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Flax is an important cash crop globally with a variety of commercial uses. It has been widely used for fiber, oil, nutrition, feed and in composite materials. Growth regulatory factor (GRF) is a transcription factor family unique to plants, and is involved in regulating many processes of growth and development. Bioinformatics analysis of the GRF family in flax predicted 17 LuGRF genes, which all contained the characteristic QLQ and WRC domains. Equally, 15 of 17 LuGRFs (88%) are predicted to be regulated by lus-miR396 miRNA. Phylogenetic analysis of GRFs from flax and several other well-characterized species defined five clades; LuGRF genes were found in four clades. Most LuGRF gene promoters contained cis-regulatory elements known to be responsive to hormones and stress. The chromosomal locations and collinearity of LuGRF genes were also analyzed. The three-dimensional structure of LuGRF proteins was predicted using homology modeling. The transcript expression data indicated that most LuGRF family members were highly expressed in flax fruit and embryos, whereas LuGRF3, LuGRF12 and LuGRF16 were enriched in response to salt stress. Real-time quantitative fluorescent PCR (qRT-PCR) showed that both LuGRF1 and LuGRF11 were up-regulated under ABA and MeJA stimuli, indicating that these genes were involved in defense. LuGRF1 was demonstrated to be localized to the nucleus as expected for a transcription factor. These results provide a basis for further exploration of the molecular mechanism of LuGRF gene function and obtaining improved flax breeding lines. [ABSTRACT FROM AUTHOR]

The necessity to understand plant adaptations to environmental stressors is underscored by the role of polyploidy in species evolution. This study focuses on the superior stress resistance exhibited by autotetraploid rice, which arises from chromosome doubling, in comparison to its diploid donor. We provide a quantitative analysis that highlights the differing susceptibilities of diploid (GFD-2X) and autotetraploid (GFD-4X) rice to rice blast disease, with GFD-2X being significantly more susceptible. Our investigation centers on transcription factors (TFs), which are crucial in regulating biological stress responses, by analyzing their expression in the face of a pathogen attack. This study uncovers variations in the number and expression timing of differentially expressed TF genes, providing a quantitative view of GFD-4X's resistance. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses confirm the role of specific pathways, including "response to stimulus" and the "MAPK signaling pathway," in resistance mechanisms. An extensive analysis of protein–protein interaction networks further clarifies the complex role of TFs during stress responses. The rationale for our experimental approach is rooted in the imperative to decipher the molecular basis of disease resistance across different ploidies, which has implications for crop enhancement. The conclusion from our research is that autotetraploid rice has a unique and more effective defense response regulation system, facilitated by transcription factors, when faced with rice blast disease. This finding provides a foundation for future genetic strategies aimed at improving crop resistance. [ABSTRACT FROM AUTHOR]

Saline stress is a major abiotic stress that inhibits plant growth and yields worldwide. The plant transcription factor (TF) family plays an important role in converting abiotic stress signals into gene expression changes. In this study, a transcriptome-based comparative analysis was performed to investigate the global gene expression of all the TFs in diploid and autotetraploid rice during the early stage of NaCl stress and recovery period. The phenotypic data indicated that the tetraploid rice exhibited a superior salt-tolerant ability compared to the diploid rice. A total of 55 TF families were co-expressed in the tetraploid and diploid rice, and the cumulative number of TF-expressed genes was relatively higher in the diploid rice than in the tetraploid rice at all time points. Unlike the diploid rice, the overall gene expression levels of the tetraploid rice were comparable to the control during recovery. The number of differentially expressed TFs (DE-TFs) in the tetraploid rice decreased after recovery, whereas it increased to a large extent in the diploid rice. GO and KEGG pathway enrichment analysis of the DE-TFs discovered the early switching of the ABA-activated signaling pathway and specific circadian rhythm in the tetraploid rice. Combining the PPI network and heatmap analysis, some core DE-TFs were found that may have potential roles to play in tetraploid salt tolerance. This study will pave the way for elucidating the complex network regulatory mechanisms of salt tolerance in tetraploid rice. [ABSTRACT FROM AUTHOR]

Flax (Linum usitatissimum L.) is an important oilseed crop widely cultivated for its oil and fiber. This study conducted transcriptome analysis to analyze the gene expression profiles of roots, leaves, stamens, pistils, and fruits in the flax cultivar Longya10. A total of 43,471 genes were detected in the RNA-seq data, with 34,497 genes showing differential expression levels between different organs. Gene expression patterns varied across different organs, with differences observed in expression-regulating genes within specific organs. However, 23,448 genes were found to be commonly expressed across all organs. Further analysis revealed organ-specific gene expressions, with 236, 690, 544, 909, and 1212 genes identified in pistils, fruits, leaves, roots, and stamens, respectively. Gene Ontology (GO) enrichment analysis was performed on these organ-specific genes, and significant enrichment was observed in various biological processes, cellular components, and molecular functions, providing new insights for the specific growth patterns of flax organs. Furthermore, we investigated the expression differences of AP2 transcription factors in various tissues and organs of Longya10. We identified 96 AP2 genes that were differentially expressed in different organs and annotated them into various biological pathways. Our results suggest that AP2 transcription factors may play important roles in regulating the growth and development of flax organs including stress response. In summary, our study provides a comprehensive analysis of gene expression patterns in different organs and tissues of flax plant and identifies potential critical regulators of flax organ growth and development. These findings contribute to a better understanding of the molecular mechanisms underlying flax organ development and may have important implications for the genetic improvement of flax crops. [ABSTRACT FROM AUTHOR]

Saline–alkali stress is a significant abiotic stress factor that impacts plant growth, development, and crop yield. Consistent with the notion that genome-wide replication events can enhance plant stress resistance, autotetraploid rice exhibited a higher level of tolerance to saline–alkali stress than its donor counterparts, which is reflected by differential gene expression between autotetraploid and diploid rice in response to salt, alkali, and saline–alkali stress. In this study, we investigated the expression of the transcription factors (TFs) in the leaf tissues of autotetraploid and diploid rice under different types of saline–alkali stress. Transcriptome analysis identified a total of 1040 genes from 55 TF families that were altered in response to these stresses, with a significantly higher number in autotetraploid rice compared to diploid rice. Contrarily, under these stresses, the number of expressed TF genes in autotetraploid rice was greater than that in diploid rice for all three types of stress. In addition to the different numbers, the differentially expressed TF genes were found to be from significantly distinct TF families between autotetraploid and diploid rice genotypes. The GO enrichment analysis unraveled that all the DEGs were distributed with differentially biological functions in rice, in particular those that were enriched in the pathways of phytohormones and salt resistance, signal transduction, and physiological and biochemical metabolism in autotetraploid rice compared to its diploid counterpart. This may provide useful guidance for studying the biological roles of polyploidization in plant resilience in response to saline–alkali stress. [ABSTRACT FROM AUTHOR]

Soil salinity is a severe constraint on crop productivity that triggers plant salt stress response pathways. The salt stress responses are controlled by transcriptional regulatory networks that enhance plant stress tolerance by manipulating the expression of transcription factor (TFs)-encoding genes. Identifying TFs associated with salt tolerance contributes to salt-tolerant crop breeding. In this study, a comparative transcriptome analysis was performed to investigate the global gene expression of entire TFs in diploid and autotetraploid rice with different salt tolerance levels, considering NaCl stress, NaOH stress, and Na2CO3 stress. A total of 54, 54 and 55 TF families were co-expressed in diploid and tetraploid roots under three stresses, respectively. Furthermore, we investigated differentially expressed TFs (DE-TFs) based on different comparisons, and the statistical analysis indicated that the DE-TFs derived from the three types of stress were as follows: Na2CO3 (53 TF families, 1356 DE-TFs) > NaCl (19 TF families, 214 DE-TFs) > NaOH (18 TF families, 152 DE-TFs). These results imply that Na2CO3 stress induced a more obvious biological responses in the roots than the other two stresses. GO and KEGG pathway enrichment analysis of DE-TFs revealed the importance of plant hormone signal transduction and MAPK signaling pathways that may contribute to the saline–alkaline tolerance of tetraploid rice. This study provides gene resources that are valuable for exploring the regulatory mechanism of TFs involved in the saline–alkaline tolerance of polyploid rice. [ABSTRACT FROM AUTHOR]

Loss of Lon1 led to stunted plant growth and accumulation of nuclear‐encoded mitochondrial proteins including Lon1 substrates. However, an in‐depth label‐free proteomics quantification of mitochondrial proteins in lon1 revealed that the majority of mitochondrial‐encoded proteins decreased in abundance. Additionally, we found that lon1 mutants contained protein aggregates in the mitochondrial that were enriched in metabolic enzymes, ribosomal subunits and PPR‐containing proteins of the translation apparatus. These mutants exhibited reduced general mitochondrial translation as well as deficiencies in RNA splicing and editing. These findings support the role of Lon1 in maintaining a functional translational apparatus for mitochondrial‐encoded gene translation. Transcriptome analysis of lon1 revealed a mitochondrial unfolded protein response reminiscent of the mitochondrial retrograde signalling dependent on the transcription factor ANAC017. Notably, lon1 mutants exhibited transiently elevated ethylene production, and the shortened hypocotyl observed in lon1 mutants during skotomorphogenesis was partially alleviated by ethylene inhibitors. Furthermore, the short root phenotype was partially ameliorated by introducing a mutation in the ethylene receptor ETR1. Interestingly, the upregulation of only a select few target genes was linked to ETR1‐mediated ethylene signalling. Together this provides multiple steps in the link between loss of Lon1 and signalling responses to restore mitochondrial protein homoeostasis in plants. [ABSTRACT FROM AUTHOR]