HANABA TARANU Is a GATA Transcription Factor That Regulates Shoot Apical Meristem and Flower Development in ArabidopsisW⃞

The OsNL1-OsTOPLESS2-OsMOC1/3 pathway regulates high-order tiller outgrowth in rice

Tiller is an important factor in determining rice yield. Currently, researches mainly focus on the outgrowth of low-order tiller (LOT), while the regulation mechanism of high-order tiller (HOT) outgrowth has remained unknown. In this study, we detected one OsNL1 mutant, nl1, exhibiting HOT numbers increase, and found that OsNL1 interacts with OsTOPLESS2, which was mediated by the core motif of nine amino acids VDCTLSLGT within the HAN domain of OsNL1. The topless2 mutant exhibits similar HOT number increase as in the nl1. Through ChIP-seq analysis, we revealed that OsNL1 recruits OsTOPLESS2 to conduct histone deacetylation in the promoters of OsMOC1 and OsMOC3 to regulate HOT outgrowth. Moreover, we showed that the HAN domain is essential for OsNL1 function as a repressor. In summary, our study reveals partial mechanism of HOT outgrowth in rice and deciphers the molecular biology function of the HAN domain. This will contribute to the comprehensive understanding of tiller outgrowth and the role of HAN-domain-containing genes.

WRKY transcription factor MdWRKY71 regulates flowering time in apple

In plants, flowering is crucial to reproductive success. Receiving limited attention in apple research is the function of WRKY transcription factors in regulating flowering time. We characterized a WRKY transcription factor, MdWRKY71, from red-fleshed apple in this study, and ectopically expressed it in Arabidopsis thaliana, which revealed its role in flowering. The sequence of MdWRKY71 exhibited similarity to that of AtWRKY71, and its protein comprised a WRKY domain and a C2H2 zinc finger-like motif, placing it within subgroup IIc of the WRKY family. The similar changing trends demonstrated a significant positive correlation between the expression level of MdWRKY71 and the key flower transition genes in apical buds of apple in flower transition stage. Overexpression of MdWRKY71 promoted the upregulation of certain flower transition genes in apple calli. The ectopic expression of MdWRKY71 in A. thaliana was observed to induce early flowering. Additionally, MdWRKY71 could bind to the promoters of several floral pathway integrators directly and interact with them to enhance their expression levels. These results contribute to our understanding of the molecular mechanism through which MdWRKY71 regulates the flowering process in fruit trees, such as red-fleshed apple.

Molecular and Functional Convergences Associated with Complex Multicellularity in Eukarya

A key trait of Eukarya is the independent evolution of complex multicellularity in animals, land plants, fungi, brown algae, and red algae. This phenotype is characterized by the initial exaptation of cell-cell adhesion genes followed by the emergence of mechanisms for cell-cell communication, together with the expansion of transcription factor gene families responsible for cell and tissue identity. The number of cell types is commonly used as a quantitative proxy for biological complexity in comparative genomics studies. While expansions of individual gene families have been associated with variations in the number of cell types within individual complex multicellular lineages, the molecular and functional roles responsible for the independent evolution of complex multicellular across Eukarya remain poorly understood. We employed a phylogeny-aware strategy to conduct a genomic-scale search for associations between the number of cell types and the abundance of genomic components across a phylogenetically diverse set of 81 eukaryotic species, including species from all complex multicellular lineages. Our annotation schemas represent 2 complimentary aspects of genomic information: homology, represented by conserved sequences, and function, represented by Gene Ontology terms. We found many gene families sharing common biological themes that define complex multicellular to be independently expanded in 2 or more complex multicellular lineages, such as components of the extracellular matrix, cell-cell communication mechanisms, and developmental pathways. Additionally, we describe many previously unknown associations of biological themes and biological complexity, such as expansions of genes playing roles in wound response, immunity, cell migration, regulatory processes, and response to natural rhythms. Together, our findings unveil a set of functional and molecular convergences independently expanded in complex multicellular lineages likely due to the common selective pressures in their lifestyles.

Ubiquitin Ligase U-Box51 Positively Regulates Drought Stress in Potato (Solanum tuberosum L.)

The ubiquitin-proteasome system (UPS) is a key protein degradation pathway in eukaryotes, in which E3 ubiquitin ligases mediate protein ubiquitination, directly or indirectly targeting substrate proteins to regulate various biological processes, including plant growth, hormone signaling, immune responses, and adaptation to abiotic stress. In this study, we identified plant U-box protein 51 in Solanum tuberosum (StPUB51) as an E3 ubiquitin ligase through transcriptomic analysis, and used it as a candidate gene for gene-function analysis. Quantitative real-time PCR (qRT-PCR) was used to examine StPUB51 expression across different tissues, and its expression patterns under simulated drought stress induced by polyethylene glycol (PEG 6000) were assessed. Transgenic plants overexpressing StPUB51 and plants with down-regulated StPUB51 expression were generated to evaluate drought tolerance. The activities of key antioxidant enzymes-superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD) as well as malondialdehyde (MDA) content in transgenic plants' leaves were measured under drought conditions. Protein-protein interactions involving StPUB51 were explored via yeast two-hybrid (Y2H) screening, with interaction verification by bimolecular fluorescence complementation (BiFC). StPUB51 was predominantly expressed in stems, with lower expression observed in tubers, and its expression was significantly upregulated in response to 20% PEG-6000 simulated drought. Subcellular localization assays revealed nuclear localization of the StPUB51 protein. Under drought stress, StPUB51-overexpressing plants exhibited enhanced SOD, POD, and CAT activities and reduced MDA levels, in contrast to plants with suppressed StPUB51 expression. Y2H and BiFC analyses identified two interacting proteins, StSKP2A and StGATA1, which may be functionally linked to StPUB51. Collectively, these findings suggest that StPUB51 plays a positive regulatory role in drought tolerance, enhancing resilience in potato growth and stress adaptation.

Comparative analysis of amino acid sequence level in plant GATA transcription factors

Transcription factors (TFs) are essential regulators of gene expression, influencing numerous biological processes such as development, growth, and cellular responses in plants. Among these, GATA TFs are distinguished by their highly conserved DNA-binding domain, characterized by a class IV zinc finger motif (CX2CX18-20CX2C). This study investigates the amino acid sequence patterns of 5,335 GATA TFs across 165 plant species sourced from the PlantTFDB database ( http://planttfdb.gao-lab.org/ ), encompassing diverse taxonomic groups. Through comparative sequence analysis, I identify conserved domains and structural features that enhance the understanding functional roles, evolutionary conservation, and lineage-specific adaptations of GATA TFs. These findings provide valuable insights into the diversification and functional specialization of GATA TFs, with implications for improving stress tolerance and adaptability in crops. This study contributes to the broader knowledge of transcriptional regulation in plant biology.

Genome-Wide Identification of GATA Family Genes in Potato and Characterization of StGATA12 in Response to Salinity and Osmotic Stress

GATA factors are evolutionarily conserved transcription regulators that are implicated in the regulation of physiological changes under abiotic stress. Unfortunately, there are few studies investigating the potential role of GATA genes in potato plants responding to salt and osmotic stresses. The physicochemical properties, chromosomal distribution, gene duplication, evolutionary relationships and classification, conserved motifs, gene structure, interspecific collinearity relationship, and cis-regulatory elements were analyzed. Potato plants were treated with NaCl and PEG to induce salinity and osmotic stress responses. qRT-PCR was carried out to characterize the expression pattern of StGATA family genes in potato plants subjected to salinity and osmotic stress. StGATA12 loss-of-function and gain-of-function plants were established. Morphological phenotypes and growth were indicated. Photosynthetic gas exchange was suggested by the net photosynthetic rate, transpiration rate, and stomatal conductance. Physiological indicators and the corresponding genes were indicated by enzyme activity and mRNA expression of genes encoding CAT, SOD, POD, and P5CS, and contents of H2O2, MDA, and proline. The expression patterns of StGATA family genes were altered in response to salinity and osmotic stress. StGATA12 protein is located in the nucleus. StGATA12 is involved in the regulation of potato plant growth in response to salinity and osmotic stress. Overexpression of StGATA12 promoted photosynthesis, transpiration, and stomatal conductance under salinity and osmotic stress. StGATA12 overexpression induced biochemical responses of potato plants to salinity and osmotic stress by regulating the levels of H2O2, MDA, and proline and the activity of CAT, SOD, and POD. StGATA12 overexpression induced the up-regulation of StCAT, StSOD, StPOD, and StP5CS against salinity and osmotic stress. StGATA12 could reinforce the ability of potato plants to resist salinity and osmosis-induced damages, which may provide an effective strategy to engineer potato plants for better adaptability to adverse salinity and osmotic conditions.

A coherent feed-forward loop in the Arabidopsis root stem cell organizer regulates auxin biosynthesis and columella stem cell maintenance

Stem cells in plant meristems are kept undifferentiated by signals from surrounding cells and provide the basis for continuous organ formation. In the stem cell organizer of the Arabidopsis thaliana root, the quiescent centre (QC), the WOX5 transcription factor, functions as a central hub in regulating columella stem cell (CSC) homoeostasis. However, the processes mediating WOX5 function are only poorly understood. Here we identify the transcription factor HAN as a central mediator of WOX5-regulated stem cell maintenance. HAN is required for mitotic quiescence of QC and CSC maintenance and is sufficient to induce ectopic stem cells. WOX5 and HAN repress transcription of the differentiation factor gene CDF4 in a coherent feed-forward loop (cFFL), one output of which is the expression of the auxin biosynthesis gene TAA1 and maintenance of auxin response maxima in the organizer. These findings and mathematical modelling provide a mechanistic framework for WOX5 function in the root stem cell niche.

Genome-Wide Identification and Expression Pattern Analysis of GATA Gene Family in Orchidaceae

The GATA transcription factors play crucial roles in plant growth, development, and responses to environmental stress. Despite extensive studies of GATA genes in many plants, their specific functions and mechanisms in orchids remain unexplored. In our study, a total of 149 GATA genes were identified in the genomes of seven sequenced orchid species (20 PeqGATAs, 23 CgGATAs, 24 CeGATAs, 23 DcaGATAs, 20 DchGATAs, 27 DnoGATAs, and 12 GelGATAs), classified into four subfamilies. Subfamily I typically contains genes with two exons, while subfamily II contains genes with two or three exons. Most members of subfamilies III and IV have seven or eight exons, with longer introns compared to subfamilies I and II. In total, 24 pairs (CgGATAs-DchGATAs), 27 pairs (DchGATAs-DnoGATAs), and 14 pairs (DnoGATAs-GelGATAs) of collinear relationships were identified. Cis-acting elements in GATA promoters were mainly enriched in abscisic acid (ABA) response elements and methyl jasmonate (MeJA) elements. Expression patterns and RT-qPCR analysis revealed that GATAs are involved in the regulation of floral development in orchids. Furthermore, under high-temperature treatment, GL17420 showed an initial increase followed by a decrease, GL18180 and GL17341 exhibited a downregulation followed by upregulation and then a decrease, while GL30286 and GL20810 displayed an initial increase followed by slight inhibition and then another increase, indicating diverse regulatory mechanisms of different GATA genes under heat stress. This study explores the function of GATA genes in orchids, providing a theoretical basis and potential genetic resources for orchid breeding and stress resistance improvement.

AINTEGUMENTA and redundant AINTEGUMENTA-LIKE6 are required for bract outgrowth in Arabidopsis

Plants consist of fundamental units of growth called phytomers (leaf or bract, axillary bud, node, and internode), which are repeated and modified throughout shoot development to give plants plasticity for survival and adaptation. One phytomer modification is the suppression or outgrowth of bracts, the leaves subtending the flowers. The floral meristem identity regulator LEAFY (LFY) and the organ boundary genes BLADE-ON-PETIOLE1 (BOP1) and BOP2 have been shown to suppress bract development in Arabidopsis, as mutations in these genes result in bract outgrowth. However, much less is known about the mechanisms that promote bract outgrowth in Arabidopsis mutants such as these. Further understanding of this mechanism may provide a potential tool for modifying leaf development. Here, we showed that the MADS-box genes SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1), FRUITFUL (FUL), and AGAMOUS-LIKE24 (AGL24) play more important roles than BOP1/2 and LFY in bract suppression, and that AINTEGUMENTA (ANT) and the partially redundant AINTEGUMENTA-LIKE6 (AIL6) are necessary for bract outgrowth in these mutant backgrounds. We also demonstrated that misexpression of AIL6 alone is sufficient for bract outgrowth. Our data reveal a mechanism for bract suppression and outgrowth and provide insight into phytomer plasticity.

PLETHORA transcription factors promote early embryo development through induction of meristematic potential

Plants are dependent on divisions of stem cells to establish cell lineages required for growth. During embryogenesis, early division products are considered to be stem cells, whereas during post-embryonic development, stem cells are present in meristems at the root and shoot apex. PLETHORA/AINTEGUMENTA-LIKE (PLT/AIL) transcription factors are regulators of post-embryonic meristem function and are required to maintain stem cell pools. Despite the parallels between embryonic and post-embryonic stem cells, the role of PLTs during early embryogenesis has not been thoroughly investigated. Here, we demonstrate that the PLT regulome in the zygote, and apical and basal cells is in strong congruence with that of post-embryonic meristematic cells. We reveal that out of all six PLTs, only PLT2 and PLT4/BABY BOOM (BBM) are expressed in the zygote, and that these two factors are essential for progression of embryogenesis beyond the zygote stage and first divisions. Finally, we show that other PLTs can rescue plt2 bbm defects when expressed from the PLT2 and BBM promoters, establishing upstream regulation as a key factor in early embryogenesis. Our data indicate that generic PLT factors facilitate early embryo development in Arabidopsis by induction of meristematic potential.

GATA family transcription factors in alga Chlamydomonas reinhardtii

GATA family transcription factors (GATA-TFs) are metalloproteins that regulate many metabolic pathways. These conserved proteins recognize the consensus sequence (A/T)GATA(A/G) in the promoter regions of many genes and regulate their transcription in response to environmental signals. Currently, the study of GATA-TFs is of increasing interest. GATA genes and their proteins are most actively studied in vascular plants and fungi. Based on the results of numerous studies, it has been shown that GATA factors regulate the metabolic pathways of nitrogen and carbon, and also play a major role in the processes induced by light and circadian rhythms. In algae, GATA-TFs remain poorly studied, and information about them is scattered. In this work, all known data on GATA-TFs in the unicellular green alga Chlamydomonas reinhardtii has been collected and systematized. The genome of this alga contains 12 GATA coding genes. Using the phylogenetic analysis, we identified three classes of GATA factors in C. reinhardtii according to the structure of the zinc finger domain and showed their difference from the classification of GATA factors developed on vascular plants.

Signatures of local adaptation to current and future climate in phenology-related genes in natural populations of Quercus robur

BACKGROUND

Local adaptation is a key evolutionary process that enhances the growth of plants in their native habitat compared to non-native habitats, resulting in patterns of adaptive genetic variation across the entire geographic range of the species. The study of population adaptation to local environments and predicting their response to future climate change is important because of climate change.

RESULTS

Here, we explored the genetic diversity of candidate genes associated with bud burst in pedunculate oak individuals sampled from 6 populations in Poland. Single nucleotide polymorphism (SNP) diversity was assessed in 720 candidate genes using the sequence capture technique, yielding 18,799 SNPs. Using landscape genomic approaches, we identified 8 FST outliers and 781 unique SNPs in 389 genes associated with geography, climate, and phenotypic variables (individual/family spring and autumn phenology, family diameter at breast height (DBH), height, and survival) that are potentially involved in local adaptation. Then, using a nonlinear multivariate model, Gradient Forests, we identified vulnerable areas of the pedunculate oak distribution in Poland that are at risk from climate change.

CONCLUSIONS

The model revealed that pedunculate oak populations in the eastern part of the analyzed geographical region are the most sensitive to climate change. Our results might offer an initial evaluation of a potential management strategy for preserving the genetic diversity of pedunculate oak.

Melica as an emerging model system for comparative studies in temperate Pooideae grasses

BACKGROUND AND AIMS

Pooideae grasses contain some of the world's most important crop and forage species. Although much work has been conducted on understanding the genetic basis of trait diversification within a few annual Pooideae, comparative studies at the subfamily level are limited by a lack of perennial models outside 'core' Pooideae. We argue for development of the perennial non-core genus Melica as an additional model for Pooideae, and provide foundational data regarding the group's biogeography and history of character evolution.

METHODS

Supplementing available ITS and ndhF sequence data, we built a preliminary Bayesian-based Melica phylogeny, and used it to understand how the genus has diversified in relation to geography, climate and trait variation surveyed from various floras. We also determine biomass accumulation under controlled conditions for Melica species collected across different latitudes and compare inflorescence development across two taxa for which whole genome data are forthcoming.

KEY RESULTS

Our phylogenetic analyses reveal three strongly supported geographically structured Melica clades that are distinct from previously hypothesized subtribes. Despite less geographical affinity between clades, the two sister 'Ciliata' and 'Imperfecta' clades segregate from the more phylogenetically distant 'Nutans' clade in thermal climate variables and precipitation seasonality, with the 'Imperfecta' clade showing the highest levels of trait variation. Growth rates across Melica are positively correlated with latitude of origin. Variation in inflorescence morphology appears to be explained largely through differences in secondary branch distance, phyllotaxy and number of spikelets per secondary branch.

CONCLUSIONS

The data presented here and in previous studies suggest that Melica possesses many of the necessary features to be developed as an additional model for Pooideae grasses, including a relatively fast generation time, perenniality, and interesting variation in physiology and morphology. The next step will be to generate a genome-based phylogeny and transformation tools for functional analyses.

Interaction between phenylpropane metabolism and oil accumulation in the developing seed of Brassica napus revealed by high temporal-resolution transcriptomes

BACKGROUND

Brassica napus is an important oilseed crop providing high-quality vegetable oils for human consumption and non-food applications. However, the regulation between embryo and seed coat for the synthesis of oil and phenylpropanoid compounds remains largely unclear.

RESULTS

Here, we analyzed the transcriptomes in developing seeds at 2-day intervals from 14 days after flowering (DAF) to 64 DAF. The 26 high-resolution time-course transcriptomes are clearly clustered into five distinct groups from stage I to stage V. A total of 2217 genes including 136 transcription factors, are specifically expressed in the seed and show high temporal specificity by being expressed only at certain stages of seed development. Furthermore, we analyzed the co-expression networks during seed development, which mainly included master regulatory transcription factors, lipid, and phenylpropane metabolism genes. The results show that the phenylpropane pathway is prominent during seed development, and the key enzymes in the phenylpropane metabolic pathway, including TT5, BAN, and the transporter TT19, were directly or indirectly related to many key enzymes and transcription factors involved in oil accumulation. We identified candidate genes that may regulate seed oil content based on the co-expression network analysis combined with correlation analysis of the gene expression with seed oil content and seed coat content.

CONCLUSIONS

Overall, these results reveal the transcriptional regulation between lipid and phenylpropane accumulation during B. napus seed development. The established co-expression networks and predicted key factors provide important resources for future studies to reveal the genetic control of oil accumulation in B. napus seeds.

Comprehensive Analysis and Characterization of the GATA Gene Family, with Emphasis on the GATA6 Transcription Factor in Poplar

GATA transcription factors are ubiquitously present in eukaryotic organisms and play a crucial role in multiple biological processes, such as plant growth, stress response, and hormone signaling. However, the study of GATA factors in poplar is currently limited to a small number of proteins, despite their evident functional importance. In this investigation, we utilized the most recent genome annotation and stringent criteria to identify 38 GATA transcription factor genes in poplar. Subsequently, we conducted a comprehensive analysis of this gene family, encompassing phylogenetic classification, protein characterization, analysis of promoter cis-acting elements, and determination of chromosomal location. Our examination of gene duplication events indicated that both tandem and segmental duplications have contributed to the expansion of the GATA gene family in poplar, with segmental duplication potentially being a major driving force. By performing collinearity analysis of genes across six different species, we identified 74 pairs of co-linear genes, which provide valuable insights for predicting gene functions from a comparative genomics perspective. Furthermore, through the analysis of gene expression patterns, we identified five GATA genes that exhibited differential expression in leaf-stem-root tissues and eight genes that were responsive to salt stress. Of particular interest was GATA6, which displayed strong induction by salt stress and overlapped between the two gene sets. We discovered that GATA6 encodes a nuclear-localized protein with transcription activation activity, which is continuously induced by salt stress in leaf and root tissues. Moreover, we constructed a co-expression network centered around GATA6, suggesting the potential involvement of these genes in the growth, development, and response to abiotic stress processes in poplar through cell transport systems and protein modification mechanisms, such as vesicle-mediated transport, intracellular transport, ubiquitination, and deubiquitination. This research provides a foundation for further exploration of the functions and mechanisms of GATA transcription factors in poplar.

Heat responsive gene StGATA2 functions in plant growth, photosynthesis and antioxidant defense under heat stress conditions

Backgrounds

Potato is sensitive to heat stress particularly during plant seedling growth. However, limited studies have characterized the expression pattern of the StGATA family genes under heat stress and lacked validation of its function in potato plants.

Methods

Potato plants were cultivated at 30°C and 35°C to induce heat stress responses. qRT-PCR was carried out to characterize the expression pattern of StGATA family genes in potato plants subjected to heat stress. StGATA2 loss-of-function and gain-of-function plants were established. Morphological phenotypes and growth were indicated by plant height and mass. Photosynthesis and transpiration were suggested by stomatal aperture, net photosynthetic rate, transpiration rate, and stomatal conductance. Biochemical and genetic responses were indicated by enzyme activity and mRNA expression of genes encoding CAT, SOD, and POD, and contents of H₂O₂, MDA, and proline.

Results

The expression patterns of StGATA family genes were altered in response to heat stress. StGATA2 protein located in the nucleus. StGATA2 is implicated in regulating plant height and weight of potato plants in response to heat stresses, especially acute heat stress. StGATA2 over-expression promoted photosynthesis while inhibited transpiration under heat stress. StGATA2 overexpression induced biochemical responses of potato plant against heat stress by regulating the contents of H₂O₂, MDA and proline and the activity of CAT, SOD and POD. StGATA2 overexpression caused genetic responses (CAT, SOD and POD) of potato plant against heat stress.

Conclusion

Our data indicated that StGATA2 could enhance the ability of potato plants to resist heat stress-induced damages, which may provide an effective strategy to engineer potato plants for better adaptability to adverse heat stress conditions.

Identification of novel loci for flowering time in mungbean [Vigna radiata (L.) R. Wilczek] using genome-wide association study

BACKGROUND

Flowering time is an important crop trait. Mungbean flowers do not flower simultaneously, leading to asynchronous pod maturity and laborious multiple harvests per individual plant. The genomic and genetic mechanisms of flowering in mungbean are largely unknown.

OBJECTIVE

This study sought to discover new quantitative trait loci (QTLs) for days to first flowering in mungbean using a genome-wide association study (GWAS).

METHODS

In total, 206 mungbean accessions collected from 20 countries were sequenced using genotyping by sequencing. A GWAS was conducted using 3,596 single nucleotide polymorphisms (SNPs) using TASSEL v5.2.

RESULTS

Seven significant SNPs were associated with first flowering time. Based on the linkage disequilibrium (LD) decay distance, LD block was determined from upstream to downstream of each SNP up to 384 kb. The lead SNP (Chr2_51229568) was located in the DFF2-2 locus. Syntenic analysis between mungbean and soybean revealed the DFF2-2 locus had collinearity with soybean genomic regions containing flowering-related QTLs on Gm13 and Gm20.

CONCLUSION

Identification of flowering-related QTLs and SNPs is important for developing synchronous pod maturity and desirable flowering traits in mungbean.

Large-scale population structure and genetic architecture of agronomic traits of garlic

Garlic, an asexually propagated crop, is the second important bulb crop after the onion and is used as a vegetable and medicinal plant. Abundant and diverse garlic resources have been formed over thousands of years of cultivation. However, genome variation, population structure and genetic architecture of garlic agronomic traits were still not well elucidated. Here, 1 100 258 single nucleotide polymorphisms (SNPs) were identified using genotyping-by-sequencing in 606 garlic accessions collected from 43 countries. Population structure, principal component and phylogenetic analysis showed that these accessions were divided into five subpopulations. Twenty agronomic traits, including above-ground growth traits, bulb-related and bolt-related traits in two consecutive years were implemented in a genome-wide association study. In total, 542 SNPs were associated with these agronomic traits, among which 188 SNPs were repeatedly associated with more than two traits. One SNP (chr6: 1896135972) was repeatedly associated with ten traits. These associated SNPs were located within or near 858 genes, 56 of which were transcription factors. Interestingly, one non-synonymous SNP (Chr4: 166524085) in ribosomal protein S5 was repeatedly associated with above-ground growth and bulb-related traits. Additionally, gene ontology enrichment analysis of candidate genes for genomic selection regions between complete-bolting and non-bolting accessions showed that these genes were significantly enriched in 'vegetative to reproductive phase transition of meristem', 'shoot system development', 'reproductive process', etc. These results provide valuable information for the reliable and efficient selection of candidate genes to achieve garlic genetic improvement and superior varieties.

Patterned proliferation orients tissue-wide stress to control root vascular symmetry in Arabidopsis

Symmetric tissue alignment is pivotal to the functions of plant vascular tissue, such as long-distance molecular transport and lateral organ formation. During the vascular development of the Arabidopsis roots, cytokinins initially determine cell-type boundaries among vascular stem cells and subsequently promote cell proliferation to establish vascular tissue symmetry. Although it is unknown whether and how the symmetry of initially defined boundaries is progressively refined under tissue growth in plants, such boundary shapes in animal tissues are regulated by cell fluidity, e.g., cell migration and intercalation, lacking in plant tissues. Here, we uncover that cell proliferation during vascular development produces anisotropic compressive stress, smoothing, and symmetrizing cell arrangement of the vascular-cell-type boundary. Mechanistically, the GATA transcription factor HANABA-TARANU cooperates with the type-B Arabidopsis response regulators to form an incoherent feedforward loop in cytokinin signaling. The incoherent feedforward loop fine-tunes the position and frequency of vascular cell proliferation, which in turn restricts the source of mechanical stress to the position distal and symmetric to the boundary. By combinatorial analyses of mechanical simulations and laser cell ablation, we show that the spatially constrained environment of vascular tissue efficiently entrains the stress orientation among the cells to produce a tissue-wide stress field. Together, our data indicate that the localized proliferation regulated by the cytokinin signaling circuit is decoded into a globally oriented mechanical stress to shape the vascular tissue symmetry, representing a reasonable mechanism controlling the boundary alignment and symmetry in tissue lacking cell fluidity.

Characterization of promoter elements of isoprene-responsive genes and the ability of isoprene to bind START domain transcription factors

Isoprene has recently been proposed to be a signaling molecule that can enhance tolerance of both biotic and abiotic stress. Not all plants make isoprene, but all plants tested to date respond to isoprene. We hypothesized that isoprene interacts with existing signaling pathways rather than requiring novel mechanisms for its effect on plants. We analyzed the cis-regulatory elements (CREs) in promoters of isoprene-responsive genes and the corresponding transcription factors binding these promoter elements to obtain clues about the transcription factors and other proteins involved in isoprene signaling. Promoter regions of isoprene-responsive genes were characterized using the Arabidopsis cis-regulatory element database. CREs bind ARR1, Dof, DPBF, bHLH112, GATA factors, GT-1, MYB, and WRKY transcription factors, and light-responsive elements were overrepresented in promoters of isoprene-responsive genes; CBF-, HSF-, WUS-binding motifs were underrepresented. Transcription factors corresponding to CREs overrepresented in promoters of isoprene-responsive genes were mainly those important for stress responses: drought-, salt/osmotic-, oxidative-, herbivory/wounding and pathogen-stress. More than half of the isoprene-responsive genes contained at least one binding site for TFs of the class IV (homeodomain leucine zipper) HD-ZIP family, such as GL2, ATML1, PDF2, HDG11, ATHB17. While the HD-zipper-loop-zipper (ZLZ) domain binds to the L1 box of the promoter region, a special domain called the steroidogenic acute regulatory protein-related lipid transfer, or START domain, can bind ligands such as fatty acids (e.g., linolenic and linoleic acid). We tested whether isoprene might bind in such a START domain. Molecular simulations and modeling to test interactions between isoprene and a class IV HD-ZIP family START-domain-containing protein were carried out. Without membrane penetration by the HDG11 START domain, isoprene within the lipid bilayer was inaccessible to this domain, preventing protein interactions with membrane bound isoprene. The cross-talk between isoprene-mediated signaling and other growth regulator and stress signaling pathways, in terms of common CREs and transcription factors could enhance the stability of the isoprene emission trait when it evolves in a plant but so far it has not been possible to say what how isoprene is sensed to initiate signaling responses.

Flower Development in Arabidopsis

Like in other angiosperms, the development of flowers in Arabidopsis starts right after the floral transition, when the shoot apical meristem (SAM) stops producing leaves and makes flowers instead. On the flanks of the SAM emerge the flower meristems (FM) that will soon differentiate into the four main floral organs, sepals, petals, stamens, and pistil, stereotypically arranged in concentric whorls. Each phase of flower development-floral transition, floral bud initiation, and floral organ development-is under the control of specific gene networks. In this chapter, we describe these different phases and the gene regulatory networks involved, from the floral transition to the floral termination.

Genetic and Phenotypic Analysis of Shoot Apical and Floral Meristem Development

The shoot apical and floral meristems (SAM and FM, respectively) of Arabidopsis thaliana contain reservoirs of self-renewing stem cells that function as sources of progenitor cells for organ formation during development. The primary SAM produces all the aerial structures of the adult plant, while the FMs generate the four types of floral organs. Consequently, aberrant SAM and FM activity can profoundly affect vegetative and reproductive plant morphology. The embedded location and small size of Arabidopsis meristems make accessing these structures difficult, so specialized techniques have been developed to facilitate their analysis. Microscopic, histological, and molecular techniques provide both qualitative and quantitative data on meristem organization and function, which are crucial for the normal growth and development of the entire plant.

Genetic architecture underlying variation in floral meristem termination in Aquilegia

Floral organs are produced by floral meristems (FMs), which harbor stem cells in their centers. Since each flower only has a finite number of organs, the stem cell activity of an FM will always terminate at a specific time point, a process termed floral meristem termination (FMT). Variation in the timing of FMT can give rise to floral morphological diversity, but how this process is fine-tuned at a developmental and evolutionary level is poorly understood. Flowers from the genus Aquilegia share identical floral organ arrangement except for stamen whorl number (SWN), making Aquilegia a well-suited system for investigation of this process: differences in SWN between species represent differences in the timing of FMT. By crossing A. canadensis and A. brevistyla, quantitative trait locus (QTL) mapping has revealed a complex genetic architecture with seven QTL. We explored potential candidate genes under each QTL and characterized novel expression patterns of select loci of interest using in situ hybridization. To our knowledge, this is the first attempt to dissect the genetic basis of how natural variation in the timing of FMT is regulated, and our results provide insight into how floral morphological diversity can be generated at the meristematic level.

Overexpression of HANABA TARANU in cultivated strawberry delays flowering and leads to defective flower and fruit development

Cultivated strawberry is one of the most important horticultural crops in the world, and the fruit yields and economic benefits are largely dependent on the quality of floral initiation and floral organ development. However, the underlying regulatory mechanisms controlling these processes in strawberry are largely unknown. In this study, the function of a GATA transcription factor gene, HANABA TARANU (HAN), in floral initiation and floral organ development was characterized in strawberry. FaHAN is expressed in four whorls of the floral organs. Overexpression (OE) of FaHAN in the strawberry cultivar 'Benihoppe' delayed flowering by at least one week by affecting key genes, such as TERMINAL FLOWER 1, APETALA 1…and increased the number of runners. FaHAN-OE plants also showed malformed floral organs, especially the deformed stigmas with disordered arrangement. Several key genes for pistil apical development such as STYLISH, YUCCA 1, and auxin-related genes such as GH3.5, PIN-FORMED 1, which play important roles in pistil primordium development in many plant species, were all down-regulated in FaHAN-OE plants. Further observations showed that the fruit deformity rate was nearly 4-fold higher than in control plants. Together, this study provides a new approach for exploring floral initiation and floral organ development in strawberry.

Boundary domain genes were recruited to suppress bract growth and promote branching in maize

Grass inflorescence development is diverse and complex and involves sophisticated but poorly understood interactions of genes regulating branch determinacy and leaf growth. Here, we use a combination of transcript profiling and genetic and phylogenetic analyses to investigate tasselsheath1 (tsh1) and tsh4, two maize genes that simultaneously suppress inflorescence leaf growth and promote branching. We identify a regulatory network of inflorescence leaf suppression that involves the phase change gene tsh4 upstream of tsh1 and the ligule identity gene liguleless2 (lg2). We also find that a series of duplications in the tsh1 gene lineage facilitated its shift from boundary domain in nongrasses to suppressed inflorescence leaves of grasses. Collectively, these results suggest that the boundary domain genes tsh1 and lg2 were recruited to inflorescence leaves where they suppress growth and regulate a nonautonomous signaling center that promotes inflorescence branching, an important component of yield in cereal grasses.

The GATA factor HANABA TARANU promotes runner formation by regulating axillary bud initiation and outgrowth in cultivated strawberry

A runner, as an elongated branch, develops from the axillary bud (AXB) in the leaf axil and is crucial for the clonal propagation of cultivated strawberry (Fragaria  ×  ananassa Duch.). Runner formation occurs in at least two steps: AXB initiation and AXB outgrowth. HANABA TARANU (HAN ) encodes a GATA transcription factor that affects AXB initiation in Arabidopsis and promotes branching in grass species, but the underlying mechanism is largely unknown. Here, the function of a strawberry HAN homolog FaHAN in runner formation was characterized. FaHAN transcripts can be detected in the leaf axils. Overexpression (OE) of FaHAN increased the number of runners, mainly by enhancing AXB outgrowth, in strawberry. The expression of the strawberry homolog of BRANCHED1 , a key inhibitor of AXB outgrowth in many plant species, was significantly downregulated in the AXBs of FaHAN -OE lines, whereas the expression of the strawberry homolog of SHOOT MERISTEMLESS, a marker gene for AXB initiation in Arabidopsis, was upregulated. Moreover, several genes of gibberellin biosynthesis and cytokinin signaling pathways were activated, whereas the auxin response pathway genes were repressed. Further assays indicated that FaHAN could be directly activated by FaNAC2, the overexpression of which in strawberry also increased the number of runners. The silencing of FaNAC2 or FaHAN inhibited AXB initiation and led to a higher proportion of dormant AXBs, confirming their roles in the control of runner formation. Taken together, our results revealed a FaNAC2-FaHAN pathway in the control of runner formation and have provided a means to enhance the vegetative propagation of cultivated strawberry.

Plant GATA Factors: Their Biology, Phylogeny, and Phylogenomics

GATA factors are evolutionarily conserved transcription factors that are found in animals, fungi, and plants. Compared to that of animals, the size of the plant GATA family is increased. In angiosperms, four main GATA classes and seven structural subfamilies can be defined. In recent years, knowledge about the biological role and regulation of plant GATAs has substantially improved. Individual family members have been implicated in the regulation of photomorphogenic growth, chlorophyll biosynthesis, chloroplast development, photosynthesis, and stomata formation, as well as root, leaf, and flower development. In this review, we summarize the current knowledge of plant GATA factors. Using phylogenomic analysis, we trace the evolutionary origin of the GATA classes in the green lineage and examine their relationship to animal and fungal GATAs. Finally, we speculate about a possible conservation of GATA-regulated functions across the animal, fungal, and plant kingdoms.

Genetic Analysis of the Grapevine GATA Gene Family and Their Expression Profiles in Response to Hormone and Downy Mildew Infection

Grapevine (Vitis. vinifera L.) is one of the most economically important fruit crops throughout the world. However, grape production is increasingly impacted by numerous diseases, including downy mildew, caused by the oomycete Plasmopara viticola. In grapevine and other plants, members of the GATA family of transcription factors play key roles in light and phytohormone signaling. However, little is known about their potential roles in biotic defense responses. As a first step, we identified 27 GATA transcription factors in grapevine and defined their transcriptional responses to three biotic stress-related phytohormones (SA, MeJA, and BR) in callus cells, and challenge with P. viticola in a downy mildew-sensitive cultivar, V. vinifera ‘Pinot noir’, and a resistant cultivar, V. piasezkii ‘Liuba-8′. Many of the VvGATA genes had higher expression at 0.5 h after hormones treatments. Moreover, a group of VvGATAs was dramatically induced in ‘Liuba-8′ at 24 post infection by P. viticola. However, the same genes were significantly repressed and showed low expression levels in ‘Pinot noir’. Additionally, VvGATA27 was located in the nucleus and had transcriptional activity. Taken together, the study identified the GATA full gene families in grapes on phylogenetic analysis and protein structure. Moreover, this study provided a basis for discussing the roles of VvGATAs in response to hormones and P. viticola infection. Our results provided evidence for the selection of candidate genes against downy mildew and lay the foundation for further investigation of VvGATA transcription factors.

A novel insight into transcriptional and epigenetic regulation underlying sex expression and flower development in melon (Cucumis melo L.)

Melon (Cucumis melo L.) is an important cucurbit and has been considered as a model plant for studying sex determination. The four most common sexual morphotypes in melon are monoecious (A-G-M), gynoecious (--ggM-), andromonoecious (A-G-mm), and hermaphrodite (--ggmm). Sex expression in melons is complex, as the genes and associated networks that govern the sex expression are not fully explored. Recently, RNA-seq transcriptomic profiling, ChIP-qPCR analysis integrated with gene ontology annotation and Kyoto Encyclopedia of Genes and Genomes pathways predicted the differentially expressed genes including sex-specific ACS and ACO genes, in regulating the sex-expression, phytohormonal cross-talk, signal transduction, and secondary metabolism in melons. Integration of transcriptional control through genetic interaction in between the ACS7, ACS11, and WIP1 in epistatic or hypostatic manner, along with the recruitment of H3K9ac and H3K27me3, epigenetically, overall determine sex expression. Alignment of protein sequences for establishing phylogenetic evolution, motif comparison, and protein-protein interaction supported the structural conservation while presence of the conserved hydrophilic and charged residues across the diverged evolutionary group predicted the functional conservation of the ACS protein. Presence of the putative cis-binding elements or DNA motifs, and its further comparison with DAP-seq-based cistrome and epicistrome of Arabidopsis, unraveled strong ancestry of melons with Arabidopsis. Motif comparison analysis also characterized putative genes and transcription factors involved in ethylene biosynthesis, signal transduction, and hormonal cross-talk related to sex expression. Overall, we have comprehensively reviewed research findings for a deeper insight into transcriptional and epigenetic regulation of sex expression and flower development in melons.

Identification and expression analysis of candidate genes related to seed dormancy and germination in the wheat GATA family

GATA transcription factors have been reported to function in plant growth and development and during various biotic/abiotic stresses in Arabidopsis and rice. However, the functions of wheat GATAs, particularly in the regulation of seed dormancy and germination, remain unclear. Here, we identified 78 TaGATAs in wheat and divided them into five subfamilies. Sixty-four paralogous pairs and 52 orthologous pairs were obtained, and Ka/Ks ratios showed that the TaGATAs had undergone strong purifying election during the evolutionary process. Triplet analysis indicated that a high homologue retention rate could explain the large number of TaGATAs in wheat. Gene structure analysis revealed that most members of the same subfamily had similar structures, and subcellular localization prediction indicated that most TaGATAs were located in the nucleus. Gene ontology annotation results showed that most TaGATAs had molecular functions in DNA and zinc binding, and promoter analysis suggested that they may play important roles in growth, development, and biotic/abiotic stress response. We combined three microarray datasets with qRT-PCR expression data from wheat varieties of contrasting dormancy and pre-harvest sprouting resistance levels during imbibition in order to identify ten candidate genes (TaGATA17/-25/-34/-37/-40/-46/-48/-51/-72/-73) that may be involved in the regulation of seed dormancy and germination in wheat. These findings provide valuable information for further dissection of TaGATA functions in the regulation of seed dormancy and germination, thereby enabling the improvement of wheat pre-harvest sprouting resistance by gene pyramiding.

Genome-wide comparative analyses of GATA transcription factors among seven Populus genomes

GATA transcription factors (TFs) are widespread eukaryotic regulators whose DNA-binding domain is a class IV zinc finger motif (CX2CX17-20CX2C) followed by a basic region. We identified 262 GATA genes (389 GATA TFs) from seven Populus genomes using the pipeline of GATA-TFDB. Alternative splicing forms of Populus GATA genes exhibit dynamics of GATA gene structures including partial or full loss of GATA domain and additional domains. Subfamily III of Populus GATA genes display lack CCT and/or TIFY domains. 21 Populus GATA gene clusters (PCs) were defined in the phylogenetic tree of GATA domains, suggesting the possibility of subfunctionalization and neofunctionalization. Expression analysis of Populus GATA genes identified the five PCs displaying tissue-specific expression, providing the clues of their biological functions. Amino acid patterns of Populus GATA motifs display well conserved manner of Populus GATA genes. The five Populus GATA genes were predicted as membrane-bound GATA TFs. Biased chromosomal distributions of GATA genes of three Populus species. Our comparative analysis approaches of the Populus GATA genes will be a cornerstone to understand various plant TF characteristics including evolutionary insights.

Genome-wide comparative analyses of GATA transcription factors among 19 Arabidopsis ecotype genomes: Intraspecific characteristics of GATA transcription factors

GATA transcription factors (TFs) are widespread eukaryotic regulators whose DNA-binding domain is a class IV zinc finger motif (CX2CX17-20CX2C) followed by a basic region. Due to the low cost of genome sequencing, multiple strains of specific species have been sequenced: e.g., number of plant genomes in the Plant Genome Database (http://www.plantgenome.info/) is 2,174 originated from 713 plant species. Thus, we investigated GATA TFs of 19 Arabidopsis thaliana genome-widely to understand intraspecific features of Arabidopsis GATA TFs with the pipeline of GATA database (http://gata.genefamily.info/). Numbers of GATA genes and GATA TFs of each A. thaliana genome range from 29 to 30 and from 39 to 42, respectively. Four cases of different pattern of alternative splicing forms of GATA genes among 19 A. thaliana genomes are identified. 22 of 2,195 amino acids (1.002%) from the alignment of GATA domain amino acid sequences display variations across 19 ecotype genomes. In addition, maximally four different amino acid sequences per each GATA domain identified in this study indicate that these position-specific amino acid variations may invoke intraspecific functional variations. Among 15 functionally characterized GATA genes, only five GATA genes display variations of amino acids across ecotypes of A. thaliana, implying variations of their biological roles across natural isolates of A. thaliana. PCA results from 28 characteristics of GATA genes display the four groups, same to those defined by the number of GATA genes. Topologies of bootstrapped phylogenetic trees of Arabidopsis chloroplasts and common GATA genes are mostly incongruent. Moreover, no relationship between geographical distribution and their phylogenetic relationships was found. Our results present that intraspecific variations of GATA TFs in A. thaliana are conserved and evolutionarily neutral along with 19 ecotypes, which is congruent to the fact that GATA TFs are one of the main regulators for controlling essential mechanisms, such as seed germination and hypocotyl elongation.

Developmental Analysis of the GATA Factor HANABA TARANU Mutants in Medicago truncatula Reveals Their Roles in Nodule Formation

Formation of nodules on legume roots results from symbiosis with rhizobial bacteria. Here, we identified two GATA transcription factors, MtHAN1 and MtHAN2, in Medicago truncatula, which are the homologs of HANABA TARANU (HAN) and HANABA TARANU LIKE in Arabidopsis thaliana. Our analysis revealed that MtHAN1 and MtHAN2 are expressed in roots and shoots including the root tip and nodule apex. We further show that MtHAN1 and MtHAN2 localize to the nucleus where they interact and that single and double loss-of-function mutants of MtHAN1 and MtHAN2 did not show any obvious phenotype in flower development, suggesting their role is different than their closest Arabidopsis homologues. Investigation of their symbiotic phenotypes revealed that the mthan1 mthan2 double mutant develop twice as many nodules as wild type, revealing a novel biological role for GATA transcription factors. We found that HAN1/2 transcript levels respond to nitrate treatment like their Arabidopsis counterparts. Global gene transcriptional analysis by RNA sequencing revealed different expression genes enriched for several pathways important for nodule development including flavonoid biosynthesis and phytohormones. In addition, further studies suggest that MtHAN1 and MtHAN2 are required for the expression of several nodule-specific cysteine-rich genes, which they may activate directly, and many peptidase and peptidase inhibitor genes. This work expands our knowledge of the functions of MtHANs in plants by revealing an unexpected role in legume nodulation.

Insights into the evo-devo of plant reproduction using next-generation sequencing approaches

The development of plant model organisms has traditionally been analyzed using resource-heavy, tailored applications that are not easily transferable to distantly related non-model taxa. Thus, our understanding of plant development has been limited to a subset of traits, and evolutionary studies conducted most effectively either across very wide [e.g. Arabidopsis thaliana and Oryza sativa (rice)] or narrow (i.e. population level) phylogenetic distances. As plant biologists seek to capitalize on natural diversity for crop improvement, enhance ecosystem functioning, and better understand plant responses to climate change, high-throughput and broadly applicable forms of existing molecular biology assays are becoming an invaluable resource. Next-generation sequencing (NGS) is increasingly becoming a powerful tool in evolutionary developmental biology (evo-devo) studies, particularly through its application to understanding trait evolution at different levels of gene regulation. Here, I review some of the most common and emerging NGS-based methods, using exemplar studies in reproductive plant evo-devo to illustrate their potential.

Genome-wide identification and function characterization of GATA transcription factors during development and in response to abiotic stresses and hormone treatments in pepper

Pepper (Capsicum annuum L.) is an economically important vegetable crop whose production and quality are severely reduced under adverse environmental stress conditions. The GATA transcription factors belonging to type IV zinc-finger proteins, play a significant role in regulating light morphogenesis, nitrate assimilation, and organ development in plants. However, the functional characteristics of GATA gene family during development and in response to environmental stresses have not yet been investigated in pepper. In this study, a total of 28 pepper GATA (CaGATA) genes were identified. To gain an overview of the CaGATAs, we analyzed their chromosomal distribution, gene structure, conservative domains, cis-elements, phylogeny, and evolutionary relationship. We divided 28 CaGATAs into four groups distributed on 10 chromosomes, and identified 7 paralogs in CaGATA family of pepper and 35 orthologous gene pairs between CaGATAs and Arabidopsis GATAs (AtGATAs). The results of promoter cis-element analysis and the quantitative real-time PCR (qRT-PCR) analysis revealed that CaGATA genes were involved in regulating the plant growth and development and the responses to various abiotic stresses and hormone treatments in pepper. Tissue-specific expression analysis showed that most CaGATA genes were preferentially expressed in flower buds, flowers, and leaves. Several CaGATA genes, especially CaGATA14, were significantly regulated under multiple abiotic stresses, and CaGATA21 and CaGATA27 were highly responsive to phytohormone treatments. Taken together, our results lay a foundation for the biological function analysis of GATA gene family in pepper.

Mapping a Partial Andromonoecy Locus in Citrullus lanatus Using BSA-Seq and GWAS Approaches

The sexual expression of watermelon plants is the result of the distribution and occurrence of male, female, bisexual and hermaphrodite flowers on the main and secondary stems. Plants can be monoecious (producing male and female flowers), andromonoecious (producing male and hermaphrodite flowers), or partially andromonoecious (producing male, female, bisexual, and hermaphrodite flowers) within the same plant. Sex determination of individual floral buds and the distribution of the different flower types on the plant, are both controlled by ethylene. A single missense mutation in the ethylene biosynthesis gene CitACS4, is able to promote the conversion of female into hermaphrodite flowers, and therefore of monoecy (genotype MM) into partial andromonoecy (genotype Mm) or andromonoecy (genotype mm). We phenotyped and genotyped, for the M/m locus, a panel of 207 C. lanatus accessions, including five inbreds and hybrids, and found several accessions that were repeatedly phenotyped as PA (partially andromonoecious) in several locations and different years, despite being MM. A cosegregation analysis between a SNV in CitACS4 and the PA phenotype, demonstrated that the occurrence of bisexual and hermaphrodite flowers in a PA line is not dependent on CitACS4, but conferred by an unlinked recessive gene which we called pa. Two different approaches were performed to map the pa gene in the genome of C. lanatus: bulk segregant analysis sequencing (BSA-seq) and genome wide association analysis studies (GWAS). The BSA-seq study was performed using two contrasting bulks, the monoecious M-bulk and the partially andromonoecious PA-bulk, each one generated by pooling DNA from 20 F2 plants. For GWAS, 122 accessions from USDA gene bank, already re-sequenced by genotyping by sequencing (GBS), were used. The combination of the two approaches indicates that pa maps onto a genomic region expanding across 32.24-36.44 Mb in chromosome 1 of watermelon. Fine mapping narrowed down the pa locus to a 867 Kb genomic region containing 101 genes. A number of candidate genes were selected, not only for their function in ethylene biosynthesis and signalling as well as their role in flower development and sex determination, but also by the impact of the SNPs and indels differentially detected in the two sequenced bulks.

The Brassica napus GATA transcription factor BnA5.ZML1 is a stigma compatibility factor

Self-incompatibility (SI) is a genetic mechanism that rejects self-pollen and thus prevents inbreeding in some hermaphroditic angiosperms. In the Brassicaceae, SI involves a pollen-stigma recognition system controlled by a single locus known as the S locus, which consists of two highly polymorphic genes that encode S-locus cysteine-rich protein (SCR) and S-receptor kinase (SRK). When self-pollen lands on the stigma, the S-haplotype-specific interaction between SCR and SRK triggers SI. Here, we show that the GATA transcription factor BnA5.ZML1 suppresses SI responses in Brassica napus and is induced after compatible pollination. The loss-of-function mutant bna5.zml1 displays reduced self-compatibility. In contrast, overexpression of BnA5.ZML1 in self-incompatible stigmas leads to a partial breakdown of SI responses, suggesting that BnA5.ZML1 is a stigmatic compatibility factor. Furthermore, the expression levels of SRK and ARC1 are up-regulated in bna5.zml1 mutants, and they are down-regulated in BnA5.ZML1 overexpressing lines. SRK affects the cellular localization of BnA5.ZML1 through direct protein-protein interaction. Overall, our findings highlight the fundamental role of BnA5.ZML1 in SI responses in B. napus, establishing a direct interaction between BnA5.ZML1 and SRK in this process.

Control of cell fate during axillary meristem initiation

Axillary meristems (AMs) are located in the leaf axil and can establish new growth axes. Whereas their neighboring cells are differentiated, the undifferentiated cells in the AM endow the AM with the same developmental potential as the shoot apical meristem. The AM is, therefore, an excellent system to study stem cell fate maintenance in plants. In this review, we summarize the current knowledge of AM initiation. Recent findings have shown that AMs derive from a stem cell lineage that is maintained in the leaf axil. This review covers AM progenitor cell fate maintenance, reactivation, and meristem establishment. We also highlight recent work that links transcription factors, phytohormones, and epigenetic regulation to AM initiation.

Gene regulatory network controlling carpel number variation in cucumber

The WUSCHEL-CLAVATA3 pathway genes play an essential role in shoot apical meristem maintenance and floral organ development, and under intense selection during crop domestication. The carpel number is an important fruit trait that affects fruit shape, size and internal quality in cucumber, but the molecular mechanism remains elusive. Here, we found that CsCLV3 expression was negatively correlated with carpel number in cucumber cultivars. CsCLV3-RNAi led to increased number of petals and carpels, whereas overexpression of CsWUS resulted in more sepals, petals and carpels, suggesting that CsCLV3 and CsWUS function as a negative and a positive regulator for carpel number variation, respectively. Biochemical analyses indicated that CsWUS directly bound to the promoter of CsCLV3 and activated its expression. Overexpression of CsFUL1^A , a FRUITFULL-like MADS-box gene, resulted in more petals and carpels. CsFUL1^A can directly bind to the CsWUS promoter to stimulate its expression. Furthermore, we found that auxin participated in carpel number variation in cucumber through interaction of CsARF14 with CsWUS. Therefore, we have identified a gene regulatory pathway involving CsCLV3, CsWUS, CsFUL1^A and CsARF14 in determining carpel number variation in an important vegetable crop - cucumber.

The wheat LLM-domain-containing transcription factor TaGATA1 positively modulates host immune response to Rhizoctonia cerealis

Wheat (Triticum aestivum) is essential for global food security. Rhizoctonia cerealis is the causal pathogen of sharp eyespot, an important disease of wheat. GATA proteins in model plants have been implicated in growth and development; however, little is known about their roles in immunity. Here, we report a defence role for a wheat LLM-domain-containing B-GATA transcription factor, TaGATA1, against R. cerealis infection and explore the underlying mechanism. Through transcriptomic analysis, TaGATA1 was identified to be more highly expressed in resistant wheat genotypes than in susceptible wheat genotypes. TaGATA1 was located on chromosome 3B and had two homoeologous genes on chromosomes 3A and 3D. TaGATA1 was found to be localized in the nucleus, possessed transcriptional activation activity, and bound to GATA-core cis-elements. TaGATA1 overexpression significantly enhanced resistance of transgenic wheat to R. cerealis, whereas silencing of TaGATA1 suppressed the resistance. Quantitative reverse transcription-PCR and ChIP-qPCR results indicated that TaGATA1 directly bound to and activated certain defence genes in host immune response to R. cerealis. Collectively, TaGATA1 positively regulates immune responses to R. cerealis through activating expression of defence genes in wheat. This study reveals a new function of plant GATAs in immunity and provides a candidate gene for improving crop resistance to R. cerealis.

Implications of region-specific gene expression for development of the partially fused petunia corolla

Angiosperm petal fusion (sympetaly) has evolved multiple times independently and is associated with increased specificity between plants and their pollinators. To uncover developmental genetic changes that might have led to the evolution of sympetaly in the asterid core eudicot genus Petunia (Solanaceae), we carried out global and fine-scale gene expression analyses in different regions of the corolla. We found that, despite several similarities with the choripetalous model species Arabidopsis thaliana in the proximal-distal transcriptome, the Petunia axillaris fused and proximal corolla tube expresses several genes that in A. thaliana are associated with the distal petal region. This difference aligns with variation in petal shape and fusion across ontogeny of the two species. Moreover, differential gene expression between the unfused lobes and fused tube of P. axillaris petals revealed three strong candidate genes for sympetaly based on functional annotation in organ boundary specification. Partial silencing of one of these, the HANABA TARANU (HAN)-like gene PhGATA19, resulted in reduced fusion of Petunia hybrida petals, with silencing of both PhGATA19 and its close paralog causing premature plant senescence. Finally, detailed expression analyses for the previously characterized organ boundary gene candidate NO APICAL MERISTEM (NAM) supports the hypothesis that it establishes boundaries between most P. axillaris floral organs, with the exception of boundaries between petals.

Biological roles and an evolutionary sketch of the GRF-GIF transcriptional complex in plants

GROWTH-REGULATING FACTORs (GRFs) are sequence-specific DNA-binding transcription factors that regulate various aspects of plant growth and development. GRF proteins interact with a transcription cofactor, GRF-INTERACTING FACTOR (GIF), to form a functional transcriptional complex. For its activities, the GRF-GIF duo requires the SWITCH2/SUCROSE NONFERMENTING2 chromatin remodeling complex. One of the most conspicuous roles of the duo is conferring the meristematic potential on the proliferative and formative cells during organogenesis. GRF expression is post-transcriptionally down-regulated by microRNA396 (miR396), thus constructing the GRF-GIF-miR396 module and fine-tuning the duo’s action. Since the last comprehensive review articles were published over three years ago, many studies have added further insight into its action and elucidated new biological roles. The current review highlights recent advances in our understanding of how the GRF-GIF-miR396 module regulates plant growth and development. In addition, I revise the previous view on the evolutionary origin of the GRF gene family.

ATML1 activity is restricted to the outermost cells of the embryo through post-transcriptional repressions

Cell fate determination in plants relies on positional cues. To investigate the position-dependent gene regulation in plants, we focused on shoot epidermal cell specification, which occurs only in the outermost cells. ATML1, which encodes an HD-ZIP class IV transcription factor, is a positive regulator of shoot epidermal cell identity. Despite the presence of a weak ATML1 promoter activity in the inner cells, ATML1 protein was detected mostly in the outermost cells, which suggests that ATML1 accumulation is inhibited in the inner cells. ATML1 nuclear localization was reduced in the epidermis and there was a positive, albeit weak, correlation between the amount of ATML1 in the nuclei and the expression of a direct target of ATML1. Nuclear accumulation of ATML1 was more strongly inhibited in the inner cells than in the outermost cells. Domain deletion analyses revealed that the ZLZ-coding sequence was necessary and partially sufficient for the post-transcriptional repression of ATML1 Our results suggest that post-transcriptional repressions contribute to the restriction of master transcriptional regulator activity in specific cells to enable position-dependent cell differentiation.

A gene expression map of shoot domains reveals regulatory mechanisms

Gene regulatory networks control development via domain-specific gene expression. In seed plants, self-renewing stem cells located in the shoot apical meristem (SAM) produce leaves from the SAM peripheral zone. After initiation, leaves develop polarity patterns to form a planar shape. Here we compare translating RNAs among SAM and leaf domains. Using translating ribosome affinity purification and RNA sequencing to quantify gene expression in target domains, we generate a domain-specific translatome map covering representative vegetative stage SAM and leaf domains. We discuss the predicted cellular functions of these domains and provide evidence that dome seemingly unrelated domains, utilize common regulatory modules. Experimental follow up shows that the RABBIT EARS and HANABA TARANU transcription factors have roles in axillary meristem initiation. This dataset provides a community resource for further study of shoot development and response to internal and environmental signals.

The shoot apical meristem (SAM) maintains stem cells and generates new leaves and flowers from its periphery. Here via spatially resolved translatome profiling, Tian et al. define distinct molecular signatures of different SAM and leaf domains and identify regulators of axillary meristem initiation.

INDEL variation in the regulatory region of the major flowering time gene LanFTc1 is associated with vernalization response and flowering time in narrow-leafed lupin (Lupinus angustifolius L.)

Narrow-leafed lupin (Lupinus angustifolius L.) cultivation was transformed by 2 dominant vernalization-insensitive, early flowering time loci known as Ku and Julius (Jul), which allowed expansion into shorter season environments. However, reliance on these loci has limited genetic and phenotypic diversity for environmental adaptation in cultivated lupin. We recently predicted that a 1,423-bp deletion in the cis-regulatory region of LanFTc1, a FLOWERING LOCUS T (FT) homologue, derepressed expression of LanFTc1 and was the underlying cause of the Ku phenotype. Here, we surveyed diverse germplasm for LanFTc1 cis-regulatory variation and identified 2 further deletions of 1,208 and 5,162 bp in the 5' regulatory region, which overlap the 1,423-bp deletion. Additionally, we confirmed that no other polymorphisms were perfectly associated with vernalization responsiveness. Phenotyping and gene expression analyses revealed that Jul accessions possessed the 5,162-bp deletion and that the Jul and Ku deletions were equally capable of removing vernalization requirement and up-regulating gene expression. The 1,208-bp deletion was associated with intermediate phenology, vernalization responsiveness, and gene expression and therefore may be useful for expanding agronomic adaptation of lupin. This insertion/deletion series may also help resolve how the vernalization response is mediated at the molecular level in legumes.

Genome-wide identification and analysis of the evolution and expression patterns of the GATA transcription factors in three species of Gossypium genus

GATA transcription factors (TFs), which bind to DNA in regulatory regions, are involved in cell differentiation and possess a type-IV zinc finger and a DNA-binding domain. GATA genes have been characterized in plant species such as Arabidopsis thaliana, Oryza sativa, and Glycine max, and their functions have been elucidated in A. thaliana. Although many Gossypium quantitative trait loci for fiber quality harbor GATA TFs, GATA genes have not yet been characterized in cotton. In this study, we identified 179 GATA genes from the genomes of three Gossypium species. We analyzed the phylogenetic relationships, chromosomal distribution, gene structure, expression pattern, and predicted promoters of all 179 Gossypium GATA genes (46 in G. raimondii, 46 in G. arboreum, and 87 in G. hirsutum). Phylogenetic analysis grouped the 179 GATA genes into four subfamilies. Domain analysis revealed that GATA domains in subfamilies I, II, and III were located near the C-terminal, whereas those in subfamily IV were adjacent to the N-terminal. RNA-seq and (Real-time PCR) qRT-PCR revealed that 39.1% (34/87) of GATA genes were expressed in growing plant tissues in G. hirsutum, but only 12.6% (11/87) were expressed during fiber development. In addition, 45.7% (21/46) and 26.1% (12/46) of GATA genes were expressed in G. arboreum and G. raimondii, respectively. Our results may be useful for elucidating the evolution, expression patterns, and functional divergence of GATA genes in Gossypium.