Functional identification of apple MdJAZ2 in Arabidopsis with reduced JA-sensitivity and increased stress tolerance

CwJAZ4/9 negatively regulates jasmonate-mediated biosynthesis of terpenoids through interacting with CwMYC2 and confers salt tolerance in Curcuma wenyujin

Plant JASMONATE ZIM-DOMAIN (JAZ) genes play crucial roles in regulating the biosynthesis of specialized metabolites and stressful responses. However, understanding of JAZs controlling these biological processes lags due to numerous JAZ copies. Here, we found that two leaf-specific CwJAZ4/9 genes from Curcuma wenyujin are strongly induced by methyl-jasmonate (MeJA) and negatively correlated with terpenoid biosynthesis. Yeast two-hybrid, luciferase complementation imaging and in vitro pull-down assays confirmed that CwJAZ4/9 proteins interact with CwMYC2 to form the CwJAZ4/9-CwMYC2 regulatory cascade. Furthermore, transgenic hairy roots showed that CwJAZ4/9 acts as repressors of MeJA-induced terpenoid biosynthesis by inhibiting the terpenoid pathway and jasmonate response, thus reducing terpenoid accumulation. In addition, we revealed that CwJAZ4/9 decreases salt sensitivity and sustains the growth of hairy roots under salt stress by suppressing the salt-mediated jasmonate responses. Transcriptome analysis for MeJA-mediated transgenic hairy root lines further confirmed that CwJAZ4/9 negatively regulates the terpenoid pathway genes and massively alters the expression of genes related to salt stress signaling and responses, and crosstalks of multiple phytohormones. Altogether, our results establish a genetic framework to understand how CwJAZ4/9 inhibits terpenoid biosynthesis and confers salt tolerance, which provides a potential strategy for producing high-value pharmaceutical terpenoids and improving resistant C. wenyujin varieties by a genetic approach.

Genome-wide identification of JAZ gene family members in autotetraploid cultivated alfalfa (Medicago sativa subsp. sativa) and expression analysis under salt stress

BACKGROUND

Jasmonate ZIM-domain (JAZ) proteins, which act as negative regulators in the jasmonic acid (JA) signalling pathway, have significant implications for plant development and response to abiotic stress.

RESULTS

Through a comprehensive genome-wide analysis, a total of 20 members of the JAZ gene family specific to alfalfa were identified in its genome. Phylogenetic analysis divided these 20 MsJAZ genes into five subgroups. Gene structure analysis, protein motif analysis, and 3D protein structure analysis revealed that alfalfa JAZ genes in the same evolutionary branch share similar exon‒intron, motif, and 3D structure compositions. Eight segmental duplication events were identified among these 20 MsJAZ genes through collinearity analysis. Among the 32 chromosomes of the autotetraploid cultivated alfalfa, there were 20 MsJAZ genes distributed on 17 chromosomes. Extensive stress-related cis-acting elements were detected in the upstream sequences of MsJAZ genes, suggesting that their response to stress has an underlying function. Furthermore, the expression levels of MsJAZ genes were examined across various tissues and under the influence of salt stress conditions, revealing tissue-specific expression and regulation by salt stress. Through RT‒qPCR experiments, it was discovered that the relative expression levels of these six MsJAZ genes increased under salt stress.

CONCLUSIONS

In summary, our study represents the first comprehensive identification and analysis of the JAZ gene family in alfalfa. These results provide important information for exploring the mechanism of JAZ genes in alfalfa salt tolerance and identifying candidate genes for improving the salt tolerance of autotetraploid cultivated alfalfa via genetic engineering in the future.

Genome-wide identification and expression analysis of the Eriobotrya japonica TIFY gene family reveals its functional diversity under abiotic stress conditions

BACKGROUND

Plant-specific TIFY proteins are widely found in terrestrial plants and play important roles in plant adversity responses. Although the genome of loquat at the chromosome level has been published, studies on the TIFY family in loquat are lacking. Therefore, the EjTIFY gene family was bioinformatically analyzed by constructing a phylogenetic tree, chromosomal localization, gene structure, and adversity expression profiling in this study.

RESULTS

Twenty-six EjTIFY genes were identified and categorized into four subfamilies (ZML, JAZ, PPD, and TIFY) based on their structural domains. Twenty-four EjTIFY genes were irregularly distributed on 11 of the 17 chromosomes, and the remaining two genes were distributed in fragments. We identified 15 covariate TIFY gene pairs in the loquat genome, 13 of which were involved in large-scale interchromosomal segmental duplication events, and two of which were involved in tandem duplication events. Many abiotic stress cis-elements were widely present in the promoter region. Analysis of the Ka/Ks ratio showed that the paralogous homologs of the EjTIFY family were mainly subjected to purifying selection. Analysis of the RNA-seq data revealed that a total of five differentially expressed genes (DEGs) were expressed in the shoots under gibberellin treatment, whereas only one gene was significantly differentially expressed in the leaves; under both low-temperature and high-temperature stresses, there were significantly differentially expressed genes, and the EjJAZ15 gene was significantly upregulated under both low- and high-temperature stress. RNA-seq and qRT-PCR expression analysis under salt stress conditions revealed that EjJAZ2, EjJAZ4, and EjJAZ9 responded to salt stress in loquat plants, which promoted resistance to salt stress through the JA pathway. The response model of the TIFY genes in the jasmonic acid pathway under salt stress in loquat was systematically summarized.

CONCLUSIONS

These results provide a theoretical basis for exploring the characteristics and functions of additional EjTIFY genes in the future. This study also provides a theoretical basis for further research on breeding for salt stress resistance in loquat. RT-qPCR analysis revealed that the expression of one of the three EjTIFY genes increased and the expression of two decreased under salt stress conditions, suggesting that EjTIFY exhibited different expression patterns under salt stress conditions.

A High-K+ Affinity Transporter (HKT) from Actinidia valvata Is Involved in Salt Tolerance in Kiwifruit

Ion transport is crucial for salt tolerance in plants. Under salt stress, the high-affinity K+ transporter (HKT) family is mainly responsible for the long-distance transport of salt ions which help to reduce the deleterious effects of high concentrations of ions accumulated within plants. Kiwifruit is well known for its susceptibility to salt stress. Therefore, a current study was designed to decipher the molecular regulatory role of kiwifruit HKT members in the face of salt stress. The transcriptome data from Actinidia valvata revealed that salt stress significantly induced the expression of AvHKT1. A multiple sequence alignment analysis indicated that the AvHKT1 protein contains three conserved amino acid sites for the HKT family. According to subcellular localization analysis, the protein was primarily present in the cell membrane and nucleus. Additionally, we tested the AvHKT1 overexpression in 'Hongyang' kiwifruit, and the results showed that the transgenic lines exhibited less leaf damage and improved plant growth compared to the control plants. The transgenic lines displayed significantly higher SPAD and Fv/Fm values than the control plants. The MDA contents of transgenic lines were also lower than that of the control plants. Furthermore, the transgenic lines accumulated lower Na+ and K+ contents, proving this protein involvement in the transport of Na+ and K+ and classification as a type II HKT transporter. Further research showed that the peroxidase (POD) activity in the transgenic lines was significantly higher, indicating that the salt-induced overexpression of AvHKT1 also scavenged POD. The promoter of AvHKT1 contained phytohormone and abiotic stress-responsive cis-elements. In a nutshell, AvHKT1 improved kiwifruit tolerance to salinity by facilitating ion transport under salt stress conditions.

Role of F-box E3-ubiquitin ligases in plant development and stress responses

KEY MESSAGE

F-box E3-ubiquitin ligases regulate critical biological processes in plant development and stress responses. Future research could elucidate why and how plants have acquired a large number of F-box genes. The ubiquitin-proteasome system (UPS) is a predominant regulatory mechanism employed by plants to maintain the protein turnover in the cells and involves the interplay of three classes of enzymes, E1 (ubiquitin-activating), E2 (ubiquitin-conjugating), and E3 ligases. The diverse and most prominent protein family among eukaryotes, F-box proteins, are a vital component of the multi-subunit SCF (Skp1-Cullin 1-F-box) complex among E3 ligases. Several F-box proteins with multifarious functions in different plant systems have evolved rapidly over time within closely related species, but only a small part has been characterized. We need to advance our understanding of substrate-recognition regulation and the involvement of F-box proteins in biological processes and environmental adaptation. This review presents a background of E3 ligases with particular emphasis on the F-box proteins, their structural assembly, and their mechanism of action during substrate recognition. We discuss how the F-box proteins regulate and participate in the signaling mechanisms of plant development and environmental responses. We highlight an urgent need for research on the molecular basis of the F-box E3-ubiquitin ligases in plant physiology, systems biology, and biotechnology. Further, the developments and outlooks of the potential technologies targeting the E3-ubiquitin ligases for developing crop improvement strategies have been discussed.

Regulatory Mechanism of the Constitutive Photomorphogenesis 9 Signalosome Complex in Response to Abiotic Stress in Plants

The constitutive photomorphogenesis 9 (COP9) signalosome (CSN) is a highly conserved protein complex that regulates signaling pathways in plants under abiotic stress. We discuss the potential molecular mechanisms of CSN under abiotic stress, including oxidative stress with reactive oxygen species signaling, salt stress with jasmonic acid, gibberellic acid, and abscisic acid signaling, high-temperature stress with auxin signaling, and optical radiation with DNA damage and repair response. We conclude that CSN likely participates in affecting antioxidant biosynthesis and hormone signaling by targeting receptors, kinases, and transcription factors in response to abiotic stress, which potentially provides valuable information for engineering stress-tolerant crops.

Identification of TIFY gene family in walnut and analysis of its expression under abiotic stresses

Background

Walnuts (Juglans regia L.) are known for their nutrient-rich nuts and are one of the important economic tree species in the world. However, due to global warming and soil salinization, walnuts suffer from various abiotic stresses. TIFY (TIF[F/Y]XG) proteins play an essential role in the growth and development of plants, signal transduction, and stress response in plants. At present, although the TIFY gene family of a number of plants has been identified and studied, how TIFY takes part in stress tolerance remains obscure and many functions of TIFY require further investigation.

Result

In this study, twenty-one TIFY transcription factors were identified in the walnut genome database, and they were divided into four subfamilies (TIFY, JAZ, ZML, and PPD) by bioinformatics analysis. Chromosome location revealed tandem duplication of some genes. Phylogenetic tree analysis showed JrTIFYs were closely related to the TIFY gene family of Arabidopsis thaliana (A. thaliana). qRT-PCR (quantitative real-time PCR) analysis revealed the TIFY genes have different expression patterns in ‘Qingxiang’ and ‘Xiangling’ walnut varieties under drought, heat, and salt stress. JAZ subfamily was more expressed in different abiotic stress than other subfamilies. The expressions of JrTIFY14 under heat and salt stress were significantly higher than those under drought stress. However, the expression of JrTIFYs was not significant in ‘Xiangling’.

Conclusion

This study reveals the TIFY gene family plays an important role in walnuts facing abiotic stresses and provides a theoretical basis for walnut breeding.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08416-9.

Key Genes in the JAZ Signaling Pathway Are Up-Regulated Faster and More Abundantly in Caterpillar-Resistant Maize

Jasmonic acid (JA) and its derivatives, collectively known as jasmonates (JAs), are important signaling hormones for plant responses against chewing herbivores. In JA signaling networks, jasmonate ZIM-domain (JAZ) proteins are transcriptional repressors that regulate JA-modulated downstream herbivore defenses. JAZ repressors are widely presented in land plants, however, there is only limited information about the regulation/function of JAZ proteins in maize. In this study, we performed a comprehensive expression analysis of ZmJAZ genes with other selected genes in the jasmonate pathway in response to feeding by fall armyworm (Spodoptera frugiperda, FAW), mechanical wounding, and exogenous hormone treatments in two maize genotypes differing in FAW resistance. Results showed that transcript levels of JAZ genes and several key genes in JA-signaling and biosynthesis pathways were rapidly and abundantly expressed in both genotypes in response to these various treatments. However, there were key differences between the two genotypes in the expression of ZmJAZ1 and ZmCOI1a, these two genes were expressed significantly rapidly and abundantly in the resistant line which was tightly regulated by endogenous JA level upon feeding. For instance, transcript levels of ZmJAZ1 increase dramatically within 30 min of FAW-fed Mp708 but not Tx601, correlating with the JA accumulation. The results also demonstrated that wounding or JA treatment alone was not as effective as FAW feeding; this suggests that insect-derived factors are required for optimal defense responses.

Overexpression of watermelon m6A methyltransferase ClMTB enhances drought tolerance in tobacco by mitigating oxidative stress and photosynthesis inhibition and modulating stress-responsive gene expression

N6-methyladenosine (m6A) in RNA is a very important post-transcriptional modification mechanism in eukaryotes. It has been reported to have important regulatory roles in some stress responses in model plants, but there has been no research regarding m6A modifications in watermelon. In this study, we cloned and characterized m6A methyltransferase, ClMTB (mRNA adenosine methylase B, METTL14 human homolog protein) in watermelon. ClMTB expression could be weakly induced by drought stress as determined by the quantitative real-time PCR (qRT-PCR) and Promoter::GUS analyses. ClMTB over-expressed in tobacco plants increased drought tolerance via enhancing reactive oxygen species (ROS) scavenging system and alleviating photosynthesis inhibition under drought. Transcriptome profiles indicated the multiple hormone and stress-responsive genes were specifically induced in over-expressed ClMTB plants under drought conditions. These results suggest that ClMTB-mediated m6A modification serves as a positive regulatory factor of drought tolerance. This study is the first one to provide an understanding of the specific roles of ClMTB in watermelon adaptation to drought stress, and may also provide important insights into the signaling pathway mediated by m6A modification in response to stress conditions.

New Insights Into Structure and Function of TIFY Genes in Zea mays and Solanum lycopersicum: A Genome-Wide Comprehensive Analysis

The TIFY gene family, a key plant-specific transcription factor (TF) family, is involved in diverse biological processes including plant defense and growth regulation. Despite TIFY proteins being reported in some plant species, a genome-wide comparative and comprehensive analysis of TIFY genes in plant species can reveal more details. In the current study, the members of the TIFY gene family were significantly increased by the identification of 18 and six new members using maize and tomato reference genomes, respectively. Thus, a genome-wide comparative analysis of the TIFY gene family between 48 tomato (Solanum lycopersicum, a dicot plant) genes and 26 maize (Zea mays, a monocot plant) genes was performed in terms of sequence structure, phylogenetics, expression, regulatory systems, and protein interaction. The identified TIFYs were clustered into four subfamilies, namely, TIFY-S, JAZ, ZML, and PPD. The PPD subfamily was only detected in tomato. Within the context of the biological process, TIFY family genes in both studied plant species are predicted to be involved in various important processes, such as reproduction, metabolic processes, responses to stresses, and cell signaling. The Ka/Ks ratios of the duplicated paralogous gene pairs indicate that all of the duplicated pairs in the TIFY gene family of tomato have been influenced by an intense purifying selection, whereas in the maize genome, there are three duplicated blocks containing Ka/Ks > 1, which are implicated in evolution with positive selection. The amino acid residues present in the active site pocket of TIFY proteins partially differ in each subfamily, although the Mg or Ca ions exist heterogeneously in the centers of the active sites of all the predicted TIFY protein models. Based on the expression profiles of TIFY genes in both plant species, JAZ subfamily proteins are more associated with the response to abiotic and biotic stresses than other subfamilies. In conclusion, globally scrutinizing and comparing the maize and tomato TIFY genes showed that TIFY genes play a critical role in cell reproduction, plant growth, and responses to stress conditions, and the conserved regulatory mechanisms may control their expression.

Jasmonates and Plant Salt Stress: Molecular Players, Physiological Effects, and Improving Tolerance by Using Genome-Associated Tools

Soil salinity is one of the most limiting stresses for crop productivity and quality worldwide. In this sense, jasmonates (JAs) have emerged as phytohormones that play essential roles in mediating plant response to abiotic stresses, including salt stress. Here, we reviewed the mechanisms underlying the activation and response of the JA-biosynthesis and JA-signaling pathways under saline conditions in Arabidopsis and several crops. In this sense, molecular components of JA-signaling such as MYC2 transcription factor and JASMONATE ZIM-DOMAIN (JAZ) repressors are key players for the JA-associated response. Moreover, we review the antagonist and synergistic effects between JA and other hormones such as abscisic acid (ABA). From an applied point of view, several reports have shown that exogenous JA applications increase the antioxidant response in plants to alleviate salt stress. Finally, we discuss the latest advances in genomic techniques for the improvement of crop tolerance to salt stress with a focus on jasmonates.

Overexpression of SlMYB75 enhances resistance to Botrytis cinerea and prolongs fruit storage life in tomato

SlMYB75 increased the accumulation of JA and improved the scavenging of excess H₂O₂ to resist B. cinerea. Overexpression of SlMYB75 greatly prolongs tomato fruit storage life. Botrytis cinerea (B. cinerea) is a major threat to the production and storage life of tomato (Solanum lycopersicum) fruit around the world. SlMYB75 is an R2R3MYB transcription factor associated with the biosynthesis of anthocyanidin, but little is known about its function in the resistance of tomato to B. cinerea. In this study, we found that the overexpression of SlMYB75 regulated the accumulation of jasmonic acid (JA) and promoted the JA-mediated signaling pathway to resist B. cinerea infection. Moreover, the activities of peroxidase and superoxide dismutase, which were activated to scavenge hydrogen peroxide produced as a result of the B. cinerea infection, were enhanced in the transgenic tomato plants. Scanning electron microscopy images showed that the wax on the fruit skin surface was significantly decreased in the transgenic tomatoes compared with the wild type. However, SlMYB75 prolonged fruit storage life by both enhancing resistance to B. cinerea and directly downregulating the fruit shelf life-related gene SlFSR. Collectively, this study provides a good candidate gene for breeding high-quality tomatoes with a long storage life and high disease resistance.

A new functional JAZ degron sequence in strawberry JAZ1 revealed by structural and interaction studies on the COI1-JA-Ile/COR-JAZs complexes

The phytohormone jasmonoyl-isoleucine (JA-Ile) regulates fundamental plant processes as developmental and defense responses. JA-Ile mediates the interaction between the F-box protein COI1 (part of the SCF^COI1 E3 ubiquitin ligase) and a JAZ repressor leading to early jasmonate responses. The Arabidopsis JAZ1 protein contains the canonical LPIARR degron sequence, which is responsible for the stabilization of the AtCOI1-JA-Ile-AtJAZ1 complex. In strawberry (Fragaria × ananassa) JAZ family was described at the transcriptional level during fruit development but the information about the interaction mode of this complex is still scarce at the molecular level. To gain insight into the strawberry JA-Ile receptor complex, we evaluated the interaction at the structural level, and protein models were built and analyzed for FaCOI1 and FaJAZ1, FaJAZ8.1, and FaJAZ10. The interaction between FaCOI1 and FaJAZ1, FaJAZ8.1 and FaJAZ10 were explored using several ligands, through molecular docking and molecular dynamics (MD) simulations, finding the strongest interaction with (+)-7-iso-JA-Ile than other ligands. Additionally, we tested interactions between FaCOI1 and FaJAZs by yeast two-hybrid assays in the presence of coronatine (COR, a JA-Ile mimic). We detected strong COR-dependent interactions between FaCOI1 and FaJAZ1. Interestingly, FaJAZ1 contains a new non-canonical (IPMQRK) functional degron sequence, in which Arg and Lys are the key residues for maintaining the interaction of the FaCOI1–COR–FaJAZ1 complex as we observed in mutated versions of the FaJAZ1 degron. Phylogenetic analysis showed that the IPMQRK degron is only present in orthologs belonging to the Rosoideae but not in other Rosaceae subfamilies. Together, this study uncovers a new degron sequence in plants, which could be required to make an alternative and functional JA-Ile perception complex in strawberry.

Genome-wide identification and expression analysis of jasmonate ZIM domain gene family in tuber mustard (Brassica juncea var. tumida)

Tuber mustard, which is the raw material of Fuling pickle, is a crop with great economic value. However, during growth and development, tuber mustard is frequently attacked by the pathogen Plasmodiophora brassicae and frequently experiences salinity stress. Jasmonic acid (JA) is a hormone related to plant resistance to biotic and abiotic stress. Jasmonate ZIM domain proteins (JAZs) are crucial components of the JA signaling pathway and play important roles in plant responses to biotic and abiotic stress. To date, no information is available about the characteristics of the JAZ family genes in tuber mustard. Here, 38 BjJAZ genes were identified in the whole genome of tuber mustard. The BjJAZ genes are located on 17 of 18 chromosomes in the tuber mustard genome. The gene structures and protein motifs of the BjJAZ genes are conserved between tuber mustard and Arabidopsis. The results of qRT-PCR analysis showed that BjuA030800 was specifically expressed in root, and BjuA007483 was specifically expressed in leaf. In addition, 13 BjJAZ genes were transiently induced by P. brassicae at 12 h, and 7 BjJAZ genes were induced by salt stress from 12 to 24 h. These results provide valuable information for further studies on the role of BjJAZ genes in the regulation of plant growth and development and in the response to biotic and abiotic stress.

Functional identification of apple on MdHIR4 in biotic stress

In plants, hypersensitive-induced reaction (HIR) proteins are involved in stress responses, especially biotic stress. However, the potential molecular mechanisms of HIR-mediated biotic resistance in plants are rarely reported. We found that apple (Malus domestica) MdHIR4 was localized in the cell nucleus and membrane similar to AtHIR1 in Arabidopsis. Moreover, salicylic acid and the bacterial flagellin flg22 (a conserved, 22-amino acid motif), which are relevant to biotic stress, could induce MdHIR4 expression. Additionally, the transcription level of MdHIR4 was increased by Methyl jasmonate treatment. Ectopic expression of MdHIR4 in Arabidopsis and Nicotiana benthamiana reduced sensitivity to Methyl jasmonate and enhanced resistance to the bacterial pathogen Pst DC3000 (Pseudomonas syringae tomato DC3000). The interaction between MdHIR4 and AtJAZs proteins (AtJAZ3, AtJAZ4, and AtJAZ9) implied that MdHIR4 participated in the jasmonic acid (JA) signaling pathway. We found the expression of JA-related genes and PRs to change in transgenic plants, further demonstrating that MdHIR4 mediated biotic stress through the JA signaling pathway. Repressing the expression of MdHIR4 in apple leaves and calli increased resistance to Botryosphaeria dothidea by influencing the transcription of resistance-related genes. Our findings reveal the resistant function to biotic stress of MdHIR4 in transgenic plants, including Arabidopsis, tobacco, and apple, and identify the regulating mechanism of MdHIR4-related biotic resistance.

The ICE-like transcription factor HbICE2 is involved in jasmonate-regulated cold tolerance in the rubber tree (Hevea brasiliensis)

An ICE-like transcription factor mediates jasmonate-regulated cold tolerance in the rubber tree (Hevea brasiliensis), and confers cold tolerance in transgenic Arabidopsis. The rubber tree (Hevea brasiliensis) is susceptible to low temperatures, and understanding the mechanisms regulating cold stress is of great potential value for enhancing tolerance to this environmental variable. In this study, we find that treatment with exogenous methyl jasmonate (MeJA) could significantly enhance Hevea brasiliensis cold tolerance. In addition, yeast two-hybrid and bimolecular fluorescence complementation (BiFC) experiments show that JASMONATE ZIM-DOMAIN(JAZ) proteins, HbJAZ1 and HbJAZ12, key repressors of JA signaling pathway, interact with HbICE2, a novel ICE (Inducer of CBF Expression)-like protein. HbICE2 was nuclear-localised and bound to the MYC recognition (MYCR) sequence. The transcriptional activation activity of HbICE2 in yeast cells was dependent on the N-terminus, and overexpression of HbICE2 in Arabidopsis resulted in elevated tolerance to chilling stress. Furthermore, dual-luciferase transient assay reveals that HbJAZ1 and HbJAZ12 proteins inhibit the transcriptional function of HbICE2. The expression of C-repeat-binding factor (CBF) signalling pathway genes including HbCBF1, HbCBF2 and HbCOR47 were up-regulated by MeJA. Taken together, our data suggest that the new ICE-like transcription factor HbICE2 is involved in jasmonate-regulated cold tolerance in Hevea brasiliensis.

Comprehensive Analysis of TIFY Transcription Factors and Their Expression Profiles under Jasmonic Acid and Abiotic Stresses in Watermelon

The TIFY gene family is plant-specific and encodes proteins involved in the regulation of multiple biological processes. Here, we identified 15 TIFY genes in the watermelon genome, which were divided into four subfamilies (eight JAZs, four ZMLs, two TIFYs, and one PPD) in the phylogenetic tree. The ClTIFY genes were unevenly located on eight chromosomes, and three segmental duplication events and one tandem duplication event were identified, suggesting that gene duplication plays a vital role in the expansion of the TIFY gene family in watermelon. Further analysis of the protein architectures, conserved domains, and gene structures provided additional clues for understanding the putative functions of the TIFY family members. Analysis of qRT-PCR and RNA-seq data revealed that the detected ClTIFY genes had preferential expression in specific tissues. qRT-PCR analysis revealed that nine selected TIFY genes were responsive to jasmonic acid (JA) and abiotic stresses including salt and drought. JA activated eight genes and suppressed one gene, among which ClJAZ1 and ClJAZ7 were the most significantly induced. Salt and drought stress activated nearly all the detected genes to different degrees. These results lay a foundation for further functional characterization of TIFY family genes in Citrullus lanatus.

Genome-wide identification and analysis of the COI gene family in wheat (Triticum aestivum L.)

Background

COI (CORONATINE INSENSITIVE), an F-box component of the Skp1-Cullin-F-box protein (SCF^COI1) ubiquitin E3 ligase, plays important roles in the regulation of plant growth and development. Recent studies have shown that COIs are involved in pollen fertility. In this study, we identified and characterized COI genes in the wheat genome and analyzed expression patterns under abiotic stress.

Results

A total of 18 COI candidate sequences for 8 members of COI gene family were isolated in wheat (Triticum aestivum L.). Phylogenetic and structural analyses showed that these COI genes could be divided into seven distinct subfamilies. The COI genes showed high expression in stamens and glumes. The qRT-PCR results revealed that wheat COIs were involved in several abiotic stress responses and anther/glume dehiscence in the photoperiod-temperature sensitive genic male sterile (PTGMS) wheat line BS366.

Conclusions

The structural characteristics and expression patterns of the COI gene family in wheat as well as the stress-responsive and differential tissue-specific expression profiles of each TaCOI gene were examined in PTGMS wheat line BS366. In addition, we examined SA- and MeJA-induced gene expression in the wheat anther and glume to investigate the role of COI in the JA signaling pathway, involved in the regulation of abnormal anther dehiscence in the PTGMS wheat line. The results of this study contribute novel and detailed information about the TaCOI gene family in wheat and could be used as a benchmark for future studies of the molecular mechanisms of PTGMS in other crops.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5116-9) contains supplementary material, which is available to authorized users.

Genome-Wide Association Mapping of Flowering and Ripening Periods in Apple

Deciphering the genetic control of flowering and ripening periods in apple is essential for breeding cultivars adapted to their growing environments. We implemented a large Genome-Wide Association Study (GWAS) at the European level using an association panel of 1,168 different apple genotypes distributed over six locations and phenotyped for these phenological traits. The panel was genotyped at a high-density of SNPs using the Axiom®Apple 480 K SNP array. We ran GWAS with a multi-locus mixed model (MLMM), which handles the putatively confounding effect of significant SNPs elsewhere on the genome. Genomic regions were further investigated to reveal candidate genes responsible for the phenotypic variation. At the whole population level, GWAS retained two SNPs as cofactors on chromosome 9 for flowering period, and six for ripening period (four on chromosome 3, one on chromosome 10 and one on chromosome 16) which, together accounted for 8.9 and 17.2% of the phenotypic variance, respectively. For both traits, SNPs in weak linkage disequilibrium were detected nearby, thus suggesting the existence of allelic heterogeneity. The geographic origins and relationships of apple cultivars accounted for large parts of the phenotypic variation. Variation in genotypic frequency of the SNPs associated with the two traits was connected to the geographic origin of the genotypes (grouped as North+East, West and South Europe), and indicated differential selection in different growing environments. Genes encoding transcription factors containing either NAC or MADS domains were identified as major candidates within the small confidence intervals computed for the associated genomic regions. A strong microsynteny between apple and peach was revealed in all the four confidence interval regions. This study shows how association genetics can unravel the genetic control of important horticultural traits in apple, as well as reduce the confidence intervals of the associated regions identified by linkage mapping approaches. Our findings can be used for the improvement of apple through marker-assisted breeding strategies that take advantage of the accumulating additive effects of the identified SNPs.