Search Results (354)

Background/Objectives: Low-temperature stress during the grain-filling stage negatively affects rice grain quality and yield. Understanding the physiological and molecular mechanisms underlying cold tolerance is critical for breeding rice varieties with improved resilience. Methods: In this study, eight rice varieties with differential cold tolerance—LD1603, 13108, LD18, and 4-1021 (cold-tolerant) and LD3, LD4, LD121, and LD1604 (cold-sensitive)—were subjected to 17.5 °C low-temperature stress during grain filling in a naturally illuminated phytotron. Amylose and protein content, as well as taste quality, were analyzed. RNA sequencing was performed to identify differentially expressed genes and transcription factors associated with cold response. Results: Under low-temperature stress, amylose and protein content significantly increased in all eight varieties. The taste quality of cold-sensitive varieties declined markedly, whereas cold-tolerant varieties maintained higher and more stable taste quality values. Transcriptomic analysis revealed that key enzyme genes (INV, SUS, HXK, FRK, amyA, and TPP) in the starch and sucrose metabolism pathway were significantly upregulated in cold-tolerant varieties (LD18 and 4-1021), but suppressed in cold-sensitive varieties. Several cold-responsive transcription factors from the NAC, WRKY, AP2/ERF, MYB, and bZIP families were also identified. Weighted gene co-expression network analysis (WGCNA) further revealed hub TFs (OsWRKY1, OsWRKY24, OsWRKY53, and OsMYB4) and structural genes (OsPAL04 and OsCDPK7) potentially involved in cold tolerance during grain filling. Conclusions: This study enhanced our understanding of the molecular response to low temperature during rice grain filling and provided candidate genes for developing cold-tolerant rice varieties through molecular breeding. Full article

Chrysanthemum morifolium Ramat. is an important ornamental plant, holding dual economic value as a medicinal and edible plant. Jinsi Huangju is a popular healthy tea drink prepared from the large and elegant shaped flowers of C. morifolium. However, the suboptimal accumulation of bioactive flavonoids during conventional harvest (full bloom stage) limits its commercial potential. To elucidate the molecular mechanisms governing flavonoid biosynthesis in Jinsi Huangju flowers and identify key genetic regulators for metabolic engineering, we performed integrated metabolomic and transcriptomic analyses of flowers at distinct developmental stages using ultra-performance liquid chromatography–tandem mass spectrometry (UPLC-MS/MS) and RNA-seq. Differential metabolites were screened, and candidate genes were validated via transient transformation assays. Among 2146 identified metabolites, flavonoids were the predominant differential compounds, with accumulation patterns being strongly stage dependent. Thirty-eight flavonoid biosynthetic genes and key transcription factors from the MYB, bHLH, and WD40 families exhibited dynamic expression. The CmMYB8a was confirmed as a positive regulator of flavonoid biosynthesis through transient overexpression. This study deciphers the stage-specific flavonoid accumulation in Jinsi Huangju and identifies CmMYB8a as a pivotal regulatory target. Our findings provide genetic resources for breeding high-flavonoid cultivars via molecular design. Full article

Fruit shape is an important quality and yield trait of pear, and the fruit shape of ‘Laiyang Cili’ presents a spindle shape which seriously affects its commercial value. Calyx excision treatment could change the fruit shape, while the underlying genes and their regulatory mechanism remain poorly understood. In this study, we constructed RNA-seq libraries of pear treated with calyx excision to explore underlying regulatory mechanisms. At the early stage of the calyx excision treatment, the numbers of differentially expressed genes (DEGs) between each comparison group were relatively high and gradually decreased along with fruit development. The expression pattern of the DEGs ranked in the top 30 of the six groups had obvious divergence, and DEGs were mainly distributed in the “after calyx excision treatment (0 days)” (AC0d) and AC2d groups. The DEGs were mainly enriched in plant hormone signal transduction and plant defense response. We identified 17 candidate genes related to fruit shape and tested their expression patterns along with fruit development. Among them, nine candidate genes expression trends were consistent with fragments per kilobase of exon model per million mapped fragment (FPKM) values, including MYB62, outer envelope pore protein 62 (OEP62), auxin response factor 3 (ARF3), auxin-responsive protein 50 (SAUR50), protein phosphatase 2C 51 (PP2C 51), major allergen Pyr c 1 (PYRC1), aquaporin TIP1-3 (TIP1-3), transcription factor TGA4 (TGA4) and auxin-responsive protein 17 (IAA17). And then, weighted gene co-expression network analysis (WGCNA) analysis revealed that the OVATE family protein (OFP) and SUN domain-containing protein (SUN) were divided into the MEblue model, which had a positive correlation with calyx excision treatment, and the expression trend of LOC103960706 (OFP8) appeared cohesive with FPKM values. Pbr014104.1 and Pbr016952.1, which were the ortholog genes of LOC103960706, were further identified from the pear genome, and were found to be highly expressed in pear fruit through RT-PCR analysis. Taken together, the key stage determining the development of fruit shape was in the early stage after calyx excision treatment, and fruit shape regulation and development were co-regulated by multiple genes. Full article

Passion fruit (Passiflora edulis Sims), belonging to the Passifloraceae family, is an economically important plant in tropical and subtropical regions. The advances in functional genomics research of passion fruit have been significantly hindered by its recalcitrance to regeneration and stable transformation. This study establishes the first efficient Agrobacterium rhizogenes-mediated hairy root transformation system for passion fruit. Utilizing the eGFP marker gene, transformation efficiencies of 11.3% were initially achieved with strains K599, MSU440, and C58C1, with K599 proving most effective. Key transformation parameters were systematically optimized to achieve the following: OD₆₀₀ = 0.6, infection duration 30 min, acetosyringone concentration 100 μM, and a dark co-cultivation period of 2 days. The system’s utility was further enhanced by incorporating the red visual marker RUBY, enabling direct, instrument-free identification of transgenic roots via betaxanthin accumulation. Finally, this system was applied for functional analysis using PeMYB123, which may be involved in proanthocyanidin accumulation. Overexpression of PeMYB123 produced a higher content of proanthocyanidin in hairy roots. Additionally, the PeANR gene involved in the proanthocyanidin pathway was strongly activated in the transgenic hairy roots. This rapid and efficient visually simplified hairy root transformation system provides a powerful tool for functional gene studies in passion fruit. Full article

Background/Objectives: Moso bamboo (Phyllostachys edulis), the most widely distributed bamboo species in China, is valued for both its shoots and timber. This species often faces challenges from high-temperature stress. To cope with this stress, Moso bamboo has evolved various adaptive mechanisms at the physiological and molecular levels. Although numerous studies have revealed that a large number of transcription factors (TFs) and genes play important roles in the regulatory network of plant heat stress responses, the regulatory network involved in heat responses remains incompletely understood. Methods: In this study, Moso bamboo was placed in a high-temperature environment of 42 °C for 1 h and 24 h, and transcriptome sequencing was carried out to accurately identify key molecules affected by high temperature and their related biological pathways. Results: Through a differential expression analysis, we successfully identified a series of key candidate genes and transcription factors involved in heat stress responses, including members of the ethylene response factor, HSF, WRKY, MYB, and bHLH families. Notably, in addition to traditional heat shock proteins/factors, multiple genes related to lipid metabolism, antioxidant enzymes, dehydration responses, and hormone signal transduction were found to play significant roles in heat stress responses. To further verify the changes in the expression of these genes, we used qRT-PCR technology for detection, and the results strongly supported their key roles in cellular physiological processes and heat stress responses. Conclusions: This study not only deepens our understanding of plant strategies for coping with and defending against extreme abiotic stresses but also provides valuable insights for future research on heat tolerance in Moso bamboo and other plants. Full article

Dunaliella salina, a unicellular and eukaryotic alga, has been found to be one of the most salt-tolerant eukaryotes with a wide range of practical applications. To elucidate the underlying molecular mechanisms of D. salina in response to salinity stress, we performed transcriptome sequencing on samples under different stress conditions. A total of 82,333 unigenes were generated, 4720, 1111 and 2611 differentially expressed genes (DEGs) were identified under high salt stress, oxidative stress and hypertonic stress, respectively. Our analysis revealed that D. salina responds to salinity stress through a complex network of molecular mechanisms. Under high salt stress, starch degradation is regulated by AMY (α-amylase) and PYG (glycogen phosphorylase) with alternative expression patterns. This process is hypothesized to be initially constrained by low ATP levels due to impaired photosynthesis. The clustering analysis of DEGs indicated that starch and sucrose metabolism, as well as glycerol metabolism, are specifically reprogrammed under high salt stress. Glycerol metabolism, particularly involving GPDHs, plays a crucial role in maintaining osmotic balance under salinity stress. Key glycerol metabolism genes were up-regulated under salinity conditions, indicating the importance of this pathway in osmotic regulation. The G3P shuttle, involving mitochondrial GPDHs (c25199_g1 and c23777_g1), contributes to redox imbalance management under high salt, oxidative and hypertonic stresses. Notably, c23777_g1 is involved in the G3P shuttle under high salt, oxidative and hypertonic stresses, while c25199_g1 is specifically induced by hypertonic stress. The R2R3-MYB gene (c23845_g1) may respond to different effects of salinity stress by regulating the transcription of ROS-related genes. Our study provides a detailed understanding of the molecular responses of D. salina to salinity stress. We reveal the critical roles of starch and sucrose metabolism, glycerol metabolism and transcription factors in the D. salina adaptation to salinity. Full article

Background/Objectives: Chinese cabbage (Brassica rapa ssp. Pekinensis, AA) growth and development is highly sensitive to cold temperatures. Prolonged low-temperature exposure during early growth stages can induce premature bolting, which reduces market quality and yield. Methods: Here, using comparative leaf RNA-seq transcriptome analysis of plants grown at 6, 9, 12, and 15 °C, we explored key genes and metabolic pathways regulating Chinese cabbage cold response. Results: RNA-seq transcriptome analysis identified a total of 1832 differentially expressed genes (DEGs) in the three comparison groups, with 5452, 1861, and 752 DEGs specifically expressed in the A6_vs_A15, A9_vs_A15, and A12_vs_A15 groups, respectively. KEGG enrichment analysis of DEGs showed that sulfur metabolism, secondary metabolites biosynthesis and photosynthesis pathways were mostly affected by cold stress. K-means clustering revealed distinct expression profiles among the DEGs enriched in cold stress response-associated clusters. Subsequently, DEGs were divided into 18 modules by WGCNA, whereupon co-expression genes that clustered into similar modules exhibited diverse expression and were annotated to various GO terms at different temperatures. Module-trait association analysis revealed M1, M2, M3, and M6 modules as key clusters potentially linked to vernalization-related processes. These modules harbored candidate hub genes encoding transcription factors (including MYB, bZIP, and WRKY), protein kinases, and cold-stress-responsive genes. Additionally, phenotypic analysis showed that 12 °C to 15 °C supported optimal growth, whereas <9 °C temperature inhibited growth. Physiological measurements showed increased antioxidant enzyme activity and proline accumulation at 6 °C. Conclusions: Overall, our study provides a set of candidate cold-stress-responsive genes and co-expression modules that may support cold stress tolerance breeding in Chinese cabbage. Full article

The establishment of a transient expression system in petals is significant for elucidating gene functions in flowering trees characterized by a prolonged juvenile phase. Genetic improvements in Camellia japonica have been hindered due to the absence of a functional validation platform. In this study, we explored an Agrobacterium-mediated and readily observable transient expression system in camellia petals to systematically optimize four critical factors affecting transformation efficiency. As a result, the bud stage, ‘Banliuxiang’ genotype, OD600 of 1.0, and 1-day co-cultivation achieved the highest intensity of transient expression, and overexpression of the Ruby1 reporter gene induced substantial anthocyanin synthesis, manifested as distinct red pigmentation. Furthermore, the optimized transient expression system revealed that the R2R3-MYB transcription factor CjMYB5, which interacted with CjGL3, promoted anthocyanin biosynthesis in camellia petals by transactivating key DFR structural genes. This transient expression platform not only advances functional genomics studies in ornamental woody species but also lays a foundation for molecular breeding programs in C. japonica. Full article

Tomato (Solanum lycopersicum) is a globally important crop, and enhancing its fruit quality and phenotypic traits is a key objective in modern breeding. This study investigates the role of the LEAFY-COTYLEDON1-LIKE4 (L1L4), an NF-YB subunit of the nuclear factor Y (NF-Y) transcription factor, in tomato fruit development using RNA-sequencing data from zinc-finger nuclease (ZFN)-targeted disruption lines. Differential gene expression (DEG) analyses of two independent l1l4 mutant lines compared to the wild-type line revealed significant alterations in key metabolic pathways and regulatory networks that are implicated in fruit ripening. Specifically, L1L4 disruption impacted the genes and pathways related to the fruit’s color development (carotenoid and flavonoids), texture (cell wall modification), flavor (sugar and volatile organic compound metabolism), and ripening-related hormone signaling. The analyses also revealed multiple differentially expressed histones, histone modifiers, and transcription factors (ERFs, MYBs, bHLHs, WRKYs, C2H2s, NACs, GRAS, MADs, and bZIPs), indicating that L1L4 participates in a complex regulatory network. These findings provide valuable insights into the role of L1L4 in orchestrating tomato fruit development and highlight it as a potential target for genetically improving the fruit quality. Full article

Plant protein phosphatase 2C (PP2C) represents the largest and most functionally diverse group of protein phosphatases in plants, playing pivotal roles in regulating metabolic processes, hormone signaling, stress responses, and growth regulation. Despite its significance, a comprehensive genome-wide analysis of the PP2C gene family in oat (Avena sativa L.) has remained unexplored. Leveraging the recently published oat genome, we identified 194 AsaPP2C genes, which were unevenly distributed across all 21 chromosomes. A phylogenetic analysis of PP2C classified these genes into 13 distinct subfamilies (A-L), with conserved motif compositions and exon-intron structures within each subfamily, suggesting evolutionary functional specialization. Notably, a promoter analysis revealed an abundance of stress-responsive cis-regulatory elements (e.g., MYB, MYC, ARE, and MBS), implicating AsaPP2Cs in hormones and biotic stress adaptation. To elucidate their stress-responsive roles, we analyzed transcriptomic data and identified seven differentially expressed AsaPP2C (Asa_chr6Dg00217, Asa_chr6Ag01950, Asa_chr3Ag01998, Asa_chr5Ag00079, Asa_chr4Cg03270, Asa_chr6Cg02197, and Asa_chr7Dg02992) genes, which were validated via qRT-PCR. Intriguingly, these genes exhibited dynamic expression patterns under varying stress conditions, with their transcriptional responses being both time-dependent and stress-dependent, highlighting their regulatory roles in oat stress adaptation. Collectively, this study provides the first comprehensive genomic and functional characterization of the PP2C family in oat, offering valuable insights into their evolutionary diversification and functional specialization. Full article

Annexins (ANNs) are a family of calcium (Ca²⁺)-dependent and phospholipid-binding proteins, which are implicated in the regulation of plant growth and development as well as protection from biotic and abiotic stresses. Corydalis saxicola Bunting, an endangered benzylisoquinoline alkaloid (BIA)-rich herbaceous plant, widely used in traditional Chinese medicine, is endemic to the calciphilic karst region of China. However, whether and how ANNs are involved in the biosynthesis pathway of BIAs and/or help C. saxicola plants cope with abiotic properties, such as calcareous soils, are largely unknown. Here, nine CsANN genes were identified from C. saxicola, and they were divided into three subfamilies, namely subfamilies I, II, and IV, based on the phylogenetic tree. The CsANNs clustered into the same clade, sharing similar gene structures and conserved motifs. The nine CsANN genes were located on five chromosomes, and their expansions were mainly attributed to tandem and whole-genome duplications. The CsANN transcripts displayed organ-specific and Ca²⁺-responsive expression patterns across various tissues. In addition, transient overexpression assays showed that CsANN1 could positively regulate the accumulation of BIA compounds in C. saxicola leaves, probably by directly interacting with key BIA-biosynthetic-pathway enzymes or by interacting with BIA-biosynthetic regulatory factors, such as MYBs. This study sheds light on the profiles and functions of the CsANN gene family and paves the way for unraveling the molecular mechanism of BIA accumulation, which is regulated by Ca²⁺ through CsANNs. Full article

The occurrence of anthocyanins in rice (Oryza sativa) and barley (Hordeum vulgare) varies among cultivars, with pigmented varieties (e.g., black rice and purple barley) accumulating higher concentrations due to genetic and environmental factors. The biosynthesis of anthocyanins is regulated by a complex network of structural and regulatory genes. Key enzymes in the pathway include chalcone synthase (CHS), chalcone isomerase (CHI), flavanone 3-hydroxylase (F3H), dihydroflavonol 4-reductase (DFR), anthocyanidin synthase (ANS), and UDP-glucose flavonoid 3-O-glucosyltransferase (UFGT). These genes are tightly controlled by transcription factors (TFs) from the MYB, bHLH (basic helix–loop–helix), and WD40 repeat families, which form the MBW (MYB-bHLH-WD40) regulatory complex. In rice, OsMYB transcription factors such as OsMYB3, OsC1, and OsPL (Purple Leaf) interact with OsbHLH partners (e.g., OsB1, OsB2) to activate anthocyanin biosynthesis. Similarly, in barley, HvMYB genes (e.g., HvMYB10) coordinate with HvbHLH TFs to regulate pigment accumulation. Environmental cues, such as light, temperature, and nutrient availability, further modulate these TFs, influencing the production of anthocyanin. Understanding the genetic and molecular mechanisms behind the biosynthesis of anthocyanins in rice and barley provides opportunities for the development of biofortification strategies that enhance their nutritional value. Full article

Polyembryonic maize, capable of producing multiple seedlings from a single kernel, holds great potential value in agricultural and industrial applications, but the seedling quality needs to be improved. In this study, seedlings of two waxy maize (Zea mays L. sinensis Kulesh) inbred lines, D35 (a polyembryonic line with twin shoots) and N6110 (single-shoot), exhibited similar relative growth rates during 1 to 5 days post-germination. UPLC-MS/MS profiling of 3- to 5-day-old seedling roots and shoots revealed that H2JA, MeSAG, and IAA-Val-Me were the common differentially accumulated metabolites (DAMs) of the 3-day-old vs. 5-day-old seedlings of D35 and N6110 in the same tissues, and MeSAG, tZ9G, cZROG, and DHZROG were identified in D35 vs. N6110 across the same tissues and the same periods. RNA-seq analyses showed various processes involved in seedling development, including DNA replication initiation, rhythmic processes, the cell cycle, secondary metabolic processes, and hormone biosynthetic regulation. The differentially expressed genes (DEGs) between D35 and N6110 were significantly enriched in organic hydroxy compound biosynthetic, alcohol biosynthetic, organic hydroxy compound metabolic, abscisic acid biosynthetic, and apocarotenoid biosynthetic processes. The KEGG-enriched pathways of DAMs and DEGs identified that AUX1, AHP, A-ARR, JAR1, SIMKK, ERF1, and GID2 might be conserved genes regulating seedling growth. The integrated analyses revealed that 98 TFs were potentially associated with multiple hormones, and 24 of them were identified to be core genes, including 11 AP2/ERFs, 4 Dofs, 2 bZIPs, 2 MADS-box genes, 2 MYBs, 1 GATA, 1 LOB, and 1 RWP-RK member. This study promotes a valuable understanding of the complex hormone interactions governing twin-shoot seedling growth and offers potential targets for improving crop establishment via seedling quality. Full article

The SWEET gene family is a group of genes with important functions in plants that is mainly involved in the transport and metabolism of carbohydrate substances. In this study, 32 mango (Mangifera indica L.) SWEET genes were screened and identified at the whole-genome level through bioinformatics methods. A systematic predictive analysis was conducted on their physicochemical properties, homology relationships, phylogenetic relationships, chromosomal locations, genomic structures, promoter cis-acting elements, and transcription factor regulatory networks. Meanwhile, the transcription levels of mango SWEET genes in different varieties and at different fruit development stages were also analyzed to obtain information about their functions. These results showed that 32 mango SWEET genes were unevenly distributed on 12 chromosomes. Phylogenetic analysis divided the SWEET proteins of mango, Arabidopsis thaliana (L.) Heynh., and Oryza sativa L. into four clades; in each clade, the mango SWEET proteins were more closely related to those of Arabidopsis. Four types of cis-acting elements were also found in the promoter regions of mango SWEET genes, including light-responsive elements, development-related elements, plant hormone-responsive elements, and stress-responsive elements. Interestingly, we found that the Misweet3 and Misweet10 genes showed strong expression in different mango varieties and at different fruit development stages, and they both belonged to the fourth Clade IV (G4) in the phylogenetic tree, indicating that they play a key role in the sugar accumulation process of mango. In this study, the upstream transcription factors of Misweet3, Misweet8, Misweet9, Misweet10, Misweet17, Misweet18, Misweet19, Misweet21, Misweet23, Misweet25, Misweet27, and Misweet31, those that had high expression levels in the transcriptome data, were predicted, and transcription factors such as ERF, NAC, WRKY, MYB, and C₂H₂ were screened. The results of this study provide a new way to further study the regulation of mango SWEET family genes on sugar accumulation, highlight their potential role in fruit quality improvement, and lay an important foundation for further study of mango SWEET function and enhance mango competitiveness in fruit market. Full article

Fruit color serves as a crucial visual indicator in chili peppers and is closely linked to the bioactive components that determine their economic and nutritional value. However, the specific components and potential molecular mechanisms that impact fruits’ development and color changes are less thoroughly understood. Here, we utilized three chili pepper varieties (CS03, CS29, and L816) at different developmental stages (young fruit stage, turning color stage, and mature stage) as research materials and integrated transcriptome and non-targeted metabolome analyses to explore the variation in bioactive components and color to explain the molecular regulatory mechanisms underlying different colors of chili peppers during the young fruit stage. Our results showed that flavonoids were the most enriched differential metabolites; aromadendrin 4′-glucoside, diospyrin, precarthamin, kaempferol-3-O-rutinoside, and kaempferol-3-O-Glucoside were significantly enriched in the young fruit stage of pepper CS03; and cyanidin, delphinidin, and cyanidin 3-glucoside were major contributors to the color formation. The upregulation of anthocyanin was related to the structural genes CaC4H, Ca4CL, CaCHS, CaF3H, CaANS, and CaUFGT, and key transcription factors such as CaMYBs and CabHLHs may have contributed to the differential accumulation of anthocyanins in CS03; in addition, RT-qPCR validation was correlated with anthocyanins, but also with flavonoids. This article mainly focuses on the changes in chili pigments, particularly anthocyanins, and explores the molecular mechanisms involved. This provides a reference for research on color in solanaceae vegetables and lays a theoretical foundation for further research on the bioactive components of chili peppers, as well as for optimizing harvesting practices and dietary recommendations. Full article