Genome-wide identification of WRKY genes and their expression profiles under different abiotic stresses in Elaeis guineensis

Genome-wide identification, characterization and expression analysis of WRKY transcription factors under abiotic stresses in Carthamus tinctorius L

BACKGROUND

WRKY transcription factors constitute one of the largest families of plant transcriptional regulators, playing pivotal roles in plant responses to biotic and abiotic stresses, as well as in hormonal signaling and secondary metabolism regulation. However, a comprehensive analysis of the WRKY family in Carthamus tinctorius (safflower) is lacking. This study aims to identify and characterize WRKY genes in safflower to enhance understanding of their roles in stress responses and metabolic regulation. Safflower, valued for its ornamental, medicinal, and culinary uses, exhibits significant resilience to salt, alkali, and drought. By elucidating the functions and expression patterns of WRKY genes, we aim to enhance breeding strategies for improved stress tolerance and metabolic traits in crops.

RESULTS

In this study, we identified 84 WRKY genes within the safflower genome, and classified them into three primary groups (Groups I, II, and III) based on molecular structure and phylogenetic relationships. Group II was further subdivided into five subgroups (II-a, II-b, II-c, II-d, and II-e). Gene structure, conserved domain, motif, cis-elements, and expression profiling were performed. Syntenic analysis revealed that there were 27 pairs of repetitive fragments. Expression profiles of CtWRKY genes were assessed across diverse tissues, colored cultivars, and abiotic stresses such as ABA, drought, and cold conditions. Several CtWRKY genes (e.g., CtWRKY44, CtWRKY63, CtWRKY65, CtWRKY70 and CtWRKY72) exhibited distinct expression patterns in response to cold stress and during different developmental stages. Additionally, CtWRKY13, CtWRKY69, CtWRKY29, CtWRKY56, and CtWRKY36 were upregulated across different flower colors. The expression patterns of CtWRKY48, CtWRKY58, and CtWRKY70 varied among safflower cultivars and flower colors. After exposure to drought stress, the expression levels of CtWRKY29 and CtWRKY58 were downregulated, while those of CtWRKY56 and CtWRKY62 were upregulated.

CONCLUSION

This study identified 84 WRKY genes in Carthamus tinctorius and classified them into three groups, with detailed analyses of their structure, conserved domains, motifs, and expression profiles under various stresses. Notably, several WRKY genes such as CtWRKY44, CtWRKY63, and CtWRKY72 displayed significant expression changes under cold stress, while CtWRKY56 and CtWRKY62 were responsive to drought stress. These findings highlight the critical roles of specific WRKY genes in abiotic stress tolerance and developmental regulation in safflower.

Molecular basis of resistance to leaf spot disease in oil palm

Introduction

Leaf spot disease caused by the fungal pathogen Curvularia oryzae is one of the most common diseases found in oil palm (Elaeis guineensis) nurseries in South East Asia, and is most prevalent at the seedling stage. Severe infections result in localized necrotic regions of leaves that rapidly spread within nurseries leading to poor quality seedlings and high economic losses.

Methods

To understand the molecular mechanisms of this plant-pathogen interaction, RNA-Seq was used to elucidate the transcriptomes of three oil palm genotypes with contrasting pathogen responses (G10 and G12, resistant and G14, susceptible) following infection with C. oryzae spores. Transcriptomes were obtained from Illumina NovaSeq 6000 sequencing of mRNA at four different time points (day 0, before treatment; day 1, 7, and 21 post treatment).

Results and discussion

Analysis of differentially expressed gene (DEG) profiles in these three genotypes provided an overview of the genes involved in the plant defence. Genes involved in disease resistance, phytohormone biosynthesis, gene regulation (transcription factors), and those encoding proteins associated with cell wall hardening were identified and likely contribute to the resistance of oil palm to C. oryzae. Such genes represent good candidates for targets to enhance oil palm productivity and resilience through molecular breeding approaches.

The WRKY gene family in the halophyte Limonium bicolor: identification, expression analysis, and regulation of salt stress tolerance

KEY MESSAGE

63 L. bicolor WRKY genes were identified and their informatics was analyzed. The results suggested that the LbWRKY genes involved in the development and salt secretion of salt glands in L. bicolor. Salt stress, as a universal abiotic stress, severely inhibits the growth and development of plants. WRKY transcription factors play a vital role in plant growth and development, as well as in response to various stresses. Nevertheless, little is known of systematic genome-wide analysis of the WRKY genes in Limonium bicolor, a model recretohalophyte. In this study, 63 L. bicolor WRKY genes were identified (LbWRKY1-63), which were unevenly distributed across seven chromosomes and one scaffold. Based on the structural and phylogenetic characteristics, 63 LbWRKYs are divided into three main groups. Cis-elements in the LbWRKY promoters were related to growth and development, phytohormone responses, and stress responses. Colinearity analysis showed strong colinearity between LbWRKYs and GmWRKYs from soybean (Glycine max). Therefore, LbWRKY genes maybe have similar functions to GmWRKY genes. Expression analysis showed that 28 LbWRKY genes are highly expressed in roots, 9 in stems, 26 in leaves, and 12 in flowers and most LbWRKY genes responded to NaCl, ABA, and PEG6000. Silencing LbWRKY10 reduced salt gland density and salt secretion ability of leaves, and the salt tolerance of the species. Consistent with this, genes associated with salt gland development were markedly down-regulated in the LbWRKY10-silenced lines. Our findings suggested that the LbWRKY genes involved in the development and salt secretion of salt glands in L. bicolor. Our research provides new insights into the functions of the WRKY family in halophytes.

WRKY Transcription Factors in Jasminum sambac: An Insight into the Regulation of Aroma Synthesis

WRKY transcription factors are one of the largest families of transcription regulators that play essential roles in regulating the synthesis of secondary metabolites in plants. Jasmine (Jasminum sambac), renowned for its aromatic nature and fragrant blossoms, possesses a significant abundance of volatile terpene compounds. However, the role of the WRKY family in terpene synthesis in jasmine remains undetermined. In this study, 72 WRKY family genes of J. sambac were identified with their conserved WRKY domains and were categorized into three main groups based on their structural and phylogenetic characteristics. The extensive segmental duplications contributed to the expansion of the WRKY gene family. Expression profiles derived from the transcriptome data and qRT-PCR analysis showed that the majority of JsWRKY genes were significantly upregulated in fully bloomed flowers compared to buds. Furthermore, multiple correlation analyses revealed that the expression patterns of JsWRKYs (JsWRKY27/33/45/51/55/57) were correlated with both distinct terpene compounds (monoterpenes and sesquiterpenes). Notably, the majority of jasmine terpene synthase (JsTPS) genes related to terpene synthesis and containing W-box elements exhibited a significant correlation with JsWRKYs, particularly with JsWRKY51, displaying a strong positive correlation. A subcellular localization analysis showed that JsWRKY51 was localized in the nucleus. Moreover, transgenic tobacco leaves and jasmine calli experiments demonstrated that overexpression of JsWRKY51 was a key factor in enhancing the accumulation of β-ocimene, which is an important aromatic terpene component. Collectively, our findings suggest the roles of JsWRKY51 and other JsWRKYs in regulating the synthesis of aromatic compounds in J. sambac, providing a foundation for the potential utilization of JsWRKYs to facilitate the breeding of fragrant plant varieties with an improved aroma.

A Chromosome-level Reference Genome of African Oil Palm Provides Insights into Its Divergence and Stress Adaptation

The palm family (Arecaceae), consisting of ∼ 2600 species, is the third most economically important family of plants. The African oil palm (Elaeis guineensis) is one of the most important palms. However, the genome sequences of palms that are currently available are still limited and fragmented. Here, we report a high-quality chromosome-level reference genome of an oil palm, Dura, assembled by integrating long reads with ∼ 150× genome coverage. The assembled genome was 1.7 Gb in size, covering 94.5% of the estimated genome, of which 91.6% was assigned into 16 pseudochromosomes and 73.7% was repetitive sequences. Relying on the conserved synteny with oil palm, the existing draft genome sequences of both date palm and coconut were further assembled into chromosomal level. Transposon burst, particularly long terminal repeat retrotransposons, following the last whole-genome duplication, likely explains the genome size variation across palms. Sequence analysis of the VIRESCENS gene in palms suggests that DNA variations in this gene are related to fruit colors. Recent duplications of highly tandemly repeated pathogenesis-related proteins from the same tandem arrays play an important role in defense responses to Ganoderma. Whole-genome resequencing of both ancestral African and introduced oil palms in Southeast Asia reveals that genes under putative selection are notably associated with stress responses, suggesting adaptation to stresses in the new habitat. The genomic resources and insights gained in this study could be exploited for accelerating genetic improvement and understanding the evolution of palms.

Bioinformatics Analysis of WRKY Family Genes in Flax (Linum usitatissimum)

WRKY gene family is one of the largest transcription factor families involved in various physiological processes of plants. Flax (Linum usitatissimum) is an important stem fiber crop, and it is also an economically important crop in natural fiber and textile industries around the world. In this study, 105 WRKY genes were obtained by screening the whole genome of flax. There were 26 in group I, 68 in group II, 8 in group III and 3 in group UN. The characteristics of the WRKY motif and gene structure in each group are similar. The promoter sequence of WRKY genes includes photoresponsive elements, core regulatory elements and 12 cis-acting elements under abiotic stress. Similar to A. thaliana and Compositae plants, WRKY genes are evenly distributed on each chromosome, with segmental and tandem repeated events, which play a major role in the evolution of WRKY genes. The flax WRKY gene family is mainly concentrated in group I and group II. This study is mainly based on genome-wide information to classify and analyze the flax WRKY gene family, laying a foundation for further understanding the role of WRKY transcription factors in species evolution and functional analysis.

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.

Abiotic stress tolerance in plants: a fascinating action of defense mechanisms

Climate fluctuation mediated abiotic stress consequences loss in crop yields. These stresses have a negative impact on plant growth and development by causing physiological and molecular changes. In this review, we have attempted to outline recent studies (5 years) associated with abiotic stress resistance in plants. We investigated the various factors that contribute to coping with abiotic challenges, such as transcription factors (TFs), microRNAs (miRNAs), epigenetic changes, chemical priming, transgenic breeding, autophagy, and non-coding RNAs. Stress responsive genes are regulated mostly by TFs, and these can be used to enhance stress resistance in plants. Plants express some miRNA during stress imposition that act on stress-related target genes to help them survive. Epigenetic alterations govern gene expression and facilitate stress tolerance. Chemical priming enhances growth in plants by modulating physiological parameters. Transgenic breeding enables identification of genes involved in precise plant responses during stressful situations. In addition to protein coding genes, non-coding RNAs also influence the growth of the plant by causing alterations at gene expression levels. For achieving sustainable agriculture for a rising world population, it is crucial to develop abiotic-resistant crops with anticipated agronomical traits. To achieve this objective, understanding the diverse mechanisms by which plants protect themselves against abiotic stresses is imperative. This review emphasizes on recent progress and future prospects for abiotic stress tolerance and productivity in plants.

Genome-wide analysis of WRKY transcription factor genes in Toona sinensis: An insight into evolutionary characteristics and terpene synthesis

WRKY transcription factors (TFs), one of the largest TF families, serve critical roles in the regulation of secondary metabolite production. However, little is known about the expression pattern of WRKY genes during the germination and maturation processes of Toona sinensis buds. In the present study, the new assembly of the T. sinensis genome was used for the identification of 78 TsWRKY genes, including gene structures, phylogenetic features, chromosomal locations, conserved protein domains, cis-regulatory elements, synteny, and expression profiles. Gene duplication analysis revealed that gene tandem and segmental duplication events drove the expansion of the TsWRKYs family, with the latter playing a key role in the creation of new TsWRKY genes. The synteny and evolutionary constraint analyses of the WRKY proteins among T. sinensis and several distinct species provided more detailed evidence of gene evolution for TsWRKYs. Besides, the expression patterns and co-expression network analysis show TsWRKYs may multi-genes co-participate in regulating terpenoid biosynthesis. The findings revealed that TsWRKYs potentially play a regulatory role in secondary metabolite synthesis, forming the basis for further functional characterization of WRKY genes with the intention of improving T. sinensis.

Genome-wide identification and expression analysis of MYB gene family under nitrogen stress in Panax notoginseng

The myeloblastosis (MYB) gene family, involved in regulating many important physiological and biochemical processes, is one of the largest transcript factor superfamilies in plants. Since the identification of genome sequencing of Panax notoginseng has been completed, there was little known about the whole genome of its specific MYB gene family and the response to abiotic stresses, in consideration of the excessive application of nitrogen fertilizers in P. notoginseng. In this study, 123 PnMYB genes (MYB genes of P. notoginseng) have been identified and divided into 3 subfamilies by the phylogenetic analysis. These PnMYB genes were unevenly located on 12 chromosomes. Meanwhile, the gene structure and protein conserved domain were established by MEME Suite. The analysis of collinear relationships reflected that there were 121 homologous genes between P. notoginseng and Arabidopsis and 30 between P. notoginseng and rice. Moreover, cis-acting elements of PnMYB gene promoters were predicted which indicated that PnMYBs are involved in biotic, abiotic stress, and hormone induction. The expressions of PnMYB transcription factors in its roots, flowers, and leaves were detected by qRT-PCR and they had tissue-specific expressions and related to the growth of different tissues. Under nitrogen stress, MYB transcription factors had great feedback. Ten R2R3-MYB subfamily genes were significantly induced and indicated the possible function of protecting P. notoginseng from excess nitrogen. With further knowledge on identification of PnMYB gene related to tissue selectivity and abiotic stresses, this study laid the foundation for the functional development of PnMYB gene family and improved the cultivation of P. notoginseng.

Co-expression of stress-responsive regulatory genes, MuNAC4, MuWRKY3 and MuMYB96 associated with resistant-traits improves drought adaptation in transgenic groundnut (Arachis hypogaea l.) plants

Groundnut, cultivated under rain-fed conditions is prone to yield losses due to intermittent drought stress. Drought tolerance is a complex phenomenon and multiple gene expression required to maintain the cellular tolerance. Transcription factors (TFs) regulate many functional genes involved in tolerance mechanisms. In this study, three stress-responsive regulatory TFs cloned from horse gram, (Macrotyloma uniflorum (Lam) Verdc.), MuMYB96, involved in cuticular wax biosynthesis; MuWRKY3, associated with anti-oxidant defense mechanism and MuNAC4, tangled with lateral root development were simultaneously expressed to enhance drought stress resistance in groundnut (Arachis hypogaea L.). The multigene transgenic groundnut lines showed reduced ROS production, membrane damage, and increased superoxide dismutase (SOD) and ascorbate peroxidase (APX) enzyme activity, evidencing improved antioxidative defense mechanisms under drought stress. Multigene transgenic plants showed lower proline content, increased soluble sugars, epicuticular wax content and higher relative water content suggesting higher maintenance of tissue water status compared to wildype and mock plants. The scanning electron microscopy (SEM) analysis showed a substantial increase in deposition of cuticular waxes and variation in stomatal number in multigene transgenic lines compared to wild type and mock plants. The multigene transgenic plants showed increased growth of lateral roots, chlorophyll content, and stay-green nature in drought stress compared to wild type and mock plants. Expression analysis of transgenes, MuMYB96, MuWRKY3, and MuNAC4 and their downstream target genes, KCS6, KCR1, APX3, CSD1, LBD16 and DBP using qRT-PCR showed a two- to four-fold increase in transcript levels in multigene transgenic groundnut plants over wild type and mock plants under drought stress. Our study demonstrate that introducing multiple genes with simultaneous expression of genes is a viable option to improve stress tolerance and productivity under drought stress.

Structural and functional analysis of stress-inducible genes and their promoters selected from young oil palm (Elaeis guineensis) under salt stress

Background

Soil salinity is a problem in more than 100 countries across all continents. It is one of the abiotic stress that threatens agriculture the most, negatively affecting crops and reducing productivity. Transcriptomics is a technology applied to characterize the transcriptome in a cell, tissue, or organism at a given time via RNA-Seq, also known as full-transcriptome shotgun sequencing. This technology allows the identification of most genes expressed at a particular stage, and different isoforms are separated and transcript expression levels measured. Once determined by this technology, the expression profile of a gene must undergo validation by another, such as quantitative real-time PCR (qRT-PCR). This study aimed to select, annotate, and validate stress-inducible genes—and their promoters—differentially expressed in the leaves of oil palm (Elaeis guineensis) plants under saline stress.

Results

The transcriptome analysis led to the selection of 14 genes that underwent structural and functional annotation, besides having their expression validated using the qRT-PCR technique. When compared, the RNA-Seq and qRT-PCR profiles of those genes resulted in some inconsistencies. The structural and functional annotation analysis of proteins coded by the selected genes showed that some of them are orthologs of genes reported as conferring resistance to salinity in other species. There were those coding for proteins related to the transport of salt into and out of cells, transcriptional regulatory activity, and opening and closing of stomata. The annotation analysis performed on the promoter sequence revealed 22 distinct types of cis-acting elements, and 14 of them are known to be involved in abiotic stress.

Conclusion

This study has helped validate the process of an accurate selection of genes responsive to salt stress with a specific and predefined expression profile and their promoter sequence. Its results also can be used in molecular-genetics-assisted breeding programs. In addition, using the identified genes is a window of opportunity for strategies trying to relieve the damages arising from the salt stress in many glycophyte crops with economic importance.

Optimized Method for the Identification of Candidate Genes and Molecular Maker Development Related to Drought Tolerance in Oil Palm (Elaeis guineensis Jacq.)

Drought is a major constraint in oil palm (Elaeis guineensis Jacq.) production. As oil palm breeding takes a long time, molecular markers of genes related to drought tolerance characteristics were developed for effective selection. Two methods of gene identification associated with drought, differential display reverse transcription polymerase chain reaction (DDRT-PCR) and pyrosequencing platform, were conducted before developing the EST-SSR marker. By DDRT-PCR, fourteen out of twenty-four primer combinations yielded the polymorphism in leaf as 77.66% and root as 96.09%, respectively. BLASTN and BLASTX revealed nucleotides from 8 out of 236 different banding similarities to genes associated with drought stress. Five out of eight genes gave a similarity with our pyrosequencing sequencing database. Furthermore, pyrosequencing analysis of two oil palm libraries, drought-tolerant, and drought sensitive, found 117 proteins associated with drought tolerance. Thirteen out of sixty EST-SSR primers could be distinguished in 119 oil palm parents in our breeding program. All of our found genes revealed an ability to develop as a molecular marker for drought tolerance. However, the function of the validated genes on drought response in oil palm must be evaluated.

A De Novo Transcriptome Analysis Identifies Cold-Responsive Genes in the Seeds of Taxillus chinensis (DC.) Danser

Taxillus chinensis (DC.) Danser, a parasitic plant of the Loranthaceae family, grows by attacking other plants. It has a long history of being used in Chinese medicine to treat multiple chronic diseases. We previously observed that T. chinensis seeds are sensitive to cold. In this study, we performed transcriptome sequencing for T. chinensis seeds treated by cold (0°C) for 0 h, 12 h, 24 h, and 36 h. TRINITY assembled 257,870 transcripts from 223,512 genes. The GC content and N50 were calculated as 42.29% and 1,368, respectively. Then, we identified 42,183 CDSs and 35,268 likely proteins in the assembled transcriptome, which contained 1,622 signal peptides and 6,795 transmembrane domains. Next, we identified 17,217 genes (FPKM > 5) and 2,333 differentially expressed genes (DEGs) in T. chinensis seeds under cold stress. The MAPK pathway, as an early cold response, was significantly enriched by the DEGs in the T. chinensis seeds after 24 h of cold treatment. Known cold-responsive genes encoding abscisic acid-associated, aquaporin, C-repeat binding factor (CBF), cold-regulated protein, heat shock protein, protein kinase, ribosomal protein, transcription factor (TF), zinc finger protein, and ubiquitin were deregulated in the T. chinensis seeds under cold stress. Notably, the upregulation of CBF gene might be the consequences of the downregulation of MYB and GATA TFs. Additionally, we identified that genes encoding CDC20, YLS9, EXORDIUM, and AUX1 and wound-responsive family protein might be related to novel mechanisms of T. chinensis seeds exposed to cold. This study is first to report the differential transcriptional induction in T. chinensis seeds under cold stress. It will improve our understanding of parasitic plants in response to cold and provide a valuable resource for future studies.

Genome-wide identification and expression analysis of bZIP transcription factors in oil palm (Elaeis guineensis Jacq.) under abiotic stress

The bZIP transcription factors are well-known transcription regulators and play a key role in regulating various developmental, biological processes, and stress responses in plants. However, information on bZIP transcription factors is not yet available in oil palm, an important oil yielding crop. The present study identified the 97 bZIP transcription factor family members in oil palm genome via a genome-wide approach. Phylogenetic analysis clustered all EgbZIPs into 12 clusters with Arabidopsis and rice bZIPs. EgbZIP gene structure analysis showed a distinct variation in the intron-exon organization among all EgbZIPs. Conserved motif analysis demonstrated the occurrence of ten additional conserved motifs besides having a common bZIP domain. All the identified 97 EgbZIPs were unevenly distributed on 16 chromosomes and exhibited tandem duplication in oil palm genome. Our results aslo demonstrated that tissue-specific expression patterns of EgbZIPs based on the available transcriptome data of six different tissue of oil palm. Stress-responsive expression analysis showed that 11EgbZIP transcription factors were highly expressed under cold, salinity, drought stress conditions. Taken together, our findings will provide insightful information on bZIP transcription factors as one of the stress-responsive regulators in oil palm.

Identification of drought responsive Elaeis guineensis WRKY transcription factors with sensitivity to other abiotic stresses and hormone treatments

BACKGROUND

The ability of plants to withstand and thrive in an adverse environment is crucial to ensure their survivability and yield performance. The WRKY transcription factors (TFs) have crucial roles in plant growth, development and stress response, particularly drought stress. In oil palm, drought is recognized as one of the major yield limiting factors. However, the roles of WRKY TFs in the drought response of oil palm is unclear.

RESULTS

Herein, we studied the transcriptome of drought treated oil palm leaf and identified 40 differentially expressed genes (DEGs) of WRKY TFs, of which 32 DEGs were upregulated and 8 DEGs were downregulated in response to drought stress in oil palm. They were categorized into Groups I to IV based on the numbers of WRKY domain and the structural difference in the zinc finger domain. Multiple stress- and hormone-responsive cis-regulatory elements were detected in the drought responsive oil palm EgWRKY (Dro-EgWRKY) genes. Fourteen of the 15 selected oil palm WRKY (EgWRKY) genes demonstrated a tissue-specific expression profile except for EgWRKY28 (Group I), which was expressed in all tissues tested. The expression levels of 15 candidate EgWRKYs were upregulated upon salinity and heat treatments, while several genes were also inducible by abscisic acid, methyl jasmonate, salicylic acid and hydrogen peroxide treatments. Members of the Group III WRKY TFs including EgWRKY07, 26, 40, 52, 59, 73 and 81 displayed multiple roles in drought- and salinity-response under the modulation of phytohormones.

CONCLUSIONS

EgWRKY TFs of oil palm are involved in phytohormones and abiotic stress responses including drought, salinity and heat. EgWRKY07, 26, 59 and 81 from Group III maybe important regulators in modulating responses of different abiotic stresses. Further functional analysis is required to understand the underlying mechanism of WRKY TFs in the regulatory network of drought stress.

The auxin response factor (ARF) gene family in Oil palm (Elaeis guineensis Jacq.): Genome-wide identification and their expression profiling under abiotic stresses

Auxin response factors (ARFs) play vital role in controlling growth and developmental processes of plants via regulating the auxin signaling pathways. However, the identification and functional roles of ARFs in oil palm plants remain elusive. Here, we identified a total of 23 ARF (EgARF) genes in oil palm through a genome-wide identification approach. The EgARF gene structure analysis revealed the presence of intron-rich ARF gene family in genome of oil palm. Further analysis demonstrated the uneven distribution of 23EgARFs on 16 chromosomes of oil palm. Phylogenetic analysis clustered all the EgARFs into four groups. Twenty-one EgARFs contained BDD, ARF, and CTD domains, whereas EgARF5 and EgARF7 lacked the CTD domain. The evolution of ARF genes in oil palm genome has been expanded by segmental duplication events. The cis-acting regulatory elements of EgARF gene family were predominantly associated with the stress and hormone responses. Expression profiling data demonstrated the constitutive and tissue-specific expression of EgARF genes in various tissues of oil palm. Real-time PCR analysis of 19 EgARF genes expression levels under cold, drought, and salt stress conditions proved their prominent role under abiotic stress responses. Altogether, our study provides a basis for studying the molecular and functional roles of ARF genes in oil palm.

Problems and Prospects of Improving Abiotic Stress Tolerance and Pathogen Resistance of Oil Palm

Oil palm crops are the most important determinant of the agricultural economy within the segment of oilseed crops. Oil palm growing in their natural habitats are often challenged simultaneously by multiple stress factors, both abiotic and biotic that limit crop productivity and are major constraints to meeting global food demands. The stress-tolerant oil palm crops that mitigate the effects of abiotic stresses on crop productivity are crucially needed to sustain agricultural production. Basal stem rot threatens the development of the industry, and the key to solving the problem is to breed new oil palm varieties resistant to adversity. This has created a need for genetic improvement which involves evaluation of germplasm, pest and disease resistance, earliness and shattering resistance, quality of oil, varieties for different climatic conditions, etc. In recent years, insights into physiology, molecular biology, and genetics have significantly enhanced our understanding of oil palm response towards such stimuli as well as the reason for varietal diversity in tolerance. In this review, we explore the research progress, existing problems, and prospects of oil palm stress resistance-based physiological mechanisms of stress tolerance as well as the genes and metabolic pathways that regulate stress response.

Genome-Wide Identification and Transcriptional Expression Profiles of Transcription Factor WRKY in Common Walnut (Juglans regia L.)

The transcription factor WRKY is widely distributed in the plant kingdom, playing a significant role in plant growth, development and response to stresses. Walnut is an economically important temperate tree species valued for both its edible nuts and high-quality wood, and its response to various stresses is an important factor that determines the quality of its fruit. However, in walnut trees themselves, information about the WRKY gene family remains scarce. In this paper, we perform a comprehensive study of the WRKY gene family in walnut. In total, we identified 103 WRKY genes in the common walnut that are clustered into 4 groups and distributed on 14 chromosomes. The conserved domains all contained a WRKY domain, and motif 2 was observed in most WRKYs, suggesting a high degree of conservation and similar functions within each subfamily. However, gene structure was significantly differentiated between different subfamilies. Synteny analysis indicates that there were 56 gene pairs in J. regia and A. thaliana, 76 in J. regia and J. mandshurica, 75 in J. regia and J. microcarpa, 76 in J. regia and P. trichocarpa, and 33 in J. regia and Q. robur, indicating that the WRKY gene family may come from a common ancestor. GO and KEGG enrichment analysis showed that the WRKY gene family was involved in resistance traits and the plant-pathogen interaction pathway. In anthracnose-resistant F26 fruits (AR) and anthracnose-susceptible F423 fruits (AS), transcriptome and qPCR analysis results showed that JrWRKY83, JrWRKY73 and JrWRKY74 were expressed significantly more highly in resistant cultivars, indicating that these three genes may be important contributors to stress resistance in walnut trees. Furthermore, we investigate how these three genes potentially target miRNAs and interact with proteins. JrWRKY73 was target by the miR156 family, including 12 miRNAs; this miRNA family targets WRKY genes to enhance plant defense. JrWRKY73 also interacted with the resistance gene AtMPK6, showing that it may play a crucial role in walnut defense.

Genome-wide analysis and characterization of R2R3-MYB family in pigeon pea (Cajanus cajan) and their functional identification in phenylpropanoids biosynthesis

Thirty CcMYB were identified to involve in flavonoid and lignin biosynthesis in pigeon pea genome. A comprehensive analysis of gene structure, phylogenetic relationships, distribution on chromosomes, gene duplication, and expression patterns was performed. MYB transcription factor is one of the largest gene families in plants and plays critical roles in plant growth and development, as well as resistance to biotic and abiotic stress. However, the function of MYB genes in pigeon pea (Cajanus cajan) remains largely unknown. Here, 30 R2R3-MYB which involved flavonoid and lignin biosynthesis were identified in the pigeon pea genome and were classified into five groups based on phylogenetic analysis. Simultaneously, another 122 key enzyme genes from biosynthetic pathways of flavonoid and lignin were identified and all of them were mapped on 11 chromosomes with the co-linearity relationship. Among these genes, the intron/exon organization and motif compositions were conserved and they have undergone a strong purifying selection and tandem duplications during evolution. Expression profile analysis demonstrated most of these genes were expressed in different tissues and responded significantly to MeJA, RNA-seq analysis revealed clear details of genes varied with time of induction. Ten key genes from the phenylpropanoid pathway were selected to further verify whether they responded to induction under different abiotic stress conditions (UV-B, cold, heat, salt, drought, and GA₃). This study elaborates on potential regulatory relationships between R2R3-MYB genes and some key genes involved in flavonoid and lignin biosynthesis under MeJA treatment, as well as adding to the understanding of improving abiotic stress tolerance and regulating the secondary metabolism in woody crops. A simplified discussion model for the different regulation networks involved with flavonoid and lignin biosynthesis in pigeon pea is proposed.

Genome-Wide Identification and Characterization of AP2/ERF Transcription Factor Family Genes in Oil Palm under Abiotic Stress Conditions

The AP2/ERF transcription factor family members play crucial roles in controlling plant growth and development, as well as responses to various abiotic stresses. Genome-wide identification and characterization of AP2/ERF genes has not yet been carried out in the oil palm genome. In the present work, we reported the occurrence of 172 EgAP2/ERFs (AP2, ERF, RAV & Soloist members) through genome-wide identification. Phylogenetic analysis was used to divide them into four groups, including: 34 AP2, 131 ERF, 5 RAV, and 2 Soloist gene family members. All 172 AP2/ERF members were unevenly distributed across 16 chromosomes of oil palm. Gene duplication analysis elucidated the tandem duplication of AP2/ERFs on chromosome blocks of the oil palm genome during evolution. Gene structure as well as conserved motif analysis demonstrated the conserved nature of intron/exon organization and motifs among the AP2/ERF genes. Several cis-regulatory elements—related to hormone, stress, and defense responses—were identified in the promoter regions of AP2/ERFs. Tissue-specific expression of 172 AP2/ERFs in five different tissues of oil palm was also revealed by heatmap analysis using the available transcriptome data. Finally, abiotic stress (salinity, cold & drought)-responsive AP2/ERFs in the oil palm genome were validated through qPCR analysis. Our study provided valuable information on oil palm AP2/ERF superfamily members and dissected their role in abiotic stress conditions.

Genome-Wide Analysis of Dof Genes and Their Response to Abiotic Stress in Rose (Rosa chinensis)

Dof (DNA binding with one finger) proteins play important roles in plant development and defense regulatory networks. In the present study, we report a genome-wide analysis of rose Dof genes (RchDof), including phylogenetic inferences, gene structures, chromosomal locations, gene duplications, and expression diversity. A total of 24 full-length RchDof genes were identified in Rosa chinensis, which were assigned to nine distinct subgroups. These RchDof genes were unevenly distributed on rose chromosomes. The genome-scale analysis of synteny indicated that segmental duplication events may have played a major role in the evolution of the RchDof gene family. Analysis of cis-acting elements revealed putative functions of Dofs in rose during development as well as under numerous biotic and abiotic stress conditions. Moreover, the expression profiles derived from qRT-PCR experiments demonstrated distinct expression patterns in various tissues, and gene expression divergence existed among the duplicated RchDof genes, suggesting a fundamentally functional divergence of the duplicated Dof paralogs in rose. The gene expression analysis of RchDofs under drought and salt stress conditions was also performed. The present study offered novel insights into the evolution of RchDofs and can aid in the further functional characterization of its candidate genes.

Phenomics, genomics of oil palm (Elaeis guineensis Jacq.): way forward for making sustainable and high yielding quality oil palm

Oil palm (Elaeis guineensis Jacq.) is a heterogeneous, perennial crop having long breeding cycle with a genome size of 1.8 Gb. The demand for vegetable oil is steadily increasing, and expected that nearly 240-250 million tons of vegetable oil may be required by 2050. Genomics and next generation technologies plays crucial role in achieving the sustainable availability of oil palm with good yield and high quality. A successful breeding programme in oil palm depends on the availability of diverse gene pool, ex-situ conservation and their proper utilization for generating elite planting material. The major breeding methods adopted in oil palm are either modified recurrent selection or the modified reciprocal recurrent selection method. The QTLs of yield and related traits are chiefly located on chromosome 4, 10, 12 and 15 which is discussed in the current review. The probable chromosomal regions influencing the less height increment is observed to be on chromosomes 4, 10, 14 and 15. Advanced genomic approaches together with bioinformatics tools were discussed thoroughly for achieving sustainable oil palm where more efforts are needed. Major emphasis is given on oil palm crop improvement using holistic approaches of various genomic tools. Also a road map given on the milestones in the genomics and way forward for making oil palm to high yielding quality oil palm.

Isolation and characterization of PoWRKY, an abiotic stress-related WRKY transcription factor from Polygonatum odoratum

WRKY transcription factors play vital roles in response to biotic and abiotic stresses in plants. As a kind of high value medicinal plant, Polygonatum odoratum has an ability to tolerate various abiotic stresses because of the special growth condition. In current study, a novel WRKY gene from P. odoratum is isolated and compared with homologous sequences from other plants. PoWRKY1 possesses two typical WRKY domains and two C₂H₂ zinc-finger motifs. Evolutionary analysis indicated that PoWRKY1 is most closely related to WRKY protein from Asparagus officinalis. Expression analysis showed that expression of PoWRKY1 is induced by cold and drought stresses but not salt stress. Overexpression of PoWRKY1 in Arabidopsis improved seed germination and root growth of transgenic plants during cold stress and drought. In addition, super oxide dismutase activity and proline content in transgenic plants increased under cold and drought stresses, whereas malondialdehyde levels and relative electrolyte leakage reduced under similar stress conditions. Taken together, these results showed that PoWRKY1 enhances the tolerance to cold and drought stresses. This study lays a potential foundation to understand the molecular mechanism of tolerance to abiotic stress in P. odoratum.

CRISPR/Cas mediated base editing: a practical approach for genome editing in oil palm

The improvement of the yield and quality of oil palm via precise genome editing has been indispensable goal for oil palm breeders. Genome editing via the CRISPR/Cas9 (CRISPR-associated protein 9) system, ZFN (zinc finger nucleases) and TALEN (transcription activator-like effector nucleases) has flourished as an efficient technology for precise target modifications in the genomes of various crops. Among the genome editing technologies, base editing approach has emerged as novel technology that could generate single base changes i.e. irreversible conversion of one target base in to other in a programmable manner. A base editor (adenine or cytosine) is a fusion of catalytically inactive CRISPR-Cas9 domain (Cas9 variants) and cytosine or adenosine deaminase domain that introduces desired point mutations. However, till date no such genetic modifications have ever been developed in oil palm via base editing technology. Precise genome editing via base editing approach can be a challenging task in oil palm due to its complex genome as well as difficulties in tissue culture and genetic transformation methods. However, availability of whole genome sequencing data in oil palm provides a platform for developing the base editing technology. Here, we briefly review the potential application and future implications of base editing technology for the genetic improvement of oil palm.

Seed Germination in Oil Palm (Elaeis guineensis Jacq.): A Review of Metabolic Pathways and Control Mechanisms

Oil palm is an oil-producing crop of major importance at the global scale. Oil palm mesocarp lipids are used for myriads industrial applications, and market demand has been growing for decades. In addition, oil palm seeds are oleaginous, and the oil extracted therefrom can be used for several purposes, from food to cosmetics. As such, there is a huge need in oil palm seeds to maintain the global cohort of more than 2 billion trees. However, oil palm seed germination is a rather difficult process, not only to break dormancy, but also because it is long and often reaches lower-than-expected germination rates. Surprisingly, despite the crucial importance of germination for oil palm plantation management, our knowledge is still rather limited, in particular about germinating oil palm seed metabolism. The present review incorporates different pieces of information that have been obtained in the past few years, in oil palm and in other palm species, in order to provide an overview of germination metabolism and its control. Further insights can also be gained from other oleaginous model plants, such as Arabidopsis or canola, however, palm seeds have peculiarities that must be accounted for, to gain a better understanding of germinating seed metabolism.

Phylogenetic and Transcription Analysis of Hibiscus hamabo Sieb. et Zucc. WRKY Transcription Factors

WRKY transcription factors are known to play important roles in the regulation of various aspects of plant growth and development, including germination, stress resistance, and senescence. Nevertheless, there is little information about the WRKY genes in Hibiscus hamabo Sieb. et Zucc., an important semimangrove plant. In this study, HhWRKY genes in H. hamabo were identificated based on Illumina RNA-sequencing and isoform sequencing from salt-treated roots. Then phylogenetic analysis and conserved motif analysis of the WRKY family in H. hamabo and Arabidopsis thaliana were used to classify WRKY genes. Sixteen HhWRKY genes were selected from different groups to detect their expression patterns using real-time quantitative PCR in different organ (root, old leaf, tender leaf, receptacle, petal, or stamen) from 10-year-old H. hamabo plants grown in their natural environment and in seedlings with 8 to 10 true leaves challenged by phytohormone (salicylic acid, methyl jasmonate, or abscisic acid) and abiotic stress (drought, salt, or high temperature). As a result, the identified 78 HhWRKY genes were divided into two major groups and several subgroups based on their structural and phylogenetic features. Most transcripts of the selected 16 HhWRKY genes were more abundant in old than in tender leaves of H. hamabo. HhWRKY genes were regulated in reaction to abiotic stresses and phytohormone treatments and may participate in signaling networks to improve plant stress resistance. Some of HhWRKY genes behaved as would be predicted based on their homology with A. thaliana WRKY genes, but others showed divergent behavior. This systematic analysis lays the foundation for further identification of WRKY gene functions, with the aim of improving woody plants.

Transgenic Breeding Approaches for Improving Abiotic Stress Tolerance: Recent Progress and Future Perspectives

The recent rapid climate changes and increasing global population have led to an increased incidence of abiotic stress and decreased crop productivity. Environmental stresses, such as temperature, drought, nutrient deficiency, salinity, and heavy metal stresses, are major challenges for agriculture, and they lead to a significant reduction in crop growth and productivity. Abiotic stress is a very complex phenomenon, involving a variety of physiological and biochemical changes in plant cells. Plants exposed to abiotic stress exhibit enhanced levels of ROS (reactive oxygen species), which are highly reactive and toxic and affect the biosynthesis of chlorophyll, photosynthetic capacity, and carbohydrate, protein, lipid, and antioxidant enzyme activities. Transgenic breeding offers a suitable alternative to conventional breeding to achieve plant genetic improvements. Over the last two decades, genetic engineering/transgenic breeding techniques demonstrated remarkable developments in manipulations of the genes for the induction of desired characteristics into transgenic plants. Transgenic approaches provide us with access to identify the candidate genes, miRNAs, and transcription factors (TFs) that are involved in specific plant processes, thus enabling an integrated knowledge of the molecular and physiological mechanisms influencing the plant tolerance and productivity. The accuracy and precision of this phenomenon assures great success in the future of plant improvements. Hence, transgenic breeding has proven to be a promising tool for abiotic stress improvement in crops. This review focuses on the potential and successful applications, recent progress, and future perspectives of transgenic breeding for improving abiotic stress tolerance and productivity in plants.

Correlation analysis of cold-related gene expression with physiological and biochemical indicators under cold stress in oil palm

Oil palm (Elaeis guineensis Jacq.) is a representative tropical oil crop that is sensitive to low temperature. Oil palm can experience cold damage when exposed to low temperatures for a long period. During these unfavorable conditions, a series of gene induction/repression and physico-chemical changes occur in oil palm. To better understand the link between these events, we investigated the expression levels of various genes (including COR410, COR413, CBF1, CBF2, CBF3, ICE1-1, ICE1-2, ICE1-4, SIZ1-1, SIZ1-2, ZAT10, ZAT12) and the accumulation of osmolytes (proline, malondialdehyde and sucrose). Likewise, the activity of superoxide dismutase (SOD) in oil palm under cold stress (4°C, 8°C and 12°C) was examined. The results showed a clear link among the expression of CBFs (especially CBF1 and CBF3) and the all genes examined under cold stress (12°C). The expression of CBF1 and CBF2 also exhibited a positive link with the accumulation of sucrose and proline under cold stress in oil palm. At 4°C, the proline content exhibited a very significant correlation with electrolyte leakage in oil palm. The results of this study provide necessary information regarding the mechanism of the response and adaption of oil palm to cold stress. Additionally, they offer clues for the selection or development of cold-tolerant cultivars from the available germplasms of oil palm.

Progress in Tissue Culture and Genetic Transformation of Oil Palm: An Overview

Oil palm (Elaeis guineensis, Jacq.) is a prominent vegetable-oil-yielding crop. Cultivating high-yielding oil palm with improved traits is a pre-requisite to meet the increasing demands of palm oil consumption. However, tissue culture and biotechnological approaches can resolve these concerns. Over the past three decades, significant research has been carried out to develop tissue culture and genetic transformation protocols for oil palm. Somatic embryogenesis is an efficient platform for the micropropagation of oil palm on a large scale. In addition, various genetic transformation techniques, including microprojectile bombardment, Agrobacterium tumefaciens mediated, Polyethylene glycol mediated mediated, and DNA microinjection, have been developed by optimizing various parameters for the efficient genetic transformation of oil palm. This review mainly emphasizes the methods established for in vitro propagation and genetic transformation of oil palm. Finally, we propose the application of the genome editing tool CRISPR/Cas9 to improve the various traits in this oil yielding crop.

Genome-Wide Identification of WRKY Transcription Factors in the Asteranae

The WRKY transcription factors family, which participates in many physiological processes in plants, constitutes one of the largest transcription factor families. The Asterales and the Apiales are two orders of flowering plants in the superorder Asteranae. Among the members of the Asterales, globe artichoke (Cynara cardunculus var. scolymus L.), sunflower (Helianthus annuus L.), and lettuce (Lactuca sativa L.) are important economic crops worldwide. Within the Apiales, ginseng (Panax ginseng C. A. Meyer) and Panax notoginseng (Burk.) F.H. Chen are important medicinal plants, while carrot (Daucus carota subsp. carota L.) has significant economic value. Research involving genome-wide identification of WRKY transcription factors in the Asterales and the Apiales has been limited. In this study, 490 WRKY genes, 244 from three species of the Apiales and 246 from three species of the Asterales, were identified and categorized into three groups. Within each group, WRKY motif characteristics and gene structures were similar. WRKY gene promoter sequences contained light responsive elements, core regulatory elements, and 12 abiotic stress cis-acting elements. WRKY genes were evenly distributed on each chromosome. Evidence of segmental and tandem duplication events was found in all six species in the Asterales and the Apiales, with segmental duplication inferred to play a major role in WRKY gene evolution. Among the six species, we uncovered 54 syntenic gene pairs between globe artichoke and lettuce. The six species are thus relatively closely related, consistent with their traditional taxonomic placement in the Asterales. This study, based on traditional species classifications, was the first to identify WRKY transcription factors in six species from the Asteranae. Our results lay a foundation for further understanding of the role of WRKY transcription factors in species evolution and functional differentiation.

Transcriptome analysis of Polygonatum cyrtonema Hua: identification of genes involved in polysaccharide biosynthesis

BACKGROUND

Polygonatum cyrtonema Hua (P. cyrtonema) is one of the most important herbs in traditional Chinese medicine. Polysaccharides in P. cyrtonema plants comprise a class of important secondary metabolites and exhibit a broad range of pharmacological functions.

RESULTS

In order to identify genes involved in polysaccharide biosynthesis, we performed RNA sequencing analysis of leaf, root, and rhizome tissues of P. cyrtonema. A total of 164,573 unigenes were obtained by assembling transcripts from all three tissues and 86,063 of these were annotated in public databases. Differentially expressed genes (DEGs) were determined based on expression profile analysis, and DEG levels in rhizome tissues were then compared with their counterparts in leaf and root tissues. This analysis revealed numerous genes that were either up-regulated or uniquely expressed in the rhizome. Multiple genes encoding important enzymes, such as UDP glycosyltransferases (UGTs), or transcription factors involved in polysaccharide biosynthesis were identified and further analyzed, while a few genes encoding key enzymes were experimentally validated using quantitative real-time PCR.

CONCLUSION

Our results substantially expand the public transcriptome dataset of P. cyrtonema and provide valuable clues for the identification of candidate genes involved in metabolic pathways.

Genome-Wide Analysis of WRKY Genes and Their Response to Hormone and Mechanic Stresses in Carrot

The WRKY gene family plays a vital role in plant development and environment response. Although previous studies suggested that the WRKY genes in carrot (Kuroda type) involved in biotic and abiotic stress responses, the information of WRKY genes in the latest version of the carrot genome (Daucus carota v2.0, Nantes type carrot) and their response to hormone and injury stresses have not been reported. In this study, we performed a genome-wide analysis of WRKYs using a chromosome-scale genome assembly of carrot (Daucus carota subsp. sativus L.). We identified a total of 67 WRKY genes, which were further classified into the three groups. These WRKY genes are unevenly distributed on carrot chromosomes. We found that more than half of them were derived from whole-genome duplication (WGD) events, suggesting that WGDs have played a major role during the evolution of the WRKY gene family. We experimentally ascertained the expression divergence existed between WGD-derived WRKY duplicated gene pairs, which is indicative of functional differentiation between duplicated genes. Our analysis of cis-acting elements indicated that WRKY genes were transcriptionally regulated upon hormone and mechanic injury stresses. Gene expression analyses by qRT-PCR further presented that WRKY genes were involved in hormone and mechanic injury stresses.

GmWRKY16 Enhances Drought and Salt Tolerance Through an ABA-Mediated Pathway in Arabidopsis thaliana

The WRKY transcription factors (TFs) are one of the largest families of TFs in plants and play multiple roles in plant development and stress response. In the present study, GmWRKY16 encoding a WRKY transcription factor in soybean was functionally characterized in Arabidopsis. GmWRKY16 is a nuclear protein that contains a highly conserved WRKY domain and a C2H2 zinc-finger structure, and has the characteristics of transcriptional activation ability, presenting a constitutive expression pattern with relative expression levels of over fourfold in the old leaves, flowers, seeds and roots of soybean. The results of quantitative real time polymerase chain reaction (qRT-PCR) showed that GmWRKY16 could be induced by salt, alkali, ABA, drought and PEG-6000. As compared with the control, overexpression of GmWRKY16 in Arabidopsis increased the seed germination rate and root growth of seedlings in transgenic lines under higher concentrations of mannitol, NaCl and ABA. In the meantime, GmWRKY16 transgenic lines showed over 75% survival rate after rehydration and enhanced Arabidopsis tolerance to salt and drought with higher proline and lower MDA accumulation, less water loss of the detached leaves, and accumulated more endogenous ABA than the control under stress conditions. Further studies showed that AtWRKY8, KIN1, and RD29A were induced in GmWRKY16 transgenic plants under NaCl treatment. The expressions of the ABA biosynthesis gene (NCED3), signaling genes (ABI1, ABI2, ABI4, and ABI5), responsive genes (RD29A, COR15A, COR15B, and RD22) and stress-related marker genes (KIN1, LEA14, LEA76, and CER3) were regulated in transgenic lines under drought stress. In summary, these results suggest that GmWRKY16 as a WRKY TF may promote tolerance to drought and salt stresses through an ABA-mediated pathway.

Genome-wide identification and expression analyses of WRKY transcription factor family members from chickpea (Cicer arietinum L.) reveal their role in abiotic stress-responses

BACKGROUND

WRKY proteins play a vital role in the regulation of several imperative plant metabolic processes and pathways, especially under biotic and abiotic stresses. Although WRKY genes have been characterized in various major crop plants, their identification and characterization in pulse legumes is still in its infancy. Chickpea (Cicer arietinum L.) is the most important pulse legume grown in arid and semi-arid tropics.

OBJECTIVE

In silico identification and characterization of WRKY transcription factor-encoding genes in chickpea genome.

METHODS

For this purpose, a systematic genome-wide analysis was carried out to identify the non-redundant WRKY transcription factors in the chickpea genome.

RESULTS

We have computationally identified 70 WRKY-encoding non-redundant genes which were randomly distributed on all the chickpea chromosomes except chromosome 8. The evolutionary phylogenetic analysis classified the WRKY proteins into three major groups (I, II and III) and seven sub-groups (IN, IC, IIa, IIb, IIc, IId and IIe). The gene structure analysis revealed the presence of 2-7 introns among the family members. Along with the presence of absolutely conserved signatory WRKY domain, 19 different domains were also found to be conserved in a group-specific manner. Insights of gene duplication analysis revealed the predominant role of segmental duplications for the expansion of WRKY genes in chickpea. Purifying selection seems to be operated during the evolution and expansion of paralogous WRKY genes. The transcriptome data-based in silico expression analysis revealed the differential expression of CarWRKY genes in root and shoot tissues under salt, drought, and cold stress conditions. Moreover, some of these genes showed identical expression pattern under these stresses, revealing the possibility of involvement of these genes in conserved abiotic stress-response pathways.

CONCLUSION

This genome-wide computational analysis will serve as a base to accelerate the functional characterization of WRKY TFs especially under biotic and abiotic stresses.

Genome-wide identification of WRKY family genes and their response to abiotic stresses in tea plant (Camellia sinensis)

The WRKY transcription factors (TFs) family is one of the largest TF families in plants and plays a central role in diverse regulation and multiple stress responses. However, the systematical analysis of the WRKY gene family in tea plant (Camellia sinensis) based on genomic data has been lacking. The primary objective of this study was to set a systematic analysis of the WRKY gene family based on genomic data in tea plant and analyze their expression profiles under various abiotic stresses. We searched the tea plant genome using the consensus model of the WRKY domain (PF03106) and then used these search results to identify all the WRKY family members by SMART and the CDD program. Analyze their phylogeny, classification, structure, conserved motifs, Cis-elements, interactors and expression profiles. 56 putative WRKY genes were identified from the tea plant genome and divided into three main groups (I-III) and five subgroups (IIa-IIe) according to the WRKY domains and the zinc-finger structure. The gene structure and conserved motifs of the CsWRKY genes were also characterized and were consistent with the classification results. Annotation analysis showed that 34 CsWRKY genes may be involved in stress responses. Promoter analysis implied that CsWRKY genes, except for CsWRKY55, possessed at least one abiotic stress response cis-element. Expression profiles of CsWRKY genes in different tissues were analyzed with RNA-seq data. The results showed that 56 CsWRKY genes had differential expression in their transcript abundance. The expression profiles also showed that many identified CsWRKY genes were possibly involved in the response to cold, drought, salt, or ABA treatment. Tea plant genome contains at least 56 WRKY genes. These results provide useful information for further exploring the function and regulatory mechanism of CsWRKY genes in the growth, development, and adaption to abiotic stresses in tea plant.

Application of CRISPR/Cas9 Genome Editing Technology for the Improvement of Crops Cultivated in Tropical Climates: Recent Progress, Prospects, and Challenges

The world population is expected to increase from 7.3 to 9.7 billion by 2050. Pest outbreak and increased abiotic stresses due to climate change pose a high risk to tropical crop production. Although conventional breeding techniques have significantly increased crop production and yield, new approaches are required to further improve crop production in order to meet the global growing demand for food. The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 (CRISPR-associated protein9) genome editing technology has shown great promise for quickly addressing emerging challenges in agriculture. It can be used to precisely modify genome sequence of any organism including plants to achieve the desired trait. Compared to other genome editing tools such as zinc finger nucleases (ZFNs) and transcriptional activator-like effector nucleases (TALENs), CRISPR/Cas9 is faster, cheaper, precise and highly efficient in editing genomes even at the multiplex level. Application of CRISPR/Cas9 technology in editing the plant genome is emerging rapidly. The CRISPR/Cas9 is becoming a user-friendly tool for development of non-transgenic genome edited crop plants to counteract harmful effects from climate change and ensure future food security of increasing population in tropical countries. This review updates current knowledge and potentials of CRISPR/Cas9 for improvement of crops cultivated in tropical climates to gain resiliency against emerging pests and abiotic stresses.