Genome-wide identification, characterisation and functional evaluation of WRKY genes in the sweet potato wild ancestor Ipomoea trifida (H.B.K.) G. Don. under abiotic stresses

Genome-Wide Identification and Expression Analysis of the DA1 Gene Family in Sweet Potato and Its Two Diploid Relatives

The DA1-like gene family plays a crucial role in regulating seed and organ size in plants. The DA1 gene family has been identified in several species but has not yet been reported in sweet potatoes. In this study, nine, eleven, and seven DA1s were identified in cultivated sweet potato (Ipomoea batatas, 2n = 6x = 90) and its two diploid wild relatives, I. trifida (2n = 2x = 30) and I. triloba (2n = 2x = 30), respectively. The DA1 genes were classified into three subgroups based on their phylogenetic relationships with Arabidopsis thaliana and Oryza sativa (rice). Their protein physiological properties, chromosomal localization, phylogenetic relationships, gene structure, promoter cis-elements, and expression patterns were systematically analyzed. The qRT-PCR results showed that the expression levels of four genes, IbDA1-1, IbDA1-3, IbDA1-6, and IbDA1-7, were higher in the sweet potato leaves than in the roots, fiber roots, and stems. In our study, we provide a comprehensive comparison and further the knowledge of DA1-like genes in sweet potatoes, and provide a theoretical basis for functional studies.

Genome-wide identification and expression analysis of the glutamate receptor gene family in sweet potato and its two diploid relatives

Plant glutamate receptor (GLR) homologs are crucial calcium channels that play an important role in plant development, signal transduction, and response to biotic and abiotic stresses. However, the GLR gene family has not yet been thoroughly and systematically studied in sweet potato. In this study, a total of 37 GLR genes were identified in the cultivated hexaploid sweet potato (Ipomoea batatas), and 32 GLR genes were discovered in each of the two diploid relatives (Ipomoea trifida and Ipomoea triloba) for the first time. Based on their evolutionary relationships to those of Arabidopsis, these GLRs were split into five subgroups. We then conducted comprehensive analysis to explore their physiological properties, protein interaction networks, promoter cis-elements, chromosomal placement, gene structure, and expression patterns. The results indicate that the homologous GLRs of the cultivated hexaploid sweet potato and its two relatives are different. These variations are reflected in their functions related to plant growth, hormonal crosstalk, development of tuberous roots, resistance to root rot, and responses to abiotic stress factors, all of which are governed by specific individual GLR genes. This study offers a comprehensive analysis of GLR genes in sweet potato and its two diploid relatives. It also provides a theoretical basis for future research into their regulatory mechanisms, significantly influencing the field of molecular breeding in sweet potatoes.

Transcriptome profiling reveals multiple regulatory pathways of Tamarix chinensis in response to salt stress

KEY MESSAGE

Multiple regulatory pathways of T. chinensis to salt stress were identified through transcriptome data analysis. Tamarix chinensis (Tamarix chinensis Lour.) is a typical halophyte capable of completing its life cycle in soils with medium to high salinity. However, the mechanisms underlying its resistance to high salt stress are still largely unclear. In this study, transcriptome profiling analyses in different organs of T. chinensis plants in response to salt stress were carried out. A total number of 2280, 689, and 489 differentially expressed genes (DEGs) were, respectively, identified in roots, stems, and leaves, with more DEGs detected in roots than in stems and leaves. Gene Ontology (GO) term analysis revealed that they were significantly enriched in "biological processes" and "molecular functions". Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that "Beta-alanine metabolism" was the most differentially enriched pathway in roots, stems, and leaves. In pair-to-pair comparison of the most differentially enriched pathways, a total of 14 pathways, including 5 pathways in roots and leaves, 6 pathways in roots and stems, and 3 pathways in leaves and stems, were identified. Furthermore, genes encoding transcription factor, such as bHLH, bZIP, HD-Zip, MYB, NAC, WRKY, and genes associated with oxidative stress, starch and sucrose metabolism, and ion homeostasis, were differentially expressed with distinct organ specificity in roots, stems, and leaves. Our findings in this research provide a novel approach for exploring the salt tolerance mechanism of halophytes and identifying new gene targets for the genetic breeding of new plant cultivars with improved resistance to salt stress.

The transcription factor BnaA9.WRKY47 coordinates leaf senescence and nitrogen remobilization in Brassica napus

Nitrogen (N) is an essential macronutrient for plants, and its remobilization is key for adaptation to deficiency stress. However, there is limited understanding of the regulatory mechanisms of N remobilization in the important crop species Brassica napus (oilseed rape). Here, we report the identification of a transcription factor, BnaA9.WRKY47, that is induced by N starvation in a canola variety. At the seedling stage, BnaA9.WRKY47-overexpressing (OE) lines displayed earlier senescence of older leaves and preferential growth of juvenile leaves compared to the wild type under N starvation. At the field scale, the seed yield was significantly increased in the BnaA9.WRKY47-OE lines compared with the wild type when grown under N deficiency conditions and, conversely, it was reduced in BnaA9.WRKY47-knockout mutants. Biochemical analyses demonstrated that BnaA9.WRKY47 directly activates BnaC7.SGR1 to accelerate senescence of older leaves. In line with leaf senescence, the concentration of amino acids in the older leaves of the OE lines was elevated, and the proportion of plant N that they contained was reduced. This was associated with BnaA9.WRKY47 activating the amino acid permease BnaA9.AAP1 and the nitrate transporter BnaA2.NRT1.7. Thus, the expression of BnaA9.WRKY47 efficiently facilitated N remobilization from older to younger leaves or to seeds. Taken together, our results demonstrate that BnaA9.WRKY47 up-regulates the expression of BnaC7.SGR1, BnaA2.NRT1.7, and BnaA9AAP1, thus promoting the remobilization of N in B. napus under starvation conditions.

Comprehensive Evaluation and Transcriptome Analysis Reveal the Salt Tolerance Mechanism in Semi-Wild Cotton (Gossypium purpurascens)

Elevated salinity significantly threatens cotton growth, particularly during the germination and seedling stages. The utilization of primitive species of Gossypium hirsutum, specifically Gossypium purpurascens, has the potential to facilitate the restoration of genetic diversity that has been depleted due to selective breeding in modern cultivars. This investigation evaluated 45 G. purpurascens varieties and a salt-tolerant cotton variety based on 34 morphological, physiological, and biochemical indicators and comprehensive salt tolerance index values. This study effectively identified a total of 19 salt-tolerant and two salt-resistant varieties. Furthermore, transcriptome sequencing of a salt-tolerant genotype (Nayanmian-2; NY2) and a salt-sensitive genotype (Sanshagaopao-2; GP2) revealed 2776, 6680, 4660, and 4174 differentially expressed genes (DEGs) under 0.5, 3, 12, and 24 h of salt stress. Gene ontology enrichment analysis indicated that the DEGs exhibited significant enrichment in biological processes like metabolic (GO:0008152) and cellular (GO:0009987) processes. MAPK signaling, plant-pathogen interaction, starch and sucrose metabolism, plant hormone signaling, photosynthesis, and fatty acid metabolism were identified as key KEGG pathways involved in salinity stress. Among the DEGs, including NAC, MYB, WRKY, ERF, bHLH, and bZIP, transcription factors, receptor-like kinases, and carbohydrate-active enzymes were crucial in salinity tolerance. Weighted gene co-expression network analysis (WGCNA) unveiled associations of salt-tolerant genotypes with flavonoid metabolism, carbon metabolism, and MAPK signaling pathways. Identifying nine hub genes (MYB4, MYB105, MYB36, bZIP19, bZIP43, FRS2 SMARCAL1, BBX21, F-box) across various intervals offered insights into the transcriptional regulation mechanism of salt tolerance in G. purpurascens. This study lays the groundwork for understanding the important pathways and gene networks in response to salt stress, thereby providing a foundation for enhancing salt tolerance in upland cotton.

Multi-algorithm cooperation research of WRKY genes under nitrogen stress in Panax notoginseng

WRKY transcription factors play an important role in the immune system and the innate defense response of plants. WRKY transcription factors have great feedback on nitrogen stress. In this study, bioinformatics was used to detect the WRKYs of Panax notoginseng (PnWRKYs). The response of PnWRKYs under nitrogen stress was also well studied. PnWRKYs were distributed on 11 chromosomes. According to PnWRKY and Arabidopsis thaliana WRKY (AtWRKY) domains, these PnWRKY proteins were divided into three groups by phylogenetic analysis. MEME analysis showed that almost every member contained motif 1 and motif 2. PlantCARE online predicted the cis-acting elements of the promoter. PnWRKY gene family members obtained 22 pairs of repeat fragments by collinearity analysis. The expression levels of PnWRKYs in different parts (roots, flowers, and leafs) were analyzed by the gene expression pattern. They reflected tissue-specific expressions. The qRT-PCR experiments were used to detect 74 PnWRKYs under nitrogen stress. The results showed that the expression levels of 8 PnWRKYs were significantly induced. The PnWRKY gene family may be involved in biotic/abiotic stresses and hormone induction. This study will not only lay the foundation to explore the functions of PnWRKYs but also provide candidate genes for the future improvement of P. notoginseng.

Genome-Wide Comparative Analysis of the R2R3-MYB Gene Family in Six Ipomoea Species and the Identification of Anthocyanin-Related Members in Sweet Potatoes

Sweet potatoes (Ipomoea batatas) are one of the important tuberous root crops cultivated worldwide, and thier storage roots are rich in antioxidants, such as anthocyanins. R2R3-MYB is a large gene family involved in various biological processes, including anthocyanin biosynthesis. However, few reports about the R2R3-MYB gene family of sweet potatoes have been released to date. In the present study, a total of 695 typical R2R3-MYB genes were identified in six Ipomoea species, including 131 R2R3-MYB genes in sweet potatoes. A maximum likelihood phylogenetic analysis divided these genes into 36 clades, referring to the classification of 126 R2R3-MYB proteins of Arabidopsis. Clade C25(S12) has no members in six Ipomoea species, whereas four clades (i.e., clade C21, C26, C30, and C36), including 102 members, had no members in Arabidopsis, and they were identified as Ipomoea-specific clades. The identified R2R3-MYB genes were unevenly distributed on all chromosomes in six Ipomoea species genomes, and the collinearity analysis among hexaploid I. batatas and another five diploid Ipomoea species suggested that the sweet potato genome might have undergone a larger chromosome rearrangement during the evolution process. Further analyses of gene duplication events showed that whole-genome duplication, transposed duplication, and dispersed duplication events were the primary forces driving the R2R3-MYB gene family expansion of Ipomoea plants, and these duplicated genes experienced strong purifying selection because of their Ka/Ks ratio, which is less than 1. Additionally, the genomic sequence length of 131 IbR2R3-MYBs varied from 923 bp to ~12.9 kb with a mean of ~2.6 kb, and most of them had more than three exons. The Motif 1, 2, 3, and 4 formed typical R2 and R3 domains and were identified in all IbR2R3-MYB proteins. Finally, based on multiple RNA-seq datasets, two IbR2R3-MYB genes (IbMYB1/g17138.t1 and IbMYB113/g17108.t1) were relatively highly expressed in pigmented leaves and tuberous root flesh and skin, respectively; thus, they were identified to regulate tissue-specific anthocyanin accumulation in sweet potato. This study provides a basis for the evolution and function of the R2R3-MYB gene family in sweet potatoes and five other Ipomoea species.

WRKY transcription factors: evolution, regulation, and functional diversity in plants

The recent advancements in sequencing technologies and informatic tools promoted a paradigm shift to decipher the hidden biological mysteries and transformed the biological issues into digital data to express both qualitative and quantitative forms. The transcriptomic approach, in particular, has added new dimensions to the versatile essence of plant genomics through the large and deep transcripts generated in the process. This has enabled the mining of super families from the sequenced plants, both model and non-model, understanding their ancestry, diversity, and evolution. The elucidation of the crystal structure of the WRKY proteins and recent advancement in computational prediction through homology modeling and molecular dynamic simulation has provided an insight into the DNA-protein complex formation, stability, and interaction, thereby giving a new dimension in understanding the WRKY regulation. The present review summarizes the functional aspects of the high volume of sequence data of WRKY transcription factors studied from different species, till date. The review focuses on the dynamics of structural classification and lineage in light of the recent information. Additionally, a comparative analysis approach was incorporated to understand the functions of the identified WRKY transcription factors subjected to abiotic (heat, cold, salinity, senescence, dark, wounding, UV, and carbon starvation) stresses as revealed through various sets of studies on different plant species. The review will be instrumental in understanding the events of evolution and the importance of WRKY TFs under the threat of climate change, considering the new scientific evidences to propose a fresh perspective.

In-depth analysis of large-scale screening of WRKY members based on genome-wide identification

With the rapid advancement of high-throughput sequencing technology, it is now possible to identify individual gene families from genomes on a large scale in order to study their functions. WRKY transcription factors are a key class of regulators that regulate plant growth and abiotic stresses. Here, a total of 74 WRKY genes were identified from Dendrobium officinale Kimura et Migo genome. Based on the genome-wide analysis, an in-depth analysis of gene structure and conserved motif was performed. The phylogenetic analysis indicated that DoWRKYs could be classified into three main groups: I, II, and III, with group II divided into five subgroups: II-a, II-b, II-c, II-d, and II-e. The sequence alignment indicated that these WRKY transcriptional factors contained a highly conserved WRKYGQK heptapeptide. The localization analysis of chromosomes showed that WRKY genes were irregularly distributed across several chromosomes of D. officinale. These genes comprised diverse patterns in both number and species, and there were certain distinguishing motifs among subfamilies. Moreover, the phylogenetic tree and chromosomal location results indicated that DoWRKYs may have undergone a widespread genome duplication event. Based on an evaluation of expression profiles, we proposed that DoWRKY5, 54, 57, 21, etc. may be involved in the transcriptional regulation of the JA signaling pathway. These results provide a scientific reference for the study of DoWRKY family genes.

A systematical genome-wide analysis and screening of WRKY transcription factor family engaged in abiotic stress response in sweetpotato

BACKGROUND

WRKY transcription factors play pivotal roles in regulating plant multiple abiotic stress tolerance, however, a genome-wide systematical analysis of WRKY genes in sweetpotato is still missing.

RESULTS

Herein, 84 putative IbWRKYs with WRKY element sequence variants were identified in sweetpotato reference genomes. Fragment duplications, rather than tandem duplications, were shown to play prominent roles in IbWRKY gene expansion. The collinearity analysis between IbWRKYs and the related orthologs from other plants further depicted evolutionary insights into IbWRKYs. Phylogenetic relationships displayed that IbWRKYs were divided into three main groups (I, II and III), with the support of the characteristics of exon-intron structures and conserved protein motifs. The IbWRKY genes, mainly from the group Ib, displayed remarkable and diverse expression profiles under multiple abiotic stress (NaCl, PEG6000, cold and heat) and hormone (ABA, ACC, JA and SA) treatments, which were determined by RNA-seq and qRT-PCR assays, suggesting their potential roles in mediating particular stress responses. Moreover, IbWRKY58L could interact with IbWRKY82 as revealed by yeast two-hybrid based on the protein interaction network screening. And abiotic stress-remarkably induced IbWRKY21L and IbWRKY51 were shown to be localized in the nucleus and had no transactivation activities.

CONCLUSION

These results provide valuable insights into sweetpotato IbWRKYs and will lay a foundation for further exploring functions and possible regulatory mechanisms of IbWRKYs in abiotic stress tolerance.

Genome-Wide Identification and Expression Analysis of SWEET Family Genes in Sweet Potato and Its Two Diploid Relatives

Sugar Will Eventually be Exported Transporter (SWEET) proteins are key transporters in sugar transportation. They are involved in the regulation of plant growth and development, hormone crosstalk, and biotic and abiotic stress responses. However, SWEET family genes have not been explored in the sweet potato. In this study, we identified 27, 27, and 25 SWEETs in cultivated hexaploid sweet potato (Ipomoea batatas, 2n = 6x = 90) and its two diploid relatives, Ipomoea trifida (2n = 2x = 30) and Ipomoea triloba (2n = 2x = 30), respectively. These SWEETs were divided into four subgroups according to their phylogenetic relationships with Arabidopsis. The protein physiological properties, chromosome localization, phylogenetic relationships, gene structures, promoter cis-elements, protein interaction networks, and expression patterns of these 79 SWEETs were systematically investigated. The results suggested that homologous SWEETs are differentiated in sweet potato and its two diploid relatives and play various vital roles in plant growth, tuberous root development, carotenoid accumulation, hormone crosstalk, and abiotic stress response. This work provides a comprehensive comparison and furthers our understanding of the SWEET genes in the sweet potato and its two diploid relatives, thereby supplying a theoretical foundation for their functional study and further facilitating the molecular breeding of sweet potato.

Comparative transcriptome analysis unveiling reactive oxygen species scavenging system of Sonneratia caseolaris under salinity stress

Many mangrove forests have undergone major changes as a result of human activity and global climate change. Sonneratia caseolaris is a common tree located in inner mangroves, and its range extends inland along tidal creeks, as far as the influence of salinity extends. This study investigated the physiological and molecular response mechanisms of S. caseolaris by analyzing its antioxidant defense capacity, including its differentially expressed genes (DEGs) under similar salt stress conditions. Salt treatment significantly affected the osmoprotectants and lipid peroxidation in S. caseolaris seedlings, which increased proline (Pro) content by 31.01-54.90% during all sample periods and decreased malonaldehyde (MDA) content by 12.81 and 18.17% at 25 and 40 days under 3.0% NaCl treatment. Antioxidant enzyme activities increased significantly following 3.0% NaCl treatment. Transcriptome analysis following De novo assembly showed 26,498 matched unigenes. The results showed that 1,263 DEGs responded to transcription factors (TFs) and plant phytohormones and mediated oxidoreductase activity to scavenge reactive oxygen species (ROS) in the control vs. 3.0% NaCl comparison. In addition, the transcription levels of genes associated with auxin and ethylene signal transduction also changed. Under salt stress, ROS scavenging genes (POD, CAT, and APX) and part of AP2, MYB, NAC, C2C2, bHLH, and WRKY TFs were upregulated. This study identified important pathways and candidate genes involved in S. caseolaris salinity tolerance and provided suggestions for further research into the mechanisms of salt tolerance in S. caseolaris.

Genome-wide survey and expression analysis of GRAS transcription factor family in sweetpotato provides insights into their potential roles in stress response

BACKGROUND

The plant-specific GRAS transcription factors play pivotal roles in various adverse environmental conditions. Numerous GRAS genes have been explored and characterized in different plants, however, comprehensive survey on GRASs in sweetpotato is lagging.

RESULTS

In this study, 72 putative sweetpotato IbGRAS genes with uneven distribution were isolated on 15 chromosomes and classified into 12 subfamilies supported by gene structures and motif compositions. Moreover, both tandem duplication and segmental duplication events played critical roles in the expansion of sweetpotato GRAS genes, and the collinearity between IbGRAS genes and the related orthologs from nine other plants further depicted evolutionary insights into GRAS gene family. RNA-seq analysis under salt stress and qRT-PCR detection of 12 selected IbGRAS genes demonstrated their significant and varying inductions under multiple abiotic stresses (salt, drought, heat and cold) and hormone treatments (ABA, ACC and JA). Consistently, the promoter regions of IbGRAS genes harbored a series of stress- and hormone-associated cis-acting elements. Among them, IbGRAS71, the potential candidate for breeding tolerant plants, was characterized as having transactivation activity in yeasts, while IbGRAS-2/-4/-9 did not. Moreover, a complex interaction relationship between IbGRASs was observed through the interaction network analysis and yeast two-hybrid assays.

CONCLUSIONS

Our results laid a foundation for further functional identifications of IbGRAS genes, and multiple members may serve as potential regulators for molecular breeding of tolerant sweetpotato.

Genome-wide identification of the Liriodendron chinense WRKY gene family and its diverse roles in response to multiple abiotic stress

BACKGROUND

Liriodendron chinense (Lchi) is a tree species within the Magnoliaceae family and is considered a basal angiosperm. The too low or high temperature or soil drought will restrict its growth as the adverse environmental conditions, thus improving L. chinense abiotic tolerance was the key issues to study. WRKYs are a major family of plant transcription factors known to often be involved in biotic and abiotic stress responses. So far, it is still largely unknown if and how the LchiWRKY gene family is tied to regulating L. chinense stress responses. Therefore, studying the involvement of the WRKY gene family in abiotic stress regulation in L. chinense could be very informative in showing how this tree deals with such stressful conditions.

RESULTS

In this research, we performed a genome-wide analysis of the Liriodendron chinense (Lchi) WRKY gene family, studying their classification relationships, gene structure, chromosomal locations, gene duplication, cis-element, and response to abiotic stress. The 44 members of the LchiWRKY gene family contain a significant amount of sequence diversity, with their lengths ranging from 525 bp to 40,981 bp. Using classification analysis, we divided the 44 LchiWRKY genes into three phylogenetic groups (I, II, II), with group II then being further divided into five subgroups (IIa, IIb, IIc, IId, IIe). Comparative phylogenetic analysis including the WRKY families from 17 plant species suggested that LchiWRKYs are closely related to the Magnolia Cinnamomum kanehirae WRKY family, and has fewer family members than higher plants. We found the LchiWRKYs to be evenly distributed across 15 chromosomes, with their duplication events suggesting that tandem duplication may have played a major role in LchiWRKY gene expansion model. A Ka/Ks analysis indicated that they mainly underwent purifying selection and distributed in the group IId. Motif analysis showed that LchiWRKYs contained 20 motifs, and different phylogenetic groups contained conserved motif. Gene ontology (GO) analysis showed that LchiWRKYs were mainly enriched in two categories, i.e., biological process and molecular function. Two group IIc members (LchiWRKY10 and LchiWRKY37) contain unique WRKY element sequence variants (WRKYGKK and WRKYGKS). Gene structure analysis showed that most LchiWRKYs possess 3 exons and two different types of introns: the R- and V-type which are both contained within the WRKY domain (WD). Additional promoter cis-element analysis indicated that 12 cis-elements that play different functions in environmental adaptability occur across all LchiWRKY groups. Heat, cold, and drought stress mainly induced the expression of group II and I LchiWRKYs, some of which had undergone gene duplication during evolution, and more than half of which had three exons. LchiWRKY33 mainly responded to cold stress and LchiWRKY25 mainly responded to heat stress, and LchiWRKY18 mainly responded to drought stress, which was almost 4-fold highly expressed, while 5 LchiWRKYs (LchiWRKY5, LchiWRKY23, LchiWRKY14, LchiWRKY27, and LchiWRKY36) responded equally three stresses with more than 6-fold expression. Subcellular localization analysis showed that all LchiWRKYs were localized in the nucleus, and subcellular localization experiments of LchiWRKY18 and 36 also showed that these two transcription factors were expressed in the nucleus.

CONCLUSIONS

This study shows that in Liriodendron chinense, several WRKY genes like LchiWRKY33, LchiWRKY25, and LchiWRKY18, respond to cold or heat or drought stress, suggesting that they may indeed play a role in regulating the tree's response to such conditions. This information will prove a pivotal role in directing further studies on the function of the LchiWRKY gene family in abiotic stress response and provides a theoretical basis for popularizing afforestation in different regions of China.

A Novel WRKY Transcription Factor from Ipomoea trifida, ItfWRKY70, Confers Drought Tolerance in Sweet Potato

WRKY transcription factors are one of the important families in plants, and have important roles in plant growth, abiotic stress responses, and defense regulation. In this study, we isolated a WRKY gene, ItfWRKY70, from the wild relative of sweet potato Ipomoea trifida (H.B.K.) G. Don. This gene was highly expressed in leaf tissue and strongly induced by 20% PEG6000 and 100 μM abscisic acid (ABA). Subcellar localization analyses indicated that ItfWRKY70 was localized in the nucleus. Overexpression of ItfWRKY70 significantly increased drought tolerance in transgenic sweet potato plants. The content of ABA and proline, and the activity of SOD and POD were significantly increased, whereas the content of malondialdehyde (MDA) and H2O2 were decreased in transgenic plants under drought stress. Overexpression of ItfWRKY70 up-regulated the genes involved in ABA biosynthesis, stress-response, ROS-scavenging system, and stomatal aperture in transgenic plants under drought stress. Taken together, these results demonstrated that ItfWRKY70 plays a positive role in drought tolerance by accumulating the content of ABA, regulating stomatal aperture and activating the ROS scavenging system in sweet potato.

Overexpression of EcDREB2A transcription factor from finger millet in tobacco enhances tolerance to heat stress through ROS scavenging

An extreme temperature regime beyond desired level imposes significant stress in crop plants. The low and high temperature stresses are one of the primary constraints for plant development and yield. Finger millet, being a climate resilient crop, is a potential source of novel stress tolerant genes. In this study, functional characterization of finger millet DREB2A gene in different abiotic stress conditions was done. This novel EcDREB2A transcription factor isolated from finger millet is a truncated version of DREB2A gene compared to previously reported DREB genes from other plant species. The overexpression of EcDREB2A in transgenic tobacco exhibits improved tolerance against heat stress 42 °C for up to 7 days, by altering physiology and biochemical means. However, same transgenic lines were unable to provide tolerance to 200 mM NaCl and 200 mM Mannitol stress. Under heat stress conditions, increased seed germination with improved lateral roots, fresh and dry weight relative to wild type (WT) was observed. The EcDREB2A transgenics exposed to heat stress showed improved rate of stomatal conductance, chlorophyll and carotenoids contents, and other photosynthesis parameters compared to WT plants. EcDREB2A overexpression also resulted in increased antioxidant enzyme activity (SOD, CAT, GR, POD and, APX) with decreased electrolyte leakage (EL), H2O2, and malondialdehyde (MDA) content than WT plants under heat stress. Quantitative real time expression analysis demonstrated that all eight downstream genes were significantly upregulated in transgenic plants only after heat stress. Our data provide a clear demonstration of the positive impact of overexpression of EcDREB2A providing heat stress tolerance to plants.

WRKY transcription factors and plant defense responses: latest discoveries and future prospects

WRKY transcription factors are among the largest families of transcriptional regulators. In this review, their pivotal role in modulating various signal transduction pathways during biotic and abiotic stresses is discussed. Transcription factors (TFs) are important constituents of plant signaling pathways that define plant responses against biotic and abiotic stimuli besides playing a role in response to internal signals which coordinate different interacting partners during developmental processes. WRKY TFs, deriving their nomenclature from their signature DNA-binding sequence, represent one of the largest families of transcriptional regulators found exclusively in plants. By modulating different signal transduction pathways, these TFs contribute to various plant processes including nutrient deprivation, embryogenesis, seed and trichome development, senescence as well as other developmental and hormone-regulated processes. A growing body of research suggests transcriptional regulation of WRKY TFs in adapting plant to a variety of stressed environments. WRKY TFs can regulate diverse biological functions from receptors for pathogen triggered immunity, modulator of chromatin for specific interaction and signal transfer through a complicated network of genes. Latest discoveries illustrate the interaction of WRKY proteins with other TFs to form an integral part of signaling webs that regulate several seemingly disparate processes and defense-related genes, thus establishing their significant contributions to plant immune response. The present review starts with a brief description on the structural characteristics of WRKY TFs followed by the sections that present recent evidence on their roles in diverse biological processes in plants. We provide a comprehensive overview on regulatory crosstalks involving WRKY TFs during multiple stress responses in plants and future prospects of WRKY TFs as promising molecular diagnostics for enhancing crop improvement.

Integrating transcriptome and metabolome analyses of the response to cold stress in pumpkin (Cucurbita maxima)

Cucurbita maxima belong to the genus Cucurbita and are of nutritional and economic importance. Physiological activity, transcriptome, and metabolome analyses of leaf samples from the C. maxima inbreding line IL7 treated at 5 °C and 25 °C were performed. Cold stress resulted in a significant increase in the malondialdehyde content, relative electrical conductivity, soluble protein, sugar content, and catalase activity. A total of 5,553 differentially expressed genes were identified, of which 2,871 were up-regulated and 2,682 down-regulated. In addition, the transcription of differentially expressed genes in the plant hormone signal transduction pathway and transcription factor families of AP2/ERF, bHLH, WRKY, MYB, and HSF was activated. Moreover, 114 differentially expressed metabolites were identified by gas chromatography time-of-flight mass spectrometry, particularly through the analysis of carboxylic acids and derivatives, and organooxygen compounds. The demonstration of a series of potential metabolites and corresponding genes highlighted a comprehensive regulatory mechanism. These findings will provide novel insights into the molecular mechanisms associated with the response to cold stress in C. maxima.

Phylogenetic Analysis of the SQUAMOSA Promoter-Binding Protein-Like Genes in Four Ipomoea Species and Expression Profiling of the IbSPLs During Storage Root Development in Sweet Potato (Ipomoea batatas)

As a major plant-specific transcription factor family, SPL genes play a crucial role in plant growth, development, and stress tolerance. The SPL transcription factor family has been widely studied in various plant species; however, systematic studies on SPL genes in the genus Ipomoea are lacking. Here, we identified a total of 29, 27, 26, and 23 SPLs in Ipomoea batatas, Ipomoea trifida, Ipomoea triloba, and Ipomoea nil, respectively. Based on the phylogenetic analysis of SPL proteins from model plants, the Ipomoea SPLs were classified into eight clades, which included conserved gene structures, domain organizations and motif compositions. Moreover, segmental duplication, which is derived from the Ipomoea lineage-specific whole-genome triplication event, was speculated to have a predominant role in Ipomoea SPL expansion. Particularly, tandem duplication was primarily responsible for the expansion of SPL subclades IV-b and IV-c. Furthermore, 25 interspecific orthologous groups were identified in Ipomoea, rice, Arabidopsis, and tomato. These findings support the expansion of SPLs in Ipomoea genus, with most of the SPLs being evolutionarily conserved. Of the 105 Ipomoea SPLs, 69 were predicted to be the targets of miR156, with seven IbSPLs being further verified as targets using degradome-seq data. Using transcriptomic data from aboveground and underground sweet potato tissues, IbSPLs showed diverse expression patterns, including seven highly expressed IbSPLs in the underground tissues. Furthermore, the expression of 11 IbSPLs was validated using qRT-PCR, and two (IbSPL17/IbSPL28) showed significantly increased expression during root development. Additionally, the qRT-PCR analysis revealed that six IbSPLs were strongly induced in the roots under phytohormone treatments, particularly zeatin and abscisic acid. Finally, the transcriptomic data of storage roots from 88 sweet potato accessions were used for weighted gene co-expression network analysis, which revealed four IbSPLs (IbSPL16/IbSPL17/IbSPL21/IbSPL28) clusters with genes involved in "regulation of root morphogenesis," "cell division," "cytoskeleton organization," and "plant-type cell wall organization or biogenesis," indicating their potential role in storage root development. This study not only provides novel insights into the evolutionary and functional divergence of the SPLs in the genus Ipomoea but also lays a foundation for further elucidation of the potential functional roles of IbSPLs on storage root development.

Overexpression of transcription factor SlWRKY28 improved the tolerance of Populus davidiana × P. bolleana to alkaline salt stress

BACKGROUND

WRKY transcription factors (TFs) have been suggested to play crucial roles in the response to biotic and abiotic stresses. This study is the first to report the alkaline salt regulation of the WRKY gene.

RESULTS

In this study, we cloned a WRKY gene (SlWRKY28) from the Salix linearistipularis and then transferred to the Populus davidiana × P. bolleana for expression. Sequence analysis on the transcriptome of Salix linearistipular showed the significant up-regulation of WRKY gene expression in response to salt-alkali stress in seedlings. Our data showed that SlWRKY28 localized to the nucleus. Furthermore, the expression of the SlWRKY28 from female plants increased with saline-alkali stress according to the northern blot analysis results. The results of 3,3'-Diaminobenzidine (DAB) staining showed that hydrogen peroxide (H2O2) concentration was lower under stress, but ascorbate peroxidase (APX) enzyme activity was significantly higher in the overexpressed plants than that in non-transgenic (NT) plants.

CONCLUSIONS

We found out the SlWRKY28 induced regulation of the enzyme gene in the reactive oxygen species (ROS) scavenging pathway is a potential mechanism for transgenic lines to improve their resistance to alkaline salt. This study shows theoretical and practical significance in determining SlWRKY28 transcription factors involved in the regulation of alkaline salt tolerance.

Genome-wide Identification of WRKY transcription factor family members in sorghum (Sorghum bicolor (L.) moench)

WRKY transcription factors regulate diverse biological processes in plants, including abiotic and biotic stress responses, and constitute one of the largest transcription factor families in higher plants. Although the past decade has seen significant progress towards identifying and functionally characterizing WRKY genes in diverse species, little is known about the WRKY family in sorghum (Sorghum bicolor (L.) moench). Here we report the comprehensive identification of 94 putative WRKY transcription factors (SbWRKYs). The SbWRKYs were divided into three groups (I, II, and III), with those in group II further classified into five subgroups (IIa–IIe), based on their conserved domains and zinc finger motif types. WRKYs from the model plant Arabidopsis (Arabidopsis thaliana) were used for the phylogenetic analysis of all SbWRKY genes. Motif analysis showed that all SbWRKYs contained either one or two WRKY domains and that SbWRKYs within the same group had similar motif compositions. SbWRKY genes were located on all 10 sorghum chromosomes, and some gene clusters and two tandem duplications were detected. SbWRKY gene structure analysis showed that they contained 0–7 introns, with most SbWRKY genes consisting of two introns and three exons. Gene ontology (GO) annotation functionally categorized SbWRKYs under cellular components, molecular functions and biological processes. A cis-element analysis showed that all SbWRKYs contain at least one stress response-related cis-element. We exploited publicly available microarray datasets to analyze the expression profiles of 78 SbWRKY genes at different growth stages and in different tissues. The induction of SbWRKYs by different abiotic stresses hinted at their potential involvement in stress responses. qRT-PCR analysis revealed different expression patterns for SbWRKYs during drought stress. Functionally characterized WRKY genes in Arabidopsis and other species will provide clues for the functional characterization of putative orthologs in sorghum. Thus, the present study delivers a solid foundation for future functional studies of SbWRKY genes and their roles in the response to critical stresses such as drought.

Comparative Transcriptome and Proteome Analysis of Salt-Tolerant and Salt-Sensitive Sweet Potato and Overexpression of IbNAC7 Confers Salt Tolerance in Arabidopsis

Salt stress is one of the major devastating factors affecting the growth and yield of almost all crops, including the crucial staple food crop sweet potato. To understand their molecular responses to salt stress, comparative transcriptome and proteome analysis of salt-tolerant cultivar Xushu 22 and salt-sensitive cultivar Xushu 32 were investigated. The results showed the two genotypes had distinct differences at the transcription level and translation level even without salt stress, while inconsistent expression between the transcriptome and proteome data was observed. A total of 16,396 differentially expressed genes (DEGs) and 727 differentially expressed proteins (DEPs) were identified. Wherein, 1,764 DEGs and 93 DEPs were specifically expressed in the tolerant genotype. Furthermore, the results revealed that the significantly upregulated genes were mainly related to the regulation of ion accumulation, stress signaling, transcriptional regulation, redox reactions, plant hormone signal transduction, and secondary metabolite accumulation, which may be involved in the response of sweet potato to salt stress and/or may determine the salt tolerance difference between the two genotypes. In addition, 1,618 differentially expressed regulatory genes were identified, including bZIP, bHLH, ERF, MYB, NAC, and WRKY. Strikingly, transgenic Arabidopsis overexpressing IbNAC7 displayed enhanced salt tolerance compared to WT plants, and higher catalase (CAT) activity, chlorophyll and proline contents, and lower malondialdehyde (MDA) content and reactive oxygen species (ROS) accumulation were detected in transgenic plants compared with that of WT under salt stress. Furthermore, RNA-seq and qRT-PCR analysis displayed that the expression of many stress-related genes was upregulated in transgenic plants. Collectively, these findings provide revealing insights into sweet potato molecular response to salt stress and underlie the complex salt tolerance mechanisms between genotypes, and IbNAC7 was shown as a promising candidate gene to enhance salt tolerance of sweet potato.