Genome-wide analysis of the 6B-INTERACTING PROTEIN1 gene family with functional characterization of MdSIP1-2 in Malus domestica

Genome-wide identification of potato Trihelix gene family and its response to different abiotic stresses

The Trihelix transcription factor family, characterized by its unique triple-helix structure (helix-loop-helix-loop-helix), plays a significant role in plant growth, development, and responses to various abiotic stresses. Potato (Solanum tuberosum L.), as a globally important food crop, experiences significant impacts on its growth and yield due to abiotic stresses such as drought, low temperature, and salt stress. Although the functions of Trihelix transcription factors have been extensively studied in various plants, systematic analysis in potatoes remains relatively scarce. This study aims to comprehensively identify the Trihelix gene family in potatoes through bioinformatics methods and analyze their expression patterns under abiotic stresses to reveal the potential functions of this gene family in potato growth, development, and stress responses. Through genome database searches and BLAST comparisons, 35 StTrihelix genes were identified in potatoes, and phylogenetic, gene structure, functional motif, and cis-acting element analyses were conducted. The expression patterns of these genes in different tissues and under low-temperature and drought stresses were analyzed using qRT-PCR technology. Additionally, the nuclear localization of StTrihelix30 was verified through subcellular localization experiments. The results indicate that the 35 StTrihelix genes are unevenly distributed across 12 chromosomes and can be classified into five subfamilies: GT-1, GT-2, GTγ, SH4, and SIP1. Gene structure and functional motif analyses revealed high conservation within the same subfamily. Cis-acting element analysis showed that these genes are closely related to hormone responses, stress responses, and growth and development processes. Tissue expression analysis showed that StTrihelix4 is highly expressed in stamens, while StTrihelix13 is highly expressed in roots. qRT-PCR results indicated that most StTrihelix genes are significantly upregulated under low-temperature and drought stresses. This study systematically identified the Trihelix gene family in potatoes and revealed its important role in abiotic stress responses. It provides new insights into the functions of the Trihelix transcription factor family in potato growth, development, and stress adaptation, offering theoretical references for stress-resistant potato breeding.

Late embryogenesis abundant gene GhLEA-5 of semi-wild cotton positively regulates salinity tolerance in upland cotton

The productivity and quality of cotton are significantly compromised by salt stress. In this study, the full length of encoding region and genomic DNA sequences of GhLEA_5A/D (Gh_A10G166600 and Gh_D10G188300), which belong to the late embryogenesis abundant gene family in allotetraploid upland cotton (Gossypium hirsutum L.) and semi-wild cotton (Gossypium purpurascens), were isolated and their salt tolerance was experimentally confirmed. Analysis of sequence alignments and phylogenetic trees indicated a significant level of homology between GhLEA-5A and GhLEA-5D. Additionally, a conserved protein motif was consistently identified across these sequences. The transcriptome data analysis showed that the expression level of GhLEA-5A/D was substantially enhanced in the leaves of salt-tolerant G. purpurascens accessions compared to salt-sensitive materials. In the real-time quantitative reverse transcription PCR (qRT-PCR) assays, notable expression levels of the GhLEA-5D gene were detected in salt-tolerant upland cotton materials following exposure to salt stress at 3 and 12-hour time points. The suppression of GhLEA-5A/D transcription via Virus-induced Gene Silencing (VIGS) technology significantly exacerbates salt sensitivity in cotton. This is evidenced by the nearly 50 % increase in malondialdehyde (MDA) content alongside a 60 % reduction in peroxidase (POD) levels in salt-treated plants when compared to the control group. The overexpression of the GhLEA-5A/D gene conferred enhanced salt tolerance in Arabidopsis, resulting in a 25 % increase in root length, a 30 % improvement in survival rate, a 15 % increase in water retention, and a 15 % boost in photosynthetic efficiency. The chlorophyll fluorescence parameters, enzyme activities, diaminobenzine, and nitroblue tetrazolium staining suggested that GhLEA-5A/D likely exhibited a positive regulatory role for cotton responding to salt stress. Furthermore, we identified 76 candidate proteins that potentially interact with GhLEA-5 in the yeast two-hybrid screening library. These results provide a theoretical basis for studying the mechanism of cotton salt tolerance and offer new resources for improving cotton salt tolerance genes.

New insights into the evolution analysis of trihelix gene family in eggplant (Solanum melongena L.) and expression analysis under abiotic stress

BACKGROUND

Trihliex transcription factors (TFs) play crucial roles in plant growth and development, stress response, and plant hormone signaling network transmission. In order to comprehensively investigate the functions of trihliex genes in eggplant development and the abiotic stress response, we conducted an extensive analysis of the trihliex gene family in the eggplant genome.

RESULTS

In this study, 30 trihelix gene family members were unevenly distributed on 12 chromosomes. On the basis of their phylogenetic relationships, these genes were conserved in different plant species and could be divided into six subfamilies, with trihelix genes within the same subfamily sharing similar structures. The promoter regions of trihelix genes contained cis-acting elements related to plant growth and development, plant hormones, and abiotic stress responses, suggesting potential applications in the development of more resistant crops. Selective pressure assessments indicated that trihliex genes have undergone purifying selection pressure. Expression analysis on the basis of transcriptomic profiles revealed that SmGT18, SmGT29, SmGT6, and SmGT28 are highly expressed in roots, leaves, flowers, and fruits, respectively. Expression analysis via quantitative real-time PCR (qRT‒PCR) revealed that most trihelix genes respond to low temperature, abscisic acid (ABA), and salicylic acid (SA), with SmGT29 exhibiting significant upregulation under cold stress conditions. The SmGT29 gene was subsequently successfully cloned from eggplant, which was located in the nucleus, robust transcriptional activity, and a protein molecular weight of 74.59 kDa. On the basis of these findings, SmGT29 was postulated to be a pivotal candidate gene that actively responds to biotic stress stimuli, thereby supporting the plant's innate stress resistance mechanisms.

CONCLUSION

In summary, this study was the first report on trihelix genes and their potential roles in eggplant plants. These results provided valuable insights for enhancing stress resistance and quality traits in eggplant breeding, thereby serving as a crucial reference for future improvement efforts.

Brassinosteroids biosynthetic gene MdBR6OX2 regulates salt stress tolerance in both apple and Arabidopsis

Salt stress is a critical limiting factor for fruit yield and quality of apples. Brassinosteroids (BRs) play an important role in response to abiotic stresses. In the present study, application of 2,4- Epicastasterone on seedlings of Malus 'M9T337' and Malus domestica 'Gala3' alleviated the physiological effects, such as growth inhibition and leaf yellowing, induced by salt stress. Further analysis revealed that treatment with NaCl induced expression of genes involved in BR biosynthesis in 'M9T337' and 'Gala3'. Among which, the expression of BR biosynthetic gene MdBR6OX2 showed a three-fold upregulation upon salt treatment, suggesting its potential role in response to salt stress in apple. MdBR6OX2, belonging to the CYP450 family, contains a signal peptide region and a P450 domain. Expression patterns analysis showed that the expression of MdBR6OX2 can be significantly induced by different abiotic stresses. Overexpressing MdBR6OX2 enhanced the tolerance of apple callis to salt stress, and the contents of endogenous BR-related compounds, such as Typhastero (TY), Castasterone (CS) and Brassinolide (BL) were significantly increased in transgenic calli compared with that of wild-type. Extopic expression of MdBR6OX2 enhanced tolerance to salt stress in Arabidopsis. Genes associated with salt stress were significantly up-regulated, and the contents of BR-related compounds were significantly elevated under salt stress. Our data revealed that BR-biosynthetic gene MdBR6OX2 positively regulates salt stress tolerance in both apple calli and Arabidopsis.

Cloning and functional identification of apple LATERAL ORGAN BOUNDARY DOMAIN 3 (LBD3) transcription factor in the regulation of drought and salt stress

MAIN CONCLUSION

Overexpression of MdLBD3 in Arabidopsis reduced sensitivity to salt and drought stresses and was instrumental in promoting early flowering. Salt and drought stresses have serious effects on plant growth. LATERAL ORGAN BOUNDARY DOMAIN (LBD) proteins are a plant-specific transcription factors (TFs) family and play important roles in plants in resisting to abiotic stress. However, about the function of LBDs in apple and other woody plants is little known. In this study, protein sequences of the LBD family TFs in apples were identified which contained conserved LOB domains. The qRT-PCR analysis showed that the MdLBD3 gene was widely expressed in various tissues and organs. The subcellular localization assay showed that the MdLBD3 protein was localized in the nucleus. Ectopic expression of MdLBD3 in Arabidopsis positively regulated its salt and drought resistance, and promoted early flowering. Collectively, these results showed that MdLBD3 improved the abiotic stress resistance, plant growth and development. Overall, this study provided a new gene for breeding that can increase the abiotic stress tolerance in apple.

The apple lipoxygenase MdLOX3 positively regulates zinc tolerance

Various abiotic stresses, especially heavy metals near factories around the world, limit plant growth and productivity worldwide. Zinc is a light gray transition metal, and excessive zinc will inactivate enzymes in the soil, weaken the biological function of microorganisms, and enter the food chain through enrichment, thus affecting human health. Lipoxygenase (LOX) can catalyze the production of fatty acid derivatives from phenolic triglycerides in plants and is an important pathway of fatty acid oxidation in plants, which usually begins under unfavorable conditions, especially under biotic and abiotic stresses. Lipoxygenase can be divided into 9-LOX and 13-LOX. MdLOX3 is a homolog of AtLOX3 and has been identified in apples (housefly apples). MdLOX3 has a typical conserved lipoxygenase domain, and promoter analysis shows that it contains multiple stress response elements. In addition, different abiotic stresses and hormonal treatments induced the MdLOX3 response. In order to explore the inherent anti-heavy metal mechanism of MdLOX3, this study verified the properties of MdLOX3 based on genetic analysis and overexpression experiments, including plant taproots length, plant fresh weight, chlorophyll, anthocyanins, MDA, relative electrical conductivity, hydrogen peroxide and superoxide anion, NBT\DAB staining, etc. In the experiment, overexpression of MdLOX3 in apple callus and Arabidopsis effectively enhanced the tolerance to zinc stress by improving the ability to clear ROS. Meanwhile, tomato materials with overexpression of ectopia grew better under excessive zinc ion stress. These results indicated that MdLOX3 had a good tolerance to heavy metal zinc. Homologous mutants are more sensitive to zinc, which proves that MdLOX3 plays an important positive role in zinc stressed apples, which broadens the range of action of LOX3 in different plants.

Transcriptome-Wide Integrated Analysis of the PgGT25-04 Gene in Controlling Ginsenoside Biosynthesis in Panax ginseng

Panax ginseng is a valuable medicinal herb of the Araliaceae family with various pharmacological activities. The Trihelix transcription factors family is involved in growth and secondary metabolic processes in plants, but no studies have been reported on the involvement of Trihelix genes in secondary metabolic processes in ginseng. In this study, weighted co-expression network analysis, correlation analysis between PgGTs and ginsenosides and key enzyme genes, and interaction network analysis between PgGTs and key enzyme genes were used to screen out the PgGT25-04 gene, which was negatively correlated with ginsenoside synthesis. Using ABA treatment of ginseng hair roots, PgGT genes were found to respond to ABA signals. Analysis of the sequence characteristics and expression pattern of the PgGT25-04 gene in ginseng revealed that its expression is spatiotemporally specific. The interfering vector pBI121-PgGT25-04 containing the PgGT25-04 gene was constructed, and the ginseng adventitious roots were transformed using the Agrobacterium-mediated method to obtain the pBI121-PgGT25-04 positive hairy root monocot line. The saponin contents of positive ginseng hair roots were measured by HPLC, and the changes in PgGT25-04 and key enzyme genes in positive ginseng hair roots were detected via fluorescence quantitative RT-PCR. These results preliminarily identified the role of the PgGT25-04 gene in the secondary metabolism of ginseng in Jilin to provide a theoretical basis for the study of Trihelix transcription factors in Panax ginseng.

GT Transcription Factors of Rosa rugosa Thunb. Involved in Salt Stress Response

Rosa rugosa was a famous aromatic plant while poor salt tolerance of commercial cultivars has hindered its culture in saline-alkali soil. In many plants, the roles of GT (or trihelix) genes in salt stresses responses have been emerging. In the wild R. rugosa, a total of 37 GTs (RrGTs) were grouped into GT-1, GT-2, GTγ, SH4, and SIP1 lineages. SIP1 lineage expanded by transposition. The motifs involved in the binding of GT cis-elements were conserved. Four RrGTs (RrGT11/14/16/18) significantly differentially expressed in roots or leaves under salt stress. The responsive patterns within 8 h NaCl treatment indicated that RrGTγ-4 (RrGT18) and RrGT-1 (RrGT16) were significantly induced by salt in roots of R. rugosa. Subcellular localizations of RrSIP1 (RrGT11) and RrGTγ-4 were on chloroplasts while RrGT-1 and RrSIP2 (RrGT14) located on cell nucleus. Regulation of ion transport could be the most important role of RrSIPs and RrGTγ-4. And RrGT-1 could be a halophytic gene with higher transcription abundance than glycophytic GT-1. These results provide key clue for further investigations of roles of RrGTs in salt stress response and would be helpful in the understanding the salt tolerance regulation mechanism of R. rugosa.