Functions and application of the AP2/ERF transcription factor family in crop improvement

Genome-wide analysis of the DREB family genes and functional identification of the involvement of BrDREB2B in abiotic stress in wucai (Brassica campestris L.)

Dehydration responsive element binding protein (DREB) is a significant transcription factor class known to be implicated in abiotic stresses. In this study, we systematically conducted a genome-wide identification and expression analysis of the DREB gene family, including gene structures, evolutionary relationships, chromosome distribution, conserved domains, and expression patterns. A total of 65 DREB family gene members were identified in Chinese cabbage (Brassica rapa L.) and were classified into five subgroups based on phylogenetic analysis. Through analysis of the conserved domains of BrDREB family genes, only one exon existed in the gene structure. Through the analysis of cis-acting elements, these genes were mainly involved in hormone regulation and adversity stress. In order to identify the function of BrDREB2B, overexpressed transgenic Arabidopsis was constructed. After different stress treatments, the germination rate, root growth, survival rate, and various plant physiological indicators were measured. The results showed that transgenic Arabidopsis thaliana plants overexpressing BrDREB2B exhibited enhanced tolerance to salt, heat and drought stresses. Taken together, our results are the first to report the BrDREB2B gene response to drought and heat stresses in Chinese cabbage and provide a basis for further studies to determine the function of BrDREBs in response to abiotic stresses.

Overexpression of MxbHLH18 Increased Iron and High Salinity Stress Tolerance in Arabidopsis thaliana

In the life cycle of apple, it will suffer a variety of abiotic stresses, such as iron stress and salt stress. bHLH transcription factors (TFs) play an indispensable role in the response of plants to stress. In this study, a new bHLH gene named MxbHLH18 was separated from Malus xiaojinensis. According to the results of subcellular localization, MxbHLH18 was localized in the nucleus. Salt stress and iron stress affected the expression of MxbHLH18 in Malus xiaojinensis seedlings to a large extent. Due to the introduction of MxbHLH18, the resistance of Arabidopsis thaliana to salt, high iron and low iron was significantly enhanced. Under the environmental conditions of high iron and low iron, the overexpression of MxbHLH18 increased many physiological indexes of transgenic Arabidopsis compared to wild type (WT), such as root length, fresh weight and iron content. The high level expression of MxbHLH18 in transformed Arabidopsis thaliana can not only increased the content of chlorophyll and proline, as well as increasing the activities of superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT); it also reduced the content of malondialdehyde (MDA), which was more obvious under high salt conditions. In addition, the relative conductivity, H₂O₂ content and O²⁻ content in transgenic Arabidopsis decreased under salt stress. Meanwhile, MxbHLH18 can also regulate the expression of downstream genes associated with salt stress (AtCBF1/2/3, AtKIN1 and AtCOR15a/b) and iron stress (AtIRT1, AtFRO2, AtNAS2, ATACT2, AtZIF1 and AtOPT3). Therefore, MxbHLH18 can actively promote the adaptability of plants to the growth environment of salt and low and/or iron.

The Transcription Factor MdERF78 Is Involved in ALA-Induced Anthocyanin Accumulation in Apples

As a friendly plant growth regulator to the environment, 5-aminolevulinic acid (ALA) has been widely used in plant production, such as fruit coloration, stress resistance, and so on. Previous studies have identified some genes that have a function in the anthocyanin accumulation induced by ALA. However, the regulatory mechanism has not been well revealed. In the current study, we proposed that an ALA-responsive transcription factor, MdERF78, regulated anthocyanin accumulation. MdERF78, overexpressed in apple peels or calli, resulted in a significant increase of anthocyanins, while MdERF78 interference had an opposite trend. Furthermore, the anthocyanin accumulation induced by MdERF78 overexpression was enhanced by exogenous ALA treatment, suggesting that MdERF78 was involved in the ALA-induced anthocyanin accumulation. Yeast one-hybrid and dual luciferase reporter assays revealed that MdERF78 bound to the promoters of MdF3H and MdANS directly and activated their expressions. Additionally, MdERF78 interacted with MdMYB1 and enhanced the transcriptional activity of MdMYB1 to its target gene promoters. Based on these, it can be concluded that MdERF78 has a positive function in ALA-induced anthocyanin accumulation via the MdERF78-MdF3Hpro/MdANSpro and MdERF78-MdMYB1-MdDFRpro/MdUFGTpro/MdGSTF12pro regulatory network. These findings provide new insights into the regulatory mechanism of ALA-promoted anthocyanin accumulation.

Plant DNA Methylation Responds to Nutrient Stress

Nutrient stress as abiotic stress has become one of the important factors restricting crop yield and quality. DNA methylation is an essential epigenetic modification that can effectively regulate genome stability. Exploring DNA methylation responses to nutrient stress could lay the foundation for improving plant tolerance to nutrient stress. This article summarizes the plant DNA methylation patterns, the effects of nutrient stress, such as nitrogen, phosphorus, iron, zinc and sulfur stress, on plant DNA methylation and research techniques for plant DNA methylation, etc. Our discussion provides insight for further research on epigenetics response to nutrient stress in the future.

Transcriptome and metabolome profiling in different stages of infestation of Eucalyptus urophylla clones by Ralstonia solanacearum

Eucalyptus urophylla is an economically important tree species that widely planted in tropical and sub-tropical areas around the world, which suffers significant losses due to Ralstonia solanacearum. However, little is known about the molecular mechanism of pathogen-response of Eucalyptus. We collected the vascular tissues of a E. urophylla clone infected by R. solanacearum in the laboratory, and combined transcriptome and metabolome analysis to investigate the defense responses of Eucalyptus. A total of 11 flavonoids that differentially accumulated at the first stage or a later stage after infection. The phenylpropanoid of p-coumaraldehyde, the two alkaloids trigonelline and DL-ephedrine, two types of traditional Chinese medicine with patchouli alcohol and 3-dihydrocadambine, and the amino acid phenylalanine were differentially accumulated after infection, which could be biomarkers indicating a response to R. solanacearum. Differentially expressed genes involved in plant hormone signal transduction, phenylpropanoids, flavonoids, mitogen-activated protein kinase (MAPK) signaling, and amino acid metabolism were activated at the first stage of infection or a later stage, indicating that they may participate in the defense against infection. This study is expected to deliver several insights into the molecular mechanism in response to pathogens in E. urophylla, and the findings have far-reaching implications in the control of E. urophylla pathogens.

Morphological Characterization and Integrated Transcriptome and Proteome Analysis of Organ Development Defective 1 (odd1) Mutant in Cucumis sativus L

Cucumber (Cucumis sativus L.) is an economically important vegetable crop with the unique growth habit and typical trailing shoot architecture of Cucurbitaceae. Elucidating the regulatory mechanisms of growth and development is significant for improving quality and productivity in cucumber. Here we isolated a spontaneous cucumber mutant organ development defective 1 (odd1) with multiple morphological changes including root, plant stature, stem, leaf, male and female flowers, as well as fruit. Anatomical and cytological analyses demonstrated that both cell size and number decreased, and the shoot apical meristem (SAM) was smaller in odd1 compared with WT. Pollen vigor and germination assays and cross tests revealed that odd1 is female sterile, which may be caused by the absence of ovules. Genetic analysis showed that odd1 is a recessive single gene mutant. Using the MutMap strategy, the odd1 gene was found to be located on chromosome 5. Integrated profiling of transcriptome and proteome indicated that the different expression genes related to hormones and SAM maintenance might be the reason for the phenotypic changes of odd1. These results expanded the insight into the molecular regulation of organ growth and development and provided a comprehensive reference map for further studies in cucumber.

Comprehensive Profiling of Tubby-Like Proteins in Soybean and Roles of the GmTLP8 Gene in Abiotic Stress Responses

Tubby-like proteins (TLPs) are transcription factors that are widely present in eukaryotes and generally participate in growth and developmental processes. Using genome databases, a total of 22 putative TLP genes were identified in the soybean genome, and unevenly distributed across 13 chromosomes. Phylogenetic analysis demonstrated that the predicted GmTLP proteins were divided into five groups (I-V). Gene structure, protein motifs, and conserved domains were analyzed to identify differences and common features among the GmTLPs. A three-dimensional protein model was built to show the typical structure of TLPs. Analysis of publicly available gene expression data showed that GmTLP genes were differentially expressed in response to abiotic stresses. Based on those data, GmTLP8 was selected to further explore the role of TLPs in soybean drought and salt stress responses. GmTLP8 overexpressors had improved tolerance to drought and salt stresses, whereas the opposite was true of GmTLP8-RNAi lines. 3,3-diaminobenzidine and nitro blue tetrazolium staining and physiological indexes also showed that overexpression of GmTLP8 enhanced the tolerance of soybean to drought and salt stresses; in addition, downstream stress-responsive genes were upregulated in response to drought and salt stresses. This study provides new insights into the function of GmTLPs in response to abiotic stresses.

Negligible Impact of Drought-Resistant Genetically Modified Maize on Arthropod Community Structure Observed in a 2-Year Field Investigation

Dehydration-responsive element-binding (DREB) transcription factors regulate diverse processes during plant development. Here, a 2-year field study was conducted to assess the potential effects of DREB-genetically modified maize (GM1) on arthropod species and ecological communities. Arthropod abundance, diversity, and community composition in GM1 and its non-transformed counterpart maize variety, Chang 7-2, were compared using whole plant inspection, pitfall trap, and suction sampler methods. Based on Shannon–Wiener diversity, Simpson’s diversity, Pielou’s indexes, number of species, and total number of individuals, GM1 had a negligible effect on arthropod abundance and diversity. Redundancy analysis indicated that the composition of arthropod community was not associated with maize type in the three investigation methods, while it exhibited significant correlation with year and sampling time in whole plant inspection and suction sample methods, and distinctly correlated with sampling time in the pitfall trap method. Nonmetric multidimensional scaling analysis of variable factors in the three investigation methods showed that sampling time, rather than maize type or year, was closely related to the composition of arthropod community in the field. Our results provide direct evidence to support that DREB-GM maize had negligible effects on arthropods in the Jilin Province under natural conditions.

The DREB A-5 Transcription Factor ScDREB5 From Syntrichia caninervis Enhanced Salt Tolerance by Regulating Jasmonic Acid Biosynthesis in Transgenic Arabidopsis

Salinity is a major limiting factor in crop productivity. Dehydration-responsive element-binding protein (DREB) transcription factors have been widely identified in a variety of plants and play important roles in plant stress responses. Studies on DREBs have primarily focused on the A-1 and A-2 DREB groups, while few have focused on the A-5 group. In this study, we concentrated on ScDREB5, an A-5b type DREB gene from the desiccation-tolerant moss Syntrichia caninervis. ScDREB5 is a transcription factor localized to the nucleus that exhibits transactivation activity in yeast. Ectopic ScDREB5 expression in Arabidopsis thaliana increased seed germination and improved seedling tolerance under salt stress. ScDREB5-overexpression transgenic Arabidopsis lines showed lower methane dicarboxylic aldehyde (MDA) and hydrogen peroxide (H₂O₂) contents, but higher peroxidase (POD), superoxide dismutase (SOD), and catalase (CAT) activities compared to wild plants. Moreover, the transcriptional levels of stress marker genes, including RD29B, COR47, LEA6, LEA7, ERD1, P5CS1, and salt overly sensitive (SOS) genes (SOS1, SOS2, and SOS3), were upregulated in the transgenic lines when subjected to salt treatment. Transcriptome and real-time quantitative PCR (RT-qPCR) analyses indicated that transgenic lines were accompanied by an increased expression of jasmonic acid (JA) biosynthesis genes, as well as a higher JA content under salt stress. Our results suggest that ScDREB5 could improve salt tolerance by enhancing the scavenging abilities of reactive oxygen species (ROS), increasing JA content by upregulating JA synthesis gene expression, regulating ion homeostasis by up-regulating stress-related genes, osmotic adjustment, and protein protection, making ScDREB5 a promising candidate gene for crop salt stress breeding.

Genome-wide characterization and expression analysis of Erf gene family in cotton

BACKGROUND

AP2/ERF transcription factors are important in a variety of biological activities, including plant growth, development, and responses to biotic and abiotic stressors. However, little study has been done on cotton's AP2/ERF genes, although cotton is an essential fibre crop. We were able to examine the tissue and expression patterns of AP2/ERF genes in cotton on a genome-wide basis because of the recently published whole genome sequence of cotton. Genome-wide analysis of ERF gene family within two diploid species (G. arboreum & G. raimondii) and two tetraploid species (G. barbadense, G. hirsutum) was performed.

RESULTS

A total of 118, 120, 213, 220 genes containing the sequence of single AP2 domain were identified in G. arboreum, G. raimondii, G. barbadense and G. hirsutum respectively. The identified genes were unevenly distributed across 13/26 chromosomes of A and D genomes of cotton. Synteny and collinearity analysis revealed that segmental duplications may have played crucial roles in the expansion of the cotton ERF gene family, as well as tandem duplications played a minor role. Cis-acting elements of the promoter sites of Ghi-ERFs genes predict the involvement in multiple hormone responses and abiotic stresses. Transcriptome and qRT-PCR analysis revealed that Ghi-ERF-2D.6, Ghi-ERF-12D.13, Ghi-ERF-6D.1, Ghi-ERF-7A.6 and Ghi-ERF-11D.5 are candidate genes against salinity tolerance in upland cotton.

CONCLUSION

Overwhelmingly, the present study paves the way to better understand the evolution of cotton ERF genes and lays a foundation for future investigation of ERF genes in improving salinity stress tolerance in cotton.

Comparative transcriptome analysis of cold-tolerant and -sensitive asparagus bean under chilling stress and recovery

Background

Low temperature is a type of abiotic stress that threatens the growth and yield of asparagus bean. However, the key genes and regulatory pathways involved in low temperature response in this legume are still poorly understood. Methodology. The present study analyzed the transcriptome of seedlings from two asparagus bean cultivars-Dubai bean and Ningjiang 3-using Illumina RNA sequencing (RNA-seq). Correlations between samples were determined by calculating Pearson correlation coefficients (PCC) and principal component analysis (PCA). Differentially expressed genes (DEGs) between two samples were identified using the DESeq package. Transcription factors (TF) prediction, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of DEGs were also performed.

Results

Phenotypes and physiological indices indicated that Ningjiang 3 seedlings tolerated cold better than Dubai bean seedlings, in contrast to adult stage. The transcriptome dynamics of the two cultivars were closely compared using Illumina RNA-seq following 0, 3, 12, and 24 h of cold stress at 5 °C and recovery for 3 h at 25 °C room temperature. Global gene expression patterns displayed relatively high correlation between the two cultivars (>0.88), decreasing to 0.79 and 0.81, respectively, at 12 and 24 h of recovery, consistent with the results of principal component analysis. The major transcription factor families identified from differentially expressed genes between the two cultivars included bHLH, NAC, C2H2, MYB, WRKY, and AP2/ERF. The representative GO enrichment terms were protein phosphorylation, photosynthesis, oxidation-reduction process, and cellular glucan metabolic process. Moreover, KEGG analysis of DEGs within each cultivar revealed 36 transcription factors enriched in Dubai bean and Ningjiang 3 seedlings under cold stress.

Conclusions

These results reveal new information that will improve our understanding of the molecular mechanisms underlying the cold stress response of asparagus bean and provide genetic resources for breeding cold-tolerant asparagus bean cultivars.

Genome-Wide Analysis of DREB Genes Identifies a Novel Salt Tolerance Gene in Wild Soybean (Glycine soja)

Salt stress is a major factor limiting the growth and yield of soybean (Glycine max). Wild soybeans (Glycine soja) contain high allelic diversity and beneficial alleles that can be re-introduced into domesticated soybeans to improve adaption to the environment. However, very few beneficial alleles have been identified from wild soybean. Here, we demonstrate that wild soybean is more salt tolerant than cultivated soybean and examine dehydration responsive element-binding (DREB) family transcription factor genes to look for advantageous alleles that might improve drought tolerance in cultivated soybean. Our genome-wide analysis identified 103 DREB genes from the Glycine max genome. By combined RNA-sequencing and population genetics of wild, landrace, and cultivated soybean accessions, we show that the natural variation in DREB3a and DREB3b is related to differences in salt tolerance in soybean accessions. Interestingly, DREB3b, but not DREB3a, appears to have undergone artificial selection. Soybean plants carrying the wild soybean DREB3b allele (DREB3b^39Del ) are more salt tolerant than those containing the reference genome allele (DREB3b^Ref ). Together, our results suggest that the loss of the DREB3b^39Del allele through domestication of cultivated soybean may be associated with a reduction in salt tolerance. Our findings provide crucial information for improving salt tolerance in soybean through molecular breeding.

ZmERF21 directly regulates hormone signaling and stress-responsive gene expression to influence drought tolerance in maize seedlings

Drought stress adversely impacts crop development and yield. Maize frequently encounters drought stress during its life cycle. Improvement of drought tolerance is a priority of maize breeding programs. Here, we identified a novel transcription factor encoding gene, APETALA2 (AP2)/Ethylene response factor (ERF), which is tightly associated with drought tolerance in maize seedlings. ZmERF21 is mainly expressed in the root and leaf and it can be highly induced by polyethylene glycol treatment. Genetic analysis showed that the zmerf21 mutant plants displayed a reduced drought tolerance phenotype, accompanied by phenotypical and physiological changes that are commonly observed in drought conditions. Overexpression of ZmERF21 in maize significantly increased the chlorophyll content and activities of antioxidant enzymes under drought conditions. RNA-Seq and DNA affinity purification sequencing analysis further revealed that ZmERF21 may directly regulate the expression of genes related to hormone (ethylene, abscisic acid) and Ca signaling as well as other stress-response genes through binding to the promoters of potential target genes. Our results thereby provided molecular evidence of ZmERF21 is involved in the drought stress response of maize.

ERF Transcription Factor OsBIERF3 Positively Contributes to Immunity against Fungal and Bacterial Diseases but Negatively Regulates Cold Tolerance in Rice

We previously showed that overexpression of the rice ERF transcription factor gene OsBIERF3 in tobacco increased resistance against different pathogens. Here, we report the function of OsBIERF3 in rice immunity and abiotic stress tolerance. Expression of OsBIERF3 was induced by Xanthomonas oryzae pv. oryzae, hormones (e.g., salicylic acid, methyl jasmonate, 1-aminocyclopropane-1-carboxylic acid, and abscisic acid), and abiotic stress (e.g., drought, salt and cold stress). OsBIERF3 has transcriptional activation activity that depends on its C-terminal region. The OsBIERF3-overexpressing (OsBIERF3-OE) plants exhibited increased resistance while OsBIERF3-suppressed (OsBIERF3-Ri) plants displayed decreased resistance to Magnaporthe oryzae and X. oryzae pv. oryzae. A set of genes including those for PRs and MAPK kinases were up-regulated in OsBIERF3-OE plants. Cell wall biosynthetic enzyme genes were up-regulated in OsBIERF3-OE plants but down-regulated in OsBIERF3-Ri plants; accordingly, cell walls became thicker in OsBIERF3-OE plants but thinner in OsBIERF3-Ri plants than WT plants. The OsBIERF3-OE plants attenuated while OsBIERF3-Ri plants enhanced cold tolerance, accompanied by altered expression of cold-responsive genes and proline accumulation. Exogenous abscisic acid and 1-aminocyclopropane-1-carboxylic acid, a precursor of ethylene biosynthesis, restored the attenuated cold tolerance in OsBIERF3-OE plants while exogenous AgNO₃, an inhibitor of ethylene action, significantly suppressed the enhanced cold tolerance in OsBIERF3-Ri plants. These data demonstrate that OsBIERF3 positively contributes to immunity against M. oryzae and X. oryzae pv. oryzae but negatively regulates cold stress tolerance in rice.

Genome-wide investigation of AP2/ERF gene family in the desert legume Eremosparton songoricum: Identification, classification, evolution, and expression profiling under drought stress

Eremosparton songoricum (Litv.) Vass. is a rare leafless legume shrub endemic to central Asia which grows on bare sand. It shows extreme drought tolerance and is being developed as a model organism for investigating morphological, physiological, and molecular adaptations to harsh desert environments. APETALA2/Ethylene Responsive Factor (AP2/ERF) is a large plant transcription factor family that plays important roles in plant responses to various biotic and abiotic stresses and has been extensively studied in several plants. However, our knowledge on the AP2/ERF family in legume species is limited, and no respective study was conducted so far on the desert shrubby legume E. songoricum. Here, 153 AP2/ERF genes were identified based on the E. songoricum genome data. EsAP2/ERFs covered AP2 (24 genes), DREB (59 genes), ERF (68 genes), and Soloist (2 genes) subfamilies, and lacked canonical RAV subfamily genes based on the widely used classification method. The DREB and ERF subfamilies were further divided into A1-A6 and B1-B6 groups, respectively. Protein motifs and exon-intron structures of EsAP2/ERFs were also examined, which matched the subfamily/group classification. Cis-acting element analysis suggested that EsAP2/ERF genes shared many stress- and hormone-related cis-regulatory elements. Moreover, the gene numbers and the ratio of each subfamily and the intron-exon structures were systematically compared with other model plants ranging from algae to angiosperms, including ten legumes. Our results supported the view that AP2 and ERF evolved early and already existed in algae, whereas RAV and DREB began to appear in moss species. Almost all plant AP2 and Soloist genes contained introns, whereas most DREB and ERF genes did not. The majority of EsAP2/ERFs were induced by drought stress based on RNA-seq data, EsDREBs were highly induced and had the largest number of differentially expressed genes in response to drought. Eight out of twelve representative EsAP2/ERFs were significantly up-regulated as assessed by RT-qPCR. This study provides detailed insights into the classification, gene structure, motifs, chromosome distribution, and gene expression of AP2/ERF genes in E. songoricum and lays a foundation for better understanding of drought stress tolerance mechanisms in legume plants. Moreover, candidate genes for drought-resistant plant breeding are proposed.

Stress-regulated elements in Lotus spp., as a possible starting point to understand signalling networks and stress adaptation in legumes

Although legumes are of primary economic importance for human and livestock consumption, the information regarding signalling networks during plant stress response in this group is very scarce. Lotus japonicus is a major experimental model within the Leguminosae family, whereas L. corniculatus and L. tenuis are frequent components of natural and agricultural ecosystems worldwide. These species display differences in their perception and response to diverse stresses, even at the genotype level, whereby they have been used in many studies aimed at achieving a better understanding of the plant stress-response mechanisms. However, we are far from the identification of key components of their stress-response signalling network, a previous step for implementing transgenic and editing tools to develop legume stress-resilient genotypes, with higher crop yield and quality. In this review we scope a body of literature, highlighting what is currently known on the stress-regulated signalling elements so far reported in Lotus spp. Our work includes a comprehensive review of transcription factors chaperones, redox signals and proteins of unknown function. In addition, we revised strigolactones and genes regulating phytochelatins and hormone metabolism, due to their involvement as intermediates in several physiological signalling networks. This work was intended for a broad readership in the fields of physiology, metabolism, plant nutrition, genetics and signal transduction. Our results suggest that Lotus species provide a valuable information platform for the study of specific protein-protein (PPI) interactions, as a starting point to unravel signalling networks underlying plant acclimatation to bacterial and abiotic stressors in legumes. Furthermore, some Lotus species may be a source of genes whose regulation improves stress tolerance and growth when introduced ectopically in other plant species.

Sorghum in dryland: morphological, physiological, and molecular responses of sorghum under drought stress

Droughts negatively affect sorghum's productivity and nutritional quality. Across its diversity centers, however, there exist resilient genotypes that function differently under drought stress at various levels, including molecular and physiological. Sorghum is an economically important and a staple food crop for over half a billion people in developing countries, mostly in arid and semi-arid regions where drought stress is a major limiting factor. Although sorghum is generally considered tolerant, drought stress still significantly hampers its productivity and nutritional quality across its major cultivation areas. Hence, understanding both the effects of the stress and plant response is indispensable for improving drought tolerance of the crop. This review aimed at enhancing our understanding and provide more insights on drought tolerance in sorghum as a contribution to the development of climate resilient sorghum cultivars. We summarized findings on the effects of drought on the growth and development of sorghum including osmotic potential that impedes germination process and embryonic structures, photosynthetic rates, and imbalance in source-sink relations that in turn affect seed filling often manifested in the form of substantial reduction in grain yield and quality. Mechanisms of sorghum response to drought-stress involving morphological, physiological, and molecular alterations are presented. We highlighted the current understanding about the genetic basis of drought tolerance in sorghum, which is important for maximizing utilization of its germplasm for development of improved cultivars. Furthermore, we discussed interactions of drought with other abiotic stresses and biotic factors, which may increase the vulnerability of the crop or enhance its tolerance to drought stress. Based on the research reviewed in this article, it appears possible to develop locally adapted cultivars of sorghum that are drought tolerant and nutrient rich using modern plant breeding techniques.

Analysis of long non-coding RNAs and mRNAs in harvested kiwifruit in response to the yeast antagonist, Wickerhamomyces anomalus

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W. anomalus exhibits good biocontrol activity against blue and gray mold on kiwifruit.

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LncRNAs in kiwifruit may be involved in activating plant hormone signal transduction pathways in response to the biocontrol yeast.

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LncRNAs in kiwifruit may modulate the production of related TFs and secondary metabolites.

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The expression of downstream defense-related genes in kiwifruit increases in response to the application of the biocontrol yeast.

Biological control utilizing antagonistic yeasts is an effective method for controlling postharvest diseases. Long non-coding RNAs (lncRNAs) have been found to be involved in a variety of plant growth and development processes, including those associated with plant disease resistance. In the present study, the yeast antagonist, Wickerhamomyces anomalus, was found to strongly inhibit postharvest blue mold (Penicillium expansum) and gray mold (Botrytis cinerea) decay of kiwifruit. Additionally, lncRNA high-throughput sequencing and bioinformatic analysis was used to identify lncRNAs in W. anomalus-treated wounds in kiwifruit and predict their function based on putative target genes. Our results indicate that lncRNAs may be involved in increasing ethylene (ET), jasmonic acid (JA), abscisic acid (ABA), and auxin (IAA) levels, as well as activating signal transduction pathways that regulate the expression of several transcription factors (WRKY72, WRKY53, JUB1AP2). These transcription factors (TFs) then mediate the expression of downstream, defense-related genes (ZAR1, PAD4, CCR4, NPR4) and the synthesis of secondary metabolites, thus, potentially enhancing disease resistance. Notably, by stimulating the accumulation of antifungal compounds, such as phenols and lignin, disease resistance in kiwifruit was enhanced. Our study provides new information on the mechanism underlying the induction of disease resistance in kiwifruit by W. anomalus, as well as a new disease resistance strategy that can be used to enhance the defense response of fruit to pathogenic fungi.

The MdMEK2-MdMPK6-MdWRKY17 pathway stabilizes chlorophyll levels by directly regulating MdSUFB in apple under drought stress

Drought stress severely limits plant growth and production in apple (Malus domestica Borkh.). To breed water-deficit-tolerant apple cultivars that maintain high yields under slight or moderate drought stress, it is important to uncover the mechanisms underlying the transcriptional regulation of chlorophyll metabolism in apple. To explore this mechanism, we generated transgenic 'Gala3' apple plants with overexpression or knockdown of MdWRKY17, which encodes a transcription factor whose expression is significantly induced by water deficit. Under moderate drought stress, we observed significantly higher chlorophyll contents and photosynthesis rates in overexpression transgenic plants than in controls, whereas these were dramatically lower in the knockdown lines. MdWRKY17 directly regulates MdSUFB expression, as demonstrated by in vitro and in vivo experiments. MdSUFB, a key component of the sulfur mobilization (SUF) system that assembles Fe-S clusters, is essential for inhibiting chlorophyll degradation and stabilizing electron transport during photosynthesis, leading to higher chlorophyll levels in transgenic apple plants overexpressing MdWRKY17. The activated MdMEK2-MdMPK6 cascade by water-deficit stress fine-tunes the MdWRKY17-MdSUFB pathway by phosphorylating MdWRKY17 under water-deficit stress. This fine-tuning of the MdWRKY17-MdSUFB regulatory pathway is important for balancing plant survival and yield losses (chlorophyll degradation and reduced photosynthesis) under slight or moderate drought stress. The phosphorylation by MdMEK2-MdMPK6 activates the MdWRKY17-MdSUFB pathway at S66 (identified by LC-MS), as demonstrated by in vitro and in vivo experiments. Our findings reveal that the MdMEK2-MdMPK6-MdWRKY17-MdSUFB pathway stabilizes chlorophyll levels under moderate drought stress, which could facilitate the breeding of apple varieties that maintain high yields under drought stress.

Crosstalk among plant growth regulators and signaling molecules during biotic and abiotic stresses: molecular responses and signaling pathways

Plant stress responses are extremely sophisticated which implicate changes at the cellular, physiological and transcriptome levels by activating specific gene expression related to the challenges faced by plants.

Downregulation of lncRNA PpL-T31511 and Pp-miRn182 Promotes Hydrogen Cyanamide-Induced Endodormancy Release through the PP2C-H2O2 Pathway in Pear (Pyrus pyrifolia)

Bud endodormancy is an important, complex process subject to both genetic and epigenetic control, the mechanism of which is still unclear. The endogenous hormone abscisic acid (ABA) and its signaling pathway play important roles in the endodormancy process, in which the type 2C protein phosphatases (PP2Cs) is key to the ABA signal pathway. Due to its excellent effect on endodormancy release, hydrogen cyanamide (HC) treatment is considered an effective measure to study the mechanism of endodormancy release. In this study, RNA-Seq analysis was conducted on endodormant floral buds of pear (Pyrus pyrifolia) with HC treatment, and the HC-induced PP2C gene PpPP2C1 was identified. Next, software prediction, expression tests and transient assays revealed that lncRNA PpL-T31511-derived Pp-miRn182 targets PpPP2C1. The expression analysis showed that HC treatment upregulated the expression of PpPP2C1 and downregulated the expression of PpL-T31511 and Pp-miRn182. Moreover, HC treatment inhibited the accumulation of ABA signaling pathway-related genes and hydrogen peroxide (H₂O₂). Furthermore, overexpression of Pp-miRn182 reduced the inhibitory effect of PpPP2C1 on the H₂O₂ content. In summary, our study suggests that downregulation of PpL-T31511-derived Pp-miRn182 promotes HC-induced endodormancy release in pear plants through the PP2C-H₂O₂ pathway.

Genome-wide identification, phylogeny and expression analysis of AP2/ERF transcription factors family in sweet potato

Background

In recent years, much attention has been given to AP2/ERF transcription factors because they play indispensable roles in many biological processes, such as plant development and biotic and abiotic stress responses. Although AP2/ERFs have been thoroughly characterised in many plant species, the knowledge about this family in the sweet potato, which is a vital edible and medicinal crop, is still limited. In this study, a comprehensive genome-wide investigation was conducted to characterise the AP2/ERF gene family in the sweet potato.

Results

Here, 198 IbAP2/ERF transcription factors were obtained. Phylogenetic analysis classified the members of the IbAP2/ERF family into three groups, namely, ERF (172 members), AP2 (21 members) and RAV (5 members), which was consistent with the analysis of gene structure and conserved protein domains. The evolutionary characteristics of these IbAP2/ERF genes were systematically investigated by analysing chromosome location, conserved protein motifs and gene duplication events, indicating that the expansion of the IbAP2/ERF gene family may have been caused by tandem duplication. Furthermore, the analysis of cis-acting elements in IbAP2/ERF gene promoters implied that these genes may play crucial roles in plant growth, development and stress responses. Additionally, the available RNA-seq data and quantitative real-time PCR (qRT-PCR) were used to investigate the expression patterns of IbAP2/ERF genes during sweet potato root development as well as under multiple forms of abiotic stress, and we identified several developmental stage-specific and stress-responsive IbAP2/ERF genes. Furthermore, g59127 was differentially expressed under various stress conditions and was identified as a nuclear protein, which was in line with predicted subcellular localization results.

Conclusions

This study originally revealed the characteristics of the IbAP2/ERF superfamily and provides valuable resources for further evolutionary and functional investigations of IbAP2/ERF genes in the sweet potato.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-08043-w.

Genome-Wide Identification and Expression Analysis of AP2/ERF Transcription Factor Related to Drought Stress in Cultivated Peanut (Arachis hypogaea L.)

APETALA2/ethylene response element-binding factor (AP2/ERF) transcription factors (TFs) have been found to regulate plant growth and development and response to various abiotic stresses. However, detailed information of AP2/ERF genes in peanut against drought has not yet been performed. Herein, 185 AP2/ERF TF members were identified from the cultivated peanut (A. hypogaea cv. Tifrunner) genome, clustered into five subfamilies: AP2 (APETALA2), ERF (ethylene-responsive-element-binding), DREB (dehydration-responsive-element-binding), RAV (related to ABI3/VP), and Soloist (few unclassified factors)). Subsequently, the phylogenetic relationship, intron-exon structure, and chromosomal location of AhAP2/ERF were further characterized. All of these AhAP2/ERF genes were distributed unevenly across the 20 chromosomes, and 14 tandem and 85 segmental duplicated gene pairs were identified which originated from ancient duplication events. Gene evolution analysis showed that A. hypogaea cv. Tifrunner were separated 64.07 and 66.44 Mya from Medicago truncatula L. and Glycine max L., respectively. Promoter analysis discovered many cis-acting elements related to light, hormones, tissues, and stress responsiveness process. The protein interaction network predicted the exitance of functional interaction among families or subgroups. Expression profiles showed that genes from AP2, ERF, and dehydration-responsive-element-binding subfamilies were significantly upregulated under drought stress conditions. Our study laid a foundation and provided a panel of candidate AP2/ERF TFs for further functional validation to uplift breeding programs of drought-resistant peanut cultivars.

TaFDL2-1A interacts with TabZIP8-7A protein to cope with drought stress via the abscisic acid signaling pathway

Drought has negative effects on cereal production. Studies have shown that many basic leucine zipper transcription factors (bZIP TFs) help to cope with drought stress. In this study, bZIP TF wheat (Triticum aestivum L.) FD-Like2 (TaFDL2) was isolated and functionally analyzed. Three homologs of TaFDL2 were identified and their expression was induced by drought and abscisic acid (ABA) treatment. TaFDL2-1A has transactivation activity and two activation domains, and the domain D region has different effects on the transcriptional activity of the two domains. Analysis of TaFDL2-1A overexpression plants indicated their enhanced drought tolerance and greater sensitivity to ABA. TabZIP8-7A was identified as a protein that interacts with TaFDL2-1A in the nucleus, and the overexpression of TabZIP8-7A conferred greater drought resistance and ABA sensitivity in Arabidopsis. Surprisingly, TaFDL2-1A × TabZIP8-7A double overexpression lines exhibited the highest drought resistance. Genetic and transcriptional regulation analyses demonstrated that stress-response gene transcription was initiated by TaFDL2-1A or TabZIP8-7A via the ABA signaling pathway. Importantly, TaFDL2-1A and TabZIP8-7A synergistically promoted ABA-inducible gene expression in a more efficient manner to form the transcriptional activation complex. Our findings provide new insights into the molecular mechanisms that allow bZIP TFs to regulate ABA signaling in response to drought stress.

Transcriptome-wide identification and expression profiling of the ERF gene family suggest roles as transcriptional activators and repressors of fruit ripening in durian

The involvement of the phytohormone ethylene as the main trigger of climacteric fruit ripening is well documented. However, our knowledge regarding the role of ethylene response factor (ERF) transcription factor in the transcriptional regulation of ethylene biosynthesis during fruit ripening remains limited. Here, comprehensive transcriptome analysis and expression profiling revealed 63 ERFs in durian pulps, termed DzERF1-DzERF63, of which 34 exhibited ripening-associated expression patterns at three stages (unripe, midripe, and ripe) during fruit ripening. Hierarchical clustering analysis classified 34 ripening-associated DzERFs into three distinct clades, among which, clade I consisted of downregulated DzERFs and clade III included those upregulated during ripening. Phylogenetic analysis predicted the functions of some DzERFs based on orthologs of previously characterized ERFs. Among downregulated DzERFs, DzERF6 functional prediction revealed its role as a negative regulator of ripening via ethylene biosynthetic gene repression, whereas among upregulated genes, DzERF9 was predicted to positively regulate ethylene biosynthesis. Correlation network analysis of 34 ripening-associated DzERFs with potential target genes revealed a strong negative correlation between DzERF6 and ethylene biosynthetic genes and a strong positive correlation between DzERF9 and ethylene biosynthesis. DzERF6 and DzERF9 showed differential expression patterns in association with different ripening treatments (natural, ethylene-induced, and 1-methylcyclopropene-delayed ripening). DzERF6 was downregulated, whereas DzERF9 was upregulated, during ripening and after ethylene treatment. The auxin-repressed and auxin-induced expression of DzERF6 and DzERF9, respectively, confirmed its dose-dependent responsiveness to exogenous auxin. We suggest ethylene- and auxin-mediated roles of DzERF6 and DzERF9 during fruit ripening, possibly through transcriptional regulation of ethylene biosynthetic genes.

Genome-wide association study of cyanogenic glycosides, proline, sugars, and pigments in Eucalyptus cladocalyx after 18 consecutive dry summers

Natural variation of cyanogenic glycosides, soluble sugars, proline, and nondestructive optical sensing of pigments (chlorophyll, flavonols, and anthocyanins) was examined in ex situ natural populations of Eucalyptus cladocalyx F. Muell. grown under dry environmental conditions in the southern Atacama Desert, Chile. After 18 consecutive dry seasons, considerable plant-to-plant phenotypic variation for all the traits was observed in the field. For example, leaf hydrogen cyanide (HCN) concentrations varied from 0 (two acyanogenic individuals) to 1.54 mg cyanide g^-1 DW. Subsequent genome-wide association study revealed associations with several genes with a known function in plants. HCN content was associated robustly with genes encoding Cytochrome P450 proteins, and with genes involved in the detoxification mechanism of HCN in cells (β-cyanoalanine synthase and cyanoalanine nitrilase). Another important finding was that sugars, proline, and pigment content were linked to genes involved in transport, biosynthesis, and/or catabolism. Estimates of genomic heritability (based on haplotypes) ranged between 0.46 and 0.84 (HCN and proline content, respectively). Proline and soluble sugars had the highest predictive ability of genomic prediction models (PA = 0.65 and PA = 0.71, respectively). PA values for HCN content and flavonols were relatively moderate, with estimates ranging from 0.44 to 0.50. These findings provide new understanding on the genetic architecture of cyanogenic capacity, and other key complex traits in cyanogenic E. cladocalyx.

Orchestration of plant development and defense by indirect crosstalk of salicylic acid and brassinosteorid signaling via transcription factor GhTINY2

Salicylic acid (SA) and brassinosteroids (BRs) are well known to regulate diverse processes of plant development and stress responses, but the mechanisms by which these phytohormones mediate the growth and defense trade-off are largely unclear. In addition, little is known about the roles of DEHYDRATION RESPONSIVE ELEMENT BINDING transcription factors, especially in biotic stress and plant growth. Here, we identified a cotton (Gossypium hirsutum) APETALA2/ETHYLENE RESPONSIVE FACTOR gene GhTINY2 that is strongly induced by Verticillium dahliae. Overexpression of GhTINY2 in cotton and Arabidopsis enhanced tolerance to V. dahliae, while knockdown of expression increased the susceptibility of cotton to the pathogen. GhTINY2 was found to promote SA accumulation and SA signaling transduction by directly activating expression of WRKY51. Moreover, GhTINY2-overexpressing cotton and Arabidopsis showed retardation of growth, increased sensitivity to inhibitors of BR biosynthesis, down-regulation of several BR-induced genes, and up-regulation of BR-repressed genes, while GhTINY2-RNAi cotton showed the opposite effects. We further determined that GhTINY2 negatively regulates BR signaling by interacting with BRASSINAZOLE-RESISTANT 1 (BZR1) and restraining its transcriptional activation of the expression of INDOLE-3-ACETIC ACID INDUCIBLE 19 (IAA19). These findings indicate that GhTINY2 fine-tunes the trade-off between immunity and growth via indirect crosstalk between WRKY51-mediated SA biosynthesis and BZR1-IAA19-regulated BR signaling.

Ethylene response factors 15 and 16 trigger jasmonate biosynthesis in tomato during herbivore resistance

Jasmonates (JAs) are phytohormones with crucial roles in plant defense. Plants accumulate JAs in response to wounding or herbivore attack, but how JA biosynthesis is triggered remains poorly understood. Here we show that herbivory by cotton bollworm (Helicoverpa armigera) induced both ethylene (ET) and JA production in tomato (Solanum lycopersicum) leaves. Using RNA-seq, ET mutants, and inhibitors of ET signaling, we identified ET-induced ETHYLENE RESPONSE FACTOR 15 (ERF15) and ERF16 as critical regulators of JA biosynthesis in tomato plants. Transcripts of ERF15 and ERF16 were markedly upregulated and peaked at 60 and 15 min, respectively, after simulated herbivore attack. While mutation in ERF16 resulted in the attenuated expression of JA biosynthetic genes and decreased JA accumulation 15 min after the simulated herbivory treatment, these changes were not observed in erf15 mutants until 60 min after treatment. Electrophoretic mobility shift assays and dual-luciferase assays demonstrated that both ERFs15 and 16 are transcriptional activators of LIPOXYGENASE D, ALLENE OXIDE CYCLASE, and 12-OXO-PHYTODIENOIC ACID REDUCTASE 3, key genes in JA biosynthesis. Furthermore, JA-activated MYC2 and ERF16 also function as the transcriptional activators of ERF16, contributing to dramatic increases in ERF16 expression. Taken together, our results demonstrated that ET signaling is involved in the rapid induction of the JA burst. ET-induced ERF15 and ERF16 function as powerful transcriptional activators that trigger the JA burst in response to herbivore attack.

The dual interplay of RAV5 in activating nitrate reductases and repressing catalase activity to improve disease resistance in cassava

Cassava bacterial blight (CBB) caused by Xanthomonas axonopodis pv. manihotis (Xam) seriously affects cassava yield. Nitrate reductase (NR) plays an important role in plant nitrogen metabolism in plants. However, the in vivo role of NR and the corresponding signalling pathway remain unclear in cassava. In this study, we isolated MeNR1/2 and revealed their novel upstream transcription factor MeRAV5. We also identified MeCatalase1 (MeCAT1) as the interacting protein of MeRAV5. In addition, we investigated the role of MeCatalase1 and MeRAV5-MeNR1/2 module in cassava defence response. MeNRs positively regulates cassava disease resistance against CBB through modulation of nitric oxide (NO) and extensive transcriptional reprogramming especially in mitogen-activated protein kinase (MAPK) signalling. Notably, MeRAV5 positively regulates cassava disease resistance through the coordination of NO and hydrogen peroxide (H2 O2 ) level. On the one hand, MeRAV5 directly activates the transcripts of MeNRs and NO level by binding to CAACA motif in the promoters of MeNRs. On the other hand, MeRAV5 interacts with MeCAT1 to inhibit its activity, so as to negatively regulate endogenous H2 O2 level. This study highlights the precise coordination of NR activity and CAT activity by MeRAV5 through directly activating MeNRs and interacting with MeCAT1 in plant immunity.

Transcriptome and metabolome profiling in naturally infested Casuarina equisetifolia clones by Ralstonia solanacearum

Casuarina equisetifolia is an important pioneer tree and suffers from bacterial wilt caused by Ralstonia solanacearum. We collected resistant (R) and susceptible (S) C. equisetifolia clones naturally infected by R. solanacearum and compared their transcriptome and metabolome with a clone (CK) from a non-infested forest, in order to study their response and resistance to bacterial wilt. We identified 18 flavonoids differentially accumulated among the three clonal groups as potential selection biomarkers against R. solanacearum. Flavonoid synthesis-related genes were up-regulated in the resistant clones, probably enhancing accumulation of flavonoids and boosting resistance against bacterial wilt. The down-regulation of auxin/indoleacetic acid-related genes and up-regulation of brassinosteroid, salicylic acid and jasmonic acid-related differentially expressed genes in the R vs CK and R vs S clonal groups may have triggered defense signals and increased expression of defense-related genes against R. solanacearum. Overall, this study provides an important insight into pathogen-response and resistance to bacterial wilt in C. equisetifolia.

Evolution and identification of DREB transcription factors in the wheat genome: modeling, docking and simulation of DREB proteins associated with salt stress

Soil salinity and the resulting salt stress it imposes on crop plants is a major problem for modern agriculture. Understanding how salt tolerance mechanisms in plants are regulated is therefore important. One regulatory mechanism is the APETALA2/Ethylene Responsive Factor (AP2/ERF) transcription factor family, including dehydration responsive element binding (DREB) transcription factors. By binding to DNA, specifically upstream of genes that play roles in salt tolerance pathways, DREB proteins upregulate expression of these genes. DREB in Triticum aestivum (wheat) cluster in sub-groups and in this study by scanning the recently extended predicted proteome of wheat for DREB, we increased the number of members of this sub-family. Using the wheat genome, we identified 576 genes coding for the AP2 domain of which 508 were identified to have one AP2 domain, a characteristic of the DREB/ERF subfamily. We confirmed the existing four sub-groups by sequence-based phylogenetic analyses but also identified 32 new DREB subfamily members, not belonging to any known sub-group. Transcription factor profile inference analysis identified two genes, TraesCS2B02G002700 and TraesCS2D02G015200, being homologous to DREB1A of Arabidopsis thaliana. Based on molecular simulation (25 ns) analysis, TraesCS2B02G002700 with a CCGAC motif was observed to interact very stably with DNA. In silico mutational analysis at the 19^th position in the DREB domain of TraesCS2B02G002700-DNA complex indicated this as a stable part for recognizing and forming interaction with DNA. Moreover, six target genes were predicted having an upstream CCGAC motif regulated by TraesCS2B02G002700. Our study provides an overall framework for exploring the transcription factors in plants and identifying e.g. potential salt stress target genes.Communicated by Ramaswamy H. Sarma.

The Corylus mandshurica genome provides insights into the evolution of Betulaceae genomes and hazelnut breeding

Hazelnut is popular for its flavor, and it has also been suggested that hazelnut is beneficial to cardiovascular health because it is rich in oleic acid. Here, we report the first high-quality chromosome-scale genome for the hazelnut species Corylus mandshurica (2n = 22), which has a high concentration of oleic acid in its nuts. The assembled genome is 367.67 Mb in length, and the contig N50 is 14.85 Mb. All contigs were assembled into 11 chromosomes, and 28,409 protein-coding genes were annotated. We reconstructed the evolutionary trajectories of the genomes of Betulaceae species and revealed that the 11 chromosomes of the hazelnut genus were derived from the most ancestral karyotype in Betula pendula, which has 14 protochromosomes, by inferring homology among five Betulaceae genomes. We identified 96 candidate genes involved in oleic acid biosynthesis, and 10 showed rapid evolution or positive selection. These findings will help us to understand the mechanisms of lipid synthesis and storage in hazelnuts. Several gene families related to salicylic acid metabolism and stress responses experienced rapid expansion in this hazelnut species, which may have increased its stress tolerance. The reference genome presented here constitutes a valuable resource for molecular breeding and genetic improvement of the important agronomic properties of hazelnut.

Overexpression of ZmWRKY65 transcription factor from maize confers stress resistances in transgenic Arabidopsis

Plant-specific WRKY transcription factors play important roles in regulating the expression of defense-responsive genes against pathogen attack. A multiple stress-responsive WRKY gene, ZmWRKY65, was identified in maize by screening salicylic acid (SA)-induced de novo transcriptomic sequences. The ZmWRKY65 protein was localized in the nucleus of mesophyll protoplasts. The analysis of the ZmWRKY65 promoter sequence indicated that it contains several stress-related transcriptional regulatory elements. Many environmental factors affecting the transcription of ZmWRKY65 gene, such as drought, salinity, high temperature and low temperature stress. Moreover, the transcription of ZmWRKY65 gene was also affected by the induction of defense related plant hormones such as SA and exogenous ABA. The results of seed germination and stomatal aperture assays indicated that transgenic Arabidopsis plants exhibit enhanced sensitivity to ABA and high concentrations of SA. Overexpression of ZmWRKY65 improved tolerance to both pathogen attack and abiotic stress in transgenic Arabidopsis plants and activated several stress-related genes such as RD29A, ERD10, and STZ as well as pathogenesis-related (PR) genes such as PR1, PR2 and PR5; these genes are involved in resistance to abiotic and biotic stresses in Arabidopsis. Together, this evidence implies that the ZmWRKY65 gene is involved in multiple stress signal transduction pathways.

Genomic Analysis of Soybean PP2A-B ' ' Family and Its Effects on Drought and Salt Tolerance

Abiotic stresses induce the accumulation of reactive oxygen species (ROS) and significantly affect plant growth. Protein phosphatase 2A (PP2A) plays an important role in controlling intracellular and extracellular ROS signals. However, the interaction between PP2A, ROS, and stress tolerance remains largely unclear. In this study, we found that the B ' ' subunit of PP2A (PP2A-B ' ' ) can be significantly induced and was analyzed using drought- and salt-induced soybean transcriptome data. Eighty-three soybean PP2A-B ' ' genes were identified from the soybean genome via homologous sequence alignment, which was distributed across 20 soybean chromosomes. Among soybean PP2A-B ' ' family genes, 26 GmPP2A-B ' ' members were found to be responsive to drought and salt stresses in soybean transcriptome data. Quantitative PCR (qPCR) analysis demonstrated that GmPP2A-B ' ' 71 had the highest expression levels under salt and drought stresses. Functional analysis demonstrated that overexpression of GmPP2A-B ' ' 71 in soybeans can improve plant tolerance to drought and salt stresses; however, the interference of GmPP2A-B ' ' 71 in soybean increased the sensibility to drought and salt stresses. Further analysis demonstrated that overexpression of GmPP2A-B ' ' 71 in soybean could enhance the expression levels of stress-responsive genes, particularly genes associated with ROS elimination. These results indicate that PP2A-B ' ' can promote plant stress tolerance by regulating the ROS signaling, which will contribute to improving the drought resistance of crops.

The Halophyte Halostachys caspica AP2/ERF Transcription Factor HcTOE3 Positively Regulates Freezing Tolerance in Arabidopsis

The APETALA2 (AP2) and ethylene-responsive element-binding factor (ERF) gene family is one of the largest plant-specific transcription factor gene families, which plays a critical role in plant development and evolution, as well as response to various stresses. The TARGET OF EAT3 (TOE3) gene is derived from Halostachys caspica and belongs to the AP2 subfamily with two AP2 DNA-binding domains. Currently, AP2 family mainly plays crucial roles in plant growth and evolution, yet there are few reports about the role of AP2 in abiotic stress tolerance. Here, we report HcTOE3, a new cold-regulated transcription factor gene, which has an important contribution to freezing tolerance. The main results showed that the expression of HcTOE3 in the H. caspica assimilating branches was strongly induced by different abiotic stresses, including high salinity, drought, and extreme temperature (heat, chilling, and freezing), as well as abscisic acid and methyl viologen treatments. Overexpressing HcTOE3 gene (OE) induced transgenic Arabidopsis plant tolerance to freezing stress. Under freezing treatment, the OE lines showed lower content of malondialdehyde and electrolyte leakage and less accumulation of reactive oxygen species compared with the wild type. However, the survival rates, antioxidant enzyme activities, and contents of osmotic adjustment substance proline were enhanced in transgenic plants. Additionally, the OE lines increased freezing tolerance by up-regulating the transcription level of cold responsive genes (CBF1, CBF2, COR15, COR47, KIN1, and RD29A) and abscisic acid signal transduction pathway genes (ABI1, ABI2, ABI5, and RAB18). Our results suggested that HcTOE3 positively regulated freezing stress and has a great potential as a candidate gene to improve plant freezing tolerance.

Assembly and Annotation of the Nuclear and Organellar Genomes of a Dwarf Coconut (Chowghat Green Dwarf) Possessing Enhanced Disease Resistance

Coconut (Cocos nucifera L.), an important source of vegetable oil, nutraceuticals, functional foods, and housing materials, provides raw materials for a repertoire of industries engaged in the manufacture of cosmetics, soaps, detergents, paints, varnishes, and emulsifiers, among other products. The palm plays a vital role in maintaining and promoting the sustainability of farming systems of the fragile ecosystems of islands and coastal regions of the tropics. In this study, we present the genome of a dwarf coconut variety "Chowghat Green Dwarf" (CGD) from India, possessing enhanced resistance to root (wilt) disease. Utilizing short reads from the Illumina HiSeq 4000 platform and long reads from the Pacific Biosciences RSII platform, we have assembled the draft genome assembly of 1.93 Gb. The genome is distributed over 26,855 scaffolds, with ∼81.56% of the assembled genome present in scaffolds of lengths longer than 50 kb. About 77.29% of the genome was composed of transposable elements and repeats. Gene prediction yielded 51,953 genes, which upon stringent filtering, based on Annotation Edit Distance, resulted in 13,707 genes, which coded for 11,181 proteins. Among these, we gathered transcript level evidence for a total of 6828 predicted genes based on the RNA-Seq data from different coconut tissues, since they presented assembled transcripts within the genome annotation coordinates. A total of 112 nucleotide-binding and leucine-rich repeat loci, belonging to six classes, were detected. We have also undertaken the assembly and annotation of the CGD chloroplast and mitochondrial genomes. The availability of the dwarf coconut genome shall prove invaluable for deducing the origin of dwarf coconut cultivars, dissection of genes controlling plant habit and fruit color, and accelerated breeding for improved agronomic traits.

A celery transcriptional repressor AgERF8 negatively modulates abscisic acid and salt tolerance

Ethylene response factors (ERFs) widely exist in plants and have been reported to be an important regulator of plant abiotic stress. Celery, a common economic vegetable of Apiaceae, contains lots of ERF transcription factors (TFs) with various functions. AP2/ERF TFs play positive or negative roles in plant growth and stress response. Here, AgERF8, a gene encoding EAR-type AP2/ERF TF, was identified. The AgERF8 mRNA accumulated in response to both abscisic acid (ABA) signaling and salt treatment. AgERF8 was proving to be a nucleus-located protein and could bind to GCC-box. The overexpression of AgERF8 in Arabidopsis repressed the transcription of downstream genes, AtBGL and AtBCH. Arabidopsis overexpressing AgERF8 gene showed inhibited root growth under ABA and NaCl treatments. AgERF8 transgenic lines showed low tolerance to ABA and salt stress than wild-type plants. Low increment in SOD and POD activities, increased accumulation of MDA, and significantly decreased plant fresh weights and chlorophyll levels were detected in AgERF8 hosting lines after treated with ABA and NaCl. Furthermore, the overexpression of AgERF8 also inhibited the levels of ascorbic acid and antioxidant-related genes (AtCAT1, AtSOD1, AtPOD, AtSOS1, AtAPX1, and AtP5CS1) expression in transgenic Arabidopsis. This finding indicated that AgERF8 negatively affected the resistance of transgenic Arabidopsis to ABA and salt stress through regulating downstream genes expression and relevant physiological changes. It will provide a potential sight to further understand the functions of ERF TFs in celery.

Genome-wide identification and expression analysis of AP2/ERF transcription factors in sugarcane (Saccharum spontaneum L.)

BACKGROUND

APETALA2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF) transcription factors play essential roles in plant growth, development, metabolism, and responses to biotic and abiotic stresses. However, few studies concerning AP2/ERF genes in sugarcane which are the most critical sugar and energy crops worldwide.

RESULTS

A total of 218 AP2/ERF genes were identified in the Saccharum spontaneum genome. Phylogenetic analysis showed that these genes could be divided into four groups, including 43 AP2s, 160 ERFs and Dehydration-responsive element-binding (DREB) factors, 11 ABI3/VPs (RAV), and four Soloist genes. These genes were unevenly distributed on 32 chromosomes. The structural analysis of SsAP2/ERF genes showed that 91 SsAP2/ERFs lacked introns. Sugarcane and sorghum had a collinear relationship between 168 SsAP2/ERF genes and sorghum AP2/ERF genes that reflected their similarity. Multiple cis-regulatory elements (CREs) present in the SsAP2/ERF promoter were related to abiotic stresses, suggesting that SsAP2/ERF activity could contribute to sugarcane adaptation to environmental changes. The tissue-specific analysis showed spatiotemporal expression of SsAP2/ERF in the stems and leaves of sugarcane at different development stages. In ten sugarcane samples, 39 SsAP2/ERFs were not expressed, whereas 58 SsAP2/ERFs were expressed in all samples. Quantitative PCR experiments showed that SsERF52 expression was up-regulated under salt stress, but suppressed under dehydration stress. SsSoloist4 had the most considerable upregulation in response to treatment with the exogenous hormones ABA and GA. Within 3 h of ABA or PEG6000 treatment, SsSoloist4 expression was up-regulated, indicating that this gene could play a role in the responses to ABA and GA-associated dehydration stress. Analysis of AP2/ERF gene expression patterns under different treatments indicated that SsAP2/ERF genes played an essential role in dehydration and salt stress responses of S. spontaneum.

CONCLUSIONS

In this study, a total of 218 members of the AP2 / ERF superfamily were identified in sugarcane, and their genetic structure, evolution characteristics, and expression patterns were studied and analyzed. The results of this study provide a foundation for future analyses to elucidate the importance of AP2/ERF transcription factors in the function and molecular breeding of sugarcane.

Ethylene promotes seed iron storage during Arabidopsis seed maturation via ERF95 transcription factor

Because Iron (Fe) is an essential element, Fe storage in plant seeds is necessary for seedling establishment following germination. However, the mechanisms controlling seed Fe storage during seed development remain largely unknown. Here we reveal that an ERF95 transcription factor regulates Arabidopsis seed Fe accumulation. We show that expression of ERF95 increases during seed maturation, and that lack of ERF95 reduces seed Fe accumulation, consequently increasing sensitivity to Fe deficiency during seedling establishment. Conversely, overexpression of ERF95 has the opposite effects. We show that lack of ERF95 decreases abundance of FER1 messenger RNA in developing seed, which encodes Fe-sequestering ferritin. Accordingly, a fer1-1 loss-of-function mutation confers reduced seed Fe accumulation, and suppresses ERF95-promoted seed Fe accumulation. In addition, ERF95 binds to specific FER1 promoter GCC-boxes and transactivates FER1 expression. We show that ERF95 expression in maturing seed is dependent on EIN3, the master transcriptional regulator of ethylene signaling. While lack of EIN3 reduces seed Fe content, overexpression of ERF95 rescues Fe accumulation in the seed of ein3 loss-of-function mutant. Finally, we show that ethylene production increases during seed maturation. We conclude that ethylene promotes seed Fe accumulation during seed maturation via an EIN3-ERF95-FER1-dependent signaling pathway.

Advances in AP2/ERF super-family transcription factors in plant

In the whole life process, many factors including external and internal factors affect plant growth and development. The morphogenesis, growth, and development of plants are controlled by genetic elements and are influenced by environmental stress. Transcription factors contain one or more specific DNA-binding domains, which are essential in the whole life cycle of higher plants. The AP2/ERF (APETALA2/ethylene-responsive element binding factors) transcription factors are a large group of factors that are mainly found in plants. The transcription factors of this family serve as important regulators in many biological and physiological processes, such as plant morphogenesis, responsive mechanisms to various stresses, hormone signal transduction, and metabolite regulation. In this review, we summarized the advances in identification, classification, function, regulatory mechanisms, and the evolution of AP2/ERF transcription factors in plants. AP2/ERF family factors are mainly classified into four major subfamilies: DREB (Dehydration Responsive Element-Binding), ERF (Ethylene-Responsive-Element-Binding protein), AP2 (APETALA2) and RAV (Related to ABI3/VP), and Soloists (few unclassified factors). The review summarized the reports about multiple regulatory functions of AP2/ERF transcription factors in plants. In addition to growth regulation and stress responses, the regulatory functions of AP2/ERF in plant metabolite biosynthesis have been described. We also discussed the roles of AP2/ERF transcription factors in different phytohormone-mediated signaling pathways in plants. Genomic-wide analysis indicated that AP2/ERF transcription factors were highly conserved during plant evolution. Some public databases containing the information of AP2/ERF have been introduced. The studies of AP2/ERF factors will provide important bases for plant regulatory mechanisms and molecular breeding.

Identification of a novel ERF gene, TaERF8, associated with plant height and yield in wheat

BACKGROUND

Ethylene Responsive Factor (ERF) is involved in various processes of plant development and stress responses. In wheat, several ERFs have been identified and their roles in mediating biotic or abiotic stresses have been elucidated. However, their effects on wheat plant architecture and yield-related traits remain poorly studied.

RESULTS

In this study, TaERF8, a new member of the ERF family, was isolated in wheat (Triticum aestivum L.). Three homoeologous TaERF8 genes, TaERF8-2A, TaERF8-2B and TaERF8-2D (named according to sub-genomic origin), were cloned from the common wheat cultivar Chinese Spring. The three homoeologs showed highly similar protein sequences, with identical AP2 domain. Whereas homoeologs sequence polymorphism analysis allowed the establishment of ten, two and three haplotypes, respectively. Expression analysis revealed that TaERF8s were constitutively expressed through entire wheat developmental stages. Analysis of related agronomic traits of TaERF8-2B overexpressing transgenic lines showed that TaERF8-2B plays a role in regulating plant architecture and yield-related traits. Association analysis between TaERF8-2B haplotypes (Hap-2B-1 and Hap-2B-2) and agronomic traits showed that TaERF8-2B was associated with plant height, heading date and 1000 kernel weight (TKW). The TaERF8-2B haplotypes distribution analysis revealed that Hap-2B-2 frequency increased in domesticated emmer wheat and modern varieties, being predominant in five major China wheat producing zones.

CONCLUSION

These results indicated that TaERF8s are differentially involved in the regulation of wheat growth and development. Haplotype Hap-2B-2 was favored during domestication and in Chinese wheat breeding. Unveiling that the here described molecular marker TaERF8-2B-InDel could be used for marker-assisted selection, plant architecture and TKW improvement in wheat breeding.

Association mapping for yield traits in Paeonia rockii based on SSR markers within transcription factors of comparative transcriptome

BACKGROUND

Allelic variation underlying the quantitative traits in plants is caused by the extremely complex regulation process. Tree peony originated in China is a peculiar ornamental, medicinal and oil woody plant. Paeonia rockii, one of tree peony species, is a precious emerging woody oil crop. However, in this valuable plant, the study of functional loci associated with yield traits has rarely been identified. Therefore, to explore the genetic architecture of 24 yield quantitative traits, the association mapping was first reported in 420 unrelated cultivated P. rockii individuals based on the next-generation sequencing (NGS) and single-molecule long-read sequencing (SMLRS).

RESULTS

The developed 58 pairs of polymorphic expressed sequence tag-simple sequence repeat (EST-SSR) markers from 959 candidate transcription factors (TFs) associated with yield were used for genotyping the 420 P. rockii accessions. We observed a high level of genetic diversity (polymorphic information content, PIC = 0.514) and low linkage disequilibrium (LD) between EST-SSRs. Moreover, four subpopulations in the association population were revealed by STRUCTURE analyses. Further, single-marker association analysis identified 141 significant associations, involving 17 quantitative traits and 41 EST-SSRs. These loci were mainly from AP2, TCP, MYB, HSF, bHLH, GATA, and B3 gene families and showed a small proportion of the phenotypic variance (3.79 to 37.45%).

CONCLUSIONS

Our results summarize a valuable collection of functional loci associated with yield traits in P. rockii, and provide a precious resource that reveals allelic variation underlying quantitative traits in Paeonia and other woody oil crops.

Host interactors of effector proteins of the lettuce downy mildew Bremia lactucae obtained by yeast two-hybrid screening

Plant pathogenic bacteria, fungi and oomycetes secrete effector proteins to manipulate host cell processes to establish a successful infection. Over the last decade the genomes and transcriptomes of many agriculturally important plant pathogens have been sequenced and vast candidate effector repertoires were identified using bioinformatic analyses. Elucidating the contribution of individual effectors to pathogenicity is the next major hurdle. To advance our understanding of the molecular mechanisms underlying lettuce susceptibility to the downy mildew Bremia lactucae, we mapped physical interactions between B. lactucae effectors and lettuce candidate target proteins. Using a lettuce cDNA library-based yeast-two-hybrid system, 61 protein-protein interactions were identified, involving 21 B. lactucae effectors and 46 unique lettuce proteins. The top ten interactors based on the number of independent colonies identified in the Y2H and two interactors that belong to gene families involved in plant immunity, were further characterized. We determined the subcellular localization of the fluorescently tagged lettuce proteins and their interacting effectors. Importantly, relocalization of effectors or their interactors to the nucleus was observed for four protein-pairs upon their co-expression, supporting their interaction in planta.

Transcription factors as molecular switches to regulate drought adaptation in maize

Here, we reviewed major transcription factors of maize that confer drought stress tolerance, and their target genes and involved signaling pathway. Transcription factors in maize can be promising candidates for improving comprehensive resistance of multiple environmental stimuli. Adverse environmental stress is the main influencing factor affecting plant growth and reproduction, which poses tremendous threats to sustainable agriculture development and crops productivity worldwide. Among various abiotic stress factors, drought is the most vital adversity with the characteristics of frequent occurrences, long duration, and globality. Maize (Zea mays L.) is a major source of food supply for human being and livestock and recently for biofuel. Maize is the crop that is highly susceptible to drought stress. Drought stress tolerance in plants is quite complex, and it is not ideal to improve crop drought tolerance through a single resistant gene. Transcription factors participate in the regulation of plant growth and development, morphogenesis, and various environmental stress responses via regulating the expression level of their target stress-responsive genes independently or cross talk with other transcription factors, thereby the comprehensive resistance of multiple stresses in crops is improved. This review aims to summarize the major drought-tolerant transcription factors in maize and their regulatory network. With the continuous identification of maize transcription factors, more will be demonstrated to confer drought tolerance either in maize or other crops. It is expected that the transcription factors will greatly enrich the functional gene resources and will be a benefit to drought-tolerant maize cultivars breeding.

Characterization of the AP2/ERF Transcription Factor Family and Expression Profiling of DREB Subfamily under Cold and Osmotic Stresses in Ammopiptanthus nanus

APETALA2/ethylene-responsive factor (AP2/ERF) is one of the largest transcription factor (TF) families in plants, which play important roles in regulating plant growth, development, and response to environmental stresses. Ammopiptanthus nanus, an unusual evergreen broad-leaved shrub in the arid region in the northern temperate zone, demonstrates a strong tolerance to low temperature and drought stresses, and AP2/ERF transcription factors may contribute to the stress tolerance of A. nanus. In the current study, 174 AP2/ERF family members were identified from the A. nanus genome, and they were divided into five subfamilies, including 92 ERF members, 55 dehydration-responsive element binding (DREB) members, 24 AP2 members, 2 RAV members, and 1 Soloist member. Compared with the other leguminous plants, A. nanus has more members of the DREB subfamily and the B1 group of the ERF subfamily, and gene expansion in the AP2/ERF family is primarily driven by tandem and segmental duplications. Promoter analysis showed that many stress-related cis-acting elements existed in promoter regions of the DREB genes, implying that MYB, ICE1, and WRKY transcription factors regulate the expression of DREB genes in A. nanus. Expression profiling revealed that the majority of DREB members were responsive to osmotic and cold stresses, and several DREB genes such as EVM0023336.1 and EVM0013392.1 were highly induced by cold stress, which may play important roles in cold response in A. nanus. This study provided important data for understanding the evolution and functions of AP2/ERF and DREB transcription factors in A. nanus.

Overexpression of GmNFYA5 confers drought tolerance to transgenic Arabidopsis and soybean plants

BACKGROUND

Crop productivity is challenged by abiotic stresses, among which drought stress is the most common. NF-Y genes, especially NF-YA genes, regulate tolerance to abiotic stress.

RESULTS

Soybean NF-Y gene GmNFYA5 was identified to have the highest transcript level among all 21 NF-YA genes in soybean (Glycine max L.) under drought stress. Drought-induced transcript of GmNFYA5 was suppressed by the ABA synthesis inhibitor naproxen (NAP). GmNFYA5 transcript was detected in various tissues at vegetative and reproductive growth stages with higher levels in roots and leaves than in other tissues, which was consist with the GmNFYA5 promoter: GUS fusion assay. Overexpression of GmNFYA5 in transgenic Arabidopsis plants caused enhanced drought tolerance in seedlings by decreasing stomatal aperture and water loss from leaves. Overexpression and suppression of GmNFYA5 in soybean resulted in increased and decreased drought tolerance, respectively, relative to plants with an empty vector (EV). Transcript levels of ABA-dependent genes (ABI2, ABI3, NCED3, LEA3, RD29A, P5CS1, GmWRKY46, GmNCED2 and GmbZIP1) and ABA-independent genes (DREB1A, DREB2A, DREB2B, GmDREB1, GmDREB2 and GmDREB3) in transgenic plants overexpressing GmNFYA5 were higher than those of wild-type plants under drought stress; suppression of GmNFYA5 transcript produced opposite results. GmNFYA5 probably regulated the transcript abundance of GmDREB2 and GmbZIP1 by binding to the promoters in vivo.

CONCLUSIONS

Our results suggested that overexpression of GmNFYA5 improved drought tolerance in soybean via both ABA-dependent and ABA-independent pathways.

In silico mining and functional analysis of AP2/ERF gene in Withania somnifera

Withania somnifera owing to its strong and remarkable stress tolerance property is a reliable candidate for the determination of genes involved in mechanism of adaption/tolerance of various stress conditions. 187 AP2/ERF gene related transcripts (GRTs) were identified during comprehensive search in W. somnifera transcriptome repertoire. Major hits in homology search were observed from the model plant Arabidopsis and members of Solanaceae family. Cloning, expression analysis of the gene and genetic transient transformation with the gene (WsAP2) were performed to predict its functional role in planta. Enhanced expression of some of the pathway genes for terpenoid biosynthesis was observed in transformed tissues in comparison to the control tissues. It is speculated that WsAP2 gene crucially regulates the expression of GGPPS gene in addition to the regulation of other important genes of terpenoid pathway via induction of expression of other genes such as HMGR, CAS, DXS and DXR. To the best of our knowledge, this is the first report representing detailed study of AP2/ERF gene family in W. somnifera. It is also suggested from the study that gene might have role in eliciting responses to combat stress and attribute the strong stress tolerant property associated with the plant.

Comparative Root Transcriptomics Provide Insights into Drought Adaptation Strategies in Chickpea (Cicer arietinum L.)

Drought adversely affects crop production across the globe. The root system immensely contributes to water management and the adaptability of plants to drought stress. In this study, drought-induced phenotypic and transcriptomic responses of two contrasting chickpea (Cicer arietinum L.) genotypes were compared at the vegetative, reproductive transition, and reproductive stages. At the vegetative stage, drought-tolerant genotype maintained higher root biomass, length, and surface area under drought stress as compared to sensitive genotype. However, at the reproductive stage, root length and surface area of tolerant genotype was lower but displayed higher root diameter than sensitive genotype. The shoot biomass of tolerant genotype was overall higher than the sensitive genotype under drought stress. RNA-seq analysis identified genotype- and developmental-stage specific differentially expressed genes (DEGs) in response to drought stress. At the vegetative stage, a total of 2161 and 1873 DEGs, and at reproductive stage 4109 and 3772 DEGs, were identified in the tolerant and sensitive genotypes, respectively. Gene ontology (GO) analysis revealed enrichment of biological categories related to cellular process, metabolic process, response to stimulus, response to abiotic stress, and response to hormones. Interestingly, the expression of stress-responsive transcription factors, kinases, ROS signaling and scavenging, transporters, root nodulation, and oxylipin biosynthesis genes were robustly upregulated in the tolerant genotype, possibly contributing to drought adaptation. Furthermore, activation/repression of hormone signaling and biosynthesis genes was observed. Overall, this study sheds new insights on drought tolerance mechanisms operating in roots with broader implications for chickpea improvement.

Comprehensive phylogenomic analysis of ERF genes in sorghum provides clues to the evolution of gene functions and redundancy among gene family members

APETALA2/Ethylene-Responsive transcription factors (AP2/ERF), with their multifunctional roles in plant development, hormone signaling and stress tolerance, are important candidates for engineering crop plants. Here, we report identification and analysis of gene structure, phylogenetic distribution, expression, chromosomal localization and cis-acting promoter analysis of AP2/ERF genes in the C4 crop plant sorghum. We identified 158 ERF genes in sorghum with 52 of them encoding dehydration-responsive binding elements (DREB) while 106 code for ERF subfamily proteins. Phylogenetic analysis organized sorghum ERF proteins into 11 distinct groups exhibiting clade-specific expansion. About 68% ERF genes have paralogs indicating gene duplications as major cause of expansion of ERF family in sorghum. Analysis of spatiotemporal expression patterns using publicly available data revealed their tissue/genotype-preferential accumulation. In addition, 40 ERF genes exhibited differential accumulation in response to heat and/or drought stress. About 25% of the segmental gene pairs and eleven tandem duplicated genes exhibited high correlation (> 0.7) in their expression patterns indicating genetic redundancy. Comparative phylogenomic analysis of sorghum ERFs with 74 genetically characterized ERF genes from other plant species provided significant clues to sorghum ERF functions. Overall data generated here provides an overview of evolutionary relationship among ERF gene family members in sorghum and with respect to previously characterized ERF genes from other plant species. This information will be instrumental in initiating functional genomic studies of ERF candidates in sorghum.

Identification of Pepper CaSBP08 Gene in Defense Response Against Phytophthora capsici Infection

Little information is available on the role of Squamosa promoter binding protein (SBP)-box genes in pepper plants. This family of genes is known to have transcription characteristics specific to plants and to regulate plant growth, development, stress responses, and signal transduction. To investigate their specific effects in pepper (Capsicum annuum), we screened pepper SBP-box family genes (CaSBP genes) for Phytophthora capsici (P. capsici) resistance genes using virus-induced gene silencing. CaSBP08, CaSBP11, CaSBP12, and CaSBP13, which are associated with plant defense responses against P. capsici, were obtained from among fifteen identified CaSBP genes. The function of CaSBP08 was identified in pepper defense response against P. capsici infection in particular. CaSBP08 protein was localized to the nucleus. Silencing of CaSBP08 enhanced resistance to P. capsici infection. Following P. capsici inoculation, the malondialdehyde content, peroxidase activity, and disease index percentage of the CaSBP08-silenced plants decreased compared to the control. Additionally, the expression levels of other defense-related genes, especially those of CaBPR1 and CaSAR8.2, were more strongly induced in CaSBP08-silenced plants than in the control. However, CaSBP08 overexpression in Nicotiana benthamiana enhanced susceptibility to P. capsici infection. This work provides a foundation for the further research on the role of CaSBP genes in plant defense responses against P. capsici infection.