Gibberellin Signal Transduction Research Articles

Comparative transcriptome analysis reveals the key factors regulating nitrogen use efficiency in Chrysanthemum

Nitrogen (N) is a limiting factor that determines the yield and quality of Chrysanthemum. Genetic variation in N use efficiency (NUE) has been reported among Chrysanthemum genotypes. We performed a transcriptome analysis of two Chrysanthemum genotypes, ‘Nannonglihuang’ (‘LH’, N-efficient genotype) and ‘Nannongxuefeng’ (‘XF’, N-inefficient genotype), under low N (0.4 mmol·L-1 N) and normal N (8 mmol·L-1 N) treatments for 15 d and an N recovery treatment for 12 h (low N treatment for 15 d and then normal N treatment for 12 h) to understand the genetic factors impacting NUE in Chrysanthemum. The two genotypes exhibited contrasting responses to the different N treatments. The N-efficient genotype ‘LH’ had significant superiority in agronomic traits, N accumulation and glutamine synthase activity under both normal N and low N treatments. Low N treatment promoted root growth in ‘LH’, but inhibited root growth in ‘XF’. Transcriptome analysis revealed that the low N treatment increased the expression of some N metabolism genes, genes related to auxin and abscisic acid signal transduction in the roots of both genotypes, as well as genes related to gibberellin signal transduction in roots of ‘LH’. The N recovery treatment just increased the expression of genes related to cytokinin signal transduction in roots of ‘LH’. The expression levels of the NRT2.1, AMT1.1, and Gln1 genes related to gibberellin and cytokinin signal transduction were higher in roots of ‘LH’ than in ‘XF’ under different N treatments, suggesting that the genes related to N metabolism and hormone (auxin, abscisic acid, gibberellin, and cytokinin) signal transduction in roots of ‘LH’ are more sensitive to different N treatments than those of ‘XF’. Co-expression network analysis (WGCNA) also identified hub genes like bZIP43, bHLH93, NPF6.3, IBR10, MYB62, PP2C, PP2C06 and NLP7, which may be the key regulators of N-mediated responses in Chrysanthemum and play crucial roles in enhancing NUE and resistance to low N stress in the N-efficient Chrysanthemum genotype. These results revealed the key factors involved in regulating NUE in Chrysanthemum at the genetic level, which provides new insights into the complex mechanism of efficient nitrogen utilization in Chrysanthemum, and can be useful for the improvement and breeding of high NUE Chrysanthemum genotypes.

Integrated physiological and transcriptome analyses of the effects of water-soluble amino acid fertilizer on plant growth

Tobacco is a key component of China’s economy, serving as a major cash crop. With traditional fertilizers reaching their maximum potential in promoting tobacco growth, the exploration of new fertilizers has emerged as a viable solution for advancing experimental sustainable development. Spraying foliar fertilizer is a key measure to improve tobacco yield and quality. This study employed a combination of field and pot experiments to investigate the effects of applying water-soluble amino acid fertilizers on the growth, development, and quality of tobacco. The results of transcriptome analysis and physiological index measurements indicate that the application of water-soluble amino acid fertilizer can enhance the area of tobacco leaves, promote photosynthesis, and improve the chemical composition of the leaves. This research determined that the optimal concentration for spraying water-soluble amino acid fertilizer is diluted 500 times. Transcriptome analysis identified a total of 6,489 differentially expressed genes (DEGs), including 3,843 genes that were up-regulated and 2,646 genes that were down-regulated. Gene Ontology (GO)analysis demonstrated that these DEGs were significantlyassociatedwithprocessesincludingcell recognition, photosynthesis,thylakoidcomponents, calcium ion binding, and carbohydrate binding.Additionally, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis emphasized that the DEGs were largely found in pathwaysrelated tophotosynthesis-antenna proteins, interactions between plants and pathogens, photosynthesisitself, phenylpropanoid biosynthesis, andplant hormone signaling. Further research revealed that a significant number of genes involved in the auxin, gibberellin, salicylic acid, and jasmonic acid signal transduction pathways exhibited varying expression patterns following the application of water-soluble amino acid fertilizers.Additionally, the expression levels of bZIP, MYB, WRKY, bHLH, and AP2/ERF transcription factors exhibited significant variations following the application of water-soluble amino acid fertilizer. These results analyze the mechanisms of action of water-soluble amino acid fertilizers, offering new effective strategies to enhance both the yield and quality of tobacco.

Physiology, Biochemistry, and Transcriptomics Jointly Reveal the Phytotoxicity Mechanism of Acetochlor on Pisum sativum L.

Acetochlor, as a commonly used pre-emergent herbicide, can be toxic to crops and affect production if used improperly. However, the toxic mechanism of acetochlor on plants is not fully understood. The present study used a combination of transcriptomic analysis and physiological measurements to investigate the effects of short-term (15-day) exposure to different concentrations of acetochlor (1, 10, 20 mg/kg) on the morphology, physiology, and transcriptional levels of pea seedlings, aiming to elucidate the toxic response and resistance mechanisms in pea seedlings under herbicide stress. The results showed that the toxicity of acetochlor to pea seedlings was dose-dependent, manifested as dwarfing and stem base browning with increasing concentrations, especially at 10 mg/kg and above. Analysis of the antioxidant system showed that from the 1 mg/kg treatment, malondialdehyde, superoxide dismutase, peroxidase, and glutathione peroxidase in peas increased with increasing concentrations of acetochlor, indicating oxidative damage. Analysis of the glutathione (GSH) metabolism system showed that under 10 mg/kg treatment, the GSH content of pea plants significantly increased, and GSH transferase activity and gene expression were significantly induced, indicating a detoxification response in plants. Transcriptomic analysis showed that after acetochlor treatment, differentially expressed genes in peas were significantly enriched in the phenylpropane metabolic pathway, and the levels of key metabolites (flavonoids and lignin) were increased. In addition, we found that acetochlor-induced dwarfing of pea seedlings may be related to gibberellin signal transduction. Environ Toxicol Chem 2024;43:2005-2019. © 2024 SETAC.

Integrated transcriptomic and metabolomic analyses reveal the effect of mycorrhizal colonization on trifoliate orange root hair

Trifoliate orange (Pocirus trifoliata) as an excellent stock for citrus, but it has few root hairs and relies on mycorrhiza (AM) formed by arbuscular mycorrhizal fungi (AMF) to absorb soil nutrients and water, and there are few studies on the relationship between trifoliate orange root hair and AMF. This experiment analyzed the conditioning of AMF in trifoliate orange root hair growth from multiple perspectives. The results showed that AMF inoculation promoted root hair in citrus (eg: density and length) and the AMF mycorrhizal infection rate was 49.12 %. Metabolic and transcriptomic data of root also show that AMF promotes the development of root hair mainly by influencing hormone transduction and biosynthesis. The analysis of hormone synthesis signal transduction expression profile showed that AMF infection significantly up-regulated auxin, gibberellin, ethylene and cytokinin synthesis and signal transduction pathway, and also up-regulated auxin transport and jasmonic acid transduction. Analysis of root hair growth-related genes showed that AMF infection the up-regulated genes correlate with cell wall loosening, Ca2+ gradient and cell cycle, thereby facilitate the formation and elongation of root hair. In summary, AMF regulates trifoliate orange root hair growth through plant hormone metabolism and related key genes, thus increases the root surface area and further promotes the infection of AMF. In order to provide theory foundation for exploring the mechanism of AMF regulating trifoliate orange root hair growth.

An F-box Kelch repeat protein, PmFBK2, from Persicaria minor interacts with GID1b to modulate gibberellin signalling

The F-box protein (FBP) family plays diverse functions in the plant kingdom, with the function of many members still unrevealed. In this study, a specific FBP called PmFBK2, containing Kelch repeats from Persicaria minor, was functionally investigated. Employing the yeast two-hybrid (Y2H) assay, PmFBK2 was found to interact with Skp1-like proteins from P. minor, suggesting its potential to form an E3 ubiquitin ligase, known as the SCF complex. Y2H and co-immunoprecipitation tests revealed that PmFBK2 interacts with full-length PmGID1b. The interaction marks the first documented binding between these two protein types, which have never been reported in other plants before, and they exhibited a negative effect on gibberellin (GA) signal transduction. The overexpression of PmFBK2 in the kmd3 mutant, a homolog from Arabidopsis, demonstrated the ability of PmFBK2 to restore the function of the mutated KMD3 gene. The function restoration was supported by morphophysiological and gene expression analyses, which exhibited patterns similar to the wild type (WT) compared to the kmd3 mutant. Interestingly, the overexpression of PmFBK2 or PmGID1b in Arabidopsis had opposite effects on rosette diameter, seed weight, and plant height. This study provides new insights into the complex GA signalling. It highlights the crucial roles of the interaction between FBP and the GA receptor (GID1b) in regulating GA responses. These findings have implications for developing strategies to enhance plant growth and yield by modulating GA signalling in crops.

Identification of ARF Genes and Elucidation of the Regulatory Effects of PsARF16a on the Dormancy of Tree Peony Plantlets.

The low survival rate of transplanted plantlets, which has limited the utility of tissue-culture-based methods for the rapid propagation of tree peonies, is due to plantlet dormancy after rooting. We previously determined that the auxin response factor PsARF may be a key regulator of tree peony dormancy. To clarify the mechanism mediating tree peony plantlet dormancy, PsARF genes were systematically identified and analyzed. Additionally, PsARF16a was transiently expressed in the leaves of tree peony plantlets to examine its regulatory effects on a downstream gene network. Nineteen PsARF genes were identified and divided into four classes. All PsARF genes encoded proteins with conserved B3 and ARF domains. The number of motifs, exons, and introns varied between PsARF genes in different classes. The overexpression of PsARF16a altered the expression of NCED, ZEP, PYL, GA2ox1, GID1, and other key genes in abscisic acid (ABA) and gibberellin (GA) signal transduction pathways, thereby promoting ABA synthesis and decreasing GA synthesis. Significant changes to the expression of some key genes contributing to starch and sugar metabolism (e.g., AMY2A, BAM3, BGLU, STP, and SUS2) may be associated with the gradual conversion of sugar into starch. This study provides important insights into PsARF functions in tree peonies.

Analysis Transcriptome and Phytohormone Changes Associated with the Allelopathic Effects of Ginseng Hairy Roots Induced by Different-Polarity Ginsenoside Components.

The allelopathic autotoxicity of ginsenosides is an important cause of continuous cropping obstacles in ginseng planting. There is no report on the potential molecular mechanism of the correlation between polarity of ginsenoside components and their allelopathic autotoxicity. This study applied a combination of metabolomics and transcriptomics analysis techniques, combined with apparent morphology, physiological indexes, and cell vitality detection of the ginseng hairy roots, through which the molecular mechanism of correlation between polarity and allelopathic autotoxicity of ginsenosides were comprehensively studied. The hairy roots of ginseng presented more severe cell apoptosis under the stress of low-polarity ginsenoside components (ZG70). ZG70 exerted allelopathic autotoxicity by regulating the key enzyme genes of cis-zeatin (cZ) synthesis pathway, indole-3-acetic acid (IAA) synthesis pathway, and jasmonates (JAs) signaling transduction pathway. The common pathway for high-polarity ginsenoside components (ZG50) and ZG70 to induce the development of allelopathic autotoxicity was through the expression of key enzymes in the gibberellin (GA) signal transduction pathway, thereby inhibiting the growth of ginseng hairy roots. cZ, indole-3-acetamid (IAM), gibberellin A1 (GA1), and jasmonoyl-L-isoleucine (JA-ILE) were the key response factors in this process. It could be concluded that the polarity of ginsenoside components were negatively correlated with their allelopathic autotoxicity.

Physiological, Metabolic, and Transcriptomic Analyses Reveal the Effect of Sweet Corn Plants Treated with a New Biostimulant on the Growth Enhancement, Focusing on Enhancing Gibberellin Synthesis and Signal Transduction

Physiological, Metabolic, and Transcriptomic Analyses Reveal the Effect of Sweet Corn Plants Treated with a New Biostimulant on the Growth Enhancement, Focusing on Enhancing Gibberellin Synthesis and Signal Transduction

Overexpression of SlPRE3 alters the plant morphologies in Solanum lycopersicum.

Overexpression of SlPRE3 is detrimental to the photosynthesis and alters plant morphology and root development. SlPRE3 interacts with SlAIF1/SlAIF2/SlPAR1/SlIBH1 to regulate cell expansion. Basic helix-loop-helix (bHLH) transcription factors play crucial roles as regulators in plant growth and development. In this study, we isolated and characterized SlPRE3, an atypical bHLH transcription factor gene. SlPRE3 exhibited predominant expression in the root and moderate expression in the senescent leaves. Comparative analysis with the wild type revealed significant differences in plant morphology in the 35S:SlPRE3 lines. These differences included increased internode length, rolling leaves with reduced chlorophyll accumulation, and elongated yet fewer adventitious roots. Additionally, 35S:SlPRE3 lines displayed elevated levels of GA3 (gibberellin A3) and reduced starch accumulation. Furthermore, utilizing the Y2H (Yeast two-hybrid) and the BiFC (Bimolecular Fluorescent Complimentary) techniques, we identified physical interactions between SlPRE3 and SlAIF1 (ATBS1-interacting factor 1)/SlAIF2 (ATBS1-interacting factor 2)/SlPAR1 (PHYTOCHROME RAPIDLY REGULATED 1)/SlIBH1 (ILI1-binding bHLH 1). RNA-seq analysis of root tissues revealed significant alterations in transcript levels of genes involved in gibberellin metabolism and signal transduction, cell expansion, and root development. In summary, our study sheds light on the crucial regulatory role of SlPRE3 in determining plant morphology and root development.

Transcriptome Analysis Reveals the Hormone Signalling Coexpression Pathways Involved in Adventitious Root Formation in Populus

Adventitious roots (ARs) occur naturally in many species and are important for plants to absorb nutrients and water. AR formation can also be induced from explants of trees, whose clonal propagation is needed. AR formation is gridlock for many woody plant mass propagations. Plant hormones have been regarded as playing a key role in AR formation, and the molecular regulatory mechanisms need to be elucidated. In this study, RNA-Seq was performed to reveal the molecular mechanisms in the different periods of AR formation from hybrid poplar clone 84K (Populus alba × P. glandulosa) and AUXIN SIGNALING F-BOX (PagFBL1-OE). To understand the importance of differentially expressed genes (DEGs), we found that many genes involved in signal transduction mechanisms were induced at 12, 24 and 48 h in 84K and PagFBL1-OE cells by NOG classification. We also found that many DEGs were enriched in hormone signal transduction only for the first 12 h in 84K and PagFBL1-OE by KEGG pathway enrichment. Notably, more DEGs appeared in indole-3-acetic acid (IAA), abscisic acid (ABA), ethylene (ETH), jasmonic acid (JA), brassinolide (BR), cytokinin (CTK) and gibberellin (GA) signal transduction for the first 12 h in PagFBL1-OE than in 84K. Moreover, ARF (Pop_G01G075686), IAA14 (Pop_A10G047257), SAURs (Pop_A03G019756, Pop_A12G067965, Pop_G03G055849 and Pop_G12G008821), JAR1s (Pop_A14G000375 and Pop_G14G044264), CTR1 (Pop_A17G052594 and Pop_G09G030293), CRE1s (Pop_G07G086605 and Pop_G07G086618), GID1 (Pop_A04G026477), BKI1 (Pop_A02G066155), PYR/PYLs (Pop_A03G050217 and Pop_G01G089222), and TGAs (Pop_A04G059310, Pop_G04G060065 and Pop_G05G008153) were only specifically expressed in PagFBL1-OE and could play an important role in AR formation, especially in the first 12 h under plant hormone signal transduction. These results show that the complex biological process of AR formation is primarily influenced by the hormone signalling pathway in Populus. This study reveals the initial regulation of AR formation in woody plant cuttings and thus contributes to further elucidating the molecular mechanism by which hormones interact.

Exogenous spraying of IAA improved the efficiency of microspore embryogenesis in Wucai (Brassica campestris L.) by affecting the balance of endogenous hormones, energy metabolism, and cell wall degradation

BackgroundMicrospore embryogenesis is an extraordinarily complicated process, comprehensively regulated by a composite network of physiological and molecular factors, among which hormone is one of the most crucial factors. Auxin is required for stress-induced microspore reprogramming, however, the mechanism of its regulation of microspore embryogenesis is still unclear.ResultsIn this study, we found exogenously spraying 100 mg·L− 1 IAA on the buds of Wucai significantly increased the rate of microspore embryogenesis, and moreover accelerated the process of embryogenesis. Physiological and biochemical tests showed that the contents of amino acids, soluble total sugar, soluble protein, and starch were significantly increased after IAA treatment. Furthermore, exogenously spraying 100 mg·L− 1 IAA significantly enhanced IAA, GA4, and GA9 content, increased catalase (CAT) and malondialdehyde (MDA) activity, and reduced abscisic acid (ABA), MDA and soluble protopectin content, H2O2 and O2·− production rate in the bud with the largest population of late-uninucleate-stage microspores. Transcriptome sequencing was performed on buds respectively treated with 100 mg·L− 1 IAA and fresh water. A total of 2004 DEGs were identified, of which 79 were involved in micropores development, embryonic development and cell wall formation and modification, most of which were upregulated. KEGG and GO analysis revealed that 9.52% of DEGs were enriched in plant hormone synthesis and signal transduction pathways, pentose and glucuronic acid exchange pathways, and oxidative phosphorylation pathways.ConclusionsThese findings indicated that exogenous IAA altered the contents of endogenous hormone content, total soluble sugar, amino acid, starch, soluble protein, MDA and protopectin, the activities of CAT and peroxidase (POD), and the production rate of H2O2 and O2·−. Combined with transcriptome analysis, it was found that most genes related to gibberellin (GA) and Auxin (IAA) synthesis and signal transduction, pectin methylase (PME) and polygalacturonase (PGs) genes and genes related to ATP synthesis and electron transport chain were upregulated, and genes related to ABA synthesis and signal transduction were downregulated. These results indicated that exogenous IAA treatment could change the balance of endogenous hormones, accelerate cell wall degradation, promote ATP synthesis and nutrient accumulation, inhibit ROS accumulation, which ultimately promote microspore embryogenesis.

Application of strigolactone analogs in storage of Gastrodia elata

This study explored the preservation effect of strigolactone analogs on Gastrodia elata tubers and screened out the suitable preservation measures of G. elata to provide a safer and more effective method for its storage and preservation. Fresh G. elata tubers were treated with 7FGR24, 2,4-D isooctyl ester, and maleic hydrazide, respectively. The growth of flower buds, the activities of CAT, and MDA, and the content of gastrodin and p-hydroxybenzyl alcohol were measured to compare the effects of different compounds on the storage and preservation of G. elata. The effects of different storage temperatures on the preservation of 7FGR24 were compared and analyzed. The gibberellin signal transduction receptor gene GeGID1 was cloned, and the effect of 7FGR24 on the expression level of GeGID1 was analyzed by quantitative polymerase chain reaction(qPCR). The toxicity of the G. elata preservative 7FGR24 was analyzed by intragastric administration in mice to evaluate its safety. The results showed that compared with 2,4-D isooctyl ester and maleic hydrazide, 7FGR24 treatment had a significant inhibitory effect on the growth of G. elata flower buds, and the CAT enzyme activity of G. elata was the highest, indicating that its preservation effect was stronger. Different storage temperatures had different effects on the preservation of G. elata, and the preservation effect was the strongest at 5 ℃. The open reading frame(ORF) of GeGID1 gene was 936 bp in length, and its expression level was significantly down-regulated after 7FGR24 treatment, indicating that 7FGR24 may inhibit the growth of flower buds by inhibiting the gibberellin signal of G. elata, thereby exerting a fresh-keeping effect. Feeding preservative 7FGR24 had no significant effect on the behavior and physiology of mice, indicating that it had no obvious toxicity. This study explored the application of the strigolactone analog 7FGR24 in the storage and preservation of G. elata and preliminarily established a method for the storage and preservation of G. elata, laying a foundation for the molecular mechanism of 7FGR24 in the storage and preservation of G. elata.

The E3 ubiquitin ligases SINA1 and SINA2 integrate with the protein kinase CIPK20 to regulate the stability of RGL2a, a positive regulator of anthocyanin biosynthesis.

Although DELLA protein destabilization mediated by post-translational modifications is essential for gibberellin (GA) signal transduction and GA-regulated anthocyanin biosynthesis, the related mechanisms remain largely unknown. In this study, we report the ubiquitination and phosphorylation of an apple DELLA protein MdRGL2a in response to GA signaling and its regulatory role in anthocyanin biosynthesis. MdRGL2a could interact with MdWRKY75 to enhance the MdWRKY75-activated transcription of anthocyanin activator MdMYB1 and interfere with the interaction between anthocyanin repressor MdMYB308 and MdbHLH3 or MdbHLH33, thereby promoting anthocyanin accumulation. A protein kinase MdCIPK20 was found to phosphorylate and protect MdRGL2a from degradation, and it was essential for MdRGL2a-promoting anthocyanin accumulation. However, MdRGL2a and MdCIPK20 were ubiquitinated and degraded by E3 ubiquitin ligases MdSINA1 and MdSINA2, respectively, both of which were activated in the presence of GA. Our results display the integration of SINA1/2 with CIPK20 to dynamically regulate GA signaling and will be helpful toward understanding the mechanism of GA signal transduction and GA-inhibited anthocyanin biosynthesis. The discovery of extensive interactions between DELLA and SINA and CIPK proteins in apple will provide reference for the study of ubiquitination and phosphorylation of DELLA proteins in other species.

High responsiveness to nitrogen supply in modern maize cultivars is contributed to gibberellin-dependent leaf elongation

Modern maize cultivars have high nitrogen responsiveness of grain yield. However, the underlying physiological mechanism is unclear. In the present study, from 17 cultivars released from 1950 s to 2010 s in China, three maize cultivars released in 1950 s (BMY), 1970 s (ZD2), and 1990 s (ZD958) were selected according to their growth responses to nitrogen supply. Nitrogen responsiveness of shoot biomass was highest in the new cultivar ZD958, and the lowest in the old cultivar BMY, with the medium cultivar ZD2 in between. Shoot biomass was closely related to leaf elongation rate. Leaf elongation was further analyzed using kinematic analysis method. Cell division rate and cell production rate were greater and more responsive to nitrogen supply in ZD958 than in the other cultivars. In agreement, there were more cells in the elongation zone of ZD958 and they were more responsive to increasing supply, resulting a longer leaf elongation zone. The interaction effect between cultivar and nitrogen supply on leaf elongation was in consistence with the change in gibberellin (GA1 and GA3) concentration in leaf growth zone. Accordingly, the genes encoding gibberellin biosynthesis or signal transduction was more up-regulated in ZD958, which was positively correlated to the up-regulation of genes related to cell cycle and DNA replication. On the contrary, the genes related to the inactivation of gibberellin was more down-regulated in ZD958. Exogenous application of bioactive gibberellin or its biosynthesis inhibitor eliminated the interaction effect between cultivar and nitrogen supply on leaf elongation rate. In conclusion, modern maize breeding may have increased nitrogen responsiveness in maize by enhancing the gibberellins-dependent leaf elongation response to high nitrogen supply.

Mechanism analysis of calcium nitrate application to induce gibberellin biosynthesis and signal transduction promoting stem elongation of Dendrobium officinale

Dendrobium officinale Kimura et Migo is a precious medicinal plant which has high medicinal and commercial value. The length of the stem of D. officinale is an important factor affecting the yield because of its bioactive polysaccharides found in the stem. Nitrate can promote the elongation of young stems, but the mechanisms of calcium nitrate (CN) mediated stem length growth remain largely unknown. In this study, the transcriptome, main organic components, mineral elements and microstructure of D. officinale sprayed with CN were analyzed. 659 differentially expressed genes (DEGs) were detected in the Control and CN treatment. The concentrations of the calcium and nitrate increased significantly, while the concentrations of two kinds of the aldohexoses decreased significantly. Most of the twenty key genes involved in calcium and nitrate signal transduction and carbohydrate metabolism were up-regulated. In the two pathways of gibberellin (GA) biosynthesis and signal transduction, it was found that the expression of four differential genes related to GA biosynthesis was up-regulated, and the contents of nine GAs were also significantly increased, especially the contents of bioactive GA1 and GA4. The expression levels of most genes related to GA signal transduction were also up-regulated after CN treatment. After CN treatment, the expression levels of downstream genes related to stem elongation and tillering were also up-regulated. In addition, the microstructure showed that CN treatment made cells elongate longitudinally, made cell walls and collenchyma thicken, made obvious lignification and the increased the number of vascular bundles, indicating that CN can promote stem elongation by enhancing ductility and mechanical strength. These results provide a theoretical and practical basis for studying how nitrate treatment can improve the stem length and yield of D. officinale.

Field plus lab experiments help identify freezing tolerance and associated genes in subtropical evergreen broadleaf trees: A case study of Camellia oleifera.

The molecular mechanisms of freezing tolerance are unresolved in the perennial trees that can survive under much lower freezing temperatures than annual herbs. Since natural conditions involve many factors and temperature usually cannot be controlled, field experiments alone cannot directly identify the effects of freezing stress. Lab experiments are insufficient for trees to complete cold acclimation and cannot reflect natural freezing-stress responses. In this study, a new method was proposed using field plus lab experiments to identify freezing tolerance and associated genes in subtropical evergreen broadleaf trees using Camellia oleifera as a case. Cultivated C. oleifera is the dominant woody oil crop in China. Wild C. oleifera at the high-elevation site in Lu Mountain could survive below -30°C, providing a valuable genetic resource for the breeding of freezing tolerance. In the field experiment, air temperature was monitored from autumn to winter on wild C. oleifera at the high-elevation site in Lu Mountain. Leave samples were taken from wild C. oleifera before cold acclimation, during cold acclimation and under freezing temperature. Leaf transcriptome analyses indicated that the gene functions and expression patterns were very different during cold acclimation and under freezing temperature. In the lab experiments, leaves samples from wild C. oleifera after cold acclimation were placed under -10°C in climate chambers. A cultivated C. oleifera variety "Ganwu 1" was used as a control. According to relative conductivity changes of leaves, wild C. oleifera showed more freezing-tolerant than cultivated C. oleifera. Leaf transcriptome analyses showed that the gene expression patterns were very different between wild and cultivated C. oleifera in the lab experiment. Combing transcriptome results in both of the field and lab experiments, the common genes associated with freezing-stress responses were identified. Key genes of the flg22, Ca2+ and gibberellin signal transduction pathways and the lignin biosynthesis pathway may be involved in the freezing-stress responses. Most of the genes had the highest expression levels under freezing temperature in the field experiment and showed higher expression in wild C. oleifera with stronger freezing tolerance in the lab experiment. Our study may help identify freezing tolerance and underlying molecular mechanisms in trees.

Insights into the Genetic Determination of the Autotetraploid Potato Plant Height.

Plant height is an important characteristic, the modification of which can improve the ability of stress adaptation as well as the yield. In this study, genome-wide association analysis was performed for plant height traits in 370 potato cultivars using the tetraploid potato genome as a reference. A total of 92 significant single nucleotide polymorphism (SNP) loci for plant height were obtained, which were particularly significant in haplotypes A3 and A4 on chromosome 1 and A1, A2, and A4 on chromosome 5. Thirty-five candidate genes were identified that were mainly involved in the gibberellin and brassinolide signal transduction pathways, including the FAR1 gene, methyltransferase, ethylene response factor, and ubiquitin protein ligase. Among them, PIF3 and GID1a were only present on chromosome 1, with PIF3 in all four haplotypes and GID1a in haplotype A3. This could lead to more effective genetic loci for molecular marker-assisted selection breeding as well as more precise localization and cloning of genes for plant height traits in potatoes.

Insights on the stem elongation of spur-type bud sport mutant of ‘Red Delicious’ apple

The decreased capacity of auxin-, CTK-, and BR-mediated cell division and cell enlargement pathways, combined with the enhanced capacity of GA and ETH-, JA-, ABA-, SA-mediated stress-resistant pathways were presumed to be the crucial reasons for the formation of spur-type 'Red Delicious' mutants. Vallee Spur', which exhibit short internodes and compact tree shape, is the fourth generation of the spur-type bud sport mutant of 'Red Delicious'. However, the underlying molecular mechanism of these properties remains unclear. Here, comparative phenotypic, full-length transcriptome and phytohormone analyses were performed between 'Red Delicious' (NSP) and 'Vallee Spur' (SP). The new shoot internode length of NSP was ˃ 1.53-fold higher than that of the SP mutant. Cytological analysis showed that the stem cells of the SP mutant were smaller and more tightly arranged relative to the NSP. By Iso-Seq, a total of 1426 differentially expressed genes (DEGs) were detected, including 808 upregulated and 618 downregulated genes in new shoot apex with 2 leaves of the SP mutant. Gene expressions involved in auxin, cytokinin (CTK), and brassinosteroid (BR) signal transduction were mostly downregulated in the SP mutant, whereas those involved in gibberellin (GA), ethylene (ETH), jasmonate (JA), ABA, and salicylic acid (SA) signal transduction were mostly upregulated. The overall thermogram analysis of hormone levels in the shoot apex carrying two leaves detected by LC-MS/MS absolute quantification showed that the levels of IAA-Asp, IAA, iP7G, OPDA, and 6-deoxyCS were significantly upregulated in the SP mutant, while the remaining 28 hormones were significantly downregulated. It is speculated that the decreased capacity of auxin, CTK, and BR-mediated cell division and cell enlargement pathways is crucial for the formation of the SP mutant. GA and stress-resistant pathways of ETH, JA, ABA, and SA also play vital roles in stem elongation. These results highlight the involvement of phytohormones in the formation of stem elongation occurring in 'Red Delicious' spur-type bud sport mutants and provide information for exploring its biological mechanism.

Physiological, Transcriptomic and Metabolomic Analyses of Overwintering Cryptomeria fortunei Needles

Low temperatures affect plant growth, development, and geographical distribution. Cryptomeriafortunei (Chinese cedar) is a major industrial tree species used for timber manufacturing in southern China. However, its popularization and application in northern China are limited due to its poor low-temperature resistance (approximately −6 °C), and its overwintering mechanism remains unclear. Here, we performed physiological, metabolomic, and transcriptomic analyses of overwintering C.fortunei needles at three stages: before winter, during winter, and in early spring. Physiological analyses showed that electrolyte leakage, H2O2, malondialdehyde (MDA), soluble sugar, and protein contents increased, while the maximum quantum yield of photosystem II (PSII) (Fv/Fm), effective quantum yield of PSII (YII), and chlorophyll content decreased as overwintering progressed. Metabolomic and transcriptomic analyses revealed that downregulated gibberellin (GA), salicylic acid (SA), cytokinin (CTK), and auxin signal transduction and upregulated abscisic acid (ABA), ethylene, brassinosteroids (BR), and jasmonic acid (JA) signal transduction pathways promoted the winter acclimation of C.fortunei, while the opposite expression pattern promoted the transition from dormancy to growth. In addition, upregulated genes/metabolites involved in phenylpropanoid and flavonoid biosynthesis, starch and sucrose metabolism, cold-related protein and fatty acid desaturases, and downregulated photosynthesis-related pathways promoted winter acclimation, while five (WRKY, AP2/ERF, NAC, MYB, and bHLH) and three (AP2/ERF, MYB, and bHLH) transcription factors were associated with winter acclimation and early spring transition from dormancy to growth, respectively. In summary, we report the first transcriptome of overwintering C.fortunei, providing a foundation for the cultivation of and research on overwintering varieties.

Integrative analysis of transcriptome and miRNAome reveals molecular mechanisms regulating pericarp thickness in sweet corn during kernel development.

Pericarp thickness affects the edible quality of sweet corn (Zea mays L. saccharata Sturt.). Therefore, breeding varieties with a thin pericarp is important for the quality breeding of sweet corn. However, the molecular mechanisms underlying the pericarp development remain largely unclear. We performed an integrative analysis of mRNA and miRNA sequencing to elucidate the genetic mechanism regulating pericarp thickness during kernel development (at 15 days, 19 days, and 23 days after pollination) of two sweet corn inbred lines with different pericarp thicknesses (M03, with a thinner pericarp and M08, with a thicker pericarp). A total of 2,443 and 1,409 differentially expressed genes (DEGs) were identified in M03 and M08, respectively. Our results indicate that phytohormone-mediated programmed cell death (PCD) may play a critical role in determining pericarp thickness in sweet corn. Auxin (AUX), gibberellin (GA), and brassinosteroid (BR) signal transduction may indirectly mediate PCD to regulate pericarp thickness in M03 (the thin pericarp variety). In contrast, abscisic acid (ABA), cytokinin (CK), and ethylene (ETH) signaling may be the key regulators of pericarp PCD in M08 (the thick pericarp variety). Furthermore, 110 differentially expressed microRNAs (DEMIs) and 478 differentially expressed target genes were identified. miRNA164-, miRNA167-, and miRNA156-mediated miRNA–mRNA pairs may participate in regulating pericarp thickness. The expression results of DEGs were validated by quantitative real-time PCR. These findings provide insights into the molecular mechanisms regulating pericarp thickness and propose the objective of breeding sweet corn varieties with a thin pericarp.