Arabidopsis Genes Research Articles

Genome-wide characterization of auxin response factor (ARF) genes in bermudagrass and ectopically functional analysis of CdARF6-B2 gene in Arabidopsis

Genome-wide characterization of auxin response factor (ARF) genes in bermudagrass and ectopically functional analysis of CdARF6-B2 gene in Arabidopsis

Rapid and high-throughput identification of thermal-responsive genes based on cDNA-library in Upland Cotton

Severe high temperature (HT) climate significantly impacts cotton quality and yield. Consequently, it is essential to mine thermal-responsive genes and explore the underlying mechanisms of HT response in cotton. In this study, we employed a high-throughput cDNA-library method in conjunction with the ALRS system to screen thermotolerant genes in Upland cotton. As a result, a total of 16,120, 13,216 and 172 effective survival genes were filtered after HT stress exposure (42 °C, 220 rpm) for 48 h, 60 h and 72 h, respectively. Functional annotation and enrichment analysis revealed that 170 common genes were involved in regulatory processes associated with HT stress, and the relevant transcriptome data indicated that the majority of these genes responded to temperature fluctuations. Twenty-one genes were randomly selected for verification, and it was found that these genes could enhance yeast resistance to HT stress. Additionally, we selected mutants of homologous Arabidopsis genes for four candidate genes to validate plant thermotolerance during flowering; the thermotolerances of SALK_201915 and SALK_120540.1 were significantly worse. The results demonstrate that numerous candidate genes identified from the cDNA-library contribute to the highly complex molecular network that governs the response and resistance to HT stress in Upland cotton. The high-throughput heat-screening method utilized in this study was optimized for mining thermotolerant genes including improvement in yeast library construction, screening system, gradient reverse pressure, and sequencing library construction. We hope that this new method can be applied in future studies on stress in cotton and other species.

High-throughput capture of transcription factor-driven epigenome dynamics using PHILO ChIP-seq.

Assessing the dynamics of chromatin features and transcription factor (TF) binding at scale remains a significant challenge in plants. Here, we present PHILO (Plant HIgh-throughput LOw input) ChIP-seq, a high-throughput ChIP-seq platform that enables the cost-effective and extensive capture of TF binding and genome-wide distributions of histone modifications. The PHILO ChIP-seq pipeline is adaptable to many plant species, requires very little starting material (1mg), and provides the option to use MNase (micrococcal nuclease) for chromatin fragmentation. By employing H3K9ac PHILO ChIP-seq on eight Arabidopsis thaliana jasmonic acid (JA) pathway mutants, with the simultaneous processing of over 100 samples, we not only recapitulated but also expanded the current understanding of the intricate interplay between the master TFs MYC2/3/4 and various chromatin regulators. Additionally, our analyses brought to light previously unknown histone acetylation patterns within the regulatory regions of MYC2 target genes in Arabidopsis, which is also conserved in tomato (Solanum lycopersicum). In summary, our PHILO ChIP-seq platform demonstrates its high effectiveness in investigating TF binding and chromatin dynamics on a large scale in plants, paving the way for the cost-efficient realization of complex experimental setups.

The overall regulatory network and contributions of ABC(D)E model genes in yellowhorn flower development

BackgroundSingle flowers and double flowers, exhibiting distinct flower morphologies, developmental process and regulatory networks, have garnered significant attention recently. In yellowhorn (Xanthoceras sorbifolium), the cause of double flower variation has been elucidated, yet the differences in regulatory networks between single and double flowers remain unexplored.ResultHere, we investigated transcriptional changes underlying flower development among yellowhorn single- and double-flowered-trees. Transcriptome analysis and weighted gene co-expression network analysis (WGCNA) were applied to identify key genes and reveal the characteristics of single and double flower traits. The involvement of development-specific and flower-type-specific DEGs related to hormone signaling, metabolism, growth and development was identified, and ABC(D)E model genes were found to be closely associated with floral organ development. Overexpression of yellowhorn ABC(D)E model genes in Arabidopsis demonstrated their roles in floral organ development, and the interactions between different pairs of genes were also validated by yeast two-hybrid (Y2H) experiments.ConclusionTherefore we elucidated differences between yellowhorn single and double flower development, highlighting the roles of yellowhorn ABC(D)E model genes in controlling flower structures, which not only enriches the understanding of yellowhorn flower researches, but also provides insights for studying flower development in other woody species.

GWAS-Based Prediction of Genes Regulating the Weight of Mobilized Reserved Seeds in Sweet Corn

Seed reserve mobilization is a crucial physiological process during seed germination. Enhancing the reserve mobilization in sweet corn is vital for seed germination and seedling growth. In this study, a genome-wide association analysis (GWAS) was conducted to predict candidate genes for regulating the weight of mobilized reserved seeds (WMRS) and kernel weight (KW) in sweet corn. GWAS was performed using the BLINK model with the maize 56K SNP chip. The results indicated that there was a positive correlation between the WMRS and KW, with coefficients of variation of 68.18% and 44.63%. Association analysis identified thirteen SNPs associated with two traits, and linkage disequilibrium analysis revealed that eight of these SNPs were in strong linkage. A total of 298 candidate genes were identified within the confidence interval, of which 79 were annotated. About 20 candidate genes were identified through the comparison of homologous genes in Arabidopsis. These genes were enriched in regulating ribosome biogenesis, signal transduction, hormone synthesis, and RNA degradation processes. This study provides important insights into the genetic mechanisms governing germination traits in sweet corn, aiding further research into the localization and cloning of genes involved in the mobilization of reserve materials.

Using Native and Synthetic Genes to Disrupt Inositol Pyrophosphates and Phosphate Accumulation in Plants.

Inositol pyrophosphates are eukaryotic signaling molecules that have been recently identified as key regulators of plant phosphate sensing and homeostasis. Given the importance of phosphate to current and future agronomic practices, we sought to design plants which could be used to sequester phosphate, as a step in a phytoremediation strategy. To achieve this, we expressed Diadenosine and Diphosphoinositol Polyphosphate Phosphohydrolase (DDP1), a yeast (Saccharomyces cerevisiae) enzyme demonstrated to hydrolyze inositol pyrophosphates, in Arabidopsis thaliana and pennycress (Thlaspi arvense), a spring annual cover crop with emerging importance as a biofuel crop. DDP1 expression in Arabidopsis decreased inositol pyrophosphates, activated Phosphate Starvation Response marker genes, and increased phosphate accumulation. These changes corresponded with alterations in plant growth and sensitivity to exogenously applied phosphate. Pennycress plants expressing DDP1 displayed increases in phosphate accumulation, suggesting that these plants could potentially serve to reclaim phosphate from phosphate-polluted soils. We also identified a native Arabidopsis gene, Nucleoside diphosphate-linked moiety X 13 (NUDIX13), which we show encodes an enzyme homologous to DDP1 with similar substrate specificity. Arabidopsis transgenics overexpressing NUDIX13 had lower inositol pyrophosphate levels and displayed phenotypes similar to DDP1-overexpressing transgenics, while nudix13-1 mutants had increased levels of inositol pyrophosphates. Taken together, our data demonstrates that DDP1 and NUDIX13 can be used in strategies to regulate plant inositol pyrophosphates and could serve as potential targets for engineering plants to reclaim phosphate from polluted environments.

Adaptation to reductions in chilling availability using variation in PLANT HOMOLOGOUS TO PARAFIBROMIN in Brassica napus.

Winter annual crops are sown in late summer or autumn and require chilling to promote flowering the following spring. Floral initiation begins in autumn and winter, and in winter oilseed rape (OSR), continued chilling during flower development is necessary for high yield potential. This can be a problem in areas where chilling is not guaranteed, or as a result of changing climates. Here, we used chilling disruption and low chilling to identify loci with the potential to increase chilling efficiency in winter OSR. We report that time to flowering and yield potential under low chill conditions are affected by variation at the PLANT HOMOLOGOUS TO PARAFIBROMIN gene, a component of the plant PAF1c complex. We show that increases in winter chilling given to developing flowers can improve seed yields and that loss of function of BnaPHP.A05 leads to early flowering in B. rapa and B. napus and an increase in seed set where chilling is limited. Because PHP is known to specifically target the FLOWERING LOCUS C (FLC) gene in Arabidopsis, we propose that variation at PHP is useful for breeding modifications to chilling responses in polyploid crops with multiple copies of the FLC gene.

Genome-Wide Analysis and Expression Profiling of Glyoxalase Gene Families Under Abiotic Stresses in Cucumber (Cucumis sativus L.)

The glyoxalase pathway, consisting of glyoxalase I (GLYI) and glyoxalase II (GLYII), is an enzymatic system that converts cytotoxic methylglyoxal to non-toxic S-D-lactoylglutathione. Although the GLY gene family has been analyzed in Arabidopsis, rice, grape, cabbage, and soybean, cucumber studies are lacking. Here, we analyzed the cucumber GLY gene family, identifying 13 CsGLYI and 2 CsGLYII genes. Furthermore, we investigated the physicochemical properties, phylogenetic relationships, chromosomal localization and colinearity, gene structure, conserved motifs, cis-regulatory elements, and protein–protein interaction networks of the CsGLY family. They were primarily localized in the cytoplasm, chloroplasts, and mitochondria, with a minor presence in the nucleus. The classification of CsGLYI and CsGLYII genes into five classes closely resembled the homologous genes in Arabidopsis and soybean. Additionally, hormone-responsive elements dominated the promoter region of GLY genes, alongside light- and stress-responsive elements. The predicted interaction proteins of CsGLYIs and CsGLYIIs exerted a significant role in cellular respiration, amino acid synthesis, and metabolism, as well as methylglyoxal catabolism. In addition, the expression profiles of GLY genes were distinct in different tissues of cucumber as well as under diverse abiotic stresses. This study is conducive to the further exploration of the functional diversity among glyoxalase genes and the mechanisms of stress responses in cucumber.

Insights into Genes Encoding LEA_1 Domain-Containing Proteins in Cyperus esculentus, a Desiccation-Tolerant Tuber Plant

LEA_1 domain-containing proteins constitute a class of late-embryogenesis-abundant proteins that are highly hydrophilic and predominantly accumulate in mature seeds. Though LEA_1 proteins have been proven to be essential for seed desiccation tolerance and longevity, little information is available on their roles in non-seed storage organs. In this study, a first genome-wide characterization of the LEA_1 gene family was conducted in tigernut (Cyperus esculentus L., Cyperaceae), whose underground tubers are desiccation tolerant with a moisture content of less than 6%. Five family members identified in tigernut are comparative to four to six found in seven other Cyperaceae plants, but relatively more than three reported in Arabidopsis. Further comparison of 125 members from 29 plant species supports early divergence of the LEA_1 family into two phylogenetic groups before angiosperm radiation, and gene expansion in tigernut was contributed by whole-genome duplications occurring after the split with the eudicot clade. These two phylogenetic groups could be further divided into six orthogroups in the momocot clade, five of which are present in tigernut and the remaining one is Poaceae specific. Frequent structural variation and expression divergence of paralogs were also observed. Significantly, in contrast to seed-preferential expression of LEA_1 genes in Arabidopsis, rice, and maize, transcriptional profiling and qRT-PCR analysis revealed that CeLEA1 genes have evolved to predominantly express in tubers, exhibiting a seed desiccation-like accumulation during tuber development. Moreover, CeLEA1 transcripts in tubers were shown to be considerably more than that of their orthologs in purple nutsedge, another Cyperaceae plant producing desiccation-sensitive tubers. These results imply species-specific activation and key roles of CeLEA1 genes in the acquisition of desiccation tolerance of tigernut tubers as observed in orthodox seeds. Our findings not only improve the understanding of lineage-specific evolution of the LEA_1 family, but also provide valuable information for further functional analysis and genetic improvement in tigernut.

ASYMMETRIC LEAVES1 promotes leaf hyponasty in Arabidopsis by light-mediated auxin signaling.

In plants, balancing growth and environmental responses is crucial for maximizing fitness. Close proximity among plants and canopy shade, which negatively impacts reproduction, elicits morphological adjustments such as hypocotyl growth and leaf hyponasty, mainly through changes in light quality and auxin levels. However, how auxin, synthesized from a shaded leaf blade, distally induces elongation of hypocotyl and petiole cells remains to be elucidated. We demonstrated that ASYMMETRIC LEAVES1 (AS1) promotes leaf hyponasty through the regulation of auxin biosynthesis, polar auxin transport, and auxin signaling genes in Arabidopsis (Arabidopsis thaliana). AS1 overexpression leads to elongation of the abaxial petiole cells with auxin accumulation in the petiole, resulting in hyponastic growth, which is abolished by the application of an auxin transport inhibitor to the leaf blade. In addition, the as1 mutant exhibits reduced hypocotyl growth under shade conditions. We observed that AS1 protein accumulates in the nucleus in response to shade or far-red light. Chromatin immunoprecipitation analysis identified the association of AS1 with the promoters of YUCCA8 (YUC8) and INDOLE-3-ACETIC ACID INDUCIBLE 19 (IAA19). In addition, AS1 forms complexes with PHYTOCHROME INTERACTING FACTORs in the nucleus and synergistically induces YUC8 and IAA19 expression. Our findings suggest that AS1 plays a crucial role in facilitating phenotypic plasticity to the surroundings by connecting light and phytohormone action.

The Maize Gene ZmGLYI-8 Confers Salt and Drought Tolerance in Transgenic Arabidopsis Plants.

Methylglyoxal (MG), a highly reactive and cytotoxic α-oxoaldehyde compound, can over-accumulate under abiotic stress, consequently injuring plants or even causing death. Glyoxalase I (GLYI), the first enzyme of the glyoxalase pathway, plays multiple roles in the detoxification of MG and in abiotic stress responses. However, the GLY1 gene in maize has been little studied in response to abiotic stress. In this study, we screened a glyoxalase I gene (ZmGLYI-8) and overexpressed in Arabidopsis. This gene was localized in the cytoplasm and can be induced in maize seedlings under multiple stress treatments, including salt, drought, MG, ABA, H2O2 and high temperature stress. Phenotypic analysis revealed that after MG, salt and drought stress treatments, overexpression of ZmGLYI-8 increased the tolerance of transgenic Arabidopsis to MG, salt and drought stress. Furthermore, we demonstrated that the overexpression of ZmGLYI-8 scavenges accumulated reactive oxygen species, detoxifies MG and enhances the activity of antioxidant enzymes to improve the resistance of transgenic Arabidopsis plants to salt and drought stress. In summary, this study preliminarily elucidates the molecular mechanism of the maize ZmGLYI-8 gene in transgenic Arabidopsis and provides new insight into the breeding of salt- and drought-tolerant maize varieties.

Genome-wide characterization of nitric oxide-induced NBS-LRR genes from Arabidopsis thaliana and their association in monocots and dicots

BackgroundNitric oxide (NO) is pivotal in regulating the activity of NBS-LRR specific R genes, crucial components of the plant’s immune system. It is noteworthy that previous research has not included a genome-wide analysis of NO-responsive NBS-LRR genes in plants.ResultsThe current study examined 29 NO-induced NBS-LRR genes from Arabidopsis thaliana, along with two monocots (rice and maize) and two dicots (soybean and tomato) using genome-wide analysis tools. These NBS-LRR genes were subjected to comprehensive characterization, including analysis of their physio-chemical properties, phylogenetic relationships, domain and motif identification, exon/intron structures, cis-elements, protein-protein interactions, prediction of S-Nitrosylation sites, and comparison of transcriptomic and qRT-PCR data. Results showed the diverse distribution of NBS-LRR genes across chromosomes, and variations in amino acid number, exons/introns, molecular weight, and theoretical isoelectric point, and they were found in various cellular locations like the plasma membrane, cytoplasm, and nucleus. These genes predominantly harbor the NB-ARC superfamily, LRR, LRR_8, and TIR domains, as also confirmed by motif analysis. Additionally, they feature species-specific PLN00113 superfamily and RX-CC_like domain in dicots and monocots, respectively, both responsive to defense against pathogen attacks. The NO-induced NBS-LRR genes of Arabidopsis reveal the presence of cis-elements responsive to phytohormones, light, stress, and growth, suggesting a wide range of responses mediated by NO. Protein-protein interactions, coupled with the prediction of S-Nitrosylation sites, offer valuable insights into the regulatory role of NO at the protein level within each respective species.ConclusionThese above findings aimed to provide a thorough understanding of the impact of NO on NBS-LRR genes and their relationships with key plant species.

Soybean gene GmMLP34 regulates Arabidopsis negative response to high temperature stress

The functions of major latex proteins (MLPs) in plant defense and stress responses have been widely documented; however, their roles in HT stress response in soybeans have not been elucidated. This study investigated the role of GmMLP34, a member of the major latex protein (MLP) family, in the response of soybeans to HT stress. Transcriptome analysis of HT-resistant (JD21) and HT-sensitive (HD14) soybean leaves under HT stress (43.40 ± 1.70 °C) and field conditions revealed differential expression of GmMLP34. Further examination across different HT-resistant varieties showed that GmMLP34 was down-regulated in the leaves of 6 HT-resistant varieties (85.7 %) and up-regulated in the leaves of 6 HT-sensitive varieties (85.7 %) under the HT treatment (45 °C for 3 h). The results of this study indicate that ectopic expression of the GmMLP34 gene in Arabidopsis led to a significant decrease in the survival rate of seedling when compared to the wild type (WT) under HT stress conditions of 37/28 °C (day/night) for 5 d, Moreover, the results indicated a significant decrease in primary root length and lateral root number under 45 °C/3 h HT stress followed by 12 h room temperature recovery. Additionally, the levels of abscisic acid (ABA), and flavonoids, and the activity of the peroxidase (POD) enzyme in the antioxidant system was decreased, while the activity of the superoxide dismutase (SOD) enzyme increased in GmMLP34-overexpressing transgenic Arabidopsis thaliana. The expression levels of the HT-response genes AtCHS1 and AtCHI2-A, were significantly down-regulated, whereas that of AtGBP1 was significantly up-regulated. These results suggest that GmMLP34 negatively regulates the response of Arabidopsis thaliana to HT stress by modulating flavonoid synthesis, hormone synthesis, and the antioxidant enzyme system. These findings provide theoretical information for the genetic improvement of HT tolerance in soybean and contribute to the understanding of the molecular mechanisms underlying plant responses to abiotic stress.

Systematic expression analysis of cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1 protein (CAP) superfamily in Arabidopsis.

The Cysteine-rich secretory proteins (CRISPS), Antigen 5 (Ag5), and Pathogenesis-related 1 (PR-1) protein (CAP) superfamily members are found in multiple eukaryotic organisms, including yeasts, animals, and plants. Although one of the plant CAP family genes, PR-1 is known to respond to pathogen infection in plants, the functions of other CAP family genes in Arabidopsis remain largely unknown. In this study, we conducted a comprehensive analysis of the similarities, loci, and expression patterns of 22 Arabidopsis CAP genes/proteins, providing a clue to elucidate their molecular functions. According to the promoter-β-glucuronidase (GUS) analysis, members of the Arabidopsis CAP family were expressed in various young tissues or organs, such as root and shoot meristems, reproductive tissues, and particularly at the lateral root initiation site before the formation of the lateral root primordium, with distinct expression specificity. In particular, CAP51, CAP52, and CAP53 were specifically expressed in the cortical cells at the lateral root developing regions, suggesting that these genes may function in lateral root development. Thus, the expression patterns of Arabidopsis CAP family genes suggest that CAP family proteins may have certain function in the expressed organs or tissues in Arabidopsis plant.

Ectopic and transient expression of VvDIR4 gene in Arabidopsis and grapes enhances resistance to anthracnose via affecting hormone signaling pathways and lignin production.

DIR (Dirigent) proteins play important roles in the biosynthesis of lignin and lignans and are involved in various processes such as plant growth, development, and stress responses. However, there is less information about VvDIR proteins in grapevine (Vitis vinifera L). In this study, we used bioinformatics methods to identify members of the DIR gene family in grapevine and identified 18 VvDIR genes in grapevine. These genes were classified into 5 subfamilies based on phylogenetic analysis. In promoter analysis, various plant hormones, stress, and light-responsive cis-elements were detected. Expression profiling of all genes following Colletotrichum gloeosporioides infection and phytohormones (salicylic acid (SA) and jasmonic acid (JA)) application suggested significant upregulation of 17 and 6 VvDIR genes, respectively. Further, we overexpressed the VvDIR4 gene in Arabidopsis thaliana and grapes for functional analysis. Ectopic expression of VvDIR4 in A. thaliana and transient expression in grapes increased resistance against C. gloeosporioides and C. higginsianum, respectively. Phenotypic observations showed small disease lesions in transgenic plants. Further, the expression patterns of genes having presumed roles in SA and JA signaling pathways were also influenced. Lignin contents were measured before and after C. higginsianum infection; the transgenic A. thaliana lines showed higher lignin content than wild-type, and a significant increase was observed after C. higginsianum infection. Based on the findings, we surmise that VvDIR4 is involved in hormonal and lignin synthesis pathways which regulate resistance against anthracnose. Our study provides novel insights into the function of VvDIR genes and new candidate genes for grapevine disease resistance breeding programs.

Genome-Wide Identification of WRKY Transcription Factors in Pea (Pisum sativum L.) and their Response to Sulfur and Water Stress

AbstractThe WRKY gene family is widely distributed in plants and plays essential roles in plant development and stress response. Despite extensive characterization of WRKY transcription factors in many plants, a genome-wide analysis of the WRKY gene family in Pisum sativum is still lacking. The central method of this study focused on the retrieval and characterization of WRKY gene sequences in the pea genome and further looking up for their modulation in response to sulfur and water stress. This involved a combination of bioinformatics tools and gene expression study to identify, characterize, and understand the properties of the WRKY gene family in pea. In this study, 86 PsWRKY genes were identified in the pea genome, categorized into five phylogenetic groups. They were dispersed across all seven chromosomes, with Chromosome 5 showing the highest enrichment. Synteny analysis revealed orthologs of 69 PsWRKY genes in Arabidopsis and Medicago. Transcriptome analysis identified 36 differentially expressed PsWRKY genes in response to sulfur (S) stress, water (W) stress, and their combination (W + S). Real-time PCR validation confirmed significant upregulation of PsWRKY23, PsWRKY58, PsWRKY64, and PsWRKY83 under water stress, PsWRKY58 and PsWRKY84 under sulfur stress, and PsWRKY03 under combined (W + S) stress. Overall, this study provides important insights on genetic information of the WRKY gene family in Pea and its possible role in water and sulfur stress, which will help further to study these candidate WRKY gene with a future objective of understanding their role in abiotic stress.

2-Keto-L-Gulonic Acid Enhances Cold Stress Tolerance in Arabidopsis thaliana via Augmentation of Ascorbic Acid Biosynthesis and Antioxidant Defense Systems

Cold stress severely impairs plant growth, development, and yields. L-ascorbic acid (ASA), a crucial antioxidant, is pivotal in mitigating stress-induced damage. Previous research found that 2-keto-L-gulonic acid (2KGA), a precursor of ASA in its industrial production, effectively enhances the endogenous ASA content in plants. We hypothesized that 2KGA might alleviate chilling stress and tried to verify it through a cultivation experiment of Arabidopsis thaliana. The results demonstrate that the application of 2KGA significantly increased ASA content (24.58%) and up-regulated ASA biosynthetic genes in Arabidopsis at 4 °C for 24 h. Furthermore, 2KGA alleviated the decrease in fresh weight (17.05%) and total chlorophyll content (15.85%) caused by low temperatures. The contents of proline, soluble sugar (SS), soluble protein (SP), and the activities of antioxidant enzymes including superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and ascorbate peroxidase (APX) were significantly increased under the 2KGA treatment at low temperatures, while the malondialdehyde (MDA) content was reduced. Moreover, 2KGA up-regulated the ICE-CBF-COR signaling pathway in response to cold stress. These collective findings strongly support the involvement of 2KGA in enhancing cold tolerance in Arabidopsis, presenting an innovative approach for agricultural practices aimed at enhancing crop resilience to environmental stresses.

Comparative Analysis of Casparian Strip Membrane Domain Protein Family in Oryza sativa (L.) and Arabidopsis thaliana (L.).

The Casparian strip membrane domain proteins (CASPs) are pivotal for the formation of the Casparian strip (CS) in endodermal cells and play a crucial role in a plant's response to environmental stresses. However, existing research on the CASP gene family in rice and Arabidopsis lacks a comprehensive bioinformatics analysis and necessitates further exploration. In this study, we identified 41 OsCASP and 39 AtCASP genes, which were grouped into six distinct subgroups. Collinearity analysis underscored the pivotal roles of WGD and TD events in driving the evolution of CASPs, with WGDs being the dominant force. On the one hand, the analysis of cis-elements indicated that most OsCASP and AtCASP genes contain MYB binding motifs. On the other hand, RNA-seq revealed that the majority of OsCASP and AtCASP genes are highly expressed in roots, particularly in endodermal cells, where OsCASP_like11/9 and AtCASP_like1/31 demonstrated the most pronounced expression. These results suggest that OsCASP_like11/9 and AtCASP_like1/31 might be candidate genes involved in the formation of the endodermis CS. RT-qPCR results demonstrated that OsCASP_like2/3/13/17/21/30 may be candidate genes for the ion defect process. Collectively, this study offers a theoretical foundation for unraveling the biological functions of CASP genes in rice and Arabidopsis.

A land plant phylogenetic framework for GLABROUS INFLORESCENCE STEMS (GIS), SUPERMAN, JAGGED and allies plus their TOPLESS co-repressor

Members of the plant specific family of C1-1i zincfinger transcriptionfactors (ZF-TFs), such as SUPERMAN, JAGGED, KNUCKLES or GIS,regulatediversedevelopmental processes including sexual reproduction. C1-1is consist of one zinc-finger and one to two EAR domains, connected by large intrinsically disordered regions (IDR). While the role of C1-i1 ZF-TFs in development processes is well known for some genes in Arabidopsis, rice or tomatoa comprehensive and broadphylogenetic background is lacking, yet knowledge of orthology is a requirement for a better understanding of C1-1i-Zf-TFs diverse roles in plants. Here, we provide a fine-grained and land plant wide classification of C1-1i sub-families and their known co-repressors TOPLESS and TOPLESS RELATED. Our work combines the identification of orthologous groups with Maximum-Likelihood phylogeny reconstructions and digital gene expression analyses mining high quality land plant genomes and transcriptomes to generate a comprehensive framework of C1-1i ZF-TF evolution. We show that C1-1i’s are low to moderate copy genesand that orthologous genesonly partiallyhaveconserved sub-family and life cycle stage dependent expression pattern across land plants while others are highly diverged. Our workprovides the phylogenetic framework for C1-1i ZF-TFs, s and strengthen C1-1 ZF-TFs as a potential model for IDR-research in plants.

YELLOW, SERRATED LEAF is essential for cotyledon vein patterning in Arabidopsis.

Venation develops complex patterns within the leaves of angiosperms, and the mechanism of leaf vein patterning remains poorly understood. Here, we report a spontaneous mutant that exhibits yellow serrated leaves and defective cotyledon vein patterning. We mapped and cloned the relevant gene YELLOW, SERRATED LEAF (YSL), a previously unreported gene in plants. YSL interacts with VH1-interacting kinase (VIK), a protein that functions in cotyledon venation development. VIK is a vascular-specific adaptor protein kinase that interacts with another vascular developmental protein, VASCULAR HIGHWAY1 (VH1)/BRASSINOSTEROID INSENSITIVE 1-LIKE 2 (BRL2), which is a receptor-like kinase of the BRASSINOSTEROID INSENSITIVE 1 (BRI1) family. Mutation of YSL affects the auxin response and the expression of auxin-related genes in Arabidopsis (Arabidopsis thaliana). Our results reveal that YSL affects cotyledon vein patterning by interacting with VIK in Arabidopsis.