide analysis of AP2/ERF transcription factors that regulate fruit development of Chinese prickly ash

BackgroundAP2/ERF is a large family of plant transcription factor proteins that play essential roles in signal transduction, plant growth and development, and responses to various stresses. The AP2/ERF family has been identified and verified by functional analysis in various plants, but so far there has been no comprehensive study of these factors in Chinese prickly ash. Phylogenetic, motif, and functional analyses combined with transcriptome analysis of Chinese prickly ash fruits at different developmental stages (30, 60, and 90 days after anthesis) were conducted in this study.ResultsThe analysis identified 146 ZbAP2/ERF genes that could be classified into 15 subgroups. The motif analysis revealed the presence of different motifs or elements in each group that may explain the functional differences between the groups. ZbERF13.2, ZbRAP2-12, and ZbERF2.1 showed high levels of expression in the early stages of fruit development. ZbRAP2-4, and ZbERF3.1 were significantly expressed at the fruit coloring stage (R2 and G2). ZbERF16 were significantly expressed at fruit ripening and expression level increased as the fruit continued to develop. Relative gene expression levels of 6 representative ZbAP2/ERFs assessed by RT-qPCR agreed with transcriptome analysis results.ConclusionsThese genes identified by screening can be used as candidate genes that affect fruit development. The results of the analysis can help guide future genetic improvement of Chinese prickly ash and enrich our understanding of AP2/ERF transcription factors and their regulatory functions in plants.

FvUVI4 inhibits cell division and cell expansion to modulate fruit development in Fragaria vesca

Fruit development is mainly regulated by cell division and expansion. As a negative regulator of the anaphase-promoting complex/cyclosome, UVI4 plays important roles in plant growth and development via coordinating cell cycle. However, currently there is no report on UVI4's functions in regulating fruit development in strawberry. Here, Fragaria vesca homolog FvUVI4 is identified and localizes in the nucleus. FvUVI4 has high gene expression in roots, leaves, flower, buds and green fruits, and low expression in petiole, stem, white and yellow fruit. Fruit development of F. vesca ‘Hawaii4’ is regulated by endoreduplication, and the expression of FvUVI4 is negatively correlated with fruit cell size. Overexpression of FvUVI4 inhibits endoreduplication of leaves, flowers and fruits in both Arabidopsis and F. vesca ‘Hawaii4’, thereby limiting cell expansion and decreasing cell area. Overexpression of FvUVI4 also inhibits mitotic cell cycle leading to decreased cell number, and ultimately affects the growth of leaves, petals and seeds or fruits. Arabidopsis uvi4 mutants obtained via CRISPR-Cas9 technology display opposite growth phenotypes to Arabidopsis and F. vesca ‘Hawaii4’ overexpression lines, which can be restored by overexpression of FvUVI4 in Arabidopsis uvi4 mutants. In conclusion, our study indicates that FvUVI4 inhibits cell expansion and cell division to modulate receptacle development in woodland strawberry.

Transcriptomics reveal useful resources for examining fruit development and variation in fruit size in Coccinia grandis.

The Cucurbitaceae family comprises many agronomically important members, that bear nutritious fruits and vegetables of great economic importance. Coccinia grandis, commonly known as Ivy gourd, belongs to this family and is widely consumed as a vegetable. Members of this family are known to display an impressive range of variation in fruit morphology. Although there have been studies on flower development in Ivy gourd, fruit development remains unexplored in this crop. In this study, comparative transcriptomics of two Ivy gourd cultivars namely "Arka Neelachal Kunkhi" (larger fruit size) and "Arka Neelachal Sabuja" (smaller fruit size) differing in their average fruit size was performed. A de novo transcriptome assembly for Ivy gourd was developed by collecting fruits at different stages of development (5, 10, 15, and 20 days after anthesis i.e. DAA) from these two varieties. The transcriptome was analyzed to identify differentially expressed genes, transcription factors, and molecular markers. The transcriptome of Ivy gourd consisted of 155205 unigenes having an average contig size of 1472bp. Unigenes were annotated on publicly available databases to categorize them into different biological functions. Out of these, 7635 unigenes were classified into 38 transcription factor (TF) families, of which Trihelix TFs were most abundant. A total of 11,165 unigenes were found to be differentially expressed in both the varieties and the in silico expression results were validated through real-time PCR. Also, 98768 simple sequence repeats (SSRs) were identified in the transcriptome of Ivy gourd. This study has identified a number of genes, including transcription factors, that could play a crucial role in the determination of fruit shape and size in Ivy gourd. The presence of polymorphic SSRs indicated a possibility for marker-assisted selection for crop breeding in Ivy gourd. The information obtained can help select candidate genes that may be implicated in regulating fruit development and size in other fruit crops.

A long noncoding RNA functions in pumpkin fruit development through S-adenosyl-L-methionine synthetase.

Long noncoding RNAs (lncRNAs) play important roles in various biological processes. However, the regulatory roles of lncRNAs underlying fruit development have not been extensively studied. The pumpkin (Cucurbita spp.) is a preferred model for understanding the molecular mechanisms regulating fruit development because of its variable shape and size and large inferior ovary. Here, we performed strand-specific transcriptome sequencing on pumpkin (Cucurbita maxima "Rimu") fruits at 6 developmental stages and identified 5,425 reliably expressed lncRNAs. Among the 332 lncRNAs that were differentially expressed during fruit development, the lncRNA MSTRG.44863.1 was identified as a negative regulator of pumpkin fruit development. MSTRG.44863.1 showed a relatively high expression level and an obvious period-specific expression pattern. Transient overexpression and silencing of MSTRG.44863.1 significantly increased and decreased the content of 1-aminocyclopropane carboxylic acid (a precursor of ethylene) and ethylene production, respectively. RNA pull-down and microscale thermophoresis assays further revealed that MSTRG.44863.1 can interact with S-adenosyl-L-methionine synthetase (SAMS), an enzyme in the ethylene synthesis pathway. Considering that ethylene negatively regulates fruit development, these results indicate that MSTRG.44863.1 plays an important role in the regulation of pumpkin fruit development, possibly through interacting with SAMS and affecting ethylene synthesis. Overall, our findings provide a rich resource for further study of fruit-related lncRNAs while offering insights into the regulation of fruit development in plants.

Overexpression of a BR inactivating enzyme gene GhPAG1 impacts eggplant fruit development and anthocyanin accumulation mainly by altering hormone homeostasis

Brassinosteroids (BRs) function importantly in plant growth and development, but the roles in regulating fruit development and anthocyanin pigmentation remain unclear. Eggplant (Solanum melongena L.) is an important Solanaceae vegetable crop rich in anthocyanins. The fruit size and coloration are important agronomic traits for eggplant breeding. In this study, transgenic eggplant exhibiting endogenous BRs deficiency was created by overexpressing a heterologous BRs-inactivating enzyme gene GhPAG1 driven by CaMV 35 S promoter. 35 S::GhPAG1 eggplant exhibited severe dwarfism, reduced fruit size, and less anthocyanin accumulation. Microscopic observation showed that the cell size of 35 S::GhPAG1 eggplant was significantly reduced compared to WT. Furthermore, the levels of IAA, ME-IAA, and active JAs (JA, JA-ILE, and H2JA) all decreased in 35 S::GhPAG1 eggplant fruit. RNA-Seq analyses showed a decrease in the expression of genes involved in cell elongation, auxin signaling, and JA signaling. Besides, overexpression of GhPAG1 significantly downregulated anthocyanin biosynthetic genes and associated transcription regulators. Altogether, these results strongly suggest that endogenous brassinosteroid deficiency arising from GhPAG1 overexpression impacts eggplant fruit development and anthocyanin coloration mainly by altering hormone homeostasis.

TKN3 affects cell expansion to regulate fruit development in tomato

Tomato is a model system for studying fleshy fruit development. After fertilization, cell division and expansion in the pericarp are crucial for fruit development and determine the final fruit size. TKN3 was found to be expressed in the tomato ovary wall/pericarp of zero to two days post-anthesis fruits as a KNOX I class member, but its function in fruit development was elusive. Here, we found that mutations of TKN3 by CRISPR/Cas9 caused fruit developmental defects, and fruit weight was dramatically reduced in the tkn3cr mutant. Histological observation of fruit pericarps revealed that mutation of TKN3 repressed cell expansion after fertilization, leading to flattened cells in the mesocarp and thereby thinner pericarps in red fruits. Moreover, tkn3cr mutants also displayed pleiotropic phenotypes including enlarged leaves and floral organs, indicating conserved functions in meristem maintenance and leaf development. Yeast two-hybrid and BiFC assays further showed that TKN3 could interact with Solyc10g086640 (a homolog of Arabidopsis PNY), which has a similar expression pattern as TKN3. Genome-wide identification of genes regulated by TKN3 indicated that the auxin and gibberellin (GA) pathways might mediate the function of TKN3. Our works revealed that TKN3 controls cell expansion in pericarps, and provides new insights into the roles of KNOX proteins in fruit development.

Transcriptome Analysis Reveals Candidate Genes Involved in Gibberellin-Induced Fruit Development in Rosa roxburghii.

Gibberellins (GAs) play indispensable roles in the fruit development of horticultural plants. Unfortunately, the molecular basis behind GAs regulating fruit development in R. roxburghii remains obscure. Here, GA3 spraying to R. roxburghii 'Guinong 5' at full-bloom promoted fruit size and weight, prickle development, seed abortion, ascorbic acid accumulation, and reduction in total soluble sugar. RNA-Seq analysis was conducted to generate 45.75 Gb clean reads from GA3- and non-treated fruits at 120 days after pollination. We obtained 4275 unigenes belonging to differently expressed genes (DEGs). Gene ontology and the Kyoto Encyclopedia of Genes and Genomes displayed that carbon metabolism and oxidative phosphorylation were highly enriched. The increased critical genes of DEGs related to pentose phosphate, glycolysis/gluconeogenesis, and citrate cycle pathways might be essential for soluble sugar degradation. Analysis of DEGs implicated in ascorbate revealed the myoinositol pathway required to accumulate ascorbic acid. Finally, DEGs involved in endogenous phytohormones and transcription factors, including R2R3 MYB, bHLH, and WRKY, were determined. These findings indicated that GA3-trigged morphological alterations might be related to the primary metabolites, hormone signaling, and transcription factors, providing potential candidate genes that could be guided to enhance the fruit development of R. roxburghii in practical approaches.

Biosynthesis, Mechanism and Potential Application of Hormones for Mitigating Stress, Conserving Bioactive Constituents in Fruits

The influence of plant growth regulators, including auxins, gibberellins, cytokinins, ethylene, abscisic acid, brassinosteroids, jasmonates, and salicylic acid, on fruit crop development and quality enhancement. Various stages of fruit crop growth, such as flowering, fruit set, ripening, and post-harvest attributes, are examined through comprehensive experimental approaches. Auxins play a crucial role in regulating fruit size, shape, and development by facilitating cell elongation. Gibberellins control fruit elongation, seed germination, and fruit set. Cytokinins influence fruit expansion, sugar metabolism, and overall quality by promoting cell division and differentiation. Ethylene affects fruit ripening processes, including color change, softening, and flavor development. Abscisic acid influences fruit maturation and dormancy. Brassinosteroids regulate fruit development, including size, ripening, and tolerance to abiotic stress. Jasmonates and salicylic acid, involved in defense responses, have an impact on fruit ripening, quality, and disease resistance. The application of these regulators shows promise in improving fruit quality, nutritional composition, and shelf life. This study aims to provide valuable insights into fruit crop physiology and develop strategies to optimize productivity and quality. It emphasizes the importance of proper regulation and responsible use of plant growth regulators to address environmental, health, and ecological concerns associated with excessive or improper application. Excessive use of PGRs can lead to various physiological issues, adversely affecting fruit crop productivity and quality. Therefore, careful control of application procedures, dosages, and timing is necessary to ensure fruit crop health and avoid negative consequences.

DbMADS regulates carotenoid metabolism by repressing two carotenogenic genes in the green alga Dunaliella sp. FACHB-847.

MADS transcription factors are involved in the regulation of fruit development and carotenoid metabolism in plants. However, whether and how carotenoid accumulation is regulated by algal MADS are largely unknown. In this study, we first used functional complementation to confirm the functional activity of phytoene synthase from the lutein-rich Dunaliella sp. FACHB-847 (DbPSY), the key rate-limiting enzyme in the carotenoid biosynthesis. Promoters of DbPSY and DbLcyB (lycopene β-cyclase) possessed multiple cis-acting elements such as light-, UV-B-, dehydration-, anaerobic-, and salt-responsive elements, W-box, and C-A-rich-G-box (MADS-box). Meanwhile, we isolated one nucleus-localized MADS transcription factor (DbMADS), belonging to type I MADS gene. Three carotenogenic genes, DbPSY, DbLcyB, and DbBCH (β-carotene hydroxylase) genes were upregulated at later stages, which was well correlated with the carotenoid accumulation. In contrast, DbMADS gene was highly expressed at lag phase with low carotenoid accumulation. Yeast one-hybrid assay and dual-luciferase reporter assay demonstrated that DbMADS could directly bind to the promoters of two carotenogenic genes, DbPSY and DbLcyB, and repress their transcriptions. This study suggested that DbMADS may act as a negative regulator of carotenoid biosynthesis by repressing DbPSY and DbLcyB at the lag phase, which provide new insights into the regulatory mechanisms of carotenoid metabolism in Dunaliella.

Combined Study of Transcriptome and Metabolome Reveals Involvement of Metabolites and Candidate Genes in Flavonoid Biosynthesis in Prunus avium L.

Sweet cherry (Prunus avium L.) is a popular fruit tree grown for its juicy fruit and pleasing appearance. The fruit pf the sweet cherry contains active antioxidants and other chemical compounds essential for human health. For this study, we performed the transcriptomics and metabolomics analysis using young Green Peel (GP) and mature Red Peel (RP) from sweet cherries to understand the underlying genetic mechanism regulating fruit development and ripening. Using high-throughput RNA sequencing and ultra-performance liquid chromatography, with quadrupole time-of-flight tandem mass spectrometry, respectively, metabolic and transcript profiling was obtained. Relative to GP, there were equal quantities of pronouncedly varied metabolites in RP (n = 3564). Differentially expressed genes (DEGs, n = 3564), containing 45 transcription factor (TF) families, were recorded in RP. Meanwhile, 182 differentially expressed TF (DETF) members of 37 TF families, were displayed in abundance in RP compared to GP sweet cherries. The largest quantities of DETFs were members of the ERF (25) and basic helix–loop–helix (bHLH) (19) families, followed by the MYB (18), WRKY (18), and C2H2 (12) families. Interestingly, most ERF genes were down-regulated, whereas CCCH genes were mainly up-regulated in RP. Other DETFs exhibited significant variations. In addition, RT-QPCR results and metabolomics data together with transcriptomic data revealed that the abundance of catechin, epicatechin, rhoifolin, myricetin, keracyanin, and the other six glycosyltransferase genes was highly increased in RP when compared to GP sweet cherries. The relatively higher expression of DETFs, metabolite, and flavonoid biosynthesis in RP sweet cherries suggests the accumulation of distinct metabolites that cause red coloring during fruit development and ripening. Thus, the metabolomics and transcriptomic analysis of the current study are powerful tools for providing more valuable information for the metabolic engineering of flavonoids biosynthesis in sweet cherries. They are also helpful in understanding the relationship between genotype and phenotype.

Mapping and identification of CsSF4, a gene encoding a UDP-N-acetyl glucosamine-peptide N-acetylglucosaminyltransferase required for fruit elongation in cucumber (Cucumis sativus L.).

The short fruit length phenotype in sf4 is caused by a SNP in Csa1G665390, which encodes an O-linked N-acetylglucosamine (GlcNAc) transferase in cucumber. Cucumber fruit is an excellent resource for studying fruit morphology due to its fast growth rate and naturally abundant morphological variations. The regulatory mechanisms underlying plant organ size and shape are important and fundamental biological questions. In this study, a short-fruit length mutant, sf4, was identified from an ethyl methanesulfonate (EMS) mutagenesis population derived from the North China-type cucumber inbred line WD1. Genetic analysis indicated that the short fruit length phenotype of sf4 was controlled by a recessive nuclear gene. The SF4 locus was located in a 116.7-kb genomic region between the SNP markers GCSNP75 and GCSNP82 on chromosome 1. Genomic and cDNA sequences analysis indicated that a single G to A transition at the last nucleotide of Csa1G665390 intron 21 in sf4 changed the splice site from GT-AG to GT-AA, resulting in a 42-bp deletion in exon 22. Csa1G665390 is presumed to be a candidate gene, CsSF4 that encodes an O-linked N-acetylglucosamine (GlcNAc) transferase (OGT). CsSF4 was highly expressed in the leaves and male flowers of wild-type cucumbers. Transcriptome analysis indicated that sf4 had alterations in expression of many genes involved in hormone response pathways, cell cycle regulation, DNA replication, and cell division, suggesting that cell proliferation-associated gene networks regulate fruit development in cucumber. Identification of CsSF4 will contribute to elucidating the function of OGT in cell proliferation and to understanding fruit elongation mechanisms in cucumber.

Comparative transcriptomic analysis of early fruit development in eggplant (Solanum melongena L.) and functional characterization of SmOVATE5.

Comparative transcriptome analysis of early fruits of long and round eggplants, SmOVATE5, is involved in regulating fruit development. Eggplant, a solanaceous crop that has undergone a long period of domestication, is one of the most important vegetables worldwide. The shape of its fruit is an important agronomic trait and consumers in different regions have different preferences. However, a limited understanding of the molecular mechanisms regulating fruit development and shape has hindered eggplant breeding. In this study, we performed morphological observations and transcriptome analysis of long- and round-fruited eggplant genotypes to understand the molecular regulation during the early development of different fruit shapes. Morphological studies revealed that the two varieties already exhibited distinctly different phenotypes at the initial stage of fruit development before flowering, with rapid fruit enlargement beginning on the sixth day after flowering. Comparative transcriptome analysis identified phytohormone-related genes that were significantly upregulated on the day of flowering, indicating they may be involved in regulating the initial stages of fruit development. Notably, SmARF1 showed a sustained upregulation pattern in both varieties, suggesting that it may promote eggplant fruit growth. In addition, several differentially expressed genes of the SUN, YABBY, and OVATE families are potentially involved in the regulation of fruit development or fruit shape. We demonstrated that the SmOVATE5 gene has a negative regulatory function suppressing plant growth and development. In conclusion, this study provides new insights into the molecular regulatory mechanisms of eggplant fruit development, and the genes identified may provide valuable references for different fruit shape breeding programs.

Comprehensive analysis of CYP78A family genes reveals the involvement of <i>CYP78A5</i> and <i>CYP78A10</i> in fruit development in eggplant

CYP78A family is a plant-specific family, members of which have been considered as promising targets for yield improvement due to their important roles in regulating organ size. Eggplant is an important vegetable cultivated worldwide. However, little information about the eggplant CYP78As (SmCYP78As) limits the potential utilization of SmCYP78As for crop improvement. In this study, we identified six CYP78A genes in eggplant genome and named <italic>SmCYP78A5</italic> to <italic>SmCYP78A10</italic> according to the phylogenetic relationships to Arabidopsis CYP78As. The phylogenetic analysis of CYP78As from eggplant, Arabidopsis, rice and tomato classified the 27 CYP78As into five clades. SmCYP78As were found in three of the five clades. This classification is consistently supported by their gene structures, domains and conserved motifs. Segmental duplication events were found to contribute the expansion of the SmCYP78A family. Comparative syntenic analysis provided further insight into the phylogenetic relationships of CYP78A genes from the four plants. qRT-PCR analysis revealed that the expression of the six SmCYP78As was detected in at least one of the eight tissues, showing a tissue-specific pattern. Notably, SmCYP78A5 and SmCYP78A10 were highly expressed in developing ovaries, indicating the involvement of fruit development in eggplant. Co-expression clustering and GO enrichment analysis suggested that <italic>SmCYP78A5</italic> and <italic>SmCYP78A10</italic> regulate fruit development likely through different pathways. In addition, six transcription factors were identified as promising candidates that may directly bind promoters of <italic>SmCYP78A5</italic> and <italic>SmCYP78A10</italic>. This study provides a comprehensive overview of the SmCYP78As family, which would lay a foundation for further understanding of evolution and function of SmCYP78A family.

CcMYB12 Positively Regulates Flavonoid Accumulation during Fruit Development in Carya cathayensis and Has a Role in Abiotic Stress Responses.

Flavonoid, an important secondary metabolite in plants, is involved in many biological processes. Its synthesis originates from the phenylpropane metabolic pathway, and it is catalyzed by a series of enzymes. The flavonoid biosynthetic pathway is regulated by many transcription factors, among which MYB transcription factors are thought to be key regulators. Hickory (Carya cathayensis) is an economic forest tree species belonging to the Juglandaceae family, and its fruit is rich in flavonoids. The transcriptome of exocarp and seed of hickory has previously been sequenced and analyzed by our team, revealing that CcMYB12 (CCA0691S0036) may be an important regulator of flavonoid synthesis. However, the specific regulatory role of CcMYB12 in hickory has not been clarified. Through a genome-wide analysis, a total of 153 R2R3-MYB genes were identified in hickory, classified into 23 subclasses, of which CcMYB12 was located in Subclass 7. The R2R3-MYBs showed a differential expression with the development of hickory exocarp and seed, indicating that these genes may regulate fruit development and metabolite accumulation. The phylogenetic analysis showed that CcMYB12 is a flavonol regulator, and its expression trend is the same as or opposite to that of flavonol synthesis-related genes. Moreover, CcMYB12 was found to be localized in the nucleus and have self-activation ability. The dual-luciferase reporter assay demonstrated that CcMYB12 strongly bonded to and activated the promoters of CcC4H, CcCHS, CcCHI, and CcF3H, which are key genes of the flavonoid synthesis pathway. Overexpression of CcMYB12 in Arabidopsis thaliana could increase the content of total flavonoids and the expression of related genes, including PAL, C4H, CHS, F3H, F3’H, ANS, and DFR, in the flavonoid synthesis pathway. These results reveal that CcMYB12 may directly regulate the expression of flavonoid-related genes and promote flavonoid synthesis in hickory fruit. Notably, the expression level of CcMYB12 in hickory seedlings was significantly boosted under NaCl and PEG treatments, while it was significantly downregulated under acid stress, suggesting that CcMYB12 may participate in the response to abiotic stresses. The results could provide a basis for further elucidating the regulation network of flavonoid biosynthesis and lay a foundation for developing new varieties of hickory with high flavonoid content.

Genome-wide identification and expression analysis of the MADS-box gene family during female and male flower development in Juglans mandshurica

The MADS-box gene family plays a crucial role in multiple developmental processes of plants, especially in floral organ specification and the regulation of fruit development and ripening. Juglans mandshurica is a precious fruit material whose quality and yield are determined by floral organ development. The molecular mechanism of J. mandshurica female and male flower development depending on MADS-box genes remains unclear. In our study, 67 JmMADS genes were identified and unevenly distributed on 15 of 16 J. mandshurica chromosomes. These genes were divided into two types [type I (Mα, Mγ, Mδ) and type II (MIKC)]. The gene structure and motif analyses showed that most genes belonging to the same type had similar gene structures and conserved motifs. The analysis of syntenic relationships showed that MADS-box genes in J. mandshurica, J. sigillata, and J. regia exhibited the highest homology and great collinearity. Analysis of cis-acting elements showed that JmMADS gene promoter regions contained light, stress and hormone response cis-acting elements. The gene expression patterns demonstrated that 30 and 26 JmMADS genes were specifically expressed in the female and male flowers, respectively. In addition, 12 selected genes common to J. mandshurica female and male flowers were significantly upregulated at the mature stage and were used to validate the reliability of the transcriptome data using quantitative real-time PCR. This comprehensive and systematic analysis of J. mandshurica MADS-box genes lays a foundation for future studies on MADS-box gene family functions.

Genome-wide analysis of histone acetyltransferase and histone deacetylase families and their expression in fruit development and ripening stage of pepper (Capsicum annuum).

The fruit development and ripening process involve a series of changes regulated by fine-tune gene expression at the transcriptional level. Acetylation levels of histones on lysine residues are dynamically regulated by histone acetyltransferases (HATs) and histone deacetylases (HDACs), which play an essential role in the control of gene expression. However, their role in regulating fruit development and ripening process, especially in pepper (Capsicum annuum), a typical non-climacteric fruit, remains to understand. Herein, we performed genome-wide analyses of the HDAC and HAT family in the pepper, including phylogenetic analysis, gene structure, encoding protein conserved domain, and expression assays. A total of 30 HAT and 15 HDAC were identified from the pepper genome and the number of gene differentiation among species. The sequence and phylogenetic analysis of CaHDACs and CaHATs compared with other plant HDAC and HAT proteins revealed gene conserved and potential genus-specialized genes. Furthermore, fruit developmental trajectory expression profiles showed that CaHDAC and CaHAT genes were differentially expressed, suggesting that some are functionally divergent. The integrative analysis allowed us to propose CaHDAC and CaHAT candidates to be regulating fruit development and ripening-related phytohormone metabolism and signaling, which also accompanied capsaicinoid and carotenoid biosynthesis. This study provides new insights into the role of histone modification mediate development and ripening in non-climacteric fruits.