Expansins: roles in plant growth and potential applications in crop improvement

Functional identification of mango MiEXPLA1a2 and MiEXPA4e1 genes in transgenic Arabidopsis and tomato

Expansin (EXP) is an intrinsic regulator of plant cell expansion, and have been shown to play a role in each stages of plant growth and development. But has not yet been fully studied in mango. In this experiment, two pairs of homologous genes MiEXPA1s and MiEXPA4s were firstly excavated from mango genome. qRT-PCR analysis showed that the expression of MiEXPA1a2 was gradually increased with the development of mango fruits, while MiEXPA4e1 has the opposite expression pattern. In this study, the functions of two genes were explored by overexpression in Arabidopsis and tomato. MiEXPLA1a2 and MiEXPA4e1 genes with opposite expression levels showed similar gene functions. Compared with wild-type Arabidopsis (WT), overexpression of MiEXPA1a2 and MiEXPA4e1 Arabidopsis promoted early flowering, increased rosette leaves number, caused dwarf plants, and reduced the number of seeds. In addition, MiEXPA1a2 and MiEXPA4e1 transgenic plants significantly increased root length and survival rate under drought and salt stress treatments. It was also found that MiEXPA1a2 and MiEXPA4e1 promoted root length in response to gibberellin treatment, while ABA significantly inhibited it. We found similar phenotypes to Arabidopsis in transgenic tomato plants, such as promoted early flowering, reduced plant height, increased sepal length, affected the fruit and seed quality. Interestingly, MiEXPA4e1 is significantly shorter the pod length in Arabidopsis and reduced the fruit weight in tomato, while MiEXPA1a2 does not have this phenomenon. In conclusion, MiEXPLA1a2 and MiEXPA4e1 genes have potential applications in regulating plant flowering, regulating phenotype, and improving stress response.

Size Matters: Influence of Available Soil Volume on the Root Architecture and Plant Response at Transcriptomic and Metabolomic Levels in Barley

Pot size is a critical factor in plant growth experiments, influencing root architecture, nutrient uptake, and overall plant development as well as sensing of stress. In controlled environments, variation in pot size can impact phenotypic and molecular outcomes and may bias experimental results. Here, we investigated how pot size affects the root system architecture and molecular responses of two barley genotypes, the landrace BERE and the modern elite CONCERTO, through assessment of shoot and root traits and by using X-ray computed tomography complemented by transcriptomic and metabolomic analyses. The two genotypes showed distinctly different adaptations to changes in pot size. The landrace showed greater stability and adaptability with consistent root traits and enhanced accumulation of osmoprotectant metabolites across different pot sizes with respect to CONCERTO. Conversely, the elite line was more sensitive to pot size variations, particularly showing altered root architecture and transcriptomic responses. Overall, this study highlights the importance of selecting an appropriate pot size for plant growth experiments, particularly when focused on root traits, and highlights the importance of considering the physiological and molecular changes due to growth environment choice in experimental design in barley.

Discovery of variation in genes related to agronomic traits by sequencing the genome of Cucurbita pepo varieties

BACKGROUND

Cucurbita pepo L. cultivars display high morphological traits variation. In addition, C. pepo faces numerous threats, such as viral and fungal infections, which significantly influence crop cultivation. Recent genomic advancements improved the understanding of genetic diversity and stress responses in this crop. We investigated genetic variations related to plant morphology and quality traits. Additionally, the inclusion of both powdery mildew (PM) and Zucchini yellow mosaic virus (ZYMV) susceptible and tolerant varieties facilitated the examination of genetic diversity concerning biotic stress.

RESULTS

The sequencing of eight Cucurbita pepo varieties produced an average of 40 million raw reads with a coverage of reference genome ranging from 22 to 40X. More than 4.7 million genomic variants were identified in all genomes. Based on admixture and PCA analysis, the eight C. pepo genotypes were grouped in two clusters belonging to Cocozelle and Zucchini groups, with "Whitaker" separated from the rest of the accessions. Genes involved in pathways related to gibberellin regulation, leaf development, and pigment accumulation resulted highly affected by variation suggesting that the diversity observed among varieties in plant and fruit morphology could be related to variants identified in such genes. Each variety showed its own set of genetic differences. The genomic comparison of 381e, 968Rb and SPQ allowed the identification of variants in chromosome regions affecting response to Zucchini yellow mosaic virus (ZYMV) and powdery mildew (PM). Variants in key genes associated with resistant traits were identified, suggesting potential pathways and mechanisms involved in biotic stress response and plant immunity.

CONCLUSIONS

Genetic variations affecting morphology and fruit quality in C. pepo emphasize their significance for breeding efforts. Furthermore, the genomic comparison of 381e, 968Rb and SPQ highlighted variants in chromosomal regions influencing zucchini's response to PM and ZYMV. These findings could pave the way for more targeted and effective genetic improvement strategies, thereby potentially leading to increased agricultural productivity and quality.

Cell wall remodeling during plant regeneration

Plant regeneration is the process during which differentiated tissues or cells can reverse or alter their developmental trajectory to repair damaged tissues or form new organs. In the plant regeneration process, the cell wall not only functions as a foundational barrier and scaffold supporting plant cells but also influences cell fates and identities. Cell wall remodeling involves the selective degradation of certain cell wall components or the integration of new components. Recently, accumulating evidence has underscored the importance of cell wall remodeling in plant regeneration. Wounding signals, transmitted by transcription factors, trigger the expressions of genes responsible for cell wall loosening, which is essential for tissue repair. In de novo organ regeneration and somatic embryogenesis, phytohormones orchestrate a transcriptional regulatory network to induce cell wall remodeling, which promotes cell fate reprogramming and organ formation. This review summarizes the effects of cell wall remodeling on various regenerative processes and provides novel insights into the future research of uncharacterized roles of cell wall in plant regeneration.

Phenotype and transcriptome analysis identify the key genes controlling seed size and oil accumulation in oil-Camellia

KEY MESSAGE

Phenotypic analysis of an F1 oil-Camellia population, combined with transcriptome sequencing of its parental lines, identifies pivotal genes controlling seed size and oil accumulation. Oil - Camellia is a major oil-producing tree, known for its high nutritional value and health benefits. Improving seed size and oil content is the key breeding objective, governed by intricate genetic networks. However, the molecular mechanism underlying these traits in oil-Camellia has been rarely reported. In this study, an F1 population was developed from two parental genotypes, CL4 (hexaploid with high oil content and large seed size) and XG (tetraploid with low oil content and small seed size), which exhibited significant variation in yield-related traits. Ploidy analysis of progenies of F1 population showed that most individuals were tetraploids and hexaploids, with a smaller number of diploids and octoploids present. Additionally, the analysis identified progeny individuals exhibiting both large seed and high oil content although no clear correlation with ploidy was observed. Comparative RNA sequencing (RNA seq) of developing seeds at four developmental stages revealed dynamic expression patterns, associated with seed size and oil content in the two parents. Co-expression regulatory network and differentially expressed genes of fatty acid biosynthesis pathway indicated that genes, such as Oleosin5 and ACCase α-subunit, displayed central roles in controlling seed size and oil content with notable expression peaks in S3 and S4. Additionally, the ABA signaling pathway, along with expansin proteins and transcription factors, showed co-expression with these genes, suggesting a regulatory pathway centered around Oleosin5 and ACCase α-subunit. This study identifies essential genes linked to oil seed yield traits, enhancing the understanding of oil-Camellia's molecular breeding targets.

Inherited endurance: deciphering genetic associations of transgenerational and intergenerational heat stress memory in barley

Barley (Hordeum vulgare L.), a cornerstone of global cereal crops, is increasingly vulnerable to concurrent heat stress, a critical abiotic factor that is intensified by climate change. This study employed genome-wide association studies (GWAS) to investigate "stress memory," a phenomenon where prior stress exposure enhances a plant's response to subsequent stress events. In this study, we analyzed essential agronomic traits, including plant height, spike length, grain number, and thousand-kernel weight, in conjunction with biochemical markers such as chlorophyll content, proline, and soluble proteins. These assessments spanned three successive generations under heat stress, capturing transgenerational and intergenerational effects and uncovering the cumulative impacts of prolonged stress in the third generation. Markedly, our findings highlight the critical influence of heat stress on plant physiology across generational scales, showcasing significant reductions in chlorophyll content, which reflect stress-induced limitations on photosynthetic capacity. In contrast, the observed consistent and substantial increases in proline and soluble protein content across transgenerational, intergenerational, and third-generation stress memory stages underscore their vital roles in stress mitigation and cellular homeostasis. These results provide compelling evidence of generational stress memory, suggesting potential adaptive strategies that plants employ to cope with harsh environmental conditions. Interestingly, identifying significant SNP markers within key genomic regions using GWAS analysis further highlights the potential for harnessing these loci in breeding programs. These results shed light on the intricate mechanisms of barley's stress tolerance and underscore the potential of integrating genomic, epigenomic, and advanced phenotyping tools into breeding programs to develop heat-resilient cultivars.

Nitric oxide mitigates cadmium stress by promoting the biosynthesis of cell walls in Robinia pseudoacacia roots

Cadmium (Cd) pollution is a growing concern worldwide, because it threatens human health through the food chain. Woody plants, such as the pioneer species black locust (Robinia pseudoacacia L.), are widely used in phytoremediation of Cd-contaminated soils, but strongly differ in Cd tolerance. Nitric oxide (NO), a highly reactive gas of biogenic and anthropogenic origin, has been shown to protect plants to Cd exposure. We investigated the protective mechanism of NO against Cd toxicity in black locust using physiological, transcriptomic and metabolomic approaches. We studied the correlation between cell wall traits, genes, and metabolites. The findings indicated that NO improved the growth of black locust under Cd exposure and elevated the fraction of Cd in the cell wall. NO increased cell wall thickness by stimulating the biosynthesis of pectin, cellulose, hemicellulose, and lignin. Transcriptomic and metabolomic analyses demonstrated that NO upregulated genes related to root cell wall biosynthesis and increased the accumulation of related metabolites, thereby increasing the Cd resistance of black locust. Our results elucidated a molecular mechanism underlying NO-mediated Cd tolerance in black locust and provided novel insights for phytoremediation of Cd-polluted soils by woody plants.

Integrative Proteomic and Phosphoproteomic Profiling Reveals the Salt-Responsive Mechanisms in Two Rice Varieties (Oryza Sativa subsp. Japonica and Indica)

Salinity stress induces ionic and osmotic imbalances in rice plants that in turn negatively affect the photosynthesis rate, resulting in growth retardation and yield penalty. Efforts have, therefore, been carried out to understand the mechanism of salt tolerance, however, the complexity of biological processes at proteome levels remains a major challenge. Here, we performed a comparative proteome and phosphoproteome profiling of microsome enriched fractions of salt-tolerant (cv. IR73; indica) and salt-susceptible (cv. Dongjin/DJ; japonica) rice varieties. This approach led to the identification of 5856 proteins, of which 473 and 484 proteins showed differential modulation between DJ and IR73 sample sets, respectively. The phosphoproteome analysis led to the identification of a total of 10,873 phosphopeptides of which 2929 and 3049 phosphopeptides showed significant differences in DJ and IR73 sample sets, respectively. The integration of proteome and phosphoproteome data showed activation of ABA and Ca2+ signaling components exclusively in the salt-tolerant variety IR73 in response to salinity stress. Taken together, our results highlight the changes at proteome and phosphoproteome levels and provide a mechanistic understanding of salinity stress tolerance in rice.

Integrated physiological and transcriptomic analyses reveal that cell wall biosynthesis and expansion play an important role in the regulation of plant height in alfalfa. BMC PLANT BIOLOGY 2025;25:267. [PMID: 40021950 PMCID: PMC11869670 DOI: 10.1186/s12870-025-06172-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

BACKGROUND

Alfalfa (Medicago sativa L.) is a high-quality, high-protein forage, and the improvement and breeding of key traits are important for enhancing the productivity of alfalfa. Plant height is an important trait that affects crop yield, and its regulatory network mechanism has been widely reported in model plants, however, there are fewer studies on the developmental regulatory of plant height in alfalfa.

RESULTS

In this study, we screened tall (WL525HQ) and short (WL343HQ) alfalfa materials through field experiments and analyzed the regulatory mechanism of plant height based on the multidimensional joint analysis of phenotype, cell, physiology, and molecular biology. The results showed that internode length was an important factor determining plant height in alfalfa, and cell size affected the internode elongation to a certain extent, whereas cell size was limited by cell wall. Moreover, changes in cell wall components play an important role in cell wall expansion, especially lignin synthesis. Transcriptome analysis showed that the high expression of hydrolase activity in T1 (initiation growth period) facilitates the expansion of the cell wall, the significant enrichment of the cellular modification process in T3 (rapid growth period) increases the cell size, and the synthesis of cell wall structural constituents and plant-type cell wall organization in T5 (growth stabilization) further improves and modifies the cell wall structure. Differential genes involved in cell wall biosynthesis and expansion were mainly enriched in cellulose synthesis, pectin cleavage, lignin formation, expansion protein (EXP), and xyloglucan endotransglycosidase (XTH).

CONCLUSIONS

These findings elucidated the plant height regulation mechanisms throughout the alfalfa plant and provided a theoretical basis for the generation of ideal alfalfa plant height germplasm.

CRISPR-Cas9-mediated deletions of FvMYB46 in Fragaria vesca reveal its role in regulation of fruit set and phenylpropanoid biosynthesis

The phenylpropanoid pathway, regulated by transcription factors of the MYB family, produces secondary metabolites that play important roles in fertilization and early phase of fruit development. The MYB46 transcription factor is a key regulator of secondary cell wall structure, lignin and flavonoid biosynthesis in many plants, but little is known about its activity in flowers and berries in F. vesca. For functional analysis of FvMYB46, we designed a CRISPR-Cas9 construct with an endogenous F. vesca-specific U6 promoter for efficient and specific expression of two gRNAs targeting the first exon of FvMYB46. This generated mutants with an in-frame 81-bp deletion of the first conserved MYB domain or an out-of-frame 82-bp deletion potentially knocking out gene function. In both types of mutant plants, pollen germination and fruit set were significantly reduced compared to wild type. Transcriptomic analysis of flowers revealed that FvMYB46 positively regulates the expression of genes involved in processes like xylan biosynthesis and metabolism, homeostasis of reactive oxygen species (ROS) and the phenylpropanoid pathway, including secondary cell wall biosynthesis and flavonoid biosynthesis. Genes regulating carbohydrate metabolism and signalling were also deregulated, suggesting that FvMYB46 might regulate the crosstalk between carbohydrate metabolism and phenylpropanoid biosynthesis. In the FvMYB46-mutant flowers, the flavanol and flavan-3-ol contents, especially epicatechin, quercetin-glucoside and kaempferol-3-coumaroylhexoside, were reduced, and we observed a local reduction in the lignin content in the anthers. Together, these results suggest that FvMYB46 controls fertility and efficient fruit set by regulating the cell wall structure, flavonoid biosynthesis, carbohydrate metabolism, and sugar and ROS signalling in flowers and early fruit development in F. vesca.

Transcriptomic and metabolomic analyses of Tartary buckwheat roots during cadmium stress

Cadmium (Cd) can adversely damage plant growth. Therefore, understanding the control molecular mechanisms of Cd accumulation will benefit the development of strategies to reduce Cd accumulation in plants. This study performed transcriptomic and metabolomic analyses on the roots of a Cd-tolerant Tartary buckwheat cultivar following 0 h (CK), 6 h (T1), and 48 h (T2) of Cd treatment. The fresh weight and root length were not significantly inhibited under the T1 treatment but they were in the T2 treatment. The root's ultrastructure was seriously damaged in T2 but not in T1 treatment. This was evidenced by deformed cell walls, altered shape and number of organelles. A total of 449, 999 differentially expressed genes (DEGs) and eight, 37 differentially expressed metabolites (DEMs) were identified in the CK versus T1 and CK versus T2 comparison, respectively. DEGs analysis found that the expression of genes related to cell wall function, glutathione (GSH) metabolism, and phenylpropanoid biosynthesis changed significantly during Cd stress. Several WRKY, MYB, ERF, and bHLH transcription factors and transporters also responded to Cd treatment. Our results indicate that Cd stress affects cell wall function and GSH metabolism and that changes in these pathways might contribute to mechanisms of Cd tolerance in Tartary buckwheat.

Differential expression and localization of expansins in Arabidopsis shoots: implications for cell wall dynamics and drought tolerance

Expansins are cell wall-modifying proteins implicated in plant growth and stress responses. In this study, we explored the differential localization of expansins in Arabidopsis thaliana shoots, with a focus on EXPA1, EXPA10, EXPA14, and EXPA15 utilizing pEXPA::EXPA translational fusion lines. Employing the chemically inducible system pOp6/LhGR for EXPA1 overexpression and high-throughput automatic phenotyping we evaluated the drought response and photosynthetic efficiency under stress conditions. We observed distinct expression patterns of expansins, with EXPA1 primarily localized in stomatal guard cells, while EXPA10 and EXPA15 showed strong cell wall (CW) localization in epidermal and other tissues. Overexpression of EXPA1 resulted in pronounced changes in CW-related gene expression, particularly during early stages of induction, including the upregulation of other expansins and CW-modifying enzymes. The induced EXPA1 line also displayed significant morphological changes in shoots, including smaller plant size, delayed senescence, and structural alterations in vascular tissues. Additionally, EXPA1 overexpression conferred drought tolerance, as evidenced by enhanced photosynthetic efficiency (Fv/FM), and low steady-state non-photochemical quenching (NPQ) values under drought stress. These findings highlight the critical role of EXPA1 in regulating plant growth, development, and stress response, with potential applications in improving drought tolerance in crops.

Creeping Stem 1 regulates directional auxin transport for lodging resistance in soybean

Soybean, a staple crop on a global scale, frequently encounters challenges due to lodging under high planting densities, which results in significant yield losses. Despite extensive research, the fundamental genetic mechanisms governing lodging resistance in soybeans remain elusive. In this study, we identify and characterize the Creeping Stem 1 (CS1) gene, which plays a crucial role in conferring lodging resistance in soybeans. The CS1 gene encodes a HEAT-repeat protein that modulates hypocotyl gravitropism by regulating amyloplast sedimentation. Functional analysis reveals that the loss of CS1 activity disrupts polar auxin transport, vascular bundle development and the biosynthesis of cellulose and lignin, ultimately leading to premature lodging and aberrant root development. Conversely, increasing CS1 expression significantly enhances lodging resistance and improves yield under conditions of high planting density. Our findings shed light on the genetic mechanisms that underlie lodging resistance in soybeans and highlight the potential of CS1 as a valuable target for genetic engineering to improve crop lodging resistance and yield.

BZR1 targets steroid 22-alpha hydroxylase 4 to negatively regulates cell elongation in bamboo

Moso bamboo is renowned for its exceptional growth rate, driven by rapid cell proliferation and elongation in culm internodes. This study uncovers the novel role of brassinosteroids (BRs) in regulating bamboo shoot growth, revealing a previously unknown negative correlation between BR levels and growth rates. Notably, we identify BRASSINAZOLE RESISTANT1 (BZR1) acts as a key transcription factor in BR signaling, governing the expression of genes involved in BR biosynthesis and growth. Specifically, we elucidate the interactions between PeBZR1s and the promoter of steroid 22-alpha hydroxylase gene (PeDWF4) encoding a critical enzyme of BR metabolism. Our findings show that the transcriptional expression levels of PeBZR1-4, PeBZR1-5, and PeBZR1-7 positively correlated with BRs content. Furthermore, all three can bind to the BRRE motif on the PeDWF4 gene promoter, thereby suppressing PeDWF4 expression. Additionally, we demonstration that knockdown of PeDWF4 in bamboo through planta gene editing results in shorter epidermal cells and reduced expression of cell elongation genes. Conversely, Arabidopsis overexpressing PeDWF4 exhibited enhanced cell elongation and larger leaves. These findings reveal PeBZR1-4, PeBZR1-5, and PeBZR1-7 as negative regulators of cell elongation through PeDWF4 inhibition. This discovery not only advances our understanding of BR-mediated regulatory mechanisms underlying the rapid growth of bamboo but also opens new approaches for future research, particularly in applying these insights to develop innovative strategies in bamboo targeted breeding and biotechnology to optimize growth characteristics.

Complex transcription regulation of acidic chitinase suggests fine-tuning of digestive processes in Drosera binata

MAIN CONCLUSION

DbChitI-3, Drosera binata's acidic chitinase, peaks at pH 2.5 from 15 °C to 30 °C. Gene expression is stimulated by polysaccharides and suppressed by monosaccharide digestion, implying a feedback loop in its transcriptional regulation. Here, we characterised a novel chitinase gene (DbChitI-3) isolated from the carnivorous plant species Drosera binata with strong homology to other Drosera species' extracellular class I chitinases with a role in digestive processes. The capability to cleave different forms of chitin was tested using recombinantly produced chitinase in Escherichia coli (rDbChitI-3S-His) and subsequent purification. The recombinant protein did not cleave chitin powder, the mono-, di- and tri- N-acetyl-D-glucosamine substrates, but cleaved acetic acid-swollen chitin. Fluorometric assay with acetic acid-swollen FITC-chitin as a substrate revealed the maximum enzyme activity at pH 2.5, spanning from 15 °C to 30 °C. Comparing enzymatic parameters with commercial chitinase from Streptomyces griseus showed rDbChitI-3S-His efficiency reaching 64.3% of S. griseus chitinase under optimal conditions. The highest basal expression of DbChitI-3 was detected in leaf blades. In other organs, the expression was either fivefold lower (petioles) or almost nondetectable (stems, roots and flowers). Application of gelatin, chitin, and pachyman resulted in a 3.9-, 4.6- and 5.7-fold increase in the mRNA transcript abundance of DbChitI-3 in leaves. In contrast, monosaccharides and laminarin decreased transcription of the DbChitI-3 gene by at least 70%, 5 h after treatment. The simultaneous application of suppressor and inducer (glucose and pachyman) indicated the predominant effect of the suppressor, implying that sufficient monosaccharide nutrients prioritize absorption processes in D. binata leaves over further digestion of the potential substrate.

The SmWRKY12-SmRAP2-7-SmEXPA13 module in Salix matsudana koidz enhances plant tolerance to drought stress

WRKY transcription factors play key roles in plant responses to abiotic stress. In this study, we cloned and characterized the drought-induced WRKY gene SmWRKY12 from Salix matsudana Koidz. Following drought treatment, SmWRKY12 was significantly upregulated in the roots of the drought-tolerant willow variety 9901. Overexpressing SmWRKY12 in willow calli significantly increased drought tolerance. The results of yeast one-hybrid and dual-luciferase reporter assays showed that SmWRKY12 can bind to the promoter of the expansin gene SmEXPA13 and activate its expression. The results of yeast two-hybrid and split luciferase complementation assays showed that SmWRKY12 can interact with SmRAP2-7. The results of dual-luciferase and transgenic experiments showed that the combination of SmWRKY12 and SmRAP2-7 significantly increased the transcriptional regulation of SmWRKY12 on SmEXPA13. SmEXPA13 was introduced into willow calli and tobacco plants. Overexpressing SmEXPA13 significantly improved their performance under drought conditions. The results revealed a novel mechanism to tolerate drought stress through the SmWRKY12-SmRAP2-7-SmEXPA13 module in willow. This study also provided a new strategy for the molecular design and breeding of drought-tolerant plants.

Comparative transcriptome analysis in two contrasting genotypes for Sclerotinia sclerotiorum resistance in sunflower

Sclerotinia sclerotiorum as a necrotrophic fungus causes the devastating diseases in many important oilseed crops worldwide. The preferred strategy for controlling S. sclerotiorum is to develop resistant varieties, but the molecular mechanisms underlying S. sclerotiorum resistance remain poorly defined in sunflower (Helianthus annuus). Here, a comparative transcriptomic analysis was performed in leaves of two contrasting sunflower genotypes, disease susceptible (DS) B728 and disease resistant (DR) C6 after S. sclerotiorum inoculation. At 24 h post-inoculation, the DR genotype exhibited no visible growth of the hyphae as well as greater activity of superoxide dismutase activity (SOD), peroxidase (POD), catalase (CAT), glutathione-S-transferase (GST), ascorbate peroxidase (APX) and monodehydroascorbate reductase (MDAR) than DS genotype. A total of 10151 and 7439 differentially expressed genes (DEGs) were detected in DS and DR genotypes, respectively. Most of DEGs were enriched in cell wall organisation, protein kinase activity, hormone, transcription factor activities, redox homeostasis, immune response, and secondary metabolism. Differential expression of genes involved in expansins, pectate lyase activities, ethylene biosynthesis and signaling and antioxidant activity after S. sclerotiorum infection could potentially be responsible for the differential resistance among two genotypes. In summary, these finding provide additional insights into the potential molecular mechanisms of S. sclerotiorum's defense response and facilitate the breeding of Sclerotinia-resistant sunflower varieties.

Identification and characterization of a rice expansin-like protein with metal-binding properties

Heavy metal (HM) contamination poses significant threat to agricultural productivity. This study identified and characterized Os09g29690 (OsELP), a rice expansin-like protein. We demonstrated OsELP localizes to the cell wall and is upregulated under various abiotic stresses. Sequence analysis revealed a potential metal-binding CXXXC motif in its conserved domain. Heterologous expression of OsELP in yeast mutants (Δacr3 and Δycf1) enhanced metal tolerance under arsenate [As(V)], arsenite [As(III)], and cadmium [Cd] stress. Yeast cells expressing OsELP accumulated higher amounts of As and Cd, suggesting a potential metal-binding mechanism. This was confirmed through site-directed mutagenesis on the conserved cysteine and serine residues within OsELP. Mutants lacking cysteine residues (mutCS) reduced tolerance to As(III) and Cd but enhanced tolerance to As(V), indicating a role of cysteine in As(III) and Cd binding. Conversely, mutants lacking serine residues (mutSA) reduced tolerance to As(V), suggesting serine's involvement in As(V) binding. These findings reveal the roles of cysteine and serine residues in mediating HM tolerance and binding, confirming OsELP as a key player in HM detoxification through cell wall localization and chelation. This study provides novel insights into the molecular mechanisms of HM tolerance in plants, with potential applications in developing crops with enhanced resistance to HM toxicity.

The genetics of fruit skin separation in date palm

The physical appearance of date palm (Phoenix dactylifera) fruit (dates) is important for its market value. Many date-producing countries experience significant financial losses due to the poor appearance of the fruit, skin separation or puffiness being a major reason. Previous research showed evidence linking the skin separation phenotype to environmental conditions. To investigate this further, a genome-wide association study was conducted using genome data from 199 samples collected from 14 countries. Here, we identified nine genetic loci associated with this phenotype and investigated genes in these regions that may contribute to the phenotype overall. Multiple genes in the associated regions have functional responses to growth regulators and are involved in cell wall development and modification. Analysis of gene expression data shows many are expressed during fruit development. We show that there are both environmental and genetic contributions to the fruit skin separation phenotype. Our results indicate that different date cultivars exhibit varying degrees of skin separation despite genetic similarities or differences. However, genetically different cultivars show extreme differences compared to the phenotype variation between genetically similar cultivars. We demonstrate that beyond environmental factors, genetics is a strong contributor to the most extreme skin separation in some cultivars. Identifying the genetic factors may help better understand the biology and pathways that lead to the environmental effects on skin separation and improve commercial date production. In conclusion, our key finding is that both environmental and genetic factors contribute to skin separation variation, and improvements in environmental factors alone cannot overcome the extreme level of variation observed in some cultivars.

Physiological and transcriptomic characterization of cold acclimation in endodormant grapevine under different temperature regimes

It is essential for the survival of grapevines in cool climate viticultural regions where vines properly acclimate in late fall and early winter and develop freezing tolerance. Climate change-associated abnormities in temperature during the dormant season, including oscillations between prolonged warmth in late fall and extreme cold in midwinter, impact cold acclimation and threaten the sustainability of the grape and wine industry. We conducted two experiments in controlled environment to investigate the impacts of different temperature regimes on cold acclimation ability in endodormant grapevine buds through a combination of freezing tolerance-based physiological and RNA-seq-based transcriptomic monitoring. Results show that exposure to a constant temperature, whether warm (22 and 11°C), moderate (7°C), or cool (4 and 2°C) was insufficient for triggering cold acclimation and increasing freezing tolerance in dormant buds. However, when the same buds were exposed to temperature cycling (7±5°C), acclimation occurred, and freezing tolerance was increased by 5°C. We characterized the transcriptomic response of endodormant buds to high and low temperatures and temperature cycling and identified new potential roles for the ethylene pathway, starch and sugar metabolism, phenylpropanoid regulation, and protein metabolism in the genetic control of endodormancy maintenance. Despite clear evidence of temperature-responsive transcription in endodormant buds, our current understanding of the genetic control of cold acclimation remains a challenge when generalizing across grapevine tissues and phenological stages.

Exploring Novel Genomic Loci and Candidate Genes Associated with Plant Height in Bulgarian Bread Wheat via Multi-Model GWAS

In the context of crop breeding, plant height (PH) plays a pivotal role in determining straw and grain yield. Although extensive research has explored the genetic control of PH in wheat, there remains an opportunity for further advancements by integrating genomics with growth-related phenomics. Our study utilizes the latest genome-wide association scan (GWAS) techniques to unravel the genetic basis of temporal variation in PH across 179 Bulgarian bread wheat accessions, including landraces, tall historical, and semi-dwarf modern varieties. A GWAS was performed with phenotypic data from three growing seasons, the calculated best linear unbiased estimators, and the leveraging genotypic information from the 25K Infinium iSelect array, using three statistical methods (MLM, FarmCPU, and BLINK). Twenty-five quantitative trait loci (QTL) associated with PH were identified across fourteen chromosomes, encompassing 21 environmentally stable quantitative trait nucleotides (QTNs), and four haplotype blocks. Certain loci (17) on chromosomes 1A, 1B, 1D, 2A, 2D, 3A, 3B, 4A, 5B, 5D, and 6A remain unlinked to any known Rht (Reduced height) genes, QTL, or GWAS loci associated with PH, and represent novel regions of potential breeding significance. Notably, these loci exhibit varying effects on PH, contribute significantly to natural variance, and are expressed during seedling to reproductive stages. The haplotype block on chromosome 6A contains five QTN loci associated with reduced height and two loci promoting height. This configuration suggests a substantial impact on natural variation and holds promise for accurate marker-assisted selection. The potentially novel genomic regions harbor putative candidate gene coding for glutamine synthetase, gibberellin 2-oxidase, auxin response factor, ethylene-responsive transcription factor, and nitric oxide synthase; cell cycle-related genes, encoding cyclin, regulator of chromosome condensation (RCC1) protein, katanin p60 ATPase-containing subunit, and expansins; genes implicated in stem mechanical strength and defense mechanisms, as well as gene regulators such as transcription factors and protein kinases. These findings enrich the pool of semi-dwarfing gene resources, providing the potential to further optimize PH, improve lodging resistance, and achieve higher grain yields in bread wheat.

Plant Cell Wall Loosening by Expansins

Expansins comprise an ancient group of cell wall proteins ubiquitous in land plants and their algal ancestors. During cell growth, they facilitate passive yielding of the wall's cellulose networks to turgor-generated tensile stresses, without evidence of enzymatic activity. Expansins are also implicated in fruit softening and other developmental processes and in adaptive responses to environmental stresses and pathogens. The major expansin families in plants include α-expansins (EXPAs), which act on cellulose-cellulose junctions, and β-expansins, which can act on xylans. EXPAs mediate acid growth, which contributes to wall enlargement by auxin and other growth agents. The genomes of diverse microbes, including many plant pathogens, also encode expansins designated expansin-like X. Expansins are proposed to disrupt noncovalent bonding between laterally aligned polysaccharides (notably cellulose), facilitating wall loosening for a variety of biological roles.

Characterizing seed dormancy in Epimedium brevicornu Maxim.: Development of novel chill models and determination of dormancy release mechanisms by transcriptomics

PURPOSE

Epimedium brevicornu Maxim. is a perennial persistent C3 plant of the genus Epimedium Linn. in the family Berberaceae that exhibits severe physiological and morphological seed dormancy.We placed mature E. brevicornu seeds under nine stratification treatment conditions and explored the mechanisms of influence by combining seed embryo growth status assessment with related metabolic pathways and gene co-expression analysis.

RESULTS

We identified 3.9 °C as the optimum cold-stratification temperature of E. brevicornu seeds via a chilling unit (CU) model. The best treatment was variable-temperature stratification (10/20 °C, 12/12 h) for 4 months followed by low-temperature stratification (4 °C) for 3 months (4-3). A total of 63801 differentially expressed genes were annotated to 2587 transcription factors (TFs) in 17 clusters in nine treatments (0-0, 0-3, 1-3, 2-3, 3-3, 4-3, 4-2, 4-1, 4-0). Genes specifically highly expressed in the dormancy release treatment group were significantly enriched in embryo development ending in seed dormancy and fatty acid degradation, indicating the importance of these two processes. Coexpression analysis implied that the TF GRF had the most reciprocal relationships with genes, and multiple interactions centred on zf-HD and YABBY as well as on MYB, GRF, and TCP were observed.

CONCLUSION

In this study, analyses of plant hormone signal pathways and fatty acid degradation pathways revealed changes in key genes during the dormancy release of E. brevicornu seeds, providing evidence for the filtering of E. brevicornu seed dormancy-related genes.

Overexpression of NtEXPA7 promotes seedling growth and resistance to root-knot nematode in tobacco

Root-knot nematode (RKN) is one of the most damaging plant pathogen in the world. They exhibit a wide host range and cause serious crop losses. The cell wall, encasing every plant cell, plays a crucial role in defending of RKN invasion. Expansins are a group of cell wall proteins inducing cell wall loosening and extensibility. They are widely involved in the regulation of plant growth and the response to biotic and abiotic stresses. In this study, we have characterized the biological function of tobacco (Nicotiana tabacum) NtEXPA7, the homologue of Solyc08g080060.2 (SlEXPA18), of which the transcription level was significantly reduced in susceptible tomato upon RKN infection. The expression of NtEXPA7 was up-regulated after inoculation of RKNs. The NtEXPA7 protein resided in the cell wall. Overexpression of NtEXPA7 promoted the seedling growth of transgenic tobacco. Meanwhile the increased expression of NtEXPA7 was beneficial to enhance the resistance against RKNs. This study expands the understanding of biological role of expansin in coordinate plant growth and disease resistance.

Combined BSA-Seq and RNA-Seq to Identify Potential Genes Regulating Fruit Size in Bottle Gourd (Lagenaria siceraria L.)

Fruit size is a crucial agronomic trait in bottle gourd, impacting both yield and utility. Despite its significance, the regulatory mechanism governing fruit size in bottle gourd remains largely unknown. In this study, we used bottle gourd (small-fruited H28 and large-fruited H17) parent plants to measure the width and length of fruits at various developmental stages, revealing a single 'S' growth curve for fruit expansion. Paraffin section observations indicated that both cell number and size significantly influence bottle gourd fruit size. Through bulked segregant analysis and combined genotype-phenotype analysis, the candidate interval regulating fruit size was pinpointed to 17,747,353 bp-18,185,825 bp on chromosome 9, encompassing 0.44 Mb and including 44 genes. Parental fruits in the rapid expansion stage were subjected to RNA-seq, highlighting that differentially expressed genes were mainly enriched in pathways related to cell wall biosynthesis, sugar metabolism, and hormone signaling. Transcriptome and resequencing analysis, combined with gene function annotation, identified six genes within the localized region as potential regulators of fruit size. This study not only maps the candidate interval of genes influencing fruit size in bottle gourd through forward genetics, but also offers new insights into the potential molecular mechanisms underlying this trait through transcriptome analysis.

Alpha-expansins: more than three decades of wall creep and loosening in fruits

Expansins are proteins without catalytic activity, but able to break hydrogen bonds between cell wall polysaccharides hemicellulose and cellulose. This proteins were reported for the first time in 1992, describing cell wall extension in cucumber hypocotyls caused particularly by alpha-expansins. Although these proteins have GH45 and CBM63 domains, characteristic of enzymes related with the cleavage of cell wall polysaccharides, demonstrating in vitro that they extend plant cell wall. Its participation has been associated to molecular processes such as development and growing, fruit ripening and softening, tolerance and resistance to biotic and abiotic stress and seed germination. Structural insights, facilitated by bioinformatics approaches, are highlighted, shedding light on the intricate interactions between alpha-expansins and cell wall polysaccharides. After more than thirty years of its discovery, we want to celebrate the knowledge of alpha-expansins and emphasize their importance to understand the phenomena of disassembly and loosening of the cell wall, specifically in the fruit ripening phenomena, with this state-of-the-art dedicated to them.

Transcriptome- and genome-wide systematic identification of expansin gene family and their expression in tuberous root development and stress responses in sweetpotato (Ipomoea batatas)

Introduction

Expansins (EXPs) are essential components of the plant cell wall that function as relaxation factors to directly promote turgor-driven expansion of the cell wall, thereby controlling plant growth and development and diverse environmental stress responses. EXPs genes have been identified and characterized in numerous plant species, but not in sweetpotato.

Results and methods

In the present study, a total of 59 EXP genes unevenly distributed across 14 of 15 chromosomes were identified in the sweetpotato genome, and segmental and tandem duplications were found to make a dominant contribution to the diversity of functions of the IbEXP family. Phylogenetic analysis showed that IbEXP members could be clustered into four subfamilies based on the EXPs from Arabidopsis and rice, and the regularity of protein motif, domain, and gene structures was consistent with this subfamily classification. Collinearity analysis between IbEXP genes and related homologous sequences in nine plants provided further phylogenetic insights into the EXP gene family. Cis-element analysis further revealed the potential roles of IbEXP genes in sweetpotato development and stress responses. RNA-seq and qRT-PCR analysis of eight selected IbEXPs genes provided evidence of their specificity in different tissues and showed that their transcripts were variously induced or suppressed under different hormone treatments (abscisic acid, salicylic acid, jasmonic acid, and 1-aminocyclopropane-1-carboxylic acid) and abiotic stresses (low and high temperature).

Discussion

These results provide a foundation for further comprehensive investigation of the functions of IbEXP genes and indicate that several members of this family have potential applications as regulators to control plant development and enhance stress resistance in plants.

Overexpression of Wild Soybean Expansin Gene GsEXLB14 Enhanced the Tolerance of Transgenic Soybean Hairy Roots to Salt and Drought Stresses

As a type of cell-wall-relaxing protein that is widely present in plants, expansins have been shown to actively participate in the regulation of plant growth and responses to environmental stress. Wild soybeans have long existed in the wild environment and possess abundant resistance gene resources, which hold significant value for the improvement of cultivated soybean germplasm. In our previous study, we found that the wild soybean expansin gene GsEXLB14 is specifically transcribed in roots, and its transcription level significantly increases under salt and drought stress. To further identify the function of GsEXLB14, in this study, we cloned the CDS sequence of this gene. The transcription pattern of GsEXLB14 in the roots of wild soybean under salt and drought stress was analyzed by qRT-PCR. Using an Agrobacterium rhizogenes-mediated genetic transformation, we obtained soybean hairy roots overexpressing GsEXLB14. Under 150 mM NaCl- and 100 mM mannitol-simulated drought stress, the relative growth values of the number, length, and weight of transgenic soybean hairy roots were significantly higher than those of the control group. We obtained the transcriptomes of transgenic and wild-type soybean hairy roots under normal growth conditions and under salt and drought stress through RNA sequencing. A transcriptomic analysis showed that the transcription of genes encoding expansins (EXPB family), peroxidase, H+-transporting ATPase, and other genes was significantly upregulated in transgenic hairy roots under salt stress. Under drought stress, the transcription of expansin (EXPB/LB family) genes increased in transgenic hairy roots. In addition, the transcription of genes encoding peroxidases, calcium/calmodulin-dependent protein kinases, and dehydration-responsive proteins increased significantly. The results of qRT-PCR also confirmed that the transcription pattern of the above genes was consistent with the transcriptome. The differences in the transcript levels of the above genes may be the potential reason for the strong tolerance of soybean hairy roots overexpressing the GsEXLB14 gene under salt and drought stress. In conclusion, the expansin GsEXLB14 can be used as a valuable candidate gene for the molecular breeding of soybeans.

EXPANSIN15 is involved in flower and fruit development in Arabidopsis

KEY MESSAGE

EXPANSIN15 is involved in petal cell morphology and size, the fusion of the medial tissues in the gynoecium and expansion of fruit valve cells. It genetically interacts with SPATULA and FRUITFULL. Cell expansion is fundamental for the formation of plant tissues and organs, contributing to their final shape and size during development. To better understand this process in flower and fruit development, we have studied the EXPANSIN15 (EXPA15) gene, which showed expression in petals and in the gynoecium. By analyzing expa15 mutant alleles, we found that EXPA15 is involved in petal shape and size determination, by affecting cell morphology and number. EXPA15 also has a function in fruit size, by affecting cell size and number. Furthermore, EXPA15 promotes fusion of the medial tissues in the gynoecium. In addition, we observed genetic interactions with the transcription factors SPATULA (SPT) and FRUITFULL (FUL) in gynoecium medial tissue fusion, style and stigma development and fruit development in Arabidopsis. These findings contribute to the importance of EXPANSINS in floral and fruit development in Arabidopsis.

Meta-QTL and Candidate Gene Analyses of Agronomic Salt Tolerance and Related Traits in an RIL Population Derived from Solanum pimpinellifolium

Breeding salt-tolerant crops is necessary to reduce food insecurity. Prebreeding populations are fundamental for uncovering tolerance alleles from wild germplasm. To obtain a physiological interpretation of the agronomic salt tolerance and better criteria to identify candidate genes, quantitative trait loci (QTLs) governing productivity-related traits in a population of recombinant inbred lines (RIL) derived from S. pimpinellifolium were reanalyzed using an SNP-saturated linkage map and clustered using QTL meta-analysis to synthesize QTL information. A total of 60 out of 85 QTLs were grouped into 12 productivity MQTLs. Ten of them were found to overlap with other tomato yield QTLs that were found using various mapping populations and cultivation conditions. The MQTL compositions showed that fruit yield was genetically associated with leaf water content. Additionally, leaf Cl- and K+ contents were related to tomato productivity under control and salinity conditions, respectively. More than one functional candidate was frequently found, explaining most productivity MQTLs, indicating that the co-regulation of more than one gene within those MQTLs might explain the clustering of agronomic and physiological QTLs. Moreover, MQTL1.2, MQTL3 and MQTL6 point to the root as the main organ involved in increasing productivity under salinity through the wild allele, suggesting that adequate rootstock/scion combinations could have a clear agronomic advantage under salinity.

MicroRNA (miRNA) profiling of maize genotypes with differential response to Aspergillus flavus implies zma-miR156-squamosa promoter binding protein (SBP) and zma-miR398/zma-miR394-F -box combinations involved in resistance mechanisms

Maize (Zea mays), a major food crop worldwide, is susceptible to infection by the saprophytic fungus Aspergillus flavus that can produce the carcinogenic metabolite aflatoxin (AF) especially under climate change induced abiotic stressors that favor mold growth. Several studies have used "-omics" approaches to identify genetic elements with potential roles in AF resistance, but there is a lack of research identifying the involvement of small RNAs such as microRNAs (miRNAs) in maize-A. flavus interaction. In this study, we compared the miRNA profiles of three maize lines (resistant TZAR102, moderately resistant MI82, and susceptible Va35) at 8 h, 3 d, and 7 d after A. flavus infection to investigate possible regulatory antifungal role of miRNAs. A total of 316 miRNAs (275 known and 41 putative novel) belonging to 115 miRNA families were identified in response to the fungal infection across all three maize lines. Eighty-two unique miRNAs were significantly differentially expressed with 39 miRNAs exhibiting temporal differential regulation irrespective of the maize genotype, which targeted 544 genes (mRNAs) involved in diverse molecular functions. The two most notable biological processes involved in plant immunity, namely cellular responses to oxidative stress (GO:00345990) and reactive oxygen species (GO:0034614) were significantly enriched in the resistant line TZAR102. Coexpression network analysis identified 34 hubs of miRNA-mRNA pairs where nine hubs had a node in the module connected to their target gene with potentially important roles in resistance/susceptible response of maize to A. flavus. The miRNA hubs in resistance modules (TZAR102 and MI82) were mostly connected to transcription factors and protein kinases. Specifically, the module of miRNA zma-miR156b-nb - squamosa promoter binding protein (SBP), zma-miR398a-3p - SKIP5, and zma-miR394a-5p - F-box protein 6 combinations in the resistance-associated modules were considered important candidates for future functional studies.

Integrated multi-omic approach reveals the effect of a Graminaceae-derived biostimulant and its lighter fraction on salt-stressed lettuce plants

Plant biostimulants are widely applied in agriculture for their ability to improve plant fitness. In the present work, the impact of Graminaceae-derived protein hydrolysate (P) and its lighter molecular fraction F3 (< 1 kDa) on lettuce plants, subjected to either no salt or high salt conditions, was investigated through the combination of metabolomics and transcriptomics. The results showed that both treatments significantly modulated the transcriptome and metabolome of plants under salinity stress, highlighting an induction of the hormonal response. Nevertheless, P and F3 also displayed several peculiarities. F3 specifically modulated the response to ethylene and MAPK signaling pathway, whereas P treatment induced a down-accumulation of secondary metabolites, albeit genes controlling the biosynthesis of osmoprotectants and antioxidants were up-regulated. Moreover, according with the auxin response modulation, P promoted cell wall biogenesis and plasticity in salt-stressed plants. Notably, our data also outlined an epigenetic control of gene expression induced by P treatment. Contrarily, experimental data are just partially in agreement when not stressed plants, treated with P or F3, were considered. Indeed, the reduced accumulation of secondary metabolites and the analyses of hormone pathways modulation would suggest a preferential allocation of resources towards growth, that is not coherent with the down-regulation of the photosynthetic machinery, the CO2 assimilation rate and leaves biomass. In conclusion, our data demonstrate that, although they might activate different mechanisms, both the P and F3 can result in similar benefits, as far as the accumulation of protective osmolytes and the enhanced tolerance to oxidative stress are concerned. Notably, the F3 fraction exhibits slightly greater growth promotion effects under high salt conditions. Most importantly, this research further corroborates that biostimulants' mode of action is dependent on plants' physiological status and their composition, underscoring the importance of investigating the bioactivity of the different molecular components to design tailored applications for the agricultural practice.

Short-term test for the toxicogenomic assessment of ecotoxic modes of action in Myriophyllum spicatum

In environmental risk assessment of substances, the 14-day growth inhibition test following OECD test guideline 239 is employed to assess toxicity in the macrophyte Myriophyllum spicatum. Currently, this test evaluates physiological parameters and does not allow the identification of the mode of action (MoA) by which adverse effects are induced. However, for an improved ecotoxicity assessment of substances, knowledge about their ecotoxic MoA in non-target organisms is required. It has previously been suggested that the identification of gene expression changes can contribute to MoA identification. Therefore, we developed a shortened three-day assay for M. spicatum including the transcriptomic assessment of global gene expression changes and applied this assay to two model substances, the herbicide and photosynthesis inhibitor bentazone and the pharmaceutical and HMG-CoA reductase inhibitor atorvastatin. Due to the lack of a reference genome for M. spicatum we performed a de novo transcriptome assembly followed by a functional annotation to use the toxicogenomic results for MoA discrimination. The gene expression changes induced by low effect concentrations of these substances were used to identify differentially expressed genes (DEGs) and impaired biological functions for the respective MoA. We observed both concentration-dependent numbers and differentiated patterns of DEGs for both substances. While bentazone impaired genes involved in the response to reactive oxygen species as well as light response, and also genes involved in developmental processes, atorvastatin exposure led to a differential regulation of genes related to brassinosteroid response as well as potential metabolic shifts between the mevalonate and methyl erythritol 4-phosphate pathway. Based on these responses, we identified biomarker candidates for the assessment of MoA in M. spicatum. Utilizing the shortened assay developed in this study, the investigation of the identified biomarker candidates may contribute to the development of future MoA-specific screening approaches in the ecotoxicological hazard prediction using aquatic non-standard model organisms.

Structure and growth of plant cell walls

Plant cells build nanofibrillar walls that are central to plant growth, morphogenesis and mechanics. Starting from simple sugars, three groups of polysaccharides, namely, cellulose, hemicelluloses and pectins, with very different physical properties are assembled by the cell to make a strong yet extensible wall. This Review describes the physics of wall growth and its regulation by cellular processes such as cellulose production by cellulose synthase, modulation of wall pH by plasma membrane H+-ATPase, wall loosening by expansin and signalling by plant hormones such as auxin and brassinosteroid. In addition, this Review discusses the nuanced roles, properties and interactions of cellulose, matrix polysaccharides and cell wall proteins and describes how wall stress and wall loosening cooperatively result in cell wall growth.

Phytoremediation ability and selected genetic transcription in Hydrocotyle umbellata-under cadmium stress

Cadmium (Cd) is the most toxic element which may cause serious consequences to microbial communities, animals, and plants. The use of green technologies like phytoremediation employs plants with high biomass and metal tolerance to extract toxic metals from their rooting zones. In the present work, Hydrocotyle umbellata was exposed to five Cd concentrations (2, 4, 6, 8, and 10 µmol) in triplicates to judge its phytoextraction ability. Effects of metal exposure on chlorophyll (Chl), bio-concentration factor (BCF), translocation factor (TF), and electrolyte leakage (EL) were analyzed after 10 days of treatment. Metal-responding genes were also observed through transcriptomic analysis. Roots were the primary organs for cadmium accumulation followed by stolon and leaves. There was an increase in EL. Plants showed various symptoms under increasing metal stress namely, chlorosis, browning of the leaf margins, burn-like areas on the leaves, and stunted growth, suggesting a positive relationship between EL, and programmed cell death (PCD). Metal-responsive genes, including glutathione, expansin, and cystatin were equally expressed. The phytoextraction capacity and adaptability of H. umbellata L. against Cd metal stress was also demonstrated by BCF more than 1 and TF less than 1.

Transcriptome analysis and functional verification reveal the roles of copper in resistance to potato virus Y infection in tobacco

Potato virus Y (PVY) is one of the most important pathogens in the genus Potyvirus that seriously harms agricultural production. Copper (Cu), as a micronutrient, is closely related to plant immune response. In this study, we found that foliar application of Cu could inhibit PVY infection to some extent, especially at 7 days post inoculation (dpi). To explore the effect of Cu on PVY infection, transcriptome sequencing analysis was performed on PVY-infected tobacco with or without Cu application. Several key pathways regulated by Cu were identified, including plant-pathogen interaction, inorganic ion transport and metabolism, and photosynthesis. Moreover, the results of virus-induced gene silencing (VIGS) assays revealed that NbMLP423, NbPIP2, NbFd and NbEXPA played positive roles in resistance to PVY infection in Nicotiana benthamiana. In addition, transgenic tobacco plants overexpressing NtEXPA11 showed increased resistance to PVY infection. These results contribute to clarify the role and regulatory mechanism of Cu against PVY infection, and provide candidate genes for disease resistance breeding.

PagEXPA1 combines with PagCDKB2;1 to regulate plant growth and the elongation of fibers in Populus alba × Populus glandulosa

Expansins are important plant cell wall proteins. They can loosen and soften the cell walls and lead to wall extension and cell expansion. To investigate their role in wood formation and fiber elongation, the PagEXPA1 that highly expressed in cell differentiation and expansion tissues was cloned from 84K poplar (Populus alba × P. glandulosa). The subcellular localization showed that PagEXPA1 located in the cell wall and it was highly expressed in primary stems and young leaves. Compared with non-transgenic 84K poplar, overexpression of PagEXPA1 can promote plant-growth, lignification, and fiber cell elongation, while PagEXPA1 Cas9-editing mutant lines exhibited the opposite phenotype. Transcriptome analysis revealed that DEGs were mainly enriched in some important processes, which are associated with cell wall formation and cellulose synthesis. The protein interaction prediction and expression analysis showed that PagCDKB2:1 and PagEXPA1 might have an interaction relationship. The luciferase complementary assay and bimolecular fluorescence complementary assay validated that PagEXPA1 can combined with PagCDKB2;1. So they promoted the expansion of xylem vascular tissues and the development of poplar though participating in the regulation of cell division and differentiation by programming the cell-cycle. It provides good foundation for molecular breeding of fast-growing and high-quality poplar varieties.

GWAS supported by computer vision identifies large numbers of candidate regulators of in planta regeneration in Populus trichocarpa

Plant regeneration is an important dimension of plant propagation and a key step in the production of transgenic plants. However, regeneration capacity varies widely among genotypes and species, the molecular basis of which is largely unknown. Association mapping methods such as genome-wide association studies (GWAS) have long demonstrated abilities to help uncover the genetic basis of trait variation in plants; however, the performance of these methods depends on the accuracy and scale of phenotyping. To enable a large-scale GWAS of in planta callus and shoot regeneration in the model tree Populus, we developed a phenomics workflow involving semantic segmentation to quantify regenerating plant tissues over time. We found that the resulting statistics were of highly non-normal distributions, and thus employed transformations or permutations to avoid violating assumptions of linear models used in GWAS. We report over 200 statistically supported quantitative trait loci (QTLs), with genes encompassing or near to top QTLs including regulators of cell adhesion, stress signaling, and hormone signaling pathways, as well as other diverse functions. Our results encourage models of hormonal signaling during plant regeneration to consider keystone roles of stress-related signaling (e.g. involving jasmonates and salicylic acid), in addition to the auxin and cytokinin pathways commonly considered. The putative regulatory genes and biological processes we identified provide new insights into the biological complexity of plant regeneration, and may serve as new reagents for improving regeneration and transformation of recalcitrant genotypes and species.

Jasmonic acid (JA)-mediating MYB transcription factor1, JMTF1, coordinates the balance between JA and auxin signalling in the rice defence response

The plant hormone jasmonic acid (JA) is a signalling compound involved in the regulation of cellular defence and development in plants. In this study, we investigated the roles of a JA-responsive MYB transcription factor, JMTF1, in the JA-regulated defence response against rice bacterial blight caused by Xanthomonas oryzae pv. oryzae (Xoo). JMTF1 did not interact with any JASMONATE ZIM-domain (JAZ) proteins. Transgenic rice plants overexpressing JMTF1 showed a JA-hypersensitive phenotype and enhanced resistance against Xoo. JMTF1 upregulated the expression of a peroxidase, OsPrx26, and monoterpene synthase, OsTPS24, which are involved in the biosynthesis of lignin and antibacterial monoterpene, γ-terpinene, respectively. OsPrx26 was mainly expressed in the vascular bundle. Transgenic rice plants overexpressing OsPrx26 showed enhanced resistance against Xoo. In addition to the JA-hypersensitive phenotype, the JMTF1-overexpressing rice plants showed a typical auxin-related phenotype. The leaf divergence and shoot gravitropic responses were defective, and the number of lateral roots decreased significantly in the JMTF1-overexpressing rice plants. JMTF1 downregulated the expression of auxin-responsive genes but upregulated the expression of OsIAA13, a suppressor of auxin signalling. The rice gain-of-function mutant Osiaa13 showed high resistance against Xoo. Transgenic rice plants overexpressing OsEXPA4, a JMTF1-downregulated auxin-responsive gene, showed increased susceptibility to Xoo. JMTF1 is selectively bound to the promoter of OsPrx26 in vivo. These results suggest that JMTF1 positively regulates disease resistance against Xoo by coordinating crosstalk between JA- and auxin-signalling in rice.

Contrasting plant transcriptome responses between a pierce-sucking and a chewing herbivore go beyond the infestation site

BACKGROUND

Plants have acquired a repertoire of mechanisms to combat biotic stressors, which may vary depending on the feeding strategies of herbivores and the plant species. Hormonal regulation crucially modulates this malleable defense response. Jasmonic acid (JA) and salicylic acid (SA) stand out as pivotal regulators of defense, while other hormones like abscisic acid (ABA), ethylene (ET), gibberellic acid (GA) or auxin also play a role in modulating plant-pest interactions. The plant defense response has been described to elicit effects in distal tissues, whereby aboveground herbivory can influence belowground response, and vice versa. This impact on distal tissues may be contingent upon the feeding guild, even affecting both the recovery of infested tissues and those that have not suffered active infestation.

RESULTS

To study how phytophagous with distinct feeding strategies may differently trigger the plant defense response during and after infestation in both infested and distal tissues, Arabidopsis thaliana L. rosettes were infested separately with the chewing herbivore Pieris brassicae L. and the piercing-sucker Tetranychus urticae Koch. Moderate infestation conditions were selected for both pests, though no quantitative control of damage levels was carried out. Feeding mode did distinctly influence the transcriptomic response of the plant under these conditions. Though overall affected processes were similar under either infestation, their magnitude differed significantly. Plants infested with P. brassicae exhibited a short-term response, involving stress-related genes, JA and ABA regulation and suppressing growth-related genes. In contrast, T. urticae elicited a longer transcriptomic response in plants, albeit with a lower degree of differential expression, in particular influencing SA regulation. These distinct defense responses transcended beyond infestation and through the roots, where hormonal response, flavonoid regulation or cell wall reorganization were differentially affected.

CONCLUSION

These outcomes confirm that the existent divergent transcriptomic responses elicited by herbivores employing distinct feeding strategies possess the capacity to extend beyond infestation and even affect tissues that have not been directly infested. This remarks the importance of considering the entire plant's response to localized biotic stresses.

Fungal loosenin-like proteins boost the cellulolytic enzyme conversion of pretreated wood fiber and cellulosic pulps

Microbial expansin-related proteins, including loosenins, can disrupt cellulose networks and increase enzyme accessibility to cellulosic substrates. Herein, four loosenins from Phanerochaete carnosa (PcaLOOLs), and a PcaLOOL fused to a family 63 carbohydrate-binding module, were compared for ability to boost the cellulolytic deconstruction of steam pretreated softwood (SSW) and kraft pulps from softwood (ND-BSKP) and hardwood (ND-BHKP). Amending the Cellic® CTec-2 cellulase cocktail with PcaLOOLs increased reducing products from SSW by up to 40 %, corresponding to 28 % higher glucose yield. Amending Cellic® CTec-2 with PcaLOOLs also increased the release of glucose from ND-BSKP and ND-BHKP by 82 % and 28 %, respectively. Xylose release from ND-BSKP and ND-BHKP increased by 47 % and 57 %, respectively, highlighting the potential of PcaLOOLs to enhance hemicellulose recovery. Scanning electron microscopy and fiber image analysis revealed fibrillation and curlation of ND-BSKP after PcaLOOL treatment, consistent with increasing enzyme accessibility to targeted substrates.

Genome-Wide Identification of Expansins in Rubus chingii and Profiling Analysis during Fruit Ripening and Softening

Improving fruit size or weight, firmness, and shelf life is a major target for horticultural crop breeding. It is associated with the depolymerization and rearrangement of cell components, including pectin, hemicellulose, cellulose, and other structural (glyco)proteins. Expansins are structural proteins to loosen plant cell wall polysaccharides in a pH-dependent manner and play pivotal roles in the process of fruit development, ripening, and softening. Rubus chingii Hu, a unique Chinese red raspberry, is a prestigious pharmaceutical and nutraceutical dual-function food with great economic value. Thirty-three RchEXPs were predicted by genome-wide identification in this study, containing twenty-seven α-expansins (EXPAs), three β-expansins (EXPBs), one expansin-like A (EXPLA), and two expansin-like B (EXPLBs). Subsequently, molecular characteristics, gene structure and motif compositions, phylogenetic relationships, chromosomal location, collinearity, and regulatory elements were further profiled. Furthermore, transcriptome sequencing (RNA-seq) and real-time quantitative PCR assays of fruits from different developmental stages and lineages showed that the group of RchEXPA5, RchEXPA7, and RchEXPA15 were synergistically involved in fruit expanding and ripening, while another group of RchEXPA6 and RchEXPA26 might be essential for fruit ripening and softening. They were regulated by both abscisic acid and ethylene and were collinear with phylogenetic relationships in the same group. Our new findings laid the molecular foundation for improving the fruit texture and shelf life of R. chingii medicinal and edible fruit.

Cellular dynamics in the maize leaf growth zone during recovery from chilling depends on the leaf developmental stage

KEY MESSAGE

A novel non-steady-state kinematic analysis shows differences in cell division and expansion determining a better recovery from a 3-day cold spell in emerged compared to non-emerged maize leaves. Zea mays is highly sensitive to chilling which frequently occurs during its seedling stage. Although the direct effect of chilling is well studied, the mechanisms determining the subsequent recovery are still unknown. Our goal is to determine the cellular basis of the leaf growth response to chilling and during recovery of leaves exposed before or after their emergence. We first studied the effect of a 3-day cold spell on leaf growth at the plant level. Then, we performed a kinematic analysis to analyse the dynamics of cell division and elongation during recovery of the 4th leaf after exposure to cold before or after emergence. Our results demonstrated cold more strongly reduced the final length of non-emerged than emerged leaves (- 13 vs. - 18%). This was not related to growth differences during cold, but a faster and more complete recovery of the growth of emerged leaves. This difference was due to a higher cell division rate on the 1st and a higher cell elongation rate on the 2nd day of recovery, respectively. The dynamics of cell division and expansion during recovery determines developmental stage-specific differences in cold tolerance of maize leaves.

A continuum mechanics model of the plant cell wall reveals interplay between enzyme action and cell wall structure

Plant cell growth is regulated through manipulation of the cell wall network, which consists of oriented cellulose microfibrils embedded within a ground matrix incorporating pectin and hemicellulose components. There remain many unknowns as to how this manipulation occurs. Experiments have shown that cellulose reorients in cell walls as the cell expands, while recent data suggest that growth is controlled by distinct collections of hemicellulose called biomechanical hotspots, which join the cellulose molecule together. The enzymes expansin and Cel12A have both been shown to induce growth of the cell wall; however, while Cel12A's wall-loosening action leads to a reduction in the cell wall strength, expansin's has been shown to increase the strength of the cell wall. In contrast, members of the XTH enzyme family hydrolyse hemicellulose but do not appear to cause wall creep. This experimentally observed behaviour still awaits a full explanation. We derive and analyse a mathematical model for the effective mechanical properties of the evolving cell wall network, incorporating cellulose microfibrils, which reorient with cell growth and are linked via biomechanical hotspots made up of regions of crosslinking hemicellulose. Assuming a visco-elastic response for the cell wall and using a continuum approach, we calculate the total stress resultant of the cell wall for a given overall growth rate. By changing appropriate parameters affecting breakage rate and viscous properties, we provide evidence for the biomechanical hotspot hypothesis and develop mechanistic understanding of the growth-inducing enzymes.

Industrial wastewater irrigation increased higher heavy metals uptake and expansins, metacaspases, and cystatin genes expression in Parthenium and maize

Industrial wastewater irrigation of agricultural crops can cause a lot of environmental and health problems in developing countries due to heavy metals deposition in agricultural soils as well as edible plant consumption by human beings. Therefore, this study was conducted to find out the heavy metals concentration in industrial wastewater and soil irrigated with that wastewater. In addition, the aim was to determine the impact of industrial wastewater irrigation on Parthenium hysterophorus and Zea mays genes involved in growth improvement and inhibition. For this purpose, plant samples from agriculture fields irrigated with wastewater from Hattar Industrial Estate (HIE) of Haripur, Pakistan, and control plants from non-contaminated soil irrigated with tape water were collected after 15 and 45 days of germination. Heavy metals concentration in the collected plant samples, wastewater, and soil was determined. The results revealed that the soil of the sample collection site was predominantly contaminated with Cr, Pb, Ni, Cu, Co, Zn, and Cd up to the concentrations of 38.98, 21.14, 46.01, 155.73, 12.50, 68.50, and 7.01 mg/kg, respectively. The concentrations of these heavy metals were found to surpass the permissible limit in normal agricultural soil. Expansins, cystatins (plant growth enhancers), and metacaspases (plant growth inhibitor) gene expression were studied through reverse transcription polymerase chain reaction. The results showed that the expression of these genes was higher in samples collected from wastewater-irrigated soils as compared to control. The expression of these genes was observed in 45 days old samples, 15 days old samples, and control. Taken together, this study suggests the use of Parthenium and maize for phytoremediation and that they should not be used for eating purposes if irrigated with industrial wastewater.

Expression divergence of expansin genes drive the heteroblasty in Ceratopteris chingii

BACKGROUND

Sterile-fertile heteroblasty is a common phenomenon observed in ferns, where the leaf shape of a fern sporophyll, responsible for sporangium production, differs from that of a regular trophophyll. However, due to the large size and complexity of most fern genomes, the molecular mechanisms that regulate the formation of these functionally different heteroblasty have remained elusive. To shed light on these mechanisms, we generated a full-length transcriptome of Ceratopteris chingii with PacBio Iso-Seq from five tissue samples. By integrating Illumina-based sequencing short reads, we identified the genes exhibiting the most significant differential expression between sporophylls and trophophylls.

RESULTS

The long reads were assembled, resulting in a total of 24,024 gene models. The differential expressed genes between heteroblasty primarily involved reproduction and cell wall composition, with a particular focus on expansin genes. Reconstructing the phylogeny of expansin genes across 19 plant species, ranging from green algae to seed plants, we identified four ortholog groups for expansins. The observed high expression of expansin genes in the young sporophylls of C. chingii emphasizes their role in the development of heteroblastic leaves. Through gene coexpression analysis, we identified highly divergent expressions of expansin genes both within and between species.

CONCLUSIONS

The specific regulatory interactions and accompanying expression patterns of expansin genes are associated with variations in leaf shapes between sporophylls and trophophylls.

Hydroxamic acids: New players in the multifactorial mechanisms of maize resistance to Striga hermonthica

Striga hermonthica is the most widespread and destructive plant parasite infesting maize and other major crops in sub-Saharan Africa where it causes severe yield losses and threatens food security. Several tolerant maize lines supporting reduced S. hermonthica emergence have been deployed. However, the molecular bases of such resistance are yet poorly understood. Based on a time course comparative gene expression analysis between susceptible and resistant maize lines we have confirmed resistance mechanisms known to be activated upon plant parasite infestation and identified potential novel players worth further investigation e.g. iron homeostasis and mitochondrial respiration-related genes. Most intriguingly, we show a previously unknown strategy of maize post-attachment resistance based on DIMBOA accumulation in S. hermonthica-infested maize roots. S. hermonthica infestation triggers positive regulation of gene expression in the hydroxamic acid (HA) pathway culminating with an accumulation of benzoxazinoids (BX), known for their antifeedant, insecticidal, antimicrobial, and allelopathic activities. We demonstrate that HA root content is positively correlated with S. hermonthica resistance in the resistant parent and its progenies and in unrelated maize lines. Downregulation of HA genes causes increased susceptibility to S. hermonthica infestation in loss-of-function maize mutants. While the mechanism of BX action in parasitic plant resistance is yet to be uncovered, the potential of this discovery for developing effective control and breeding strategies is enormous.

The genus Arachis: an excellent resource for studies on differential gene expression for stress tolerance

Peanut Arachis hypogaea is a segmental allotetraploid in the section Arachis of the genus Arachis along with the Section Rhizomataceae. Section Arachis has several diploid species along with Arachis hypogaea and A. monticola. The section Rhizomataceae comprises polyploid species. Several species in the genus are highly tolerant to biotic and abiotic stresses and provide excellent sets of genotypes for studies on differential gene expression. Though there were several studies in this direction, more studies are needed to identify more and more gene combinations. Next generation RNA-seq based differential gene expression study is a powerful tool to identify the genes and regulatory pathways involved in stress tolerance. Transcriptomic and proteomic study of peanut plants under biotic stresses reveals a number of differentially expressed genes such as R genes (NBS-LRR, LRR-RLK, protein kinases, MAP kinases), pathogenesis related proteins (PR1, PR2, PR5, PR10) and defense related genes (defensin, F-box, glutathione S-transferase) that are the most consistently expressed genes throughout the studies reported so far. In most of the studies on biotic stress induction, the differentially expressed genes involved in the process with enriched pathways showed plant-pathogen interactions, phenylpropanoid biosynthesis, defense and signal transduction. Differential gene expression studies in response to abiotic stresses, reported the most commonly expressed genes are transcription factors (MYB, WRKY, NAC, bZIP, bHLH, AP2/ERF), LEA proteins, chitinase, aquaporins, F-box, cytochrome p450 and ROS scavenging enzymes. These differentially expressed genes are in enriched pathways of transcription regulation, starch and sucrose metabolism, signal transduction and biosynthesis of unsaturated fatty acids. These identified differentially expressed genes provide a better understanding of the resistance/tolerance mechanism, and the genes for manipulating biotic and abiotic stress tolerance in peanut and other crop plants. There are a number of differentially expressed genes during biotic and abiotic stresses were successfully characterized in peanut or model plants (tobacco or Arabidopsis) by genetic manipulation to develop stress tolerance plants, which have been detailed out in this review and more concerted studies are needed to identify more and more gene/gene combinations.

Tapping into the plasticity of plant architecture for increased stress resilience

Plant architecture develops post-embryonically and emerges from a dialogue between the developmental signals and environmental cues. Length and branching of the vegetative and reproductive tissues were the focus of improvement of plant performance from the early days of plant breeding. Current breeding priorities are changing, as we need to prioritize plant productivity under increasingly challenging environmental conditions. While it has been widely recognized that plant architecture changes in response to the environment, its contribution to plant productivity in the changing climate remains to be fully explored. This review will summarize prior discoveries of genetic control of plant architecture traits and their effect on plant performance under environmental stress. We review new tools in phenotyping that will guide future discoveries of genes contributing to plant architecture, its plasticity, and its contributions to stress resilience. Subsequently, we provide a perspective into how integrating the study of new species, modern phenotyping techniques, and modeling can lead to discovering new genetic targets underlying the plasticity of plant architecture and stress resilience. Altogether, this review provides a new perspective on the plasticity of plant architecture and how it can be harnessed for increased performance under environmental stress.

Metabolome and transcriptome reprogramming underlying tomato drought resistance triggered by a Pseudomonas strain

Although amelioration of drought stress by Plant Growth Promoting Rhizobacteria (PGPR) is a well-documented phenomenon, the combined molecular and metabolic mechanisms governing this process remain unclear. In these lines, the present study aimed to provide new insights in the underlying drought attenuating mechanisms of tomato plants inoculated with a PGP Pseudomonas putida strain, by using a combination of metabolomic and transcriptomic approaches. Following Differentially Expressed Gene analysis, it became evident that inoculation resulted in a less disturbed plant transcriptome upon drought stress. Untargeted metabolomics highlighted the differential metabolite accumulation upon inoculation, as well as the less metabolic reprograming and the lower accumulation of stress-related metabolites for inoculated stressed plants. These findings were in line with morpho-physiological evidence of drought stress mitigation in the inoculated plants. The redox state modulation, the more efficient nitrogen assimilation, as well as the differential changes in amino acid metabolism, and the induction of the phenylpropanoid biosynthesis pathway, were the main drought-attenuating mechanisms in the SAESo11-inoculated plants. Shifts in pathways related to hormonal signaling were also evident upon inoculation at a transcript level and in conjunction with carbon metabolism regulation, possibly contributed to a drought-attenuation preconditioning. The identified signatory molecules of SAESo11-mediated priming against drought included aspartate, myo-inositol, glutamate, along with key genes related to trehalose, tryptophan and cysteine synthesis. Taken together, SAESo11-inoculation provides systemic effects encompassing both metabolic and regulatory functions, supporting both seedling growth and drought stress amelioration.