Search Results (72)

In this work, we searched for and analyzed highly divergent dispersed repeats (DRs) in the genomes of four plants: Arabidopsis thaliana, Capsicum annuum, Daucus carota, and Zea mays. DRs were detected using the iterative procedure method which has shown efficacy in searches for highly divergent repeats in bacteria and algae. The results indicated that the number of DRs in the plant genomes depended on the genome size, whereas the number of repeat families did not. The DRs covered from 36 to 50% of the studied genomes. The shortest repeats were observed in the D. carota genome, but their consensus lengths were similar to those in the other species. Analysis of periodicity in various DR families showed that most periods were 3 bp long. We created a database of the detected DRs, which contains 5,392,216 DRs grouped in 150 families and which can be accessed on the Research Center of Biotechnology RAS server. The server makes it possible to search for repeats based on various criteria and to download the obtained data. Full article

The APETALA2/ethylene response factor (AP2/ERF) is a class of plant-specific transcription factors, among which the dehydration-responsive element-binding protein (DREB) subfamily has been widely reported to enhance plant resistance to abiotic stresses. A high-temperature-related gene, Apium graveolens DREBA6b (AgDREBA6b; accession number: OR727346), was previously cloned from a heat-tolerant celery variety. In this study, we transformed this gene into Arabidopsis thaliana using an Agrobacterium rhizogenes-mediated method to explore its function. The results showed that overexpressing AgDREBA6b in Arabidopsis thaliana significantly improved plant growth under high-temperature stress (38 °C) compared to the dreb mutant and wild-type (WT) plants. The anatomical structure of the leaves revealed that the number and degree of stomatal openings in the overexpressed plants were significantly higher than those in the WT and dreb plants, suggesting that AgDREBA6b enhances stomatal opening. Additionally, the chlorophyll content, chlorophyll fluorescence properties, proline (Pro), malondialdehyde (MDA), superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD) activities were higher in the transgenic plants, indicating better stress tolerance. qPCR analysis showed that four heat tolerance-related genes (AtHSP98.7, AtHSP70-1, AtAPX1, and AtGOLS1) were upregulated in the transgenic plants, with higher expression levels than in WT and mutant plants. This study provides valuable genetic resources for understanding the molecular mechanisms of celery’s heat tolerance and offers insights for breeding heat-tolerant celery varieties. Full article

The Multi-Parent Advanced Generation Inter-Cross (MAGIC) population is a powerful tool for dissecting the genetic architecture controlling natural variation in complex traits. In this work, the natural variation available in Arabidopsis thaliana MAGIC lines was evaluated by mapping quantitative trait loci (QTLs) for primary root length (PRL), lateral root number (LRN), lateral root length (LRL), adventitious root number (ARN), and adventitious root length (ARL). We analyzed the differences in the root structure of 139 MAGIC lines by measuring PRL, LRN, LRL, ARN, and ARL. Through QTL mapping, we identified new potential genes that may be responsible for these traits. Furthermore, we detected single-nucleotide polymorphisms (SNPs) in the coding regions of candidate genes in the founder accessions and the recombinant inbred lines (RILs). We identified a significant region on chromosome 1 associated with AR formation. This region encompasses 316 genes, many of which are involved in auxin and gibberellin signaling and homeostasis. We discovered SNPs in the coding regions of these candidate genes in the founder accessions that may contribute to natural variation in AR characteristics. Additionally, we found a novel gene that encodes a protein from the hydroxyproline-rich glycoprotein family, which exhibits differential SNPs in accessions with contrasting AR formation. This study provides genetic insights into the natural variation in AR numbers using MAGIC lines linked to hormone-related genes. Full article

Large and distinct families of receptor-like kinases (RLKs) play elemental roles in many fundamental processes of plants. The proline-rich extensin-like receptor kinase (PERK) family is one of the most pivotal classes of RLKs. To date, there have been no comprehensive or published studies conducted on the PERK gene family in Glycine max. This research aimed to characterize the role of the PERK gene family in cultivated soybean using a systematic array of bioinformatic and experimental approaches. We identified 16 PERK members in G. max through local BLASTp, using PERK members from Arabidopsis thaliana as a query. Tissue expression of genes, predicted via tissue specific expression analysis from the soybean database “SoyBase”, revealed that these PERK genes exhibit differentiated expression patterns in various plant organs. The gene structure was predicted via Gene Structure Display Server (GSDS). Phylogeny was demonstrated through an evolutionary tree employing the neighbor-joining method. Subcellular localization of proteins was identified via “Softberry” and cis-acting elements were identified through PlantCARE. The KASP (Kompetitive Allele Specific PCR (KASP)) marker was developed for the GmPERK-1-C and GmPERK-1-T allele, targeting position 167 nt in the CDS region. Genotyping results indicated that GmPERK-1 exhibits promising potential for utilization in molecular breeding programs for soybean to increase crop yield. Collectively, our findings indicate that G. max accessions harboring the GmPERK-1-C allele exhibit significantly higher thousand grain weight compared to accessions carrying the GmPERK-1-T allele. This research enhances the understanding of the molecular roles of PERK genes in G. max, providing valuable insights for the utilization of favorable genetic variations in soybean molecular breeding programs. Full article

Plant flowering time is affected by endogenous and exogenous factors, but its variation patterns among different populations of a species has not been fully established. In this study, 27 Arabidopsis thaliana accessions were used to investigate the relationship between autonomous pathway gene methylation, gene expression and flowering time variation. DNA methylation analysis, RT-qPCR and transgenic verification showed that variation in the flowering time among the Arabidopsis populations ranged from 19 to 55 days and was significantly correlated with methylation of the coding regions of six upstream genes in the autonomous pathway, FLOWERING LOCUS VE (FVE), FLOWERING LOCUS Y (FY), FLOWERING LOCUS D (FLD), PEPPER (PEP), HISTONE DEACETYLASE 5 (HAD5) and Pre-mRNA Processing Protein 39-1 (PRP39-1), as well as their relative expression levels. The expression of FVE and FVE(CS) was modified separately through degenerate codon substitution of cytosine and led to earlier flowering of transgenic plants by 8 days and 25 days, respectively. An accurate determination of methylated sites in FVE and FVE(CS) among those transgenic plants and the recipient Col-0 verified the close relationship between the number of methylation sites, expression and flowering time. Our findings suggest that the methylation variation of these six key upstream transcription factors was associated with the gene expression level of the autonomous pathway and flowering time in Arabidopsis. The FVE(CS) and FVE genes in transgenic plants tended to be hypermethylated, which could be a protective mechanism for plants. However, modification of gene sequences through degenerate codon substitution to reduce cytosine can avoid hypermethylated transferred genes in transgenic plants. It may be possible to partially regulate the flowering of plants by modified trans-epigenetic technology. Full article

Cyclin B (CYCB) is a regulatory subunit of cyclin-dependent kinase (CDK), the concentration of which fluctuates to regulate cell cycle progression. Extensive studies have been performed on cyclins in numerous species, yet the evolutionary relationships and biological functions of the CYCB family genes in Brassica napus remain unclear. In this study, we identified 299 CYCB genes in 11 B. napus accessions. Phylogenetic analysis suggests that CYCB genes could be divided into three subfamilies in angiosperms and that the CYCB3 subfamily members may be a newer group that evolved in eudicots. The expansion of BnaCYCB genes underwent segmental duplication and purifying selection in genomes, and a number of drought-responsive and light-responsive cis-elements were found in their promoter regions. Additionally, expression analysis revealed that BnaCYCBs were strongly expressed in the developing seed and silique pericarp, as confirmed by the obviously reduced seed size of the mutant cycb3;1 in Arabidopsis thaliana compared with Col-0. This study provides a comprehensive evolutionary analysis of CYCB genes as well as insight into the biological function of CYCB genes in B. napus. Full article

In plant models such as Arabidopsis thaliana, phosphatidic acid (PA), a key molecule of lipid signaling, was shown not only to be involved in stress responses, but also in plant development and nutrition. In this article, we highlight lipid signaling existing in crop species. Based on open access databases, we update the list of sequences encoding phospholipases D, phosphoinositide-dependent phospholipases C, and diacylglycerol-kinases, enzymes that lead to the production of PA. We show that structural features of these enzymes from model plants are conserved in equivalent proteins from selected crop species. We then present an in-depth discussion of the structural characteristics of these proteins before focusing on PA binding proteins. For the purpose of this article, we consider RESPIRATORY BURST OXIDASE HOMOLOGUEs (RBOHs), the most documented PA target proteins. Finally, we present pioneering experiments that show, by different approaches such as monitoring of gene expression, use of pharmacological agents, ectopic over-expression of genes, and the creation of silenced mutants, that lipid signaling plays major roles in crop species. Finally, we present major open questions that require attention since we have only a perception of the peak of the iceberg when it comes to the exciting field of phospholipid signaling in plants. Full article

The analysis of plant phenotype parameters is closely related to breeding, so plant phenotype research has strong practical significance. This paper used deep learning to classify Arabidopsis thaliana from the macro (plant) to the micro level (organelle). First, the multi-output model identifies Arabidopsis accession lines and regression to predict Arabidopsis’s 22-day growth status. The experimental results showed that the model had excellent performance in identifying Arabidopsis lines, and the model’s classification accuracy was 99.92%. The model also had good performance in predicting plant growth status, and the regression prediction of the model root mean square error ($RMSE$) was 1.536. Next, a new dataset was obtained by increasing the time interval of Arabidopsis images, and the model’s performance was verified at different time intervals. Finally, the model was applied to classify Arabidopsis organelles to verify the model’s generalizability. Research suggested that deep learning will broaden plant phenotype detection methods. Furthermore, this method will facilitate the design and development of a high-throughput information collection platform for plant phenotypes. Full article

The increase in soil salinization represents a current challenge for plant productivity, as most plants, including crops, are mainly salt-sensitive species. The identification of molecular traits underpinning salt tolerance represents a primary goal for breeding programs. In this scenario, the study of intraspecific variability represents a valid tool for investigating natural genetic resources evolved by plants in different environmental conditions. As a model system, Arabidopsis thaliana, including over 750 natural accessions, represents a species extensively studied at phenotypic, metabolic, and genomic levels under different environmental conditions. Two haplogroups showing opposite root architecture (shallow or deep roots) in response to auxin flux perturbation were identified and associated with EXO70A3 locus variations. Here, we studied the influence of these genetic backgrounds on plant salt tolerance. Eight accessions belonging to the two haplogroups were tested for salt sensitivity by exposing them to moderate (75 mM NaCl) or severe (150 mM NaCl) salt stress. Salt-tolerant accessions were found in both haplogroups, and all of them showed efficient ROS-scavenging ability. Even if an exclusive relation between salt tolerance and haplogroup membership was not observed, the modulation of root system architecture might also contribute to salt tolerance. Full article

The analysis of telomere length is an important component of many studies aiming to characterize the role of telomere maintenance mechanisms in cellular lifespan, disease, or in general chromosome protection and DNA replication pathways. Several powerful methods to accurately measure the telomere length from Southern blots have been developed, but their utility for large-scale genomic studies has not been previously evaluated. Here, we performed a comparative analysis of two recently developed programs, TeloTool and WALTER, for the extraction of mean telomere length values from Southern blots. Using both software packages, we measured the telomere length in two extensive experimental datasets for the model plant Arabidopsis thaliana, consisting of 537 natural accessions and 65 T-DNA (transfer DNA for insertion mutagenesis) mutant lines in the reference Columbia (Col-0) genotype background. We report that TeloTool substantially overestimates the telomere length in comparison to WALTER, especially for values over 4500 bp. Importantly, the TeloTool- and WALTER-calculated telomere length values correlate the most in the 2100–3500 bp range, suggesting that telomeres in this size interval can be estimated by both programs equally well. We further show that genome-wide association studies using datasets from both telomere length analysis tools can detect the most significant SNP candidates equally well. However, GWAS analysis with the WALTER dataset consistently detects fewer significant SNPs than analysis with the TeloTool dataset, regardless of the GWAS method used. These results imply that the telomere length data generated by WALTER may represent a more stringent approach to GWAS and SNP selection for the downstream molecular screening of candidate genes. Overall, our work reveals the unanticipated impact of the telomere length analysis method on the outcomes of large-scale genomic screens. Full article

NAC transcription factors play a significant role in plant stress responses. In this study, an NAC transcription factor, with a CDS of 792 bp encoding 263 amino acids, was cloned from Fagopyrum tataricum (L.) Gaertn. (F. tataricum), a minor cereal crop, which is rich in flavonoids and highly stress resistant. The transcription factor was named FtNAC10 (NCBI accession number: MK614506.1) and characterized as a member of the NAP subgroup of NAC transcriptions factors. The gene exhibited a highly conserved N-terminal, encoding about 150 amino acids, and a highly specific C-terminal. The resulting protein was revealed to be hydrophilic, with strong transcriptional activation activity. FtNAC10 expression occurred in various F. tataricum tissues, most noticeably in the root, and was regulated differently under various stress treatments. The over-expression of FtNAC10 in transgenic Arabidopsis thaliana (A. thaliana) seeds inhibited germination, and the presence of FtNAC10 enhanced root elongation under saline and drought stress. According to phylogenetic analysis and previous reports, our experiments indicate that FtNAC10 may regulate the stress response or development of F. tataricum through ABA-signaling pathway, although the mechanism is not yet known. This study provides a reference for further analysis of the regulatory function of FtNAC10 and the mechanism that underlies stress responses in Tartary buckwheat. Full article

The central oscillator is believed to be the key mechanism by which plants adapt to new environments. However, impacts from hybridization, the natural environment, and human selection have rarely been assessed on the oscillator of a crop. Here, from clearly identified alleles at oscillator loci (OsCCA1/LHY, OsPRR95, OsPRR37, OsPRR59, and OsPRR1) in ten diverse genomes of Oryza sativa, additional accessions, and functional analysis, we show that rice’s oscillator was rebuilt primarily by new alleles from recombining parental sequences and subsequent 5′ or/and coding mutations. New alleles may exhibit altered transcript levels from that of a parental allele and are transcribed variably among genetic backgrounds and natural environments in RIL lines. Plants carrying more expressed OsCCA1_a and less transcribed OsPRR1_e flower early in the paddy field. 5′ mutations are instrumental in varied transcription, as shown by EMSA tests on one deletion at the 5′ region of highly transcribed OsPRR1_a. Compared to relatively balanced mutations at oscillator loci of Arabidopsis thaliana, 5′ mutations of OsPRR37 (and OsCCA1 to a less degree) were under negative selection while those of OsPRR1 alleles were under strong positive selection. Together, range expansion of Asian rice can be elucidated by human selection on OsPRR1 alleles via local flowering time-yield relationships. Full article

The realm of antimicrobial proteins in plants is extensive but remains relatively uncharted. Understanding the mechanisms underlying the action of plant antifungal proteins (AFPs) holds promise for antifungal strategies. This study aimed to bridge this knowledge gap by comprehensively screening Arabidopsis thaliana species to identify novel AFPs. Using MALDI-TOF analysis, we identified a member of the TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR1 (TCP) family of transcription factors as a novel AFP, A. thaliana TCP21 (AtTCP21; accession number NP_196450). Bacterially purified recombinant AtTCP21 inhibited the growth of various pathogenic fungal cells. AtTCP21 was more potent than melittin, a well-known AFP, in combating Colletotrichum gloeosporioides. Growth inhibition assays against various fungal pathogens and yeasts confirmed the pH-dependent antimicrobial activity of AtTCP21. Without inducing any membrane alterations, AtTCP21 penetrates the fungal cell wall and membrane, where it instigates a repressive milieu for fungal cell growth by generating intracellular reactive oxygen species and mitochondrial superoxides; resulting in morphological changes and apoptosis. Our findings demonstrate the redox-regulating effects of AtTCP21 and point to its potential as an antimicrobial agent. Full article

Spikelet number per panicle (SNP) is one of the most important yield components in rice. Rice ENHANCING BIOMASS AND SPIKELET NUMBER (OsEBS), a gene involved in improved SNP and yield, has been cloned from an accession of Dongxiang wild rice. However, the mechanism of OsEBS increasing rice SNP is poorly understood. In this study, the RNA-Seq technology was used to analyze the transcriptome of wildtype Guichao 2 and OsEBS over-expression line B102 at the heading stage, and analysis of the evolution of OsEBS was also conducted. A total of 5369 differentially expressed genes (DEGs) were identified between Guichao2 and B102, most of which were down-regulated in B102. Analysis of the expression of endogenous hormone-related genes revealed that 63 auxin-related genes were significantly down-regulated in B102. Gene Ontogeny (GO) enrichment analysis showed that the 63 DEGs were mainly enriched in eight GO terms, including auxin-activated signaling pathway, auxin polar transport, auxin transport, basipetal auxin transport, and amino acid transmembrane transport, most of which were directly or indirectly related to polar auxin transport. Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway analysis further verified that the down-regulated genes related to polar auxin transport had important effects on increased SNP. Analysis of the evolution of OsEBS found that OsEBS was involved in the differentiation of indica and japonica, and the differentiation of OsEBS supported the multi-origin model of rice domestication. Indica (XI) subspecies harbored higher nucleotide diversity than japonica (GJ) subspecies in the OsEBS region, and XI experienced strong balancing selection during evolution, while selection in GJ was neutral. The degree of genetic differentiation between GJ and Bas subspecies was the smallest, while it was the highest between GJ and Aus. Phylogenetic analysis of the Hsp70 family in O. sativa, Brachypodium distachyon, and Arabidopsis thaliana indicated that changes in the sequences of OsEBS were accelerated during evolution. Accelerated evolution and domain loss in OsEBS resulted in neofunctionalization. The results obtained from this study provide an important theoretical basis for high-yield rice breeding. Full article