The telomere-to-telomere genome of Pucai () (Typha angustifolia L.): a distinctive semiaquatic vegetable with lignin and chlorophyll as quality characteristics

Pucai () (Typha angustifolia L.), within the Typha spp., is a distinctive semiaquatic vegetable. Lignin and chlorophyll are two crucial traits and quality indicators for Pucai. In this study, we assembled a 207.00-Mb high-quality gapless genome of Pucai, telomere-to-telomere (T2T) level with a contig N50 length of 13.73 Mb. The most abundant type of repetitive sequence, comprising 16.98% of the genome, is the long terminal repeat retrotransposons (LTR-RT). A total of 30 telomeres and 15 centromeric regions were predicted. Gene families related to lignin, chlorophyll biosynthesis, and disease resistance were greatly expanded, which played important roles in the adaptation of Pucai to wetlands. The slow evolution of Pucai was indicated by the σ whole-genome duplication (WGD)-associated Ks peaks from different Poales and the low activity of recent LTR-RT in Pucai. Meanwhile, we found a unique WGD event in Typhaceae. A statistical analysis and annotation of genomic variations were conducted in interspecies and intraspecies of Typha. Based on the T2T genome, we constructed lignin and chlorophyll metabolic pathways of Pucai. Subsequently, the candidate structural genes and transcription factors that regulate lignin and chlorophyll biosynthesis were identified. The T2T genomic resources will provide molecular information for lignin and chlorophyll accumulation and help to understand genome evolution in Pucai.

A Golden2-like transcription factor regulates Brassica napus seed vigor after artificial aging

KEY MESSAGE

A novel GLK transcription factor, BnaA03.G2-like, regulates seed vigor after aging by affecting FAs composition in B. napus. Seeds, a most crucial materials for crop production, constitute the basis of agriculture. Seed aging usually occurs during storage, especially for seeds with high oil content. However, the genes and mechanisms underlying seed aging in Brassica napus, a widely grown oilseed crop, remain largely unexplored. In this study, nine SNPs associated with seed vigor after aging were identified through a genome-wide association study, and transgenic seeds confirmed that BnaA03.G2-like negatively regulated seed vigor after aging. Haplotype and gene-based association analyses revealed that S_A3.16900957 and S_A3.16901008 were two core variants located within BnaA03.G2-like. Transcriptome analysis and gas chromatography results suggested that BnaA03.G2-like regulated fatty acid biosynthesis, and the linoleic acid content significantly increased in the seeds of BnaA03.G2-like overexpression lines but decreased in the seeds of BnaA03.G2-like RNA interference lines. Further correlation analysis and malondialdehyde determination revealed that BnaA03.G2-like regulated seed vigor by affecting the linoleic acid content in mature seeds and the degree of membrane lipid peroxidation during seed aging. This study initially reported the function of BnaA03.G2-like and its favorable alleles, providing genetic resources for seed antiaging breeding in B. napus.

GLKs directly regulate carotenoid biosynthesis via interacting with GBFs in plants

Carotenoids are vital photosynthetic pigments for plants. Golden2-like transcription factors (GLKs) are widely recognized as major regulators of Chl biosynthesis and chloroplast development. However, despite GLKs being subjected to intensive investigations, whether GLKs directly regulate carotenoid biosynthesis and the molecular mechanisms by which GLKs transcriptionally activate their target genes remain unclear. Here, we report that GLKs directly regulate carotenoid biosynthesis and activate their target genes in a G-box binding factor (GBF)-dependent manner in Arabidopsis. Both in vitro and in vivo studies reveal that GLKs physically interact with GBFs to activate transcription of phytoene synthase (PSY), the gene encoding a rate-limiting enzyme for carotenoid biosynthesis. While GLKs possess transactivation activity, they depend on GBFs to directly bind to the G-box motif to modulate PSY expression. Loss of GBFs impairs GLK function in regulating carotenoid and Chl biosynthesis. Since the G-box motif is an enriched motif in the promoters of GLK-regulated genes, the GLK-GBF regulatory module likely serves as a common mechanism underlying GLK-regulated photosynthetic pigment biosynthesis and chloroplast development. Our findings uncover a novel regulatory machinery of carotenoid biosynthesis, discover a molecular mechanism of transcriptional regulation by GLKs, and divulge GLKs as important regulators to coordinate photosynthetic pigment synthesis in plants.

Chlorine Modulates Photosynthetic Efficiency, Chlorophyll Fluorescence in Tomato Leaves, and Carbohydrate Allocation in Developing Fruits

Chlorine (Cl) is an essential nutrient for higher plants, playing a critical role in their growth and development. However, excessive Cl application can be detrimental, leading to its limited use in controlled-environment agriculture. Recently, Cl has been recognized as a beneficial macronutrient, yet studies investigating its impact on plant growth and fruit quality remain scarce. In this study, we determined the optimal Cl concentration in nutrient solutions through a series of cultivation experiments. A comparative analysis of Cl treatments at 1, 2, and 3 mM revealed that 3 mM Cl- significantly enhanced chlorophyll content, biomass accumulation, and yield. Furthermore, we examined the effects of 3 mM Cl- (supplied as 1.5 mM CaCl2 and 3 mM KCl) on leaf photosynthesis, chlorophyll fluorescence, and fruit sugar metabolism. The results demonstrated that Cl- treatments enhanced the activity of Photosystem I (PS I) and Photosystem II (PS II), leading to a 25.53% and 28.37% increase in the net photosynthetic rate, respectively. Additionally, Cl- application resulted in a 12.3% to 16.5% increase in soluble sugar content in mature tomato fruits. During fruit development, Cl- treatments promoted the accumulation of glucose, fructose, and sucrose, thereby enhancing fruit sweetness and overall quality. The observed increase in glucose and fructose levels was attributed to the stimulation of invertase activity. Specifically, acidic invertase (AI) activity increased by 61.6% and 62.6% at the green ripening stage, while neutral invertase (NI) activity was elevated by 56.2% and 32.8% in the CaCl2 and KCl treatments, respectively, at fruit maturity. Furthermore, sucrose synthase (SS-I) activity was significantly upregulated by 1.5- and 1.4-fold at fruit maturity, while sucrose phosphate synthase (SPS) activity increased by 76.4% to 77.8% during the green ripening stage. These findings provide novel insights into the role of Cl- in tomato growth and metabolism, offering potential strategies for optimizing fertilization practices in protected horticulture.

Genome-Wide Identification of GLK Family Genes in Phoebe bournei and Their Transcriptional Analysis Under Abiotic Stresses

GOLDEN2-LIKE (GLK) transcription factors are crucial regulators of chloroplast development and stress responses in plants. In this study, we investigated the GLK gene family in Phoebe bournei (Hemsl.) Yen C. Yang, a near-threatened species important for forestry and wood utilization in China. We identified 61 PbGLK genes which were classified into seven subfamilies. Our analyses of their phylogenetic relationships, gene structures, and chromosomal distribution revealed diverse characteristics. Expression profiling under different tissues and abiotic stresses showed that PbGLK25 and PbGLK30 were particularly responsive to drought, heat, light, and shade stresses, with significant upregulation. These findings highlight the potential role of PbGLK genes in stress adaptation and provide insights for the genetic improvement of P. bournei.

Genome-wide identification and characterization of FORMIN gene family in cotton (Gossypium hirsutum L.) and their expression profiles in response to multiple abiotic stress treatments

FORMIN proteins distinguished by FH2 domain, are conserved throughout evolution and widely distributed in eukaryotic organisms. These proteins interact with various signaling molecules and cytoskeletal proteins, playing crucial roles in both biotic and abiotic stress responses. However, the functions of FORMINs in cotton (Gossypium hirsutum L.) remain uncovered. In this study, 46 FORMIN genes in G. hirsutum (referred to as GhFH) were systematically identified. The gene structures, conserved domains, and motifs of these GhFH genes were thoroughly explored. Phylogenetic and structural analysis classified these 46 GhFH genes into five distinct groups. In silico subcellular localization, prediction suggested that GhFH genes are distributed across various cellular compartments, including the nucleus, extracellular space, cytoplasm, mitochondria, cytoskeleton, plasma membrane, endoplasmic reticulum, and chloroplasts. Evolutionary and functional diversification analyses, based on on-synonymous (Ka) and synonymous (Ks) ratios and gene duplication events, indicated that GhFH genes have evolved under purifying selection. The analysis of cis-acting elements suggested that GhFH genes may be involved in plant growth, hormone regulation, light response, and stress response. Results from transcriptional factors TFs and gene ontology analysis indicate that FORMIN proteins regulate cell wall structure and cytoskeleton dynamics by reacting to hormone signals associated with environmental stress. Additionally, 45 putative ghr-miRNAs were identified from 32 families targeting 33 GhFH genes. Expression analysis revealed that GhFH1, GhFH10, GhFH20, GhFH24, and GhFH30 exhibited the highest levels of expression under red, blue, and white light conditions. Further, GhFH9, GhFH20, and GhFH30 displayed higher expression levels under heat stress, while GhFH20 and GhFH30 showed increased expression under salt stress compared to controls. The result suggests that GhFH20 and GhFH30 genes could play significant roles in the development of G. hirsutum under heat and salt stresses. Overall these findings enhance our understanding of the biological functions of the cotton FORMIN family, offering prospects for developing stress-resistant cotton varieties through manipulation of GhFH gene expression.

Identification and characterization of ClAPRR2, a key candidate gene controlling watermelon stripe color

The stripe color of watermelon is a vital commercial trait and is the focus of attention of consumers and researchers. However, the genetic determinants of watermelon stripe color are incompletely understood. Based on the results of preliminary localization studies, we constructed a large-capacity F2 generation population (710 plants) using light-green striped ZXG1555 and green-striped Cream of Saskatchewan (COS) watermelon strains as parental lines for fine mapping. Genes controlling stripe color were located in an 85.284 kb region on chromosome 9, which contained five candidate genes. Combined with parental phenotypes, chlorophyll contents of rinds and stripes were assayed. Gene sequence alignment and transcriptional level analysis of parental lines predicted Cla97C09G175170 (encoding a two-component response regulator-like protein, APRR2) as the best candidate gene for stripe color trait. Two SNPs in the ClAPRR2 coding region caused amino acid substitutions, but were not located in the conserved domain, while a 12 bp insertion caused premature translation termination and a 35 amino acid deletion in the conserved domain and may have affected ClAPRR2 function in ZXG1555. Subcellular localization analysis showed that ClAPRR2 was expressed in the ZXG1555 cell membrane but was located in the nucleus and cell membrane of COS. Nucleotide polymorphisms and deletions were also detected in the promoter region between parental lines and caused cis-acting element variations. Luciferase activity suggested that promoter variations may not be the main factor in the regulation of ClAPRR2 expression.

Molecular breeding of tomato: Advances and challenges

The modern cultivated tomato (Solanum lycopersicum) was domesticated from Solanum pimpinellifolium native to the Andes Mountains of South America through a "two-step domestication" process. It was introduced to Europe in the 16th century and later widely cultivated worldwide. Since the late 19th century, breeders, guided by modern genetics, breeding science, and statistical theory, have improved tomatoes into an important fruit and vegetable crop that serves both fresh consumption and processing needs, satisfying diverse consumer demands. Over the past three decades, advancements in modern crop molecular breeding technologies, represented by molecular marker technology, genome sequencing, and genome editing, have significantly transformed tomato breeding paradigms. This article reviews the research progress in the field of tomato molecular breeding, encompassing genome sequencing of germplasm resources, the identification of functional genes for agronomic traits, and the development of key molecular breeding technologies. Based on these advancements, we also discuss the major challenges and perspectives in this field.

Integrative transcriptomic and HS-SPME-GC-MS analysis reveals the influence mechanism of different altitude ecotypes on pulp aroma components and volatile metabolites in strawberry hybrid F1 and its parents

Strawberry (Fragaria × ananassa) is an important horticultural crop and is highly nutritious and valuable. However, several molecular mechanisms on the biosynthesis and metabolism of aroma compounds and the regulatory network that governs aromas remain unknown. This study investigated the influence of different altitude ecotypes on the components of pulp aroma and volatile metabolites in strawberry hybrid F1 and its parents. "Perilla alcohol" was found to be the major factor that regulated the aroma of strawberry pulp from plants at low altitudes, and "perilla alcohol, linalool, alpha-farnesene and E-2-hexenyl benzoate" were the major factors that regulated the aroma of strawberry pulp from plants at high altitudes. Furthermore, three key candidate genes were identified according to the criteria of |K.i| > 40 and |MM| > 0.90. This study will establish a theoretical foundation for the cultivation of novel varieties of strawberries characterized by superior quality and flavor.

lncRNA1471 mediates tomato-ripening initiation by binding to the ASR transcription factor

The regulatory mechanisms underlying fruit ripening, including hormone regulation, transcription factor activity, and epigenetic modifications, have been discussed extensively. Nonetheless, the role of long non-coding RNAs (lncRNAs) in fruit ripening remains unclear. Here, we identified lncRNA1471 as a negative regulator of tomato fruit-ripening initiation. Knocking out lncRNA1471 via large fragment deletion resulted in accelerated initiation of fruit ripening, a shorter color-breaking stage (BR), deeper coloration, increased levels of ethylene, lycopene, and β-carotene, accelerated chlorophyll degradation, and reduced fruit firmness. These phenotypic changes were accompanied by alterations in the carotenoid pathway flux, ethylene biosynthesis, and cell wall metabolism, primarily mediated by the direct regulation of key genes involved in these processes. For example, in the CR-lncRNA1471 mutant, lycopene-related SlPSY1 and SlZISO were upregulated. Additionally, the expression levels of ethylene biosynthetic genes (SlACS2 and SlACS4), ripening-related genes (RIN, NOR, CNR, and SlDML2), and cell wall metabolism genes (SlPL, SlPG2a, SlEXP1, SlPMEI-like, and SlBG4) were significantly upregulated, which further strengthening the findings mentioned above. Furthermore, lncRNA1471 was identified to interact with the abscisic stress-ripening protein (ASR) transcription factor by chromatin isolation by RNA purification coupled with mass spectrometry (ChIRP-MS) and protein pull-down assay in vitro, which might regulate key genes involved in tomato ripening. The discovery of the significant non-coding regulator lncRNA1471 enhances our understanding of the complex regulatory landscape governing fruit ripening. These findings provide valuable insights into the mechanisms underlying ripening, particularly regarding the involvement of lncRNAs in ripening.

A chromosome-scale genome of Hippophae neurocarpa provides new insights into serotonin biosynthesis and chlorophyll-derived brown fruit coloration

Sea buckthorn (Hippophae neurocarpa), a plant with both medicinal and edible properties, exhibits high content of serotonin with a unique brown color. Here, we assemble the 1002.54 Mb genome sequence of H. neurocarpa and find that it has evolved from two sequential polyploidizations with four sub-genomes. Based on in vitro enzyme activity and transient overexpression experiments, we confirm that the expression of both HnT5H1 and HnT5H2 genes from tandem duplication contributes to high accumulation of serotonin in sea buckthorn. Furthermore, we verify that the HnGLK1 gene plays a crucial role in continuous chlorophyll accumulation, driving the brown color formation of H. neurocarpa fruit. Collectively, the high-quality genome of H. neurocarpa offers valuable insights into the mechanisms underlying serotonin biosynthesis and abnormal coloration and serves as a valuable resource for further functional genomic studies and molecular breeding efforts in sea buckthorn.

The transcription factor CaBBX10 promotes chlorophyll and carotenoid pigment accumulation in Capsicum annuum fruit

Chlorophylls and carotenoids are 2 pivotal photosynthetic pigments directly influencing the economic value of pepper (Capsicum annuum L.) fruits. However, the coordinated regulatory mechanisms governing the accumulation of both chlorophylls and carotenoids during pepper fruit development remain elusive. In this study, pepper B-box 10 (CaBBX10), a candidate hub transcription factor, was found to play dual roles in the early development of pepper fruit. CaBBX10 virus-induced gene silencing and overexpression experiments demonstrated that the encoded transcription factor promotes both chlorophyll and carotenoid accumulation in pepper fruit. Further comprehensive analyses showed that CaBBX10 directly binds to the promoter of magnesium chelatase subunit D subunit (CaCHLD) and phytoene synthase 1 (CaPSY1), thereby activating their expression in the chlorophyll and carotenoid biosynthesis pathways, respectively. Additionally, the photomorphogenic factor CaCOP1 was found to physically interact with CaBBX10 and lead to its degradation. Therefore, CaBBX10 may serve as a critical link connecting chlorophyll and carotenoid biosynthesis to light signaling. Altogether, our findings reveal a mechanism for the complex transcriptional regulation that simultaneously promotes chlorophyll and carotenoid accumulation in pepper fruit.

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.

Influence of exogenous 24-epibrassinolide on improving carotenoid content, antioxidant capacity and gene expression in germinated maize seeds

BACKGROUND

Carotenoids have various physiological functions, such as immune regulation and cancer prevention. Germination could further improve the content of carotenoids in maize seeds. In this study, yellow maize seeds (Suyu 29) were soaked and germinated with different concentrations of 24-epibrassinolide. The changes of germination percentage, sprout length, bioactive components, antioxidant capacity and carotenoid content of the maize seeds were analyzed. Additionally, the relative expression of key genes in the carotenoid synthesis pathway was investigated.

RESULTS

The results showed that the sprout length, germination percentage, soluble protein, free amino acids, proline, endogenous abscisic acid, vitamin C, total phenolics and carotenoids displayed a significant increasing trend compared with the control group (P < 0.05). The activity of superoxide dismutase and peroxidase increased by 55.1% and 58.5% versus the control group, and the antioxidant capacity of 2,2-diphenyl-1-picrylhydrazyl, 2,2-azinobis(3-ethylbenzothiazoline-6-sulfonic acid) and ferric reducing antioxidant power was 19.8%, 13.4% and 44.1% higher than that of the control group (P < 0.05). Compared with the control group, the expression of genes was significantly up-regulated (P < 0.05). Under the treatment of 0.1 mg L-1 of 24-epibrassinolide, carotenoid content reached the highest value. The carotenoids showed a positive correspondence with antioxidant enzyme activity, antioxidant capacity and total phenolics content (P < 0.05).

CONCLUSION

This study showed that 0.1 mg L-1 of exogenous 24-epibrassinolide promoted the accumulation of carotenoids and improved the antioxidant capacity and the quality of germinated maize seeds. It could provide a method for the development of germinated maize products enriched in carotenoids. © 2024 Society of Chemical Industry.

The BES1/BZR1 transcriptional factor SlBES2 regulates photosynthetic apparatus in tomato fruit

BACKGROUND

Fruit photosynthetic apparatus development comprises a series of biological processes which is essential in determining fruit development and quality formation. However, the understanding of the regulation of fruit photosynthetic apparatus development remains poor.

RESULTS

In this study, we identified a transcriptional factor SlBES2, the closest homolog of BES1 and BZR1 in tomato BES1 family, is highly expressed in fruit at mature green (MG) stage and exhibited transcriptional inhibition activity. Down-regulation of SlBES2 resulted in fruits showing paler fruit than wild type at MG stage, in contrast, SlBES2-overexpressing tomato lines bore deeper green fruits. Notably, chlorophyll content and number of thylakoids per chloroplast in fruit was substantially increased in SlBES2-overexpressing lines, while markedly decreased in SlBES2-suppressing lines. Comparative transcriptome analysis revealed that multiple genes of the photosystem, chloroplast development and chlorophyll metabolism pathways were regulated by SlBES2. Further verification revealed that SlBES2 can significantly repress the transcriptional activity of SlNYC1 and Green-Flesh, and physically interact with protein SlHY5.

CONCLUSIONS

Collectively, this study demonstrated that SlBES2 plays an important role in regulating fruit photosynthetic apparatus development through either transcriptional repression of genes involved in chlorophyll breakdown, or posttranscriptional regulation of proteins associated with plant photomorphogenesis and chloroplast development. Our findings add a new actor to the complex mechanisms underlying photosynthetic apparatus during fruit development.

Telomere-to-telomere genome assembly of eggplant (Solanum melongena L.) promotes gene fine localization of the green stripe (GS) in pericarp

Fruit appearance of eggplant is a key commercial trait, and the precise selection of new varieties with diverse aesthetics aligns with current breeding objectives. However, functional genomics research in eggplant remains underdeveloped. Here, we assembled the first telomere-to-telomere (T2T) eggplant genome, as well as chloroplast and mitochondrial genomes for the inbred line 'NO211'. The 1.06-Gb SmT2T genome is anchored to 12 chromosomes, nine of which are gap-free, totaling three gaps. This assembly harbors 36,505 genes and 64.08 % repetitive sequences, identifying 12 centromeres and 22 telomeres. Utilizing the SmT2T genome for bulked segregant analysis (BSA) and forward genetic approach with green-striped 'NO211' and pure green 'P13' as parents, the green stripe (GS) locus was finely mapped to a 9-Kb region on Chr4, containing a single gene, eggplant.04G07850 (GLK protein). Sequence analysis and qRT-PCR revealed that a single-base deletion in the exon of SmGLK in 'P13' led to premature stop codon, and SmGLK expression was significantly higher in the pericarp of 'NO211' compared to 'P13'. A marker was developed and validated in 36 germplasms, demonstrating co-segregation with green-striped rind trait. This study provides an ideal reference genome for eggplant functional genomics studies, facilitating mechanistic research on peel stripe formation and molecular-assisted selection for fruit appearance.

Overexpression of the persimmon ABA receptor DkPYL3 gene alters fruit development and ripening in transgenic tomato

Abscisic acid (ABA) is a crucial plant hormone that regulates various aspects of plant development. However, the specific function of the ABA receptor PYL in fruit development has not been fully understood. In this study, we focused on DkPYL3, a member of the ABA receptor subfamily Ⅰ in persimmon, which exhibited high expression levels in fruit, particularly during the young fruit and turning stages. Through yeast two-hybrid (Y2H), firefly luciferase complementation imaging (LCI), protein inhibition assays, and RNA-seq techniques, we identified and characterized the DkPYL3 protein, which was found to inhibit the activity of protein phosphatase type 2 C (PP2C). By heterologous overexpressing (OE) persimmon DkPYL3 in tomatoes, we investigated the impact of the DkPYL3 gene on fruit development and ripening. DkPYL3-OE upregulated the expression of genes related to chlorophyll synthesis and development, leading to a significant increase in chlorophyll content in young fruit. Several fruit quality parameters were also affected by DkPYL3 expression, including sugar content, single fruit weight, and photosynthesis rate. Additionally, fruits overexpressing DkPYL3 exhibited earlier ripening and higher levels of carotenoids and flavonoids compared to wild-type fruits. These results demonstrate the pivotal role of DkPYL3 in ABA-mediated young fruit development, ripening onset, and fruit quality in transgenic tomatoes.

AcGLK1 promotes chloroplast division through regulating AcFtsZ1 in Actinidia chinensis

MAIN CONCLUSION

This study unravels a new regulatory member (AcGLK1) that regulates chloroplast division by affecting the expression levels of cytoskeletal filamenting temperature-sensitive Z (FtsZ) in Actinidia chinensis. GOLDEN 2-LIKE (GLK) transcription factor members of GARP subfamily play an irreplaceable role in regulating chloroplast biogenesis and development. Here we report the functional characterization of a novel GLK1 homolog (AcGLK1) isolated from kiwifruit (Actinidia chinensis cultivar 'Hongyang'). Transgenic lines overexpressing AcGLK1 (AcGLK1OE) resulted in an increase of chloroplast number, size and nutrients accumulation in a tomato variety Micro-Tom (Solanum lycopersicum). Transcriptomic data revealed a series of DEGs related to chloroplast division, in which a tomato FtsZ1 homolog (SlFtsZ1) was significantly upregulated in the transgenic lines and could be directly activated by AcGLK1. Furthermore, AcGLK1 was shown to transcriptionally activate expression of kiwifruit FtsZ1 homologous genes (Achv4p23g035689 and Achv4p19g029547) through Y1H and GUS assays. Taken together, we provide evidence showing that AcGLK1 promotes chloroplast division probably through positively regulation of the transcription of FtsZ1 homologs.

Irregular green netting of eggplant fruit peel: a domestication trait controlled by SmGLK2 with potential for fruit colour diversification

The distribution of chlorophylls in eggplant (Solanum melongena) peel exhibits either a uniform pattern or an irregular green netting pattern. The latter, manifested as a gradient of dark green netting that is intensified in the proximal part of the fruit on a pale green background, is common in wild relatives and some eggplant landraces. Despite the selection of uniform chlorophylls during domestication, the netting pattern contributes to a greater diversity of fruit colours. Here, we used over 2300 individuals from different populations, including a multi-parent advanced generation inter-cross population for candidate genomic region identification, an F2 population for bulked segregant analysis by sequencing, and advanced backcrosses for edges-to-core fine-mapping, to identify SmGLK2 gene as responsible for the irregular netting in eggplant fruits. We also analysed the gene sequence of 178 S. melongena accessions and 22 wild relative species for tracing the evolutionary changes that the gene has undergone during domestication. Three different mutations were identified leading to the absence of netting. The main causative indel induces a premature stop codon disrupting the protein conformation and function, which was confirmed by western blot analysis and confocal microscopy observations. SmGLK2 has a major role in regulating chlorophyll biosynthesis in eggplant fruit peel.

Identification of lineage-specific cis-trans regulatory networks related to kiwifruit ripening initiation

Previous research on the ripening process of many fruit crop varieties typically involved analyses of the conserved genetic factors among species. However, even for seemingly identical ripening processes, the associated gene expression networks often evolved independently, as reflected by the diversity in the interactions between transcription factors (TFs) and the targeted cis-regulatory elements (CREs). In this study, explainable deep learning (DL) frameworks were used to predict expression patterns on the basis of CREs in promoter sequences. We initially screened potential lineage-specific CRE-TF interactions influencing the kiwifruit ripening process, which is triggered by ethylene, similar to the corresponding processes in other climacteric fruit crops. Some novel regulatory relationships affecting ethylene-induced fruit ripening were identified. Specifically, ABI5-like bZIP, G2-like, and MYB81-like TFs were revealed as trans-factors modulating the expression of representative ethylene signaling/biosynthesis-related genes (e.g., ACS1, ERT2, and ERF143). Transient reporter assays and DNA affinity purification sequencing (DAP-Seq) analyses validated these CRE-TF interactions and their regulatory relationships. A comparative analysis with co-expression networking suggested that this DL-based screening can identify regulatory networks independently of co-expression patterns. Our results highlight the utility of an explainable DL approach for identifying novel CRE-TF interactions. These  imply that fruit crop species may have evolved lineage-specific fruit ripening-related cis-trans regulatory networks.

Exogenous 5-aminolevulinic acid promotes carotenoid accumulation in tomato fruits by regulating ethylene biosynthesis and signaling

5-Aminolevulinic acid (ALA) can not only improve fruit yield and quality, but also increase the lycopene content in tomato fruits. Furthermore, ALA has been shown to promote system-2 ethylene production in tomato fruits. However, the specific interactions between ALA and ethylene during fruit ripening remain unclear. In this study, we treated tomato fruits with ALA, 1-aminocyclopropane-1-carboxylic acid (ACC), aminooxyacetic acid (AOA) + AgNO3, and AOA + AgNO3 + ALA and analyzed ethylene emissions, carotenoid contents, and the relative gene expression levels related to fruit ripening, carotenoid contents, ethylene synthesis, and signal transduction. The ALA treatment significantly enhanced ethylene bursts and carotenoid accumulation, and significantly upregulated the expression of ethylene and carotenoid-related genes, such as SlACS2, SlACS4, SlACO1, SlPSY1, and SlPDS. We also observed that the gene expression levels associated with carotenoid synthesis were downregulated in fruits treated with a combination of ethylene inhibitors (AOA + AgNO3). However, there was a significant upregulation in the gene expression levels associated with carotenoid synthesis and an increase in carotenoid content when fruits were treated with AOA + AgNO3 + ALA. After silencing SlACO1 expression, the total carotenoid content and SlPSY1 expression decreased significantly, while this effect was reversed after exogenous application of ALA. These results indicated that ALA promotes carotenoid accumulation in tomato fruits by promoting ethylene biosynthesis. In conclusion, our results highlighted the role of ALA in promoting carotenoid accumulation and ripening in tomato fruits by regulating ethylene synthesis, thereby providing a novel strategy for improving fruit quality.

Releasing a sugar brake generates sweeter tomato without yield penalty

In tomato, sugar content is highly correlated with consumer preferences, with most consumers preferring sweeter fruit1-4. However, the sugar content of commercial varieties is generally low, as it is inversely correlated with fruit size, and growers prioritize yield over flavour quality5-7. Here we identified two genes, tomato (Solanum lycopersicum) calcium-dependent protein kinase 27 (SlCDPK27; also known as SlCPK27) and its paralogue SlCDPK26, that control fruit sugar content. They act as sugar brakes by phosphorylating a sucrose synthase, which promotes degradation of the sucrose synthase. Gene-edited SlCDPK27 and SlCDPK26 knockouts increased glucose and fructose contents by up to 30%, enhancing perceived sweetness without fruit weight or yield penalty. Although there are fewer, lighter seeds in the mutants, they exhibit normal germination. Together, these findings provide insight into the regulatory mechanisms controlling fruit sugar accumulation in tomato and offer opportunities to increase sugar content in large-fruited cultivars without sacrificing size and yield.

Enhancing post-harvest quality of tomato fruits with chitosan oligosaccharide-zinc oxide nanocomposites: A study on biocompatibility, quality improvement, and carotenoid enhancement

In this study, a new composite with combination of chitosan oligosaccharide (COS) and zinc oxide nanoparticles (ZnO NPs), termed Chitosan Oligosaccharide-Zinc Oxide Nanocomposites (COS-ZnO NC), was designed to enhance the quality of tomato fruits during postharvest storage. SEM analysis showed a uniform distribution of COS-ZnO NC films on tomato surfaces, indicating high biocompatibility, while the FTIR spectrum confirmed the interaction of COS and ZnO NPs via hydrogen bonds. The COS-ZnO NC exerts positive effects on post-harvest quality of tomato fruits, including significantly reduced water loss, fewer skin wrinkles, increased sugar-acid ratio, and enhanced vitamin C and carotenoids accumulation. Furthermore, COS-ZnO NC induces transcription of carotenoid biosynthesis genes and promotes carotenoids storage in the chromoplast. These results suggest that the COS-ZnO NC film can significantly improve the quality traits of tomato fruits, and therefore is potential in post-harvest storage of tomato fruits.

Genomic variation across distribution of Micro-Tom, a model cultivar of tomato (Solanum lycopersicum)

Micro-Tom is a cultivar of tomato (Solanum lycopersicum), which is known as a major crop and model plant in Solanaceae. Micro-Tom has phenotypic traits such as dwarfism, and substantial EMS-mutagenized lines have been reported. After Micro-Tom was generated in Florida, USA, it was distributed to research institutes worldwide and used as a genetic resource. In Japan, the Micro-Tom lines have been genetically fixed; currently, three lines have been re-distributed from three institutes, but many phenotypes among the lines have been observed. We have determined the genome sequence de novo of the Micro-Tom KDRI line, one of the Micro-Tom lines distributed from Kazusa DNA Research Institute (KDRI) in Japan, and have built chromosome-scale pseudomolecules. Genotypes among six Micro-Tom lines, including three in Japan, one in the United States, one in France, and one in Brazil showed phenotypic alternation. Here, we unveiled the swift emergence of genetic diversity in both phenotypes and genotypes within the Micro-Tom genome sequence during its propagation. These findings offer valuable insights crucial for the management of bioresources.

Streamlined regulation of chloroplast development in the liverwort Marchantia polymorpha

Chloroplasts develop from undifferentiated plastids in response to light. In angiosperms, after the perception of light, the Elongated Hypocotyl 5 (HY5) transcription factor initiates photomorphogenesis, and two families of transcription factors known as GOLDEN2-LIKE (GLK) and GATA are considered master regulators of chloroplast development. In addition, the MIR171-targeted SCARECROW-LIKE GRAS transcription factors also impact chlorophyll biosynthesis. The extent to which these proteins carry out conserved roles in non-seed plants is not known. Using the model liverwort Marchantia polymorpha, we show that GLK controls chloroplast biogenesis, and HY5 shows a small conditional effect on chlorophyll content. Chromatin immunoprecipitation sequencing (ChIP-seq) revealed that MpGLK has a broader set of targets than has been reported in angiosperms. We also identified a functional GLK homolog in green algae. In summary, our data support the hypothesis that GLK carries out a conserved role relating to chloroplast biogenesis in land plants and green algae.

REDUCED CHLOROPLAST COVERAGE proteins are required for plastid proliferation and carotenoid accumulation in tomato

Increasing the amount of cellular space allocated to plastids will lead to increases in the quality and yield of crop plants. However, mechanisms that allocate cellular space to plastids remain poorly understood. To test whether the tomato (Solanum lycopersicum L.) REDUCED CHLOROPLAST COVERAGE (SlREC) gene products serve as central components of the mechanism that allocates cellular space to plastids and contribute to the quality of tomato fruit, we knocked out the 4-member SlREC gene family. We found that slrec mutants accumulated lower levels of chlorophyll in leaves and fruits, accumulated lower levels of carotenoids in flowers and fruits, allocated less cellular space to plastids in leaf mesophyll and fruit pericarp cells, and developed abnormal plastids in flowers and fruits. Fruits produced by slrec mutants initiated ripening later than wild type and produced abnormal levels of ethylene and abscisic acid (ABA). Metabolome and transcriptome analyses of slrec mutant fruits indicated that the SlREC gene products markedly influence plastid-related gene expression, primary and specialized metabolism, and the response to biotic stress. Our findings and previous work with distinct species indicate that REC proteins help allocate cellular space to plastids in diverse species and cell types and, thus, play a central role in allocating cellular space to plastids. Moreover, the SlREC proteins are required for the high-level accumulation of chlorophyll and carotenoids in diverse organs, including fruits, promote the development of plastids and influence fruit ripening by acting both upstream and downstream of ABA biosynthesis in a complex network.

Recent progress on mechanisms that allocate cellular space to plastids

Mechanisms that allocate cellular space to organelles are of fundamental importance to biology but remain poorly understood. A detailed understanding of mechanisms that allocate cellular space to plastids, such as chloroplasts, will lead to high-yielding crops with enhanced nutritional value. The HIGH PIGMENT (HP) genes in tomato contribute to regulated proteolysis and abscisic acid metabolism. The HP1 gene was the first gene reported to influence the amount of cellular space occupied by chloroplasts and chromoplasts almost 20 years ago. Recently, our knowledge of mechanisms that allocate cellular space to plastids was enhanced by new information on the influence of cell type on the amount of cellular space occupied by plastids and the identification of new genes that help to allocate cellular space to plastids. These genes encode proteins with unknown and diverse biochemical functions. Several transcription factors were recently reported to regulate the numbers and sizes of chloroplasts in fleshy fruit. If these transcription factors do not induce compensating effects on cell size, they should affect the amount of cellular space occupied by plastids. Although we can now propose more detailed models for the network that allocates cellular space to plastids, many gaps remain in our knowledge of this network and the genes targeted by this network. Nonetheless, these recent breakthroughs provide optimism for future progress in this field.

The pleiotropic functions of GOLDEN2-LIKE transcription factors in plants

The regulation of gene expression is crucial for biological plant growth and development, with transcription factors (TFs) serving as key switches in this regulatory mechanism. GOLDEN2-LIKE (GLK) TFs are a class of functionally partially redundant nuclear TFs belonging to the GARP superfamily of MYB TFs that play a key role in regulating genes related to photosynthesis and chloroplast biogenesis. Here, we summarized the current knowledge of the pleiotropic roles of GLKs in plants. In addition to their primary functions of controlling chloroplast biogenesis and function maintenance, GLKs have been proven to regulate the photomorphogenesis of seedlings, metabolite synthesis, flowering time, leaf senescence, and response to biotic and abiotic stress, ultimately contributing to crop yield. This review will provide a comprehensive understanding of the biological functions of GLKs and serve as a reference for future theoretical and applied studies of GLKs.

Integrating Physiology, Cytology, and Transcriptome to Reveal the Leaf Variegation Mechanism in Phalaenopsis Chia E Yenlin Variegata Leaves

Phalaenopsis orchids, with their unique appearance and extended flowering period, are among the most commercially valuable Orchidaceae worldwide. Particularly, the variegation in leaf color of Phalaenopsis significantly enhances the ornamental and economic value and knowledge of the molecular mechanism of leaf-color variegation in Phalaenopsis is lacking. In this study, an integrative analysis of the physiology, cytology, and transcriptome profiles was performed on Phalaenopsis Chia E Yenlin Variegata leaves between the green region (GR) and yellow region (YR) within the same leaf. The total chlorophyll and carotenoid contents in the YR exhibited a marked decrease of 72.18% and 90.21%, respectively, relative to the GR. Examination of the ultrastructure showed that the chloroplasts of the YR were fewer and smaller and exhibited indistinct stromal lamellae, ruptured thylakoids, and irregularly arranged plastoglobuli. The transcriptome sequencing between the GR and YR led to a total of 3793 differentially expressed genes, consisting of 1769 upregulated genes and 2024 downregulated genes. Among these, the chlorophyll-biosynthesis-related genes HEMA, CHLH, CRD, and CAO showed downregulation, while the chlorophyll-degradation-related gene SGR had an upregulated expression in the YR. Plant-hormone-related genes and transcription factors MYBs (37), NACs (21), ERFs (20), bHLH (13), and GLK (2), with a significant difference, were also analyzed. Furthermore, qRT-PCR experiments validated the above results. The present work establishes a genetic foundation for future studies of leaf-pigment mutations and may help to improve the economic and breeding values of Phalaenopsis.

Linkage and association mapping in multi-parental populations reveal the genetic basis of carotenoid variation in maize kernels

Carotenoids are indispensable to plants and critical components of the human diet. The carotenoid metabolic pathway is conserved across plant species, but our understanding of the genetic basis of carotenoid variation remains limited for the seeds of most cereal crops. To address this issue, we systematically performed linkage and association mapping for eight carotenoid traits using six recombinant inbred line (RIL) populations. Single linkage mapping (SLM) and joint linkage mapping (JLM) identified 77 unique additive QTLs and 104 pairs of epistatic QTLs. Among these QTLs, we identified 22 overlapping hotspots of additive and epistatic loci, highlighting the important contributions of some QTLs to carotenoid levels through additive or epistatic mechanisms. A genome-wide association study based on all RILs detected 244 candidate genes significantly associated with carotenoid traits, 23 of which were annotated as carotenoid pathway genes. Effect comparisons suggested that a small number of loci linked to pathway genes have substantial effects on carotenoid variation in our tested populations, but many loci not associated with pathway genes also make important contributions to carotenoid variation. We identified ZmPTOX as the causal gene for a QTL hotspot (Q10/JLM10/GWAS019); this gene encodes a putative plastid terminal oxidase that produces plastoquinone-9 used by two enzymes in the carotenoid pathway. Natural variants in the promoter and second exon of ZmPTOX were found to alter carotenoid levels. This comprehensive assessment of the genetic mechanisms underlying carotenoid variation establishes a foundation for rewiring carotenoid metabolism and accumulation for efficient carotenoid biofortification.

The Y locus encodes a REPRESSOR OF PHOTOSYNTHETIC GENES protein that represses carotenoid biosynthesis via interaction with APRR2 in carrot

Little is known about the factors regulating carotenoid biosynthesis in roots. In this study, we characterized DCAR_032551, the candidate gene of the Y locus responsible for the transition of root color from ancestral white to yellow during carrot (Daucus carota) domestication. We show that DCAR_032551 encodes a REPRESSOR OF PHOTOSYNTHETIC GENES (RPGE) protein, named DcRPGE1. DcRPGE1 from wild carrot (DcRPGE1W) is a repressor of carotenoid biosynthesis. Specifically, DcRPGE1W physically interacts with DcAPRR2, an ARABIDOPSIS PSEUDO-RESPONSE REGULATOR2 (APRR2)-like transcription factor. Through this interaction, DcRPGE1W suppresses DcAPRR2-mediated transcriptional activation of the key carotenogenic genes phytoene synthase 1 (DcPSY1), DcPSY2, and lycopene ε-cyclase (DcLCYE), which strongly decreases carotenoid biosynthesis. We also demonstrate that the DcRPGE1W-DcAPRR2 interaction prevents DcAPRR2 from binding to the RGATTY elements in the promoter regions of DcPSY1, DcPSY2, and DcLCYE. Additionally, we identified a mutation in the DcRPGE1 coding region of yellow and orange carrots that leads to the generation of alternatively spliced transcripts encoding truncated DcRPGE1 proteins unable to interact with DcAPRR2, thereby failing to suppress carotenoid biosynthesis. These findings provide insights into the transcriptional regulation of carotenoid biosynthesis and offer potential target genes for enhancing carotenoid accumulation in crop plants.

Overexpression of Liriodendron Hybrid LhGLK1 in Arabidopsis Leads to Excessive Chlorophyll Synthesis and Improved Growth

Chloroplasts is the site for photosynthesis, which is the main primary source of energy for plants. Golden2-like (GLK) is a key transcription factor that regulates chloroplast development and chlorophyll synthesis. However, most studies on GLK genes are performed in crops and model plants with less attention to woody plants. In this study, we identified the LhGLK1 and LhGLK2 genes in the woody plant Liriodendron hybrid, and they are specifically expressed in green tissues. We showed that overexpression of the LhGLK1 gene improves rosette leaf chlorophyll content and induces ectopic chlorophyll biogenesis in primary root and petal vascular tissue in Arabidopsis. Although these exhibit a late-flowering phenotype, transgenic lines accumulate more biomass in vegetative growth with improved photochemical quenching (qP) and efficiency of photosystem II. Taken together, we verified a conserved and ancient mechanism for regulating chloroplast biogenesis in Liriodendron hybrid and evaluated its effect on photosynthesis and rosette biomass accumulation in the model plant Arabidopsis.

Transcriptome Analysis Reveals the Molecular Mechanism of the Leaf Yellowing in Allotriploid Cucumber

Yellowing leaves are ideal materials for studying the metabolic pathways of photosynthetic pigment chloroplast development, and the mechanism of photosynthetic systems. Here, we obtained a triploid material HCC (2n = 3x = 26), which was derived from hybridization between the artificial tetraploid Cucumis × hytivus (2n = 4x = 38, HHCC) and the cultivated cucumber Cucumis sativus (2n = 2x = 14, CC), and this triploid HCC showed obvious leaf yellowing characteristics. Phenotypic observation results showed that chloroplast development was impaired, the chlorophyll content decreased, and photosynthesis decreased in yellowing HCC leaves. The transcriptome results indicated that HCC-GLK is significantly downregulated in HCC and participates in the regulation of leaf yellowing. GO enrichment analysis revealed that differential genes were enriched in the heme binding and tetrapyrrole binding pathways related to leaf color. KEGG enrichment analysis revealed that differential genes were predominantly enriched in photosynthesis-related pathways. The experimental results of VIGS and yeast hybridization showed that silencing the GLK gene can induce leaf yellowing in cucumber plants, and the GLK protein can affect plant chloroplast development by interacting with the CAB3C protein (light-harvesting chlorophyll a/b binding) in the plant chlorophyll synthesis pathway. The current findings have not only enhanced our understanding of the regulatory mechanism of the GLK transcription factor in cucumber but also introduced novel insights and directions for investigating the molecular mechanism underlying polyploid leaf yellowing.

Fruit Quality Analysis and Flavor Comprehensive Evaluation of Cherry Tomatoes of Different Colors

Cherry tomatoes are popular vegetables worldwide owing to their variety of colors and nutrients. However, an integrated evaluation of color and flavor has rarely been reported. This study examined the differences among red, brown, yellow, and green cherry tomatoes grown in the Jiuquan area. A comprehensive analysis of the flavor quality of these tomatoes, including sensory evaluation, electronic nose analysis, nutritional and flavor quality measurements, targeted metabolomics, and chemometrics, was conducted. Red tomatoes had the highest lycopene content, and green tomatoes had the highest soluble protein and vitamin C content. In cherry tomatoes, K is the most abundant macro element and Fe and Zn are the most abundant trace elements. Brown cherry tomatoes had significantly higher K, P, Mg, Cu and Fe contents than other colored tomatoes, and red tomatoes had significantly higher Zn content than other cherry tomatoes (218.8-724.3%). Yellow cherry tomatoes had the highest soluble sugar content, followed by red, brown and green tomatoes. A total of 20 amino acids of tomatoes were simultaneously determined by LC-MS. Yellow cherry tomatoes have the highest content of essential amino acids, aromatic amino acids and sweetness amino acids. Red tomatoes have the highest levels of non-essential and sourness amino acid contents. An analysis of 30 flavor indicators revealed that yellow tomatoes had the best flavor, followed by red, brown, and green tomatoes. Our work lays the foundation for future research on color and flavor formation in cherry tomatoes.

Exploring the interplay between angiosperm chlorophyll metabolism and environmental factors

MAIN CONCLUSION

In this review, we summarize how chlorophyll metabolism in angiosperm is affected by the environmental factors: light, temperature, metal ions, water, oxygen, and altitude. The significance of chlorophyll (Chl) in plant leaf morphogenesis and photosynthesis cannot be overstated. Over time, researchers have made significant advancements in comprehending the biosynthetic pathway of Chl in angiosperms, along with the pivotal enzymes and genes involved in this process, particularly those related to heme synthesis and light-responsive mechanisms. Various environmental factors influence the stability of Chl content in angiosperms by modulating Chl metabolic pathways. Understanding the interplay between plants Chl metabolism and environmental factors has been a prominent research topic. This review mainly focuses on angiosperms, provides an overview of the regulatory mechanisms governing Chl metabolism, and the impact of environmental factors such as light, temperature, metal ions (iron and magnesium), water, oxygen, and altitude on Chl metabolism. Understanding these effects is crucial for comprehending and preserving the homeostasis of Chl metabolism.

Galactinol synthase 2 influences the metabolism of chlorophyll, carotenoids, and ethylene in tomato fruits

Galactinol synthase (GolS), which catalyses the synthesis of galactinol, is the first critical enzyme in the biosynthesis of raffinose family oligosaccharides (RFOs) and contributes to plant growth and development, and resistance mechanisms. However, its role in fruit development remains largely unknown. In this study, we used CRISPR/Cas9 gene-editing technology in tomato (Solanum lycopersicum) to create the gols2 mutant showing uniformly green fruits without dark-green shoulders, and promoting fruit ripening. Analysis indicated that galactinol was undetectable in the ovaries and fruits of the mutant, and the accumulation of chlorophyll and chloroplast development was suppressed in the fruits. RNA-sequencing analysis showed that genes related to chlorophyll accumulation and chloroplast development were down-regulated, including PROTOCHLOROPHYLLIDE OXIDOREDUCTASE, GOLDEN 2-LIKE 2, and CHLOROPHYLL A/B-BINDING PROTEINS. In addition, early color transformation and ethylene release was prompted in the gols2 lines by regulation of the expression of genes involved in carotenoid and ethylene metabolism (e.g. PHYTOENE SYNTHASE 1, CAROTENE CIS-TRANS ISOMERASE, and 1-AMINOCYCLOPROPANE-1-CARBOXYLIC ACID SYNTHASE2/4) and fruit ripening (e.g. RIPENING INHIBITOR, NON-RIPENING, and APETALA2a). Our results provide evidence for the involvement of GolS2 in pigment and ethylene metabolism of tomato fruits.

Class II knotted-like homeodomain protein SlKN5 with BEL1-like homeodomain proteins suppresses fruit greening in tomato fruit

Knotted1-like homeodomain (KNOX) proteins are essential in regulating plant organ differentiation. Land plants, including tomato (Solanum lycopersicum), have two classes of the KNOX protein family, namely, class I (KNOX I) and class II KNOX (KNOX II). While tomato KNOX I proteins are known to stimulate chloroplast development in fruit, affecting fruit coloration, the role of KNOX II proteins in this context remains unclear. In this study, we employ CRISPR/Cas9 to generate knockout mutants of the KNOX II member, SlKN5. These mutants display increased leaf complexity, a phenotype commonly associated with reduced KNOX II activity, as well as enhanced accumulation of chloroplasts and chlorophylls in smaller cells within young, unripe fruit. RNA-seq data analyses indicate that SlKN5 suppresses the transcriptions of genes involved in chloroplast biogenesis, chlorophyll biosynthesis, and gibberellin catabolism. Furthermore, protein-protein interaction assays reveal that SlKN5 physically interacts with three transcriptional repressors from the BLH1-clade of BEL1-like homeodomain (BLH) protein family, SlBLH4, SlBLH5, and SlBLH7, with SlBLH7 showing the strongest interaction. CRISPR/Cas9-mediated knockout of these SlBLH genes confirmed their overlapping roles in suppressing chloroplast biogenesis, chlorophyll biosynthesis, and lycopene cyclization. Transient assays further demonstrate that the SlKN5-SlBLH7 interaction enhances binding capacity to regulatory regions of key chloroplast- and chlorophyll-related genes, including SlAPRR2-like1, SlCAB-1C, and SlGUN4. Collectively, our findings elucidate that the KNOX II SlKN5-SlBLH regulatory modules serve to inhibit fruit greening and subsequently promote lycopene accumulation, thereby fine-tuning the color transition from immature green fruit to mature red fruit.

Integrative analysis of the methylome and transcriptome of tomato fruit (Solanum lycopersicum L.) induced by postharvest handling

Tomato fruit ripening is triggered by the demethylation of key genes, which alters their transcriptional levels thereby initiating and propagating a cascade of physiological events. What is unknown is how these processes are altered when fruit are ripened using postharvest practices to extend shelf-life, as these practices often reduce fruit quality. To address this, postharvest handling-induced changes in the fruit DNA methylome and transcriptome, and how they correlate with ripening speed, and ripening indicators such as ethylene, abscisic acid, and carotenoids, were assessed. This study comprehensively connected changes in physiological events with dynamic molecular changes. Ripening fruit that reached 'Turning' (T) after dark storage at 20°C, 12.5°C, or 5°C chilling (followed by 20°C rewarming) were compared to fresh-harvest fruit 'FHT'. Fruit stored at 12.5°C had the biggest epigenetic marks and alterations in gene expression, exceeding changes induced by postharvest chilling. Fruit physiological and chronological age were uncoupled at 12.5°C, as the time-to-ripening was the longest. Fruit ripening to Turning at 12.5°C was not climacteric; there was no respiratory or ethylene burst, rather, fruit were high in abscisic acid. Clear differentiation between postharvest-ripened and 'FHT' was evident in the methylome and transcriptome. Higher expression of photosynthetic genes and chlorophyll levels in 'FHT' fruit pointed to light as influencing the molecular changes in fruit ripening. Finally, correlative analyses of the -omics data putatively identified genes regulated by DNA methylation. Collectively, these data improve our interpretation of how tomato fruit ripening patterns are altered by postharvest practices, and long-term are expected to help improve fruit quality.

Identification and expression analysis of the GLK gene family in tea plant (Camellia sinensis) and a functional study of CsGLK54 under low-temperature stress

The Golden2-like (GLK) transcription factor family is a significant group of transcription factors in plantae. The currently available studies have shown that GLK transcription factors have been studied mainly in chloroplast growth and development, with fewer studies in abiotic stress regulation. In this study, all tea plant GLK transcription factors were identified for the first time in tea plants, and genome-wide identification, phylogenetic analysis, and thematic characterization were performed to identify 66 GLK transcription factors in tea plants. These genes are categorized into seven groups, and an amino acid sequence comparison analysis is performed. This study revealed that the structure of GLK genes in tea plants is highly conserved and that these genes are distributed across 14 chromosomes. Collinearity analysis revealed 17 pairs of genes with fragment duplications and one pair of genes with tandem duplications, and the analysis of Ka/Ks ratios indicated that most of the genes underwent negative purifying selection. Analysis of promoter cis-elements revealed that the promoters of tea plant GLK genes contain a large number of cis-acting elements related to phytohormones and stress tolerance. In addition, a large number of genes contain LTR elements, suggesting that tea plant GLK genes are involved in low-temperature stress. qRT‒PCR analysis revealed that the expression of CsGLK17, CsGLK38, CsGLK54, CsGLK11 and CsGLK60 significantly increased and that the expression of CsGLK7 and CsGLK13 decreased in response to low-temperature induction. Taken together, the results of the transcription profile analysis suggested that CsGLK54 may play an important regulatory role under low-temperature stress. The subcellular localization of CsGLK54 was in the nucleus. Furthermore, CsGLK54 positively regulated the transcription levels of the NbPOD and NbSOD genes under low-temperature stress, which led to an increase in POD and SOD enzyme activities and a decrease in MDA content. These findings provide valuable insights into the regulatory mechanism of low-temperature stress in tea plants.

Role of GARP family transcription factors in the regulatory network for nitrogen and phosphorus acquisition

The GARP (Golden2, ARR-B, Psr1) family proteins with a conserved DNA-binding domain, called the B-motif, are plant-specific transcription factors involved in the regulation of various physiological processes. The GARP family proteins are divided into members that function as monomeric transcription factors, and members that function as transcription factors in the dimeric form, owing to the presence of a coiled-coil dimerization domain. Recent studies revealed that the dimer-forming GARP family members, which are further divided into the PHR1 and NIGT1 subfamilies, play critical roles in the regulation of phosphorus (P) and nitrogen (N) acquisition. In this review, we present a general overview of the GARP family proteins and discuss how several members of the PHR1 and NIGT1 subfamilies are involved in the coordinated acquisition of P and N in response to changes in environmental nutrient conditions, while mainly focusing on the recent findings that enhance our knowledge of the roles of PHR1 and NIGT1 in phosphate starvation signaling and nitrate signaling.

Genome-Wide Analysis of the GLK Gene Family and Its Expression at Different Leaf Ages in the Citrus Cultivar Kanpei

The GLK gene family plays a crucial role in the regulation of chloroplast development and participates in chlorophyll synthesis. However, the precise mechanism by which GLK contributes to citrus's chlorophyll synthesis remains elusive. The GLK gene family causes variations in the photosynthetic capacity and chlorophyll synthesis of different citrus varieties. In this study, we identified tissue-specific members and the key CcGLKs involved in chlorophyll synthesis. A total of thirty CcGLK transcription factors (TFs) were discovered in the citrus genome, distributed across all nine chromosomes. The low occurrence of gene tandem duplication events and intronic variability suggests that intronic variation may be the primary mode of evolution for CcGLK TFs. Tissue-specific expression patterns were observed for various GLK family members; for instance, CcGLK12 and CcGLK15 were specifically expressed in the skin, while CcGLK30 was specific to the ovary, and CcGLK10, CcGLK6, CcGLK21, CcGLK2, CcGLK18, CcGLK9, CcGLK28, and CcGLK8 were specifically expressed in the leaves. CcGLK4, CcGLK5, CcGLK11, CcGLK23, CcGLKl7, CcGLK26, and CcGLK20 may participate in the regulation of the ALA, prochlorophylate, protoporphyrin IX, Mg-protoporphyrin IX, Chl b, T-Chl, MG-ProtoIX ME, and POR contents in citrus.

The SlGRAS9-SlZHD17 transcriptional cascade regulates chlorophyll and carbohydrate metabolism contributing to fruit quality traits in tomato

Some essential components of fleshy fruits are dependent on photosynthetic activity and carbohydrate metabolism. Nevertheless, the regulatory mechanisms linking chlorophyll and carbohydrate metabolism remain partially understood. Here, we uncovered the role of SlGRAS9 and SlZHD17 transcription factors in controlling chlorophyll and carbohydrate accumulation in tomato fruit. Knockout or knockdown of SlGRAS9 or SlZHD17 resulted in marked increase in chlorophyll content, reprogrammed chloroplast biogenesis and enhanced accumulation of starch and soluble sugars. Combined genome-wide transcriptomic profiling and promoter-binding experiments unveiled a complex mechanism in which the SlGRAS9/SlZHD17 regulatory module modulates the expression of chloroplast and sugar metabolism either via a sequential transcriptional cascade or through binding of both TFs to the same gene promoters, or, alternatively, via parallel pathways where each of the TFs act on different target genes. For instance, the regulation of SlAGPaseS1 and SlSUS1 is mediated by SlZHD17 whereas that of SlVI and SlGLK1 occurs only through SlGRAS9 without the intervention of SlZHD17. Both SlGRAS9 and SlZHD17 can also directly bind the promoter of SlPOR-B to regulate its expression. Taken together, our findings uncover two important regulators acting synergistically to manipulate chlorophyll and carbohydrate accumulation and provide new potential breeding targets for improving fruit quality in fleshy fruits.

Water saving irrigation mediates bioactive pigments metabolism and storage capacity in tomato fruit

Tomato fruit consumption is influenced by flavor and nutrient quality. In the present study, we investigate the impact of water saving irrigation (WSI) as a pre-harvest management on flavor and nutrient quality of tomato fruit. Our results demonstrate that WSI-treated tomato fruit exhibited improved sensory scores as assessed by a taste panel, accompanied by elevated levels of SlGLK2 expression, sugars, acids, and carotenoid contents compared to non-treated fruit. Notably, WSI treatment significantly enhanced the development of chloroplast and plastoglobulus in chromoplast, which served as carotenoid storage sites and upregulated the expression of carotenoid biosynthetic genes. Furthermore, integrated transcriptome and metabolome analysis revealed heightened expression of sugar and flavonoid metabolism pathways in WSI-treated tomato fruit. Remarkably, the master regulator SlMYB12 displayed a substantially increased expression due to WSI. These findings suggest that WSI is an effective and sustainable approach to enhance the pigments metabolism and storage capacity as well as the organoleptic characteristics and nutritional value of tomato fruit, offering a win-win solution for both water conservation and quality improvement in agro-food production.

PSEUDO-ETIOLATION IN LIGHT proteins reduce greening by binding GLK transcription factors

Knocking out genes encoding proteins that downregulate the accumulation of pigments may lead to increases in crop quality and yield. PSEUDO-ETIOLATION IN LIGHT 1 (PEL1) downregulates the accumulation of carotenoids in carrot and chlorophyll in Arabidopsis and rice and may inhibit GOLDEN 2-LIKE (GLK) transcription factors. PEL1 belongs to a previously unstudied gene family found only in plants. We used CRISPR/Cas9 technology to knock out each member of the 4-member PEL gene family and both GLK genes in Arabidopsis. In pel mutants, chlorophyll levels were elevated in seedlings; after flowering, chloroplasts increased in size, and anthocyanin levels increased. Although the chlorophyll-deficient phenotype of glk1 glk2 was epistatic to pel1 pel2 pel3 pel4 in most of our experiments, glk1 glk2 was not epistatic to pel1 pel2 pel3 pel4 for the accumulation of anthocyanins in most of our experiments. The pel alleles attenuated growth, altered the accumulation of nutrients in seeds, disrupted an abscisic acid-inducible inhibition of seedling growth response that promotes drought tolerance, and affected the expression of genes associated with diverse biological functions, such as stress responses, cell wall metabolism hormone responses, signaling, growth, and the accumulation of phenylpropanoids and pigments. We found that PEL proteins specifically bind 6 transcription factors that influence the accumulation of anthocyanins, GLK2, and the carboxy termini of GLK1 and Arabidopsis thaliana myeloblastosis oncogene homolog 4 (AtMYB4). Our data indicate that the PEL proteins influence the accumulation of chlorophyll and many other processes, possibly by inhibiting GLK transcription factors and via other mechanisms, and that multiple mechanisms downregulate chlorophyll content.

MdSnRK1.1 interacts with MdGLK1 to regulate abscisic acid-mediated chlorophyll accumulation in apple

Abscisic acid (ABA), as a plant hormone, plays a positive role in leaf chlorosis; however, the underlying molecular mechanism is less known. Our findings provide ABA treatment reduced the chlorophyll accumulation in apple, and Malus × domestica Sucrose Non-fermenting 1-Related Protein Kinase 1.1 (MdSnRK1.1) participates in the process. MdSnRK1.1 interacts with MdGLK1, a GOLDEN2-like transcription factor that orchestrates development of the chloroplast. Furthermore, MdSnRK1.1 affects MdGLK1 protein stability through phosphorylation. We found that Ser468 of MdGLK1 is target site of MdSnRK1.1 phosphorylation. MdSnRK1.1-mediated phosphorylation was critical for MdGLK1 binding to the target gene MdHEMA1 promoters. Collectively, our results demonstrate that ABA activates MdSnRK1.1 to degrade MdGLK1 and inhibit the accumulation of chlorophyll. These findings extend our understanding on how MdSnRK1.1 balances normal growth and hormone response.

Transcriptional regulation of tomato fruit ripening

An intrinsic and genetically determined ripening program of tomato fruits often depends upon the appropriate activation of tissue- and stage-specific transcription factors in space and time. The past two decades have yielded considerable progress in detailing these complex transcriptional as well as hormonal regulatory circuits paramount to fleshy fruit ripening. This non-linear ripening process is strongly controlled by the MADS-box and NOR family of proteins, triggering a transcriptional response associated with the progression of fruit ripening. Deepening insights into the connection between MADS-RIN and plant hormones related transcription factors, such as ERFs and ARFs, further conjugates the idea that several signaling units work in parallel to define an output fruit ripening transcriptome. Besides these TFs, the role of other families of transcription factors such as MYB, GLK, WRKY, GRAS and bHLH have also emerged as important ripening regulators. Other regulators such as EIN and EIL proteins also determine the transcriptional landscape of ripening fruits. Despite the abundant knowledge of the complex spectrum of ripening networks in the scientific domain, identifying more ripening effectors would pave the way for a better understanding of fleshy fruit ripening at the molecular level. This review provides an update on the transcriptional regulators of tomato fruit ripening.

Maize GOLDEN2-LIKE proteins enhance drought tolerance in rice by promoting stomatal closure

Drought has become one of the most severe abiotic stresses experienced in agricultural production across the world. Plants respond to water deficit via stomatal movements in the leaves, which are mainly regulated by abscisic acid (ABA). A previous study from our lab showed that constitutive expression of maize (Zea mays L.) GOLDEN2-LIKE (GLK) transcription factors in rice (Oryza sativa L.) can improve stomatal conductance and plant photosynthetic capacity under field conditions. In the present study, we uncovered a function of ZmGLK regulation of stomatal movement in rice during drought stress. We found that elevated drought tolerance in rice plants overexpressing ZmGLK1 or GOLDEN2 (ZmG2) was conferred by rapid ABA-mediated stomatal closure. Comparative analysis of RNA-sequencing (RNA-seq) data from the rice leaves and DNA affinity purification sequencing (DAP-seq) results obtained in vitro revealed that ZmGLKs played roles in regulating ABA-related and stress-responsive pathways. Four upregulated genes closely functioning in abiotic stress tolerance with strong binding peaks in the DAP-seq data were identified as putative target genes of ZmGLK1 and ZmG2 in rice. These results demonstrated that maize GLKs play an important role in regulating stomatal movements to coordinate photosynthesis and stress tolerance. This trait is a valuable target for breeding drought-tolerant crop plants without compromising photosynthetic capacity.

BPG4 regulates chloroplast development and homeostasis by suppressing GLK transcription factors and involving light and brassinosteroid signaling

Chloroplast development adapts to the environment for performing suitable photosynthesis. Brassinosteroids (BRs), plant steroid hormones, have crucial effects on not only plant growth but also chloroplast development. However, the detailed molecular mechanisms of BR signaling in chloroplast development remain unclear. Here, we identify a regulator of chloroplast development, BPG4, involved in light and BR signaling. BPG4 interacts with GOLDEN2-LIKE (GLK) transcription factors that promote the expression of photosynthesis-associated nuclear genes (PhANGs), and suppresses their activities, thereby causing a decrease in the amounts of chlorophylls and the size of light-harvesting complexes. BPG4 expression is induced by BR deficiency and light, and is regulated by the circadian rhythm. BPG4 deficiency causes increased reactive oxygen species (ROS) generation and damage to photosynthetic activity under excessive high-light conditions. Our findings suggest that BPG4 acts as a chloroplast homeostasis factor by fine-tuning the expression of PhANGs, optimizing chloroplast development, and avoiding ROS generation.

Identification, characterization, and expression of lipoxygenase genes in sweet cherry (Prunus avium L.) cv. Regina and their relationship with the development of an herbaceous off-flavor during fruit ripening

Flavor is an essential characteristic of fruit quality and is significant for consumers. Off-flavors have been reported in several fruits, including sweet cherry. This fruit has been reported to show an herbaceous/grassy-like flavor. The herbaceous off-flavor in sweet cherries detected in cultivar Regina has been related to the differential development of aroma compounds such as short-chain aldehydes and esters. One of the main biosynthesis pathways for these compounds is the fatty acid oxidation mediated by lipoxygenases (LOX). In order to have a better understanding of the biological basis of the differences in the volatile profile, the LOX gene expression profile was characterized during fruit development with and without herbaceous off-flavor. A genome-wide analysis of LOX in sweet cherry was carried out and compared to other species such as Arabidopsis, tomato, apple, prunus and strawberry. The structural features of 9-LOX and 13-LOX genes, encoded protein domains and their synteny were examined. Moreover, we analyzed the LOX expression at four developmental stages along ripening by RT-qPCR. Thirteen LOX gene candidates (six 9-LOX and seven 13-LOX) were identified. The 13-LOXs, PaLOX10, PaLOX11, and PaLOX12 were differentially expressed in herbaceous sweet cherries. Furthermore, their expression profile positively correlated with key volatile compounds linked to the herbaceous off-flavor. Overall, this study involves the genome-wide characterization of the LOX family in Prunus avium cv. Regina and provides information that can aid in studying LOX-related fruit deterioration in sweet cherries and associated species.

The AlkB Homolog SlALKBH10B Negatively Affects Drought and Salt Tolerance in Solanum lycopersicum

ALKBH proteins, the homologs of Escherichia coli AlkB dioxygenase, constitute a single-protein repair system that safeguards cellular DNA and RNA against the harmful effects of alkylating agents. ALKBH10B, the first discovered N6-methyladenosine (m6A) demethylase in Arabidopsis (Arabidopsis thaliana), has been shown to regulate plant growth, development, and stress responses. However, until now, the functional role of the plant ALKBH10B has solely been reported in arabidopsis, cotton, and poplar, leaving its functional implications in other plant species shrouded in mystery. In this study, we identified the AlkB homolog SlALKBH10B in tomato (Solanum lycopersicum) through phylogenetic and gene expression analyses. SlALKBH10B exhibited a wide range of expression patterns and was induced by exogenous abscisic acid (ABA) and abiotic stresses. By employing CRISPR/Cas9 gene editing techniques to knock out SlALKBH10B, we observed an increased sensitivity of mutants to ABA treatment and upregulation of gene expression related to ABA synthesis and response. Furthermore, the Slalkbh10b mutants displayed an enhanced tolerance to drought and salt stress, characterized by higher water retention, accumulation of photosynthetic products, proline accumulation, and lower levels of reactive oxygen species and cellular damage. Collectively, these findings provide insights into the negative impact of SlALKBH10B on drought and salt tolerance in tomato plant, expanding our understanding of the biological functionality of SlALKBH10B.