Genome-wide expression analysis of carboxylesterase (CXE) gene family implies GBCXE49 functional responding to alkaline stress in cotton

Response of different cotton genotypes to salt stress and re-watering

BACKGROUND

Cotton is a vital economic crop and reserve material and a pioneer crop planted on saline-alkaline soil. Improving the tolerance of cotton to saline alkaline environments is particularly important.

RESULTS

Salt-tolerant and salt-sensitive cotton plants at the three-leaf stage were subjected to 200 mM NaCl stress treatment, thereafter, microstructural observations beside physiological and biochemical analyses were performed on cotton leaves at 0 h (CK), 48 h (NaCl) and re-watering (RW) for 48 h. Salt stress altered microstructural observations and physiological and biochemical in ST and SS (p < 0.05). After re-watering, ST recovered fully, while SS sustained permanent oxidative and structural damage, indicating distinct salt tolerance. Transcriptome analysis was performed on cotton leaves under salt stress and re-watering conditions. KEGG analysis revealed that the response of cotton to salt stress and its adaptation to re-watering may be related to major protein families such as photosynthesis (ko 00195), photosynthesis-antenna protein (ko 00196), plant hormone signal transduction (ko 04075), starch and sucrose metabolism (ko 00500), and porphyrin and chlorophyll metabolism (ko 00860). A gray coexpression module associated with cotton restoration under salt stress was enriched according to WGCNA.

CONCLUSIONS

Salt stress did not only affect the physiological and biochemical levels of cotton but also induced structural changes in cells and tissues. Re-watering was relatively effective in stabilizing the physiological and biochemical parameters, as well as the leaf microstructure, of cotton plants under salt stress. WGCNA revealed enriched gray coexpression modules related to the recovery of cotton plants under salt stress, and screening of the pivotal genes in the gray module revealed five critical hubs, namely, GH_A01G1528, GH_A08G2688, GH_D08G2683, GH_D01G1620 and GH_A10G0617. Overall, our findings can provide new insights into enhancing cotton salt tolerance and exploring salt tolerance genes in cotton,including screening cotton genetic resources using those potential responsive genes. This study provides a theoretical basis for further exploration of the molecular mechanism of cotton salt tolerance and genetic resources for breeding salt-tolerant cotton.

Consensus genomic regions and key genes for biotic, abiotic and key nutritional traits identified using meta- QTL analysis in peanut

Peanut (Arachis hypogaea L.), a key oilseed crop in the U.S., plays a significant role in agriculture and the economy but faces challenges from biotic and abiotic stresses, including aflatoxin contamination caused by Aspergillus flavus and A. parasiticus. Despite many large-effect QTLs identified for yield and key traits, their use in breeding is limited by unfavorable genetic interactions. To overcome this, we aimed to identify consensus genomic regions and candidate genes linked to key traits by analyzing QTL data from 30 independent studies conducted over the past 12 years, focusing on biotic, abiotic, aflatoxin, morphological, nutritional, phenological, and yield-associated traits. Using genetic map information, we constructed consensus maps and performed a meta-analysis on 891 QTLs, leading to the identification of 70 Meta-QTLs (MQTLs) with confidence intervals ranging from 0.07 to 9.63 cM and an average of 2.33 cM. This reduction in confidence intervals enhances the precision of trait mapping, making the identified MQTLs more applicable for breeding purposes. Furthermore, we identified key genes associated with aflatoxin resistance in MQTL5.2 (serine/threonine-protein kinase, BOI-related E3 ubiquitin-protein ligase), MQTL5.3, MQTL7.3, and MQTL13.1. Similarly, for yield-related traits in MQTL3.1-MQTL3.4 (mitogen-activated protein kinase, auxin response factor), MQTL11.2 (MADS-box protein, squamosa promoter-binding protein), and MQTL14.1. Genes related to oil composition within MQTL5.2 (fatty-acid desaturase FAD2, linoleate 9S-lipoxygenase), MQTL9.3, MQTL19.1 (acyl-CoA-binding protein, fatty acyl-CoA reductase FAR1), MQTL19.4, and MQTL19.5. Nutritional traits like iron and zinc content are linked to MQTL1.1 (probable methyltransferase, ferredoxin C), MQTL10.1, and MQTL12.1. These regions and genes serve as precise targets for marker-assisted breeding to enhance peanut yield, resilience, and quality.

Genome-wide identification of carboxyesterase family members reveals the function of GeCXE9 in the catabolism of parishin A in Gastrodia elata

KEY MESSAGE

GeCXE9 can catalyze the hydrolysis of parishin A via two pathways during the medicinal processing of Gastrodia elata. Gastrodia elata Bl. is used in traditional Chinese medicine for its bioactive compounds, particularly phenols. The molecular mechanisms of phenols formation and regulation remain to be fully explored. Here, we identified 13 GeCXE genes in G. elata. These members were mapped to eight chromosomes and possessed motifs necessary for catalysis. Phylogenetic analyses grouped them into four categories, supported by gene structure and motif composition. The cis-acting elements analysis indicated most GeCXEs contained elements associated with plant hormones or stress response. In vitro expression experiments revealed that GeCXE9 can catalyze the hydrolysis of parishin A via two pathways, producing parishin B and parishin C, respectively. Whereas in the absence of GeCXE9, parishin A is hydrolyzed solely to parishin B. In conclusion, GeCXE9 plays a crucial role in determining the metabolic pathways of phenols in G. elata, and its discovery provides a viable approach for the artificial regulation of phenols in this species.

FveDREB1B improves cold tolerance of woodland strawberry by positively regulating FveSCL23 and FveCHS

Cold stress has seriously inhibited the growth and development of strawberry during production. CBF/DREB1 is a key central transcription factor regulating plant cold tolerance, but its regulatory mechanisms are varied in different plants. Especially in strawberry, the molecular mechanism of CBF/DREB1 regulating cold tolerance is still unclear. In this study, we found that FveDREB1B was most significantly induced by cold stress in CBF/DREB1 family of diploid woodland strawberry. FveDREB1B was localized to the nucleus, and DREB1B sequences were highly conserved in diploid and octoploid strawberry, and even similar in Rosaceae. And FveDREB1B overexpressed strawberry plants showed delayed flowering and increased cold tolerance, while FveDREB1B silenced plants showed early flowering and decreased cold tolerance. Under cold stress, FveDREB1B activated FveSCL23 expression by directly binding to its promoter. Meanwhile, FveDREB1B and FveSCL23 interacted with FveDELLA, respectively. In addition, we also found that FveDREB1B promoted anthocyanin accumulation in strawberry leaves by directly activating FveCHS expression after cold treatment and recovery to 25°C. DREB1B genes were also detected to be highly expressed in cold-tolerant strawberry resources 'Fragaria mandschurica' and 'Fragaria nipponica'. In conclusion, our study reveals the molecular mechanism of FveDREB1B-FveSCL23-FveDELLA module and FveDREB1B-FveCHS module to enhance the cold tolerance of woodland strawberry. It provides a new idea for improving the cold tolerance of cultivated strawberry and evaluating the cold tolerance of strawberry germplasm resources.

Genome-wide identification of rice CXE gene family and mining of alleles for potential application in rice improvement

Carboxylesterases (CXE, EC 3.1.1.1), a class of hydrolases with an α/β folding domain, play important roles in plant growth and development and stress response. Here, we identified 32, 63, 41, and 45 CXE genes in Oryza sativa Japonica (Nipponbare), Oryza sativa Indica (93-11), Oryza sativa Indica (Xian-1B1 var.IR64), and Oryza sativa Japonica (Geng-sbtrp var.ChaoMeo), respectively. Then, we analyzed the chromosomal location, physical and chemical properties, subcellular localization, collinearity, and selection pressure of CXE genes in four rice varieties. We also analyzed the functional interaction network, cis-regulatory elements, evolutionary relationship, and protein tertiary structure, and performed gene expression profiling and qPCR verification under abiotic stress, as well as diversity analysis of 3010 gene-CDS-haplotype (gcHap) rice samples, aiming to understand the potential function of the 32 OsCXE genes. Our results indicated that fragment replication is the main reason for amplification of the CXE gene family in rice, and the gene family has undergone strong purification selection. OsCXE3.1, OsCXE3.2, OsCXE3.3, OsCXE5.1, and OsCXE7.3 may be used to improve the tolerance of rice to abiotic stress. OsCXE play important roles in rice population differentiation and improvement, and the major gcHaps at most OsCXE locus are significantly associated with yield traits. Therefore, natural variations of most OsCXE locus have great potential value for improvement of rice productivity.

Evolutionary divergence of CXE gene family in green plants unveils that PtoCXEs overexpression reduces fungal colonization in transgenic Populus

Plant enzymes significantly contribute to the rapidly diversified metabolic repertoire since the colonization of land by plants. Carboxylesterase is just one of the ubiquitous, multifunctional and ancient enzymes that has particularly diversified during plant evolution. This study provided a status on the carboxylesterase landscape within Viridiplantae. A total of 784 carboxylesterases were identified from the genome of 31 plant species representing nine major lineages of sequenced Viridiplantae and divided into five clades based on phylogenetic analysis. Clade I carboxylesterase genes may be of bacterial origin and then expanded and diversified during plant evolution. Clade II was first gained in the ancestor of bryophytes after colonization of land by plants, Clade III and Clade IV in ferns which were considered the most advanced seedless vascular plants, while Clade V was gained in seed plants. To date, the functions of carboxylesterase genes in woody plants remain unclear. In this study, 51 carboxylesterase genes were identified from the genome of Populus trichocarpa and further divided into eight classes. Tandem and segmental duplication events both contributed to the expansion of carboxylesterase genes in Populus. Although carboxylesterase genes were proven to enhance resistance to pathogens in many herbaceous species, relevant researches on forest trees are still needed. In this study, pathogen incubation assays showed that overexpressing of six Class VI carboxylesterases in Populus tomentosa, to a greater or lesser degree, reduced colonization of detached leaves by fungus Cytospora chrysosperma. A significant difference was also found in functional divergence patterns for genes derived from different gene duplication events. Functional differentiation of duplicated carboxylesterase genes in Populus was proved for the first time by in vivo physiological analysis. The identification of the potentially anti-fungal PtoCXE06 gene also laid a theoretical foundation for promoting the genetic improvement of disease-resistance traits in forest trees.

Infection of Phytophthora palmivora Isolates on Arabidopsis thaliana

Phytophthora palmivora, a hemibiotrophic oomycete, causes diseases in several economically important tropical crops, such as oil palm, which it is responsible for a devastating disease called bud rot (BR). Despite recent progress in understanding host resistance and virulence mechanisms, many aspects remain unknown in P. palmivora isolates from oil palm. Model pathosystems are useful for understanding the molecular interactions between pathogens and hosts. In this study, we utilized detached leaves and whole seedlings of Arabidopsis thaliana Col-0 to describe and evaluate the infection process of three P. palmivora isolates (CPPhZC-05, CPPhZC-04, CPPhZOC-01) that cause BR in oil palm. Two compatible isolates (CPPhZC-05 and CPPhZOC-01) induced aqueous lesions at 72 h post-inoculation (hpi), with microscopic visualization revealing zoospore encysting and appressorium penetration at 3 hpi, followed by sporangia generation at 72 hpi. In contrast, an incompatible isolate (CPPhZC-04) exhibited cysts that could not penetrate tissue, resulting in low leaf colonization. Gene expression of ten P. palmivora infection-related genes was quantified by RT-qPCR, revealing overexpression in compatible isolates, but not in the incompatible isolate. Additionally, key genes associated with salicylic acid (SA), jasmonic acid (JA), and ethylene (ET) in Arabidopsis exhibited regulation during interaction with the three isolates. These findings demonstrate that P. palmivora can infect Arabidopsis Col-0, and variability is observed in the interaction between Arabidopsis-Col-0 and P. palmivora isolates. Establishing this pathosystem is expected to enhance our understanding of P. palmivora's pathology and physiology.

Genome-wide profiling of DNA methylome and transcriptome reveals epigenetic regulation of Urechis unicinctus response to sulfide stress

Sulfide is a well-known environmental pollutant that can have detrimental effects on most organisms. However, few metazoans living in sulfide-rich environments have developed mechanisms to tolerate and adapt to sulfide stress. Epigenetic mechanisms, including DNA methylation, have been shown to play a vital role in environmental stress adaptation. Nevertheless, the precise function of DNA methylation in biological sulfide adaptation remains unclear. Urechis unicinctus, a benthic organism inhabiting sulfide-rich intertidal environments, is an ideal model organism for studying adaptation to sulfide environments. In this study, we conducted a comprehensive analysis of the DNA methylome and transcriptome of U. unicinctus after exposure to 50 μM sulfide. The results revealed dynamic changes in the DNA methylation (5-methylcytosine) landscape in response to sulfide stress, with U. unicinctus exhibiting elevated DNA methylation levels following stress exposure. Integrating differentially expressed genes (DEGs) and differentially methylated regions (DMRs), we identified a crucial role of gene body methylation in predicting gene expression. Furthermore, using a DNA methyltransferase inhibitor, we validated the involvement of DNA methylation in the sulfide stress response and the gene regulatory network influenced by DNA methylation. The results indicated that by modulating DNA methylation levels during sulfide stress, the expression of glutathione S-transferase, glutamyl aminopeptidase, and cytochrome c oxidase could be up-regulated, thereby facilitating the metabolism and detoxification of exogenous sulfides. Moreover, DNA methylation was found to regulate and enhance the oxidative phosphorylation pathway, including NADH dehydrogenase, isocitrate dehydrogenase, and ATP synthase. Additionally, DNA methylation influenced the regulation of Cytochrome P450 and macrophage migration inhibitory factor, both of which are closely associated with oxidative stress and stress resistance. Our findings not only emphasize the role of DNA methylation in sulfide adaptation but also provide novel insights into the potential mechanisms through which marine organisms adapt to environmental changes.

Systematic identification and characterization of microRNAs with target genes involved in high night temperature stress at the filling stage of rice

High night temperature stress is one of the main environmental factors affecting rice yield and quality. More and more evidence shows that microRNA (miRNA) plays an important role in various abiotic stresses. However, the molecular network of miRNA regulation on rice tolerance to high night temperatures remains unclear. Here, small RNA, transcriptome and degradome sequencing were integrated to identify differentially expressed miRNAs, genes, and key miRNA-target gene pairs in rice heat-sensitive and heat-tolerant lines at the filling stage suffering from high night temperature stress. It was discovered that there were notable differences in the relative expression of 102 miRNAs between the two rice lines under stress. Meanwhile, 5263 and 5405 mRNAs were differentially expressed in the heat-sensitive line and heat-tolerant line, and functional enrichment analysis revealed that these genes were involved in heat-related processes and pathways. The miRNAs-mRNAs target relationship was further verified by degradome sequencing. Eventually, 49 miRNAs-222 mRNAs target pairs with reverse expression patterns showed significant relative expression changes between the heat-tolerant and the heat-sensitive line, being suggested to be responsible for the heat tolerance difference of these two rice lines. Functional analysis of these 222 mRNA transcripts showed that high night temperature-responsive miRNAs targeted these mRNAs involved in many heat-related biological processes, such as transcription regulation, chloroplast regulation, mitochondrion regulation, protein folding, hormone regulation and redox process. This study identified possible miRNA-mRNA regulation relationships in response to high night temperature stress in rice and potentially contributed to heat resistance breeding of rice in the future.

Genome-wide identification of CXE and PuCXE15 functions in the catabolism of volatile ester in 'Nanguo' pear fruit

Volatile esters are the main aromatic components that affect consumer sensory preferences. Aroma is a crucial characteristic of the 'Nanguo' pear (Pyrus ussriensis Maxim). Carboxylesterases (CXEs) are positively correlated with the catabolism of volatile esters in peaches; however, the mechanism of action of CXE family members in 'Nanguo' pear is poorly understood. In this study, 40 PuCXEs were identified in the 'Nanguo' pear and assigned into seven groups. In addition, we found that most PuCXEs were relatively conserved and contained cytoplasmic proteins. This hypothesis was supported by phylogenetic analysis, investigation of conserved domains and gene structures, and prediction of subcellular localization. Based on the content of volatile esters and expression levels of PuCXEs analysis, four PuCXEs, including PuCXE7, PuCXE15, PuCXE20, and PuCXE25, had a significant negative correlation with volatile ester accumulation. Particularly, the correlation of PuCXE15 far exceeded that of the other PuCXEs. The results of the transient expression assay showed that PuCXE15 promoted the degradation of ester in vivo. Subcellular localization experiment revealed that PuCXE15 is located in the plasma membrane and nucleus. These results show that PuCXE15 functions in the catabolism of volatile ester in 'Nanguo' pear fruit, and provides a foundation for enhancing aroma quality by artificial control in pear.

Genome-wide association analysis for drought tolerance and associated traits in faba bean (Vicia faba L.)

Faba bean (Vicia faba L.) is an important high protein legume adapted to diverse climatic conditions with multiple benefits for the overall sustainability of the cropping systems. Plant-based protein demand is being expanded and faba bean is a good candidate to cover this need. However, the crop is very sensitive to abiotic stresses, especially drought, which severely affects faba bean yield and development worldwide. Therefore, identifying genes associated with drought stress tolerance is a major challenge in faba bean breeding. Although the faba bean response to drought stress has been widely studied, the molecular approaches to improve drought tolerance in this crop are still limited. Here we built on recent genomic advances such as the development of the first high-density SNP genotyping array, to conduct a genome-wide association study (GWAS) using thousands of genetic polymorphisms throughout the entire faba bean genome. A worldwide collection of 100 faba bean accessions was grown under control and drought conditions and 10 morphological, phenological and physiological traits were evaluated to identify single nucleotide polymorphism (SNP) markers associated with drought tolerance. We identified 29 SNP markers significantly correlated with these traits under drought stress conditions. The flanking sequences were blasted to the Medicago truncatula reference genomes in order to annotate potential candidate genes underlying the causal variants. Three of the SNPs for chlorophyll content after the stress, correspond to uncharacterized proteins indicating the presence of novel genes associated with drought tolerance in faba bean. The significance of stress-inducible signal transducers provides valuable information on the possible mechanisms underlying the faba bean response to drought stress, thus providing a foundation for future marker-assisted breeding in the crop.

Genome-Wide Characterization and Functional Analysis of ABCG Subfamily Reveal Its Role in Cutin Formation in Cotton

ATP-binding cassette transporter G (ABCG) has been shown to be engaged in export of broad-spectrum compounds with structural differences, but little is known concerning its role in cutin formation of cotton (Gossypium spp.). In this study, we conduct a genome-wide survey and detected 69, 71, 124 and 131 ABCG genes within G. arboretum, G. raimondii, G. hirsutum and G. barbadense, separately. The above ABCGs could be divided into four groups (Ia, Ib, Ic, II). Some ABCG genes such as GhABCG15, whose homologous gene transports cuticular lipid in Arabidopsis, was preferentially expressed in the development of fiber. A weighted gene co-expression network analysis (WGCNA) demonstrated that GhABCG expression was significantly associated with the amount of 16-Hydroxypalmitate (a main component of cutin precursor) in cotton fibers. Further, silencing of GhABCG15 by virus-induced gene silencing (VIGS) in cotton generated brightened and crinkled leaves as well as reduced thickness of cuticle and increased permeability. Chemical composition analysis showed the cutin content in GhABCG15-silenced leaves had decreased while the wax content had increased. Our results provide an insight for better understanding of the role of the Gossypium ABCG family and revealed the essential role of GhABCGs in cotton cutin formation.

Effects of Date Palm Waste Compost Application on Root Proteome Changes of Barley (Hordeum vulgare L.)

Proteomic analysis was performed to investigate the differentially abundant proteins (DAPs) in barley roots during the tillering stage. Bioinformatic tools were used to interpret the biological function, the pathway analysis and the visualisation of the network amongst the identified proteins. A total of 72 DAPs (33 upregulated and 39 downregulated) among a total of 2580 proteins were identified in response to compost treatment, suggesting multiple pathways of primary and secondary metabolism, such as carbohydrates and energy metabolism, phenylpropanoid pathway, glycolysis pathway, protein synthesis and degradation, redox homeostasis, RNA processing, stress response, cytoskeleton organisation, and phytohormone metabolic pathways. The expression of DAPs was further validated by qRT-PCR. The effects on barley plant development, such as the promotion of root growth and biomass increase, were associated with a change in energy metabolism and protein synthesis. The activation of enzymes involved in redox homeostasis and the regulation of stress response proteins suggest a protective effect of compost, consequently improving barley growth and stress acclimation through the reduction of the environmental impact of productive agriculture. Overall, these results may facilitate a better understanding of the molecular mechanism of compost-promoted plant growth and provide valuable information for the identification of critical genes/proteins in barley as potential targets of compost.

Comprehensive analysis of the carboxylesterase gene reveals that NtCXE22 regulates axillary bud growth through strigolactone metabolism in tobacco

Carboxylesterases (CXE) are a class of hydrolytic enzymes with α/β-folding domains that play a vital role in plant growth, development, stress response, and activation of herbicide-active substances. In this study, 49 Nicotiana tabacum L. CXE genes (NtCXEs) were identified using a sequence homology search. The basic characteristics, phylogenetic evolution, gene structure, subcellular location, promoter cis-elements, and gene expression patterns of the CXE family were systematically analyzed. RNA-seq data and quantitative real-time PCR showed that the expression level of CXEs was associated with various stressors and hormones; gene expression levels were significantly different among the eight tissues examined and at different developmental periods. As a new class of hormones, strigolactones (SLs) are released from the roots of plants and can control the germination of axillary buds.NtCXE7, NtCXE9, NtCXE22, and NtCXE24 were homologous to Arabidopsis SLs hydrolase AtCXE15, and changes in their expression levels were induced by topping and by GR24 (a synthetic analogue of strigolactone). Further examination revealed that NtCXE22-mutant (ntcxe22) plants generated by CRISPR-Cas9 technology had shorter bud outgrowth with lower SLs content. Validation of NtCXE22 was also performed in NtCCD8-OE plants (with fewer axillary buds) and in ntccd8 mutant plants (with more axillary buds). The results suggest that NtCXE22 may act as an efficient SLs hydrolase and affects axillary bud development, thereby providing a feasible method for manipulating endogenous SLs in crops and ornamental plants.

Deciphering the Genetic Basis of Root and Biomass Traits in Rapeseed (Brassica napus L.) through the Integration of GWAS and RNA-Seq under Nitrogen Stress

An excellent root system is responsible for crops with high nitrogen-use efficiency (NUE). The current study evaluated the natural variations in 13 root- and biomass-related traits under a low nitrogen (LN) treatment in a rapeseed association panel. The studied traits exhibited significant phenotypic differences with heritabilities ranging from 0.53 to 0.66, and most of the traits showed significant correlations with each other. The genome-wide association study (GWAS) found 51 significant and 30 suggestive trait–SNP associations that integrated into 14 valid quantitative trait loci (QTL) clusters and explained 5.7–21.2% phenotypic variance. In addition, RNA sequencing was performed at two time points to examine the differential expression of genes (DEGs) between high and low NUE lines. In total, 245, 540, and 399 DEGs were identified as LN stress-specific, high nitrogen (HN) condition-specific, and HNLN common DEGs, respectively. An integrated analysis of GWAS, weighted gene co-expression network, and DEGs revealed 16 genes involved in rapeseed root development under LN stress. Previous studies have reported that the homologs of seven out of sixteen potential genes control root growth and NUE. These findings revealed the genetic basis underlying nitrogen stress and provided worthwhile SNPs/genes information for the genetic improvement of NUE in rapeseed.

Research Advances and Prospects of Orphan Genes in Plants

Orphan genes (OGs) are defined as genes having no sequence similarity with genes present in other lineages. OGs have been regarded to play a key role in the development of lineage-specific adaptations and can also serve as a constant source of evolutionary novelty. These genes have often been found related to various stress responses, species-specific traits, special expression regulation, and also participate in primary substance metabolism. The advancement in sequencing tools and genome analysis methods has made the identification and characterization of OGs comparatively easier. In the study of OG functions in plants, significant progress has been made. We review recent advances in the fast evolving characteristics, expression modulation, and functional analysis of OGs with a focus on their role in plant biology. We also emphasize current challenges, adoptable strategies and discuss possible future directions of functional study of OGs.