Cis-cinnamic acid-enhanced 1 gene plays a role in regulation of Arabidopsis bolting

Nitrate transporter protein NPF5.12 and major latex-like protein MLP6 are important defense factors against Verticillium longisporum

Plant defense responses to the soil-borne fungus Verticillium longisporum causing stem stripe disease on oilseed rape (Brassica napus) are poorly understood. In this study, a population of recombinant inbred lines (RILs) using the Arabidopsis accessions Sei-0 and Can-0 was established. Composite interval mapping, transcriptome data, and T-DNA mutant screening identified the NITRATE/PEPTIDE TRANSPORTER FAMILY 5.12 (AtNPF5.12) gene as being associated with disease susceptibility in Can-0. Co-immunoprecipitation revealed interaction between AtNPF5.12 and the MAJOR LATEX PROTEIN family member AtMLP6, and fluorescence microscopy confirmed this interaction in the plasma membrane and endoplasmic reticulum. CRISPR/Cas9 technology was applied to mutate the NPF5.12 and MLP6 genes in B. napus. Elevated fungal growth in the npf5.12 mlp6 double mutant of both oilseed rape and Arabidopsis demonstrated the importance of these genes in defense against V. longisporum. Colonization of this fungus depends also on available nitrates in the host root. Accordingly, the negative effect of nitrate depletion on fungal growth was less pronounced in Atnpf5.12 plants with impaired nitrate transport. In addition, suberin staining revealed involvement of the NPF5.12 and MLP6 genes in suberin barrier formation. Together, these results demonstrate a dependency on multiple plant factors that leads to successful V. longisporum root infection.

Genome-Wide Characterization and Expression Analyses of Major Latex Protein Gene Family in Populus simonii × P. nigra

Major latex proteins, or MLPs, are crucial to plants' capacity to grow, develop, and endure biotic and abiotic stresses. The MLP gene family has been found in numerous plants, but little is known about its role in Populus simonii × P. nigra. This study discovered and assessed 43 PtMLP genes that were unevenly dispersed throughout 12 chromosomes in terms of their physicochemical characteristics, gene structure, conserved motifs, and protein localization. Based on their phylogeny and protein structural characteristics, three separate subclasses of PtMLP family were identified. Segmental and tandem duplication were found to be essential variables in the expansion of the PtMLP genes. The involvement of the PtMLP genes in growth and development, as well as in the responses to different hormones and stresses, was demonstrated by cis-regulatory element prediction. The PtMLP genes showed varying expression patterns in various tissues and under different conditions (cold, salt, and drought stress), as demonstrated in RNA-Seq databases, suggesting that PsnMLP may have different functions. Following the further investigation of the genes demonstrating notable variations in expression before and after the application of three stresses, PsnMLP5 was identified as a candidate gene. Subsequent studies revealed that PsnMLP5 could be induced by ABA treatment. This study paves the way for further investigations into the MLP genes' functional mechanisms in response to abiotic stressors, as well as the ways in which they can be utilized in poplar breeding for improved stress tolerance.

Genome-Wide Evolutionary Characterization and Expression Analysis of Major Latex Protein (MLP) Family Genes in Tomato

Major latex proteins (MLPs) play a key role in plant response to abiotic and biotic stresses. However, little is known about this gene family in tomatoes (Solanum lycopersicum). In this paper, we perform a genome-wide evolutionary characterization and gene expression analysis of the MLP family in tomatoes. We found a total of 34 SlMLP members in the tomato genome, which are heterogeneously distributed on eight chromosomes. The phylogenetic analysis of the SlMLP family unveiled their evolutionary relationships and possible functions. Furthermore, the tissue-specific expression analysis revealed that the tomato MLP members possess distinct biological functions. Crucially, multiple cis-regulatory elements associated with stress, hormone, light, and growth responses were identified in the promoter regions of these SlMLP genes, suggesting that SlMLPs are potentially involved in plant growth, development, and various stress responses. Subcellular localization demonstrated that SlMLP1, SlMLP3, and SlMLP17 are localized in the cytoplasm. In conclusion, these findings lay a foundation for further dissecting the functions of tomato SlMLP genes and exploring the evolutionary relationships of MLP homologs in different plants.

Genomic insights into biased allele loss and increased gene numbers after genome duplication in autotetraploid Cyclocarya paliurus

BACKGROUND

Autopolyploidy is a valuable model for studying whole-genome duplication (WGD) without hybridization, yet little is known about the genomic structural and functional changes that occur in autopolyploids after WGD. Cyclocarya paliurus (Juglandaceae) is a natural diploid-autotetraploid species. We generated an allele-aware autotetraploid genome, a chimeric chromosome-level diploid genome, and whole-genome resequencing data for 106 autotetraploid individuals at an average depth of 60 × per individual, along with 12 diploid individuals at an average depth of 90 × per individual.

RESULTS

Autotetraploid C. paliurus had 64 chromosomes clustered into 16 homologous groups, and the majority of homologous chromosomes demonstrated similar chromosome length, gene numbers, and expression. The regions of synteny, structural variation and nonalignment to the diploid genome accounted for 81.3%, 8.8% and 9.9% of the autotetraploid genome, respectively. Our analyses identified 20,626 genes (69.18%) with four alleles and 9191 genes (30.82%) with one, two, or three alleles, suggesting post-polyploid allelic loss. Genes with allelic loss were found to occur more often in proximity to or within structural variations and exhibited a marked overlap with transposable elements. Additionally, such genes showed a reduced tendency to interact with other genes. We also found 102 genes with more than four copies in the autotetraploid genome, and their expression levels were significantly higher than their diploid counterparts. These genes were enriched in enzymes involved in stress response and plant defense, potentially contributing to the evolutionary success of autotetraploids. Our population genomic analyses suggested a single origin of autotetraploids and recent divergence (~ 0.57 Mya) from diploids, with minimal interploidy admixture.

CONCLUSIONS

Our results indicate the potential for genomic and functional reorganization, which may contribute to evolutionary success in autotetraploid C. paliurus.

Genetic diversity, population structure, and genome-wide association study for the flowering trait in a diverse panel of 428 moth bean (Vigna aconitifolia) accessions using genotyping by sequencing

BACKGROUND

Moth bean (Vigna aconitifolia) is an underutilized, protein-rich legume that is grown in arid and semi-arid areas of south Asia and is highly resistant to abiotic stresses such as heat and drought. Despite its economic importance, the crop remains unexplored at the genomic level for genetic diversity and trait mapping studies. To date, there is no report of SNP marker discovery and association mapping of any trait in this crop. Therefore, this study aimed to dissect the genetic diversity, population structure and marker-trait association for the flowering trait in a diversity panel of 428 moth bean accessions using genotyping by sequencing (GBS) approach.

RESULTS

A total of 9078 high-quality single nucleotide polymorphisms (SNPs) were discovered by genotyping of 428 moth bean accessions. Model-based structure analysis and PCA grouped the moth bean accessions into two subpopulations. Cluster analysis revealed accessions belonging to the Northwestern region of India had higher variability than accessions from the other regions suggesting that this region represents its center of diversity. AMOVA revealed more variations within individuals (74%) and among the individuals (24%) than among the populations (2%). Marker-trait association analysis using seven multi-locus models including mrMLM, FASTmrEMMA FASTmrEMMA, ISIS EM-BLASSO, MLMM, BLINK and FarmCPU revealed 29 potential genomic regions for the trait days to 50% flowering, which were consistently detected in three or more models. Analysis of the allelic effect of the major genomic regions explaining phenotypic variance of more than 10% and those detected in at least 2 environments showed 4 genomic regions with significant phenotypic effect on this trait. Further, we also analyzed genetic relationships among the Vigna species using SNP markers. The genomic localization of moth bean SNPs on genomes of closely related Vigna species demonstrated that maximum numbers of SNPs were getting localized on Vigna mungo. This suggested that the moth bean is most closely related to V. mungo.

CONCLUSION

Our study shows that the north-western regions of India represent the center of diversity of the moth bean. Further, the study revealed flowering-related genomic regions/candidate genes which can be potentially exploited in breeding programs to develop early-maturity moth bean varieties.

Arabidopsis histone H3 lysine 9 methyltransferases KYP/SUVH5/6 are involved in leaf development by interacting with AS1-AS2 to repress KNAT1 and KNAT2

The Arabidopsis H3K9 methyltransferases KRYPTONITE/SUPPRESSOR OF VARIEGATION 3-9 HOMOLOG 4 (KYP/SUVH4), SUVH5 and SUVH6 are redundantly involved in silencing of transposable elements (TEs). Our recent study indicated that KYP/SUVH5/6 can directly interact with the histone deacetylase HDA6 to synergistically regulate TE expression. However, the function of KYP/SUVH5/6 in plant development is still unclear. The transcriptional factors ASYMMETRIC LEAVES1 (AS1) and AS2 form a transcription complex, which is involved in leaf development by repressing the homeobox genes KNOTTED-LIKE FROM ARABIDOPSIS THALIANA 1 (KNAT1) and KNAT2. In this study, we found that KYP and SUVH5/6 directly interact with AS1-AS2 to repress KNAT1 and KNAT2 by altering histone H3 acetylation and H3K9 dimethylation levels. In addition, KYP can directly target the promoters of KNAT1 and KNAT2, and the binding of KYP depends on AS1. Furthermore, the genome-wide occupancy profile of KYP indicated that KYP is enriched in the promoter regions of coding genes, and the binding of KYP is positively correlated with that of AS1 and HDA6. Together, these results indicate that Arabidopsis H3K9 methyltransferases KYP/SUVH5/6 are involved in leaf development by interacting with AS1-AS2 to alter histone H3 acetylation and H3K9 dimethylation from KNAT1 and KNAT2 loci.

Genome-wide characterization of major latex protein gene family in peanut and expression analyses under drought and waterlogging stress

Peanut is an important oilseed crop around the world which provides vegetable oil, protein and vitamins for humans. Major latex-like proteins (MLPs) play important roles in plant growth and development, as well as responses to biotic and abiotic stresses. However, their biological function in peanut is still unclear. In this study, a genome-wide identification of MLP genes in cultivated peanut and two diploid ancestor species was analyzed to determine their molecular evolutionary characteristics and the expression profile under drought and waterlogging stress conditions. Firstly, a total of 135 MLP genes were identified from the genome of tetraploid peanut (Arachis hypogaea) and two diploid species Arachis. duranensis and Arachis. ipaensis. Then, phylogenetic analysis revealed that MLP proteins were divided into five different evolutionary groups. These genes were distributed unevenly at the ends of chromosomes 3, 5, 7, 8, 9 and 10 in three Arachis species. The evolution of MLP gene family in peanut was conserved and led by tandem and segmental duplication. The prediction analysis of cis-acting elements showed that the promoter region of peanut MLP genes contained different proportions of transcription factors, plant hormones-responsive elements and so on. The expression pattern analysis showed that they were differentially expressed under waterlogging and drought stress. These results of this study provide a foundation for further research on the function of the important MLP genes in peanut.

Genome-wide identification and characterization of major latex-like protein genes responsible for crop contamination in Cucurbita pepo

BACKGROUND

Zucchini plants (Cucurbita pepo) accumulate persistent organic pollutants (POPs) at high concentrations in their aerial parts, and major latex-like proteins (MLPs) play crucial roles in their accumulation. MLPs bind to POPs in root cells, MLP-POP complexes are then translocated into xylem vessels, and POPs are transported to the aerial parts. We previously identified three CpMLP genes (MLP-PG1, MLP-GR1, and MLP-GR3) as transporting factors for POPs; however, other studies have shown that the genomes of several plant species contain more than 10 MLP genes, thus, further MLP genes responsible for POP accumulation may have been overlooked.

METHODS AND RESULTS

Here, we investigated the number of CpMLP genes by performing a hidden Markov model search against the C. pepo genome database and characterized their effects on POP accumulation by performing the expression analysis in the organs and in silico structural analysis. The C. pepo genome contained 21 CpMLP genes, and several CpMLP genes, including MLP-PG1 and MLP-GR3, were highly expressed in roots. 3D structural prediction showed that all examined CpMLPs contained a cavity with a hydrophobic region, which facilitated binding to POPs.

CONCLUSIONS

The present study provides insights regarding CpMLP genes responsible for POP accumulation.

Genetic loci associated with freezing tolerance in a European rapeseed (Brassica napus L.) diversity panel identified by genome-wide association mapping

Winter biotypes of rapeseed (Brassica napus L.) require a vernalization treatment to enter the reproductive phase and generally produce greater yields than spring rapeseed. To find genetic loci associated with freezing tolerance in rapeseed, we first performed genotyping-by-sequencing (GBS) on a diversity panel consisting of 222 rapeseed accessions originating primarily from Europe, which identified 69,554 high-quality single-nucleotide polymorphisms (SNPs). Model-based cluster analysis suggested that there were eight subgroups. The diversity panel was then phenotyped for freezing survival (visual damage and Fv/Fo and Fv/Fm) after 2 months of cold acclimation (5°C) and a freezing treatment (-15°C for 4 h). The genotypic and phenotypic data for each accession in the rapeseed diversity panel was then used to conduct a genome-wide association study (GWAS). GWAS results showed that 14 significant markers were mapped to seven chromosomes for the phenotypes scored. Twenty-four candidate genes located within the mapped loci were identified as previously associated with lipid, photosynthesis, flowering, ubiquitination, and cytochrome P450 in rapeseed or other plant species.

Transport enhancement of hydrophobic pollutants by the expression of zucchini major latex-like protein genes in tobacco plants

The environmental spread of hydrophobic pollutants has been receiving attention because of specific characteristics of these compounds that make them resistant to degradation, thus causing various toxic effects on humans as a result of their bioaccumulation. Here, we report the role of zucchini major-latex like proteins (MLPs) on the accumulation of hydrophobic pollutants, as consumption of contaminated crops is one of the main routes for accumulation. Transgenic tobacco plants expressing an aryl hydrocarbon receptor (AhR) gene with a β-glucuronidase (GUS) inducible expression system were transformed with one of the three zucchini MLP genes (PG1, GR1, and GR3). MLP transgenic plants showed a significant increase in the fold induction of GUS activity compared to the parental AhR tobacco plants when one of the most toxic polychlorinated biphenyl (PCB) congeners, 3,3',4,4',5-pentachlorobiphenyl (CB126), was applied. GUS activity was detected in both aerial parts and roots after treatment with the strong carcinogen 3-methylcholanthrene. Phenotypic changes in the MLP tobacco during incubation with CB126 were also observed. The MLP transgenic plant PG1 responded to treatment with 0.32 nM CB126, whereas vector control plants significantly induced GUS activity at 200 nM CB126. Moreover, GUS activities in the MLP plants treated with other PCB congeners were significantly higher than those in the plants given the mock treatment. As GUS activities in the aerial parts of the plants were significantly correlated with the accumulation level of PCBs, these results strongly suggest that zucchini MLPs are related to the translocation of hydrophobic pollutants from the roots to the aerial parts through their binding affinity.

Review: Biological functions of major latex-like proteins in plants

Major latex-like proteins (MLPs) have been identified in dicots and monocots. They are members of the birch pollen allergen Bet v 1 family as well as pathogenesis-related proteins class 10. MLPs have two main features. One is binding affinity toward various hydrophobic compounds, such as long-chain fatty acids, steroids, and systemic acquired resistance signals, via its internal hydrophobic cavity or hydrophobic residues on its surface. MLPs transport such compounds to other organs via phloem and xylem vessels and contribute to the expression of physiologically important ligands' activity in the particular organs. The second feature is responses to abiotic and biotic stresses. MLPs are involved in drought and salt tolerance through the mediation of plant hormone signaling pathways. MLPs generate resistance against pathogens by the induction of pathogenesis-related protein genes. Therefore, MLPs play crucial roles in drought and salt tolerance and resistance against pathogens. However, knowledge of MLPs is fragmented, and an overview of them is needed. Herein, we summarize the current knowledge of the biological functions of MLPs, which to our knowledge, is the first review about MLPs that has been reported.

The Nicotiana tabacum L. major latex protein-like protein 423 (NtMLP423) positively regulates drought tolerance by ABA-dependent pathway

BACKGROUND

Drought stress is an environmental factor that limits plant growth and reproduction. Little research has been conducted to investigate the MLP gene in tobacco. Here, NtMLP423 was isolated and identified, and its role in drought stress was studied.

RESULTS

Overexpression of NtMLP423 improved tolerance to drought stress in tobacco, as determined by physiological analyses of water loss efficiency, reactive oxygen species levels, malondialdehyde content, and levels of osmotic regulatory substances. Overexpression of NtMLP423 in transgenic plants led to greater sensitivity to abscisic acid (ABA)-mediated seed germination and ABA-induced stomatal closure. NtMLP423 also regulated drought tolerance by increasing the levels of ABA under conditions of drought stress. Our study showed that the transcription level of ABA synthetic genes also increased. Overexpression of NtMLP423 reduced membrane damage and ROS accumulation and increased the expression of stress-related genes under drought stress. We also found that NtWRKY71 regulated the transcription of NtMLP423 to improve drought tolerance.

CONCLUSIONS

Our results indicated that NtMLP423-overexpressing increased drought tolerance in tobacco via the ABA pathway.

Global Quantitative Proteomics Studies Revealed Tissue-Preferential Expression and Phosphorylation of Regulatory Proteins in Arabidopsis

Organogenesis in plants occurs across all stages of the life cycle. Although previous studies have identified many genes as important for either vegetative or reproductive development at the RNA level, global information on translational and post-translational levels remains limited. In this study, six Arabidopsis stages/organs were analyzed using quantitative proteomics and phosphoproteomics, identifying 2187 non-redundant proteins and evidence for 1194 phosphoproteins. Compared to the expression observed in cauline leaves, the expression of 1445, 1644, and 1377 proteins showed greater than 1.5-fold alterations in stage 1–9 flowers, stage 10–12 flowers, and open flowers, respectively. Among these, 294 phosphoproteins with 472 phosphorylation sites were newly uncovered, including 275 phosphoproteins showing differential expression patterns, providing molecular markers and possible candidates for functional studies. Proteins encoded by genes preferentially expressed in anther (15), meiocyte (4), or pollen (15) were enriched in reproductive organs, and mutants of two anther-preferentially expressed proteins, acos5 and mee48, showed obviously reduced male fertility with abnormally organized pollen exine. In addition, more phosphorylated proteins were identified in reproductive stages (1149) than in the vegetative organs (995). The floral organ-preferential phosphorylation of GRP17, CDC2/CDKA.1, and ATSK11 was confirmed with western blot analysis. Moreover, phosphorylation levels of CDPK6 and MAPK6 and their interacting proteins were elevated in reproductive tissues. Overall, our study yielded extensive data on protein expression and phosphorylation at six stages/organs and provides an important resource for future studies investigating the regulatory mechanisms governing plant development.

Wheat RING E3 ubiquitin ligase TaDIS1 degrade TaSTP via the 26S proteasome pathway

Drought stress has a great impact on wheat yields. The ubiquitin/26S proteasome system is one of the most important mechanisms employed by plants for responding to stress. E3 ubiquitin ligase is an important part of the ubiquitin/26S proteasome system. In wheat, the mechanism of E3 ubiquitin ligase TaDIS1 has not been investigated in great detail. In this study, TaSTP was identified as an interacting partner using yeast two-hybrid screening. The results obtained from bimolecular fluorescence complementation, pull-down, and co-immunoprecipitation assays also demonstrated that TaDIS1 interacts with TaSTP. In vitro ubiquitination assays showed that TaDIS1 has an E3 ubiquitin ligase activity and the results based on two TaDIS1 mutants suggested that the RING domain is essential for its E3 ubiquitin ligase activity. In addition, we used MG132 to show that TaSTP can be degraded by TaDIS1 via the 26S proteasome pathway. The transcript levels of TaSTP showed that it can also respond to different abiotic stresses, such as drought, salt, and abscisic acid treatment. RING E3 ubiquitin ligase TaDIS1 may through the posttranslational regulation of TaSTP to play an important role in drought tolerance.

Understanding the role played by protic ionic liquids (PILs) and the substituent effect for enhancing the generation of Z-cinnamic acid derivatives†

Photoisomerization of a series of substituted E-cinnamic acids in MeCN in their acid forms and as their corresponding protic ionic liquids (PILs) with light of 300 nm is studied. The nature, strength, number, and position effects of substituents on the photochemical behavior of E-cinnamic derivatives are investigated. The photosensitization of the reaction in the presence of Michler's ketone is also studied at 366 nm and it demonstrates that the triplet-excited state is involved in the reaction. As the presence of n-butylamine needed to form the PILs significantly increases the photoproduct yields in all cases, the role of the PILs is also discussed. Thus, understanding of these fundamental aspects has allowed us to establish an excellent and practical synthetic protocol for successfully synthesizing Z-cinnamic acids.

The change of gravity vector induces short-term phosphoproteomic alterations in Arabidopsis

Plants can sense the gravitational force. When plants perceive a change in this natural force, they tend to reorient their organs with respect to the direction of the gravity vector, i.e., the shoot stem curves up. In the present study, we performed a 4C quantitative phosphoproteomics to identify those altered protein phosphosites resulting from 150 s of reorientation of Arabidopsis plants on earth. A total of 5556 phosphopeptides were identified from the gravistimulated Arabidopsis. Quantification based on the ¹⁵N-stable isotope labeling in Arabidopsis (SILIA) and computational analysis of the extracted ion chromatogram (XIC) of phosphopeptides showed eight and five unique PTM peptide arrays (UPAs) being up- and down-regulated, respectively, by gravistimulation. Among the 13 plant reorientation-responsive protein groups, many are related to the cytoskeleton dynamic and plastid movement. Interestingly, the most gravistimulation-responsive phosphosites are three serine residues, S350, S376, and S410, of a blue light receptor Phototropin 1 (PHOT1). The immunoblots experiment confirmed that the change of gravity vector indeed affected the phosphorylation level of S410 in PHOT1. The functional role of PHOT1 in gravitropic response was further validated with gravicurvature measurement in the darkness of both the loss-of-function double mutant phot1phot2 and its complementary transgenic plant PHOT1/phot1phot2. SIGNIFICANCE: The organs of sessile organisms, plants, are able to move in response to environmental stimuli, such as gravity vector, touch, light, water, or nutrients, which is termed tropism. For instance, the bending of plant shoots to the light source is called phototropism. Since all plants growing on earth are continuously exposed to the gravitational field, plants receive the mechanical signal elicited by the gravity vector change and convert it into plant morphogenesis, growth, and development. Past studies have resulted in various hypotheses for gravisensing, but our knowledge about how the signal of gravity force is transduced in plant cells is still minimal. In the present study, we performed a SILIA-based 4C quantitative phosphoproteomics on 150-s gravistimulated Arabidopsis seedlings to explore the phosphoproteins involved in the gravitropic response. Our data demonstrated that such a short-term reorientation of Arabidopsis caused changes in phosphorylation of cytoskeleton structural proteins like Chloroplast Unusual Positioning1 (CHUP1), Patellin3 (PATL3), and Plastid Movement Impaired2 (PMI2), as well as the blue light receptor Phototropin1 (PHOT1). These results suggested that protein phosphorylation plays a crucial role in gravisignaling, and two primary tropic responses of plants, gravitropism and phototropism, may share some common components and signaling pathways. We expect that the phosphoproteins detected from this study will facilitate the subsequent molecular and cellular studies on the mechanism underlying the signal transduction in plant gravitropic response.

Genome-wide identification and expression analysis of major latex protein (MLP) family genes in the apple (Malus domestica Borkh.) genome

Major latex protein/ripening-related proteins (MLP/RRP) subfamily are a class of proteins that play crucial roles in response to defense and stress response. However, their biological function is still not clear, the identification and characterization will provide essential information for understanding their roles. Here, we carried out a genome-wide evolutionary characteristics and gene expression analysis of the MLP family in apple (Malus domestica, Borkh.). A total of 36 MdMLP genes were screened in apple genome. They were uneven located on 5 chromosomes, where were mainly arranged in tandem clusters, and the phylogenetic analysis put forward further views on the evolutionary relationship and putative functions among the genes. The conserved motifs showed that the MLP proteins which contained motif 1 had the potential function, and tissue-specific expression analysis showed that apple MLP members had diverse biological roles. Furthermore, the results showed seven of the MdMLPs that harbored cis-acting regulatory elements in response to defense and stress, and our expression data proved that they were involved in biotic stresses. The present study provides new views to the evolution and regulation of MdMLP genes, which represent objectives of future research and incorporate in resistance-related molecular breeding projects.

De novo genome assembly and Hi-C analysis reveal an association between chromatin architecture alterations and sex differentiation in the woody plant Jatropha curcas

BACKGROUND

Chromatin architecture is an essential factor regulating gene transcription in different cell types and developmental phases. However, studies on chromatin architecture in perennial woody plants and on the function of chromatin organization in sex determination have not been reported.

RESULTS

Here, we produced a chromosome-scale de novo genome assembly of the woody plant Jatropha curcas with a total length of 379.5 Mb and a scaffold N50 of 30.7 Mb using Pacific Biosciences long reads combined with genome-wide chromosome conformation capture (Hi-C) technology. Based on this high-quality reference genome, we detected chromatin architecture differences between monoecious and gynoecious inflorescence buds of Jatropha. Differentially expressed genes were significantly enriched in the changed A/B compartments and topologically associated domain regions and occurred preferentially in differential contact regions between monoecious and gynoecious inflorescence buds. Twelve differentially expressed genes related to flower development or hormone synthesis displayed significantly different genomic interaction patterns in monoecious and gynoecious inflorescence buds. These results demonstrate that chromatin organization participates in the regulation of gene transcription during the process of sex differentiation in Jatropha.

CONCLUSIONS

We have revealed the features of chromatin architecture in perennial woody plants and investigated the possible function of chromatin organization in Jatropha sex differentiation. These findings will facilitate understanding of the regulatory mechanisms of sex determination in higher plants.

PERPETUAL FLOWERING2 coordinates the vernalization response and perennial flowering in Arabis alpina

The floral repressor APETALA2 (AP2) in Arabidopsis regulates flowering through the age pathway. The AP2 ortholog in the alpine perennial Arabis alpina, PERPETUAL FLOWERING 2 (PEP2), was previously reported to control flowering through the vernalization pathway via enhancing the expression of another floral repressor PERPETUAL FLOWERING 1 (PEP1), the ortholog of Arabidopsis FLOWERING LOCUS C (FLC). However, PEP2 also regulates flowering independently of PEP1. To characterize the function of PEP2, we analyzed the transcriptomes of pep2 and pep1 mutants. The majority of differentially expressed genes were detected between pep2 and the wild type or between pep2 and pep1, highlighting the importance of the PEP2 role that is independent of PEP1. Here, we demonstrate that PEP2 activity prevents the up-regulation of the A. alpina floral meristem identity genes FRUITFUL (AaFUL), LEAFY (AaLFY), and APETALA1 (AaAP1), ensuring floral commitment during vernalization. Young pep2 seedlings respond to vernalization, suggesting that PEP2 regulates the age-dependent response to vernalization independently of PEP1. The major role of PEP2 through the PEP1-dependent pathway takes place after vernalization, when it facilitates PEP1 activation both in the main shoot apex and in axillary branches. These multiple roles of PEP2 in the vernalization response contribute to the A. alpina life cycle.

Quantitative Proteomics Analysis of Lettuce (Lactuca sativa L.) Reveals Molecular Basis-Associated Auxin and Photosynthesis with Bolting Induced by High Temperature

Bolting is a key process in the growth and development of lettuce (Lactuca sativa L.). A high temperature can induce early bolting, which decreases both the quality and production of lettuce. However, knowledge of underlying lettuce bolting is still lacking. To better understand the molecular basis of bolting, a comparative proteomics analysis was conducted on lettuce stems, during the bolting period induced by a high temperature (33 °C) and a control temperature (20 °C) using iTRAQ-based proteomics, phenotypic measures, and biological verifications using qRT-PCR and Western blot. The high temperature induced lettuce bolting, while the control temperature did not. Of the 5454 identified proteins, 619 proteins presented differential abundance induced by high-temperature relative to the control group, of which 345 had an increased abundance and 274 had a decreased abundance. Proteins with an abundance level change were mainly enriched in pathways associated with photosynthesis and tryptophan metabolism involved in auxin (IAA) biosynthesis. Moreover, among the proteins with differential abundance, proteins associated with photosynthesis and tryptophan metabolism were increased. These findings indicate that a high temperature enhances the function of photosynthesis and IAA biosynthesis to promote the process of bolting, which is in line with the physiology and transcription level of IAA metabolism. Our data provide a first comprehensive dataset for gaining novel understanding of the molecular basis underlying lettuce bolting induced by high temperature. It is potentially important for further functional analysis and genetic manipulation for molecular breeding to breed new cultivars of lettuce to restrain early bolting, which is vital for improving vegetable quality.

Investigating Drought Tolerance in Chickpea Using Genome-Wide Association Mapping and Genomic Selection Based on Whole-Genome Resequencing Data

Drought tolerance is a complex trait that involves numerous genes. Identifying key causal genes or linked molecular markers can facilitate the fast development of drought tolerant varieties. Using a whole-genome resequencing approach, we sequenced 132 chickpea varieties and advanced breeding lines and found more than 144,000 single nucleotide polymorphisms (SNPs). We measured 13 yield and yield-related traits in three drought-prone environments of Western Australia. The genotypic effects were significant for all traits, and many traits showed highly significant correlations, ranging from 0.83 between grain yield and biomass to -0.67 between seed weight and seed emergence rate. To identify candidate genes, the SNP and trait data were incorporated into the SUPER genome-wide association study (GWAS) model, a modified version of the linear mixed model. We found that several SNPs from auxin-related genes, including auxin efflux carrier protein (PIN3), p-glycoprotein, and nodulin MtN21/EamA-like transporter, were significantly associated with yield and yield-related traits under drought-prone environments. We identified four genetic regions containing SNPs significantly associated with several different traits, which was an indication of pleiotropic effects. We also investigated the possibility of incorporating the GWAS results into a genomic selection (GS) model, which is another approach to deal with complex traits. Compared to using all SNPs, application of the GS model using subsets of SNPs significantly associated with the traits under investigation increased the prediction accuracies of three yield and yield-related traits by more than twofold. This has important implication for implementing GS in plant breeding programs.

Comparative proteomic study of Arabidopsis mutants mpk4 and mpk6

Arabidopsis MPK4 and MPK6 are implicated in different signalling pathways responding to diverse external stimuli. This was recently correlated with transcriptomic profiles of Arabidopsis mpk4 and mpk6 mutants, and thus it should be reflected also on the level of constitutive proteomes. Therefore, we performed a shot gun comparative proteomic analysis of Arabidopsis mpk4 and mpk6 mutant roots. We have used bioinformatic tools and propose several new proteins as putative MPK4 and MPK6 phosphorylation targets. Among these proteins in the mpk6 mutant were important modulators of development such as CDC48A and phospholipase D alpha 1. In the case of the mpk4 mutant transcriptional reprogramming might be mediated by phosphorylation and change in the abundance of mRNA decapping complex VCS. Further comparison of mpk4 and mpk6 root differential proteomes showed differences in the composition and regulation of defense related proteins. The mpk4 mutant showed altered abundances of antioxidant proteins. The examination of catalase activity in response to oxidative stress revealed that this enzyme might be preferentially regulated by MPK4. Finally, we proposed developmentally important proteins as either directly or indirectly regulated by MPK4 and MPK6. These proteins contribute to known phenotypic defects in the mpk4 and mpk6 mutants.

Proteomic Identification of Putative MicroRNA394 Target Genes in Arabidopsis thaliana Identifies Major Latex Protein Family Members Critical for Normal Development

Expression of the F-Box protein Leaf Curling Responsiveness (LCR) is regulated by microRNA, miR394, and alterations to this interplay in Arabidopsis thaliana produce defects in leaf polarity and shoot apical meristem organization. Although the miR394-LCR node has been documented in Arabidopsis, the identification of proteins targeted by LCR F-box itself has proven problematic. Here, a proteomic analysis of shoot apices from plants with altered LCR levels identified a member of the Latex Protein (MLP) family gene as a potential LCR F-box target. Bioinformatic and molecular analyses also suggested that other MLP family members are likely to be targets for this post-translational regulation. Direct interaction between LCR F-Box and MLP423 was validated. Additional MLP members had reduction in protein accumulation, in varying degrees, mediated by LCR F-Box. Transgenic Arabidopsis lines, in which MLP28 expression was reduced through an artificial miRNA technology, displayed severe developmental defects, including changes in leaf patterning and morphology, shoot apex defects, and eventual premature death. These phenotypic characteristics resemble those of Arabidopsis plants modified to over-express LCR Taken together, the results demonstrate that MLPs are driven to degradation by LCR, and indicate that MLP gene family is target of miR394-LCR regulatory node, representing potential targets for directly post-translational regulation mediated by LCR F-Box. In addition, MLP28 family member is associated with the LCR regulation that is critical for normal Arabidopsis development.

Major latex protein-like protein 43 (MLP43) functions as a positive regulator during abscisic acid responses and confers drought tolerance in Arabidopsis thaliana

Drought stress is one of the disadvantageous environmental conditions for plant growth and reproduction. Given the importance of abscisic acid (ABA) to plant growth and abiotic stress responses, identification of novel components involved in ABA signalling transduction is critical. In this study, we screened numerous Arabidopsis thaliana mutants by seed germination assay and identified a mutant mlp43 (major latex protein-like 43) with decreased ABA sensitivity in seed germination. The mlp43 mutant was sensitive to drought stress while the MLP43-overexpressed transgenic plants were drought tolerant. The tissue-specific expression pattern analysis showed that MLP43 was predominantly expressed in cotyledons, primary roots and apical meristems, and a subcellular localization study indicated that MLP43 was localized in the nucleus and cytoplasm. Physiological and biochemical analyses indicated that MLP43 functioned as a positive regulator in ABA- and drought-stress responses in Arabidopsis through regulating water loss efficiency, electrolyte leakage, ROS levels, and as well as ABA-responsive gene expression. Moreover, metabolite profiling analysis indicated that MLP43 could modulate the production of primary metabolites under drought stress conditions. Reconstitution of ABA signalling components in Arabidopsis protoplasts indicated that MLP43 was involved in ABA signalling transduction and acted upstream of SnRK2s by directly interacting with SnRK2.6 and ABF1 in a yeast two-hybrid assay. Moreover, ABA and drought stress down-regulated MLP43 expression as a negative feedback loop regulation to the performance of MLP43 in ABA and drought stress responses. Therefore, this study provided new insights for interpretation of physiological and molecular mechanisms of Arabidopsis MLP43 mediating ABA signalling transduction and drought stress responses.

Substituent effects of cis-cinnamic acid analogues as plant growh inhibitors

1-O-cis-Cinnamoyl-β-D-glucopyranose is one of the most potent allelochemicals that has been isolated from Spiraea thunbergii Sieb by Hiradate et al. It derives its strong inhibitory activity from cis-cinnamic acid (cis-CA), which is crucial for phytotoxicity. By preparing and assaying a series of cis-CA analogues, it was previously found that the key features of cis-CA for lettuce root growth inhibition are a phenyl ring, cis-configuration of the alkene moiety, and carboxylic acid. On the basis of a structure-activity relationship study, the substituent effects on the aromatic ring of cis-CA were examined by systematic synthesis and the lettuce root growth inhibition assay of a series of cis-CA analogues having substituents on the aromatic ring. While ortho- and para-substituted analogues exhibited low potency in most cases, meta-substitution was not critical for potency, and analogues having a hydrophobic and sterically small substituent were more likely to be potent. Finally, several cis-CA analogues were found to be more potent root growth inhibitors than cis-CA.

Design and synthesis of conformationally constrained analogues of cis-cinnamic acid and evaluation of their plant growth inhibitory activity

1-O-cis-Cinnamoyl-β-D-glucopyranose is known to be one of the most potent allelochemical candidates and was isolated from Spiraea thunbergii Sieb by Hiradate et al. (2004), who suggested that it derived its strong inhibitory activity from cis-cinnamic acid, which is crucial for phytotoxicity. In this study, key structural features and substituent effects of cis-cinnamic acid (cis-CA) on lettuce root growth inhibition was investigated. These structure-activity relationship studies indicated the importance of the spatial relationship of the aromatic ring and carboxylic acid moieties. In this context, conformationally constrained cis-CA analogues, in which the aromatic ring and cis-olefin were connected by a carbon bridge, were designed, synthesized, and evaluated as plant growth inhibitors. The results of the present study demonstrated that the inhibitory activities of the five-membered and six-membered bridged compounds were enhanced, up to 0.27 μM, and were ten times higher than cis-CA, while the potency of the other compounds was reduced.

Functional phosphoproteomic analysis reveals that a serine-62-phosphorylated isoform of ethylene response factor110 is involved in Arabidopsis bolting

Ethylene is a major plant hormone that plays an important role in regulating bolting, although the underlying molecular mechanism is not well understood. In this study, we report the novel finding that the serine-62 (Ser-62) phosphorylation of Ethylene Response Factor110 (ERF110) is involved in the regulation of bolting time. The gene expression and posttranslational modification (phosphorylation) of ERF110 were analyzed among ethylene-response mutants and ERF110 RNA-interfering knockout lines of Arabidopsis (Arabidopsis thaliana). Physiological and biochemical studies revealed that the Ser-62 phosphorylation of ERF110 was closely related to bolting time, that is, the ethylene-enhanced gene expression of ERF110 and the decreased Ser-62 phosphorylation of the ERF110 protein in Arabidopsis. The expression of a flowering homeotic APETALA1 gene was up-regulated by the Ser-62-phosphorylated isoform of the ERF110 transcription factor, which was necessary but not sufficient for normal bolting. The gene expression and phosphorylation of ERF110 were regulated by ethylene via both Ethylene-Insensitive2-dependent and -independent pathways, which constitute a dual-and-opposing mechanism of action for ethylene in the regulation of Arabidopsis bolting.

Cinnamic acid induced changes in reactive oxygen species scavenging enzymes and protein profile in maize (Zea mays L.) plants grown under salt stress

Plant growth and development are greatly affected due to changes in environmental conditions and become a serious challenge to scientific people. Therefore, present study was conducted to determine the role of secondary metabolites on the growth and development of maize under abiotic stress conditions. Cinnamic acid (CA) is one of the basic phenylpropanoid with antioxidant activity, produced by plants in response to stressful conditions. Response of maize seeds to the presoaking treatment with 0.5 mM CA was studied under different concentrations of NaCl stress. Exogenous CA increased growth characteristics in saline and non-saline conditions, while effects of CA were more significant under saline conditions in comparison to non-saline conditions in maize plants. CA also reduced oxidative damage through the induction of ROS scavenging enzymes such as supperoxide dismutase (SOD) (EC 1.15.1.1), peroxidase (POD) (EC 1.11.1.7), while the activity of enzyme catalase (CAT) (EC 1.11.1.6) was decreased. The content of malondialdehyde (MDA) was reduced significantly in maize leaf under CA treatment. Changes in protein banding patterns in the maize leaves showed a wide variation in response to NaCl-stress, while in the presence of CA salt-induced expression of polypeptides was reduced significantly. Present study clearly reports the alleviative effects of CA in response to salinity stress on growth, metabolic activity and changes in protein profile of 21 days old maize plants.

Identification of differentially methylated regions during vernalization revealed a role for RNA methyltransferases in bolting

Sugar beet (Beta vulgaris altissima) is a biennial root crop with an absolute requirement for cold exposure to bolt and flower, a process called vernalization. Global DNA methylation variations have been reported during vernalization in several plants. However, few genes targeted by DNA methylation during vernalization have been described. The objectives of this study were to identify differentially methylated regions and to study their involvement in bolting induction and tolerance. Restriction landmark genome scanning was applied to DNA from shoot apical meristems of sugar beet genotypes, providing a direct quantitative epigenetic assessment of several CG methylated genes without prior knowledge of gene sequence. Several differentially methylated regions exhibiting variations of gene-body DNA methylation and expression during cold exposure and/or between genotypes were identified, including an AROGENATE DEHYDRATASE and two RNA METHYLCYTOSINE TRANSFERASE sequences. One RNA METHYLCYTOSINE TRANSFERASE sequence displayed gene-body hypermethylation and activation of expression, while the other was hypomethylated and inhibited by cold exposure. Global RNA methylation and phenolic compound levels changed during cold exposure in a genotype-dependent way. The use of methyl RNA immunoprecipitation of total RNA and reverse transcription-PCR analysis revealed mRNA methylation in a vernalized bolting-resistant genotype for the FLOWERING LOCUS 1 gene, a repressor of flowering. Finally, Arabidopsis mutants for RNA METHYLCYTOSINE TRANSFERASE and AROGENATE DEHYDRATASE were shown to exhibit, under different environmental conditions, early or late bolting phenotypes, respectively. Overall, the data identified functional targets of DNA methylation during vernalization in sugar beet, and it is proposed that RNA methylation and phenolic compounds play a role in the floral transition.

Key structural features of cis-cinnamic acid as an allelochemical

1-O-cis-cinnamoyl-β-D-glucopyranose is one of the most potent allelochemicals isolated from Spiraea thunbergii Sieb. It is suggested that it derives its strong inhibitory activity from cis-cinnamic acid, which is crucial for phytotoxicity. It was synthesized to confirm its structure and bioactivity, and also a series of cis-cinnamic acid analogues were prepared to elucidate the key features of cis-cinnamic acid for lettuce root growth inhibition. The cis-cyclopropyl analogue showed potent inhibitory activity while the saturated and alkyne analogues proved to be inactive, demonstrating the importance of the cis-double bond. Moreover, the aromatic ring could not be replaced with a saturated ring. However, the 1,3-dienylcyclohexene analogue showed strong activity. These results suggest that the geometry of the C-C double bond between the carboxyl group and the aromatic ring is essential for potent inhibitory activity. In addition, using several light sources, the photostability of the cinnamic acid derivatives and the role of the C-C double bond were also investigated.