Search Results (344)

Domestication has been proven to significantly impact the biosynthesis of plant secondary metabolites. Cultivated green jujube (Ziziphus mauritiana Lam.), as an important autotetraploid fruit crop widely planted in tropical regions, exhibits differential physicochemical traits compared with its wild progenitor. To assess the traits lost in cultivated green jujube during domestication, the study performed comprehensive genomic, transcriptomic and metabolomic investigations of flavonoid pathways in wild and cultivated green jujube. Based on the four haplotype genomes of wild and cultivated green jujube, for the first time, the study bulk-identified 16 key gene families associated with flavonoid biosynthesis. Collinearity analysis revealed that tandem duplication was the predominant event in flavonoid-related genes rather than WGD. Through the expression profiles in different tissues, the distinct member of these gene families was classified as “redundant” or “functional”. Transcriptomic analyses illustrated the significant differential expressions (p < 0.05) of 13 flavonoid-related gene families in fruits of six cultivated and three wild green jujube accessions, except for FLS, LAR and PPO. The wild green jujube fruits accumulated more abundance of flavonoid metabolites than in cultivated fruits (p < 0.0001), as evidenced by upregulated chalcones, dihydroflavonol, isoflavones and flavonoid carbonoside. Gene–metabolite co-expression modules further validated the potential transcription regulators, such as BBX21, WRI1 and bZIP44. Together, the study suggested a genomic, transcriptomic and metabolic perspective for domestication regarding fruit flavonoid pathways in green jujube, which provides a valuable genetic resource for fruit quality improvement in cultivated green jujube. Full article

The blood orange arose from the insertion of a retrotransposon adjacent to the Ruby gene, an MYB-type transcriptional activator of anthocyanin production, as reported previously. However, the intricate process of anthocyanin regulation among different varieties of blood orange remains incompletely understood. In this study, mRNA levels of the transcription factors Ruby and TT8 were found to be upregulated in the juice vesicle tissues of a variety with higher concentrations of anthocyanins in the pulp compared with another variety with a lower anthocyanin content. In contrast, comparative analysis of the two varieties using two-dimensional electrophoresis and mass spectrometry did not identify differentially expressed proteins related to anthocyanin biosynthesis in the juice vesicle tissues. Furthermore, higher anthocyanin contents were observed in various tissues of transgenic Arabidopsis thaliana overexpressing the Ruby gene from blood orange compared with the wildtype plant. Moreover, the long terminal repeat (LTR) region of a retrotransposon inserted upstream of the Ruby locus exhibited the ability to drive reporter expression through histochemical assay in a transgenic seedling. Thus, a PCR-based molecular marker was developed, targeting the upstream sequence of the Ruby locus to identify Citrus hybrids with the unique trait of red-fleshed fruit. Intriguingly, bisulfite sequencing revealed differentially methylated regions within a Gag-Pol polyprotein-encoding sequence of a retrotransposon adjacent to Ruby locus when comparing two varieties with different anthocyanin contents. A higher average level of methylation status was observed in the fruit with a lower anthocyanin content. In conclusion, methylation modifications at specific upstream positions on the Ruby locus may influence anthocyanin production in blood oranges. 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

As the primary harvested organ, fruit size and weight hold significant economic importance during tomato production. Therefore, elucidating the genetic mechanisms underlying fruit size and weight is of considerable agronomic value. In this study, the Solanum pimpinellifolium introgression lines were constructed with “LA2093” as the donor and “Jina” as the recipient, and a genetic linkage map was constructed. Preliminary QTL mapping was conducted using four fruit-related traits: single fruit weight, fruit diameter, fruit length, and fruit shape index. A total of 10 QTLs were identified, including one for single fruit weight (qFw-3), five for fruit diameter (qFtd-3-1, qFtd-3-2, qFtd-4, qFtd-7, and qFtd-12), two for fruit length (qFl-3 and qFl-11), and two for fruit shape index (qFsi-2 and qFsi-3). To explore the key regulatory genes of the single fruit weight QTL qFw-3 locus, it was further finely mapped between SSR3-14 and C03M65101. The SSR3-14 and C03M65101 interval contained 57 genes on chromosome 3 (64.68–65.10 Mb) in the reference genome. Among these, eight genes, including Solyc03g114830, Solyc03g114870, Solyc03g114880, Solyc03g114890, Solyc03g114900, Solyc03g114910, Solyc03g115200, and Solyc03g115380, were identified as candidate genes involved in regulating fruit weight. These studies provide a basis for future functional validation of key regulatory genes and offer valuable genetic resources for the improvement of fruit size and weight during tomato breeding. Full article

The rugose surface trait in pepper (Capsicum annuum L.), marked by ridges and depressions on the fruit epidermis, is linked to improved fruit texture. To investigate its regulatory basis, histological, textural, and transcriptomic differences, contrasting genotypes were analyzed. Histological analysis revealed that disorganized epidermal cell layers contribute to rugosity, with morphological differences emerging around 10 days post-anthesis (DPA). A computer-aided design (CAD)-based rugosity index (RI) was developed and showed strong correlation with sensory rugosity scores (R² = 0.659, p < 0.001). Texture analysis demonstrated that increasing surface rugosity was associated with reduced rupture force and hardness, as well as elevated pectinase activity. Comparative transcriptome profiling identified 10 differentially expressed genes (DEGs) related to microtubule dynamics (e.g., CA03g18310 and CA09g13510) and phytohormone signaling (e.g., CA03g35180 and CA08g12070), which exhibited distinct spatial and temporal expression patterns. These findings suggest that coordinated cytoskeletal remodeling and hormonal regulation drive epidermal disorganization, leading to surface rugosity and altered fruit texture. The study provides novel insights into the molecular basis of fruit surface morphology and identifies promising targets for breeding high-quality pepper cultivars. Full article

The goal of this study was to build an understanding of the quality of Idesia polycarpa fruit Maxim from different ecotypes and to identify the best cultivars, with a view to providing a reference and theoretical basis for the selection and cultivation of I. polycarpa. In this study, we systematically evaluated the fruit quality characteristics of five seed sources, namely SH, SG1, GG, HX, and SG2, at four developmental stages, M1-M4, through a principal component analysis, a correlation analysis, and a significance test. Comparisons between the ecotype yielded that GG was significantly better than the other ecotype in oil content (28.7%) and fresh weight per cluster (155.56 g), while HX exhibited higher SOD content (278.18 U/g) and soluble protein content (27.50 mg·g⁻¹), suggesting a higher level of stress tolerance. The results of the correlation analysis showed that POD was significantly negatively correlated with oil content (r = −0.633) and SOD (r = −0.617) activities, indicating that the antioxidant enzyme system may affect oil accumulation. The results of the principal component analysis showed that the cumulative contribution of the first four principal components reached 89.72%, of which principal component 1 mainly reflected yield-related traits, and principal component 2 was significantly correlated with oil content and soluble protein. Through the evaluation and screening of the five ecotypes, we determined that GG can be utilized as a good single plant in the selection and improvement of new cultivars; our findings can provide theoretical support for the selection of good cultivars of I. polycarpa seed in the central region of Henan. Full article

Fruit size is an important agronomic trait affecting the yield and commercial value of melon and a key trait selected for during domestication. In this study, two respective melon accessions (large-fruited M202008 and small-fruited M202009) were crossed, and developed biparental mapping populations of the F₂ generation (160 and 382 plants) were checked across two subsequent experimental years (2023 and 2024). The phenotypic characterization and genetic inheritance analysis showed that melon fruit size is modulated by quantitative genetics. Bulked segregant sequencing analysis (BSA-seq) identified a stable and effective quantitative trait locus (QTL, named Cmfs) controlling fruit size, localized to a 3.75 Mb region on chromosome 9. To better delineate the main-effect Cmfs locus, co-dominant polymorphic molecular markers were developed in this genetic interval, and genotyping was performed within the F₂ mapping populations grown across two years. QTL analysis of the phenotypic and genotypic datasets delimited the major-effect Cmfs locus interval for fruit length [2023: logarithm of odds (LOD) value = 6.16, 16.20% phenotypic variation explained (PVE); 2024: LOD = 5.44, 6.35% PVE] and fruit diameter (2023: LOD value = 5.48, 14.59% PVE; 2024: LOD = 6.22, 7.22% PVE) to 1.88 and 2.20 Mb intervals, respectively. The annotation analysis across the melon genome and comparison of resequencing data from the two parental lines led to the preliminary identification of MELO3C021600.1 (annotated as cytochrome P450 724B1) as a candidate gene related to melon fruit size. These results provide a better understanding for further fine mapping and functional gene analysis related to melon fruit size. Full article

This study evaluated the influence of different male date palm cultivars, distinguished by their chloroplast haplotypes, on pollen quality, pollination efficiency, metaxenia effects, and gene expression during fruit development. Chloroplast DNA analysis of 37 male trees revealed multiple haplotypes, from which cultivars B25, P8, C22, and B46 were selected for further investigation. Pollen viability varied significantly among cultivars, with P8 and B25 exhibiting the highest germination rates and pollen tube elongation, while C22 showed the lowest. These differences correlated with pollination success: P8 and B25 achieved fertilization rates near 99%, whereas C22 remained below 43%. Pollination outcomes also varied in fruit traits. Despite its low pollen performance, C22 induced the production of larger fruits at the Bleh (Kimri) stage, potentially due to compensatory physiological mechanisms. Phytochemical profiling revealed significant cultivar effects: fruits from B25-pollinated trees had with lower moisture and polyphenol content but the higher sugar levels and soluble solids, suggesting accelerated maturation. Ripening patterns confirmed this finding, with B25 promoting the earliest ripening and B46 causing the most delayed. Gene expression analysis supported these phenotypic differences. Fruits pollinated by P8, B25, and B46 exhibited elevated levels of cell-division-related transcripts, particularly the PdCD_1 gene (PDK_XM_008786146.4, a gene encoding a cell division control protein), which was most abundant in P8. In contrast, fruits from C22-pollinated trees had the lowest expression of growth-related genes, suggesting a shift toward cell expansion rather than division. Overall, the results show the critical role of male genotype in influencing fertilization outcomes and fruit development, offering valuable insights for targeted breeding strategies at enhancing date palm productivity and fruit quality. Full article

Insights into dynamic regulatory factors in various stages of growth and development can guide strategies for precision and targeted breeding. Bitter gourd, as a vegetable product with medicinal value, plays a role in both agricultural and medical fields. In this study, phenotypic observations, metabolomic and transcriptomic analyses, and differential gene expression patterns, along with a correlation analysis, were conducted in different stages of fruit growth and development. The results revealed that the growth rate of fruit’s fresh weight, length, diameter, and flesh thickness during the first seven days was slow, and that it then rapidly increased after the seventh day, and finally slowed once more after 17 days, indicating that the overall process followed a “slow–fast–slow” pattern. Transcriptomic and metabolomic analyses identified several differentially expressed genes and metabolites, and joint analyses revealed that each of the glycolysis/gluconeogenesis, fructose and mannose metabolism and flavonoid biosynthesis pathways individually play significant roles in the dynamic regulation of fruit growth and development during the early, middle, and late stages. Among these, 53 differentially expressed genes (DEGs) and 12 differentially expressed metabolites (DEMs) were found in these pathways. A total of 12 randomly selected DEGs were analyzed using quantitative PCR, and the results showed that gene expression levels were generally consistent with transcriptomic sequencing results, exhibiting dynamic changes with varying expression levels. Correlation analysis revealed that 11 DEMs were positively correlated with four traits except for arbutin, while eight DEGs were related to all traits, including six significantly positive and two significantly negative correlations. These findings enhance our understanding of the regulatory network governing yield and quality and provide substantial evidence to support improvements in breeding programs. 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

Background: The Actinidia deliciosa cultivar ‘Guichang’ is a remarkable kiwifruit variety. The phenotypic traits of this variety are influenced by the climatic conditions in Guizhou. The flowering time, which is shaped by multiple environmental factors, has a substantial impact on both the fruit yield and quality. Objectives and Methods: This study was designed to explore the molecular mechanisms underlying the transition from bud to flowering in ‘Guichang’ through transcriptomic and proteomic analyses. Results: The transcriptomic results revealed that 6201 genes were up-regulated, while 5849 genes were down-regulated during this transition. Key genes related to hormone signaling, such as AdPIF4, AdBSK, AdBRI1, and AdCYCD3, were recognized as crucial regulators. The proteomic analysis detected a total of 10,488 proteins. Among them, AdBSK1 was regulated, while AdPIF4, AdBRI1, and AdCYCD3 showed stable expressions. A moderate positive correlation (with a Pearson correlation coefficient of 0.445) was found between the expression levels of transcriptomics and proteomics. When AdBSK1 was over-expressed in Arabidopsis, it promoted earlier flowering. This was achieved by down-regulating FLC and up-regulating FT and SOC1. Conclusions: This study clarifies the molecular mechanisms involved in the bud-to-flowering transition in ‘Guichang’. It emphasizes the intricate interactions among hormonal pathways, key genes, and proteins, which are consistent with the broader understanding of plant flowering regulation in recent research. These findings are significant for deepening our understanding of, and potentially controlling, the flowering mechanisms. Full article

Passion fruit is an underutilised fruit in Northeastern India, known for its unique flavour and health benefits. This study analysed 15 genotypes (P1 to P15) to explore their morphological and biochemical traits related to fruit quality and yield. P. quadrangularis L. (P15) exhibited maximum flower length, fruit size, weight, juice content, shelf-life, and yield. P. edulis f. flavicarpa (P3, P5, and P2) had the highest seed count per fruit and antioxidant activity, along with greater chlorophyll and anthocyanin levels. Passiflora edulis Sims (P8 and P11) showed superior total soluble solids, carotenoids, and vitamin C. The study found that fruit shelf life positively correlated with seed weight, while the number of fruits per vine negatively correlated with seed traits and peel weight. Additionally, certain traits, such as total carotenoids, had strong positive correlations with reducing sugar and flavonoids. Principal component analysis revealed distinct trait relationships, particularly for genotypes P7 and P10. SDS-PAGE protein profiling indicated a significant distance between P3 and P14, emphasising genetic diversity. In conclusion, this research highlights the diverse morphological and biochemical characteristics of passion fruit genotypes, paving the way for the region’s improved fruit quality, yield, and breeding strategies. Full article

The degeneration of germplasm is a key factor limiting the yield and quality of Gastrodia elata Blume. Sexual reproduction is a primary method to address this degeneration, while the number of flowers and capsules is directly related to sexual reproduction. However, the genetic mechanisms underlying the high flower/fruit-bearing traits in G. elata remain unclear. We first compared the quantitative and qualitative traits during the flowering to fruiting period of G. elata, including bolting height, flowering quantity, flowering time, fruiting quantity, capsule spacing, seed quality, etc. The natural materials were selected by multi-capsule and few-capsule for transcriptome analysis to screen the differentially expressed genes (DEGs); the candidate gene GePIF4 was suspected to regulate the formation of multiple flowers and fruits. It was confirmed that GePIF4 has multiple biological functions in the overexpression of transgenic lines, including increasing numbers of vegetative propagation corms (VPCs) and promoting the growth of G. elata. Through comparative transcriptomic analysis of EV and OE-GePIF4 transgenic lines, the transcriptional regulatory network of GePIF4 was identified, and transient expression of GePIF4 was demonstrated to significantly promote gastrodin accumulation. The dual-LUC assay and in vitro yeast one hybrid results showed that GePIF4 could directly bind to GeRAX2 to regulate multi-capsule formation, and GePIF4 could directly bind to GeC4H1 to promote gastrodin accumulation. Therefore, we elucidate the role of GePIF4 in multi-capsule formation and secondary metabolite accumulation, thereby laying the groundwork for the genetic improvement of G. elata germplasm resources. Full article

The abiotic stresses associated with spring/fall freezes and extreme winter cold cause significant economic losses in blueberry production. These problems are exacerbated by climate change and increasingly erratic weather patterns. Developing freeze-tolerant blueberry cultivars with optimized cold hardiness, chilling requirement, and flowering and fruiting phenology holds promise for mitigating the risk of these weather-related damages. These weather-resilient cultivars will ensure the long-term productivity and sustainability of the blueberry industry. The focus of this review is to present the current understanding of the major components of genetic breeding for blueberry freeze tolerance, i.e., phenotyping, genotyping, genetic association analysis, and marker development. The advancement in gene regulation and corresponding proteomic changes upon cold acclimation, dormancy, de-acclamation, and flowering and fruiting aids in the understanding of the adaptive stress response in blueberries. A wide range of genetic diversity in freeze tolerance and phenological traits has been identified among cultivated and wild blueberry relatives. Significant efforts have been made to phenotype freeze tolerance, chilling requirement, and flower and fruit development in both field and controlled environmental conditions. Recent studies emphasize the need for high-throughput, image-based phenotyping of blueberry flower development to improve the precision and efficiency of selecting freeze-resilient genotypes. In addition, advancements in blueberry genomics and pangenome resources expanded the potential of variant calling and high-density linkage map construction. Genetic association studies have identified QTL regions linked to freeze tolerance in blueberries, providing valuable targets for selection. The implementation of these advanced genomic tools and high-throughput phenotyping methodology will accelerate the development of weather-resilient blueberry cultivars. Full article

Agriculture is presently facing several ecological concerns related to the upsurging request for premium-value food produced in compliance with natural horticultural tools. The use of natural substances, such as biostimulants, principally protein hydrolysates (PHs), could be useful to maximize overall vegetable plant fitness. However, the mode of application (foliar spray or fertigation) could affect biostimulant efficiency. The current research was conducted to evaluate the effect of a Zea mays-derived PH (Surnan^®, SPAA, Pescara, Italy) and its mode of application (foliar spray and/or fertigation) on yield traits, mineral profile, nutritional and functional components, along with NUE of “Florida fortuna” strawberry cultivated under tunnel. The findings showed that the corn-based PH effectively enhanced yield and number of marketable fruits per plant (NMFP) compared with the control (+20.1% and +25.4%, respectively). Fruits from biostimulated plants also showed a higher fruit lightness and ascorbic acid and anthocyanin concentration than fruits from control plots. Furthermore, Surnan^® PH increased nitrogen use efficiency (NUE) of strawberry plants. Captivatingly, plants biostimulated via fertigation showed the highest fruit potassium (K) concentration, while those exposed to the foliar spray had the highest fruit phenolic concentration. Generally, our findings recommended that the application of Zea mays-derived PH via foliar spray could be considered a suitable tool to increase functional traits of strawberry grown under tunnel. Full article