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Research Article

ArticleID :JASHC/2025/11/01/01

Biochemical and yield response of spring wheat to drought stress through gibberellic and abscisic acids

Issue No. 01 (Jan-Mar)

Authors: Sobhi F. Lamlom, Ahmed M. Abdelghany, A. S. Farouk, E. Sh. Alwakel, Khaled M. Makled, Najat A. Bukhari, et.al.,

Drought stress significantly impacts wheat productivity, but plant growth regulators may help mitigate these effects. This study examined the influence of gibberellic acid (GA3) and abscisic acid (ABA) on wheat (Triticum aestivum L., CV: Giza 171) growth and yield under different water regimes. Using a split-plot design, we tested three drought levels as main plots: normal irrigation (80% field capacity), moderate drought (60% field capacity), and severe drought (40% field capacity). Subplots consisted of GA3 and ABA treatments at 100 and 200 ppm concentrations. Results showed that 200 ppm GA3 treatment enhanced multiple growth parameters under normal irrigation, including plant height (25–30% increase), leaf area (30–35% increase), and reproductive traits (40% increase in number of number of spikes, 35% increase in grains per spike). In contrast, ABA treatment at 200 ppm resulted in reduced plant height (35% decrease) and greater leaf area reduction (40% vs. 20% in control) under drought conditions. GA3 at 200 ppm also improved physiological parameters including catalase and superoxide dismutase activities, protein content, and proline accumulation. These findings demonstrate the distinct roles of GA3 and ABA in regulating wheat growth and stress responses, providing valuable insights for drought management in wheat cultivation.

How To Cite this Article

© The Author(s) 2024. Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit h t t p : / / c r e a t i v e c o m m o n s . o r g / l i c e n s e s / b y - n c - n d / 4. 0 / .

Research Article

ArticleID :JASHC/2025/11/01/02

Symbiotic fungal inoculation promotes the growth of Pinus tabuliformis seedlings in relation to the applied nitrogen form

Issue No. 01 (Jan-Mar)

Authors: Lingjie Xu, Yanhui Li, Xiaoyu Dai, Xueyu Jin, Qiannai Zhao, Boyu Tian and Yong Zhou

Background:  Nitrogen (N) deposition has become a major driving factor affecting the balance of terrestrial ecosystems, changing the soil environment, element balance and species coexistence relationships, driving changes in biodiversity and ecosystem structure and function. Human-induced nitrogen input leads to a high NH4 +/ NO3 - ratio in soil. However, relatively few studies have investigated the effects of different nitrogen sources on forest plantmicrobial symbionts. In this study, the effects of four nitrogen sources, N free, NH4Cl, L-glutamic acid, and Na(NO3)2 (N-, NH4 +-N, Org-N, and NO3 --N) on four fungal species, Suillus granulatus (Sg), Pisolithus tinctorius (Pt), Pleotrichocladium opacum (Po), and Pseudopyrenochaeta sp. (Ps), which were isolated from the roots of Pinus tabulaeformis, were studied in vitro. The effects of inoculation with the four fungi on the growth performance, nutrient uptake and nitrogen metabolism-related enzymes of Pinus tabuliformis under different nitrogen source conditions were subsequently studied.

Results: The biomass and N concentration of the Sg and Po strains were the highest under the NO3 --N treatment, while the biomass and N concentration of the Pt and Ps strains were significantly greater under the NH4 +-N and NO3 --N treatments than under the Org-N and N- treatments. All four fungi could effectively colonize the roots of P. tabuliformis and formed a symbiotic relationship with it. Under all nitrogen conditions, the inoculation of the four fungi had positive effects on the growth, root development and nutrient concentration of the P. tabuliformis seedlings. Under the Org-N and NO3 --N treatments, the nitrate reductase (NR) activity of the inoculated plants was significantly greater than that of the noninoculated control (CK) plants. Under all nitrogen conditions, the glutamine synthetase (GS) activity of the inoculated plants was significantly greater than that of the CK plants.

Conclusions: The four fungi can establish good symbiotic relationships with P. tabuliformis seedlings and promote their growth and development under different nitrogen source treatments.

How To Cite this Article

© The Author(s) 2024. Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit h t t p : / / c r e a t i v e c o m m o n s . o r g / l i c e n s e s / b y - n c - n d / 4. 0 / .

Research Article

ArticleID :JASHC/2025/11/01/03

Root and mycorrhizal nutrient acquisition strategies in the succession of subtropical forests under N and P limitation

Issue No. 01 (Jan-Mar)

Authors: Xue Wu, Yueming Liang, Wenwu Zhao and Fujing Pan

Background: Nutrient limitation is a universal phenomenon in terrestrial ecosystems. Root and mycorrhizal are critical to plant nutrient absorption in nutrient-limited ecosystems. However, how they are modified by N and P limitations with advancing vegetation successions in karst forests remains poorly understood. The present study compared the diversity indices, composition, and co-occurrence network of arbuscular mycorrhizal fungi (AMF) between grassland, shrubland, shrub-tree forest, and tree forest in subtropical karst forests, as well as soil nutrients and fine root functional traits (e.g., specific root length (SRL), specific root area (SRA), diameter, biomass, and N and P contents).

Results:  The fine roots diameter, biomass, and N and P contents increased with advancing succession, whereas SRL and SRA decreased. Network complexity and Richness and Chao1 indices of AMF increased from grassland to shrubtree forest but decreased in tree forest. The fine roots N and P contents were positively related to their diameter and biomass, soil nutrients, and AMF composition but were negatively correlated with SRL and SRA. Moreover, these two parameters increased with the increase of soil nutrients. The variations in fine roots N and P contents were mainly explained by soil nutrients and fine root functional traits in grassland and by the interactions of soil nutrients, fine root functional traits, and AMF in the other three stages. Additionally, the interactive explanation with AMF increased from shrubland to shrub-tree forest but decreased in tree forest.

Conclusions: Our results indicated that mycorrhizal strategy might be the main nutrient acquisition strategy under N and P co-limitation. In contrast, the root strategy is the main one when an individual is subject to limitations in N or P in karst ecosystems. Root and mycorrhizal nutrient acquisition strategies are generally mutualistic, mycorrhizal strategy enhances plant nutrient acquisition under N and P co-limitation.

How To Cite this Article

© The Author(s) 2025. Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/.

Research Article

ArticleID :JASHC/2025/11/01/04

Genome-wide identification of the adaptor protein complexes and its expression patterns analysis in foxtail millet (Setaria italica L.)

Issue No. 01 (Jan-Mar)

Authors: Dan Wang, Min Su, Jian-Hong Hao, Zi-Dong Li, Shuqi Dong, Xiangyang Yuan, Xiaorui Li, Lulu Gao, Xiaoqian Chu, Guanghui Yang, Jia-Gang Wang and Huiling Du

Backgrounds:  Adapter proteins (APs) complex is a class of heterotetrameric complexes comprising of 4-subunits with important regulatory functions in eukaryotic cell membrane vesicle trafficking. Foxtail millet (Setaria italica L.) is a significant C4 model plant for monocotyledon studies, and vesicle trafficking may plays a crucial role in various life activities related to growth and development. Despite this importance, studies on AP complexes in foxtail millet have been lacking.

Results: This research conducted genome-wide identification and systematical analysis of AP complexes in foxtail millet. 33 SiAP complex genes were identified and classified into 7 groups, distributed unevenly across 9 chromosomes in foxtail millet. Among these genes, 11 segmental duplication pairs were found. Out of the 33 SiAP complex genes, 24 exhibited collinear relationships with Setaria viridis, while only one showed relationship with Arabidopsis thaliana. Gene structure and motif composition were investigated to understand the function and evolution of these SiAP complex genes. Furthermore, these promoter region of the SiAP complex genes contains 49 cis-elements that are associated with responses to light, hormones, abiotic stress, growth and development. The interaction network between the SiAP complexes was analyzed, and there were strong interactions among the SiAP complex proteins. Expression patterns of SiAP complex genes in different organs and developmental stages of foxtail millet were investigated. The majority of the SiAP complex genes exhibited expressed in multiple tissues, with some genes being predominantly expressed in specific tissues. Subsequently, we selected SiAP4M and SiAP2M for validation of subcellular localization. The signal of 35 S:: SiAP4M: GFP (Long) and 35 S:: SiAP4M: GFP (Short) fused proteins were primarily observed in the nucleus, while the signal of 35 S:: SiAP2M: GFP fused proteins was widely distributed on the cell membrane and vesicles.

Conclusions: Overall, this study presents a comprehensive map of the SiAP complexes in foxtail millet. These findings not only administer to understanding the biological functions of AP complexes in foxtail millet growth and development but also offer insights for enhancing genetic breeding in this crop.

How To Cite this Article

© The Author(s) 2024. Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/.

Research Article

ArticleID :JASHC/2025/11/01/05

Response of Kapok seedlings were irrigated with water of different qualities and heavy metal contents for foliar application of antioxidants

Issue No. 01 (Jan-Mar)

Authors: Alaa I. B. Abou‑Sreea, Faisal M. A. Matter, Mahmoud A. Hassanain and Abdallah H. A. Hassan

Background: The imbalance between Egypt’s water requirements and supply necessitates the use of unconventional water sources, such as treated sewage water (TSW) and agricultural drainage water (ADW), to combat water scarcity. This study investigated the effects of foliar glycine betaine (GB) on vegetative growth parameters, physiological characteristics, photosynthetic pigments, leaf element contents, anatomical leaf structures, and antioxidant activity. The experiment was conducted in two successive seasons (2021/2022 and 2022/2023) using Kapok seedlings irrigated with ADW and TSW at different mixing ratios with normal irrigation water (NIW) (25%, 50%, 75%, and 100%), combined with foliar spraying of GB at concentrations of 0.0 and 50 mM.

Results: The results revealed that irrigation with 100% TSW or ADW significantly decreased vegetative growth parameters, physiological characteristics, photosynthetic pigments, leaf element contents, leaf thickness, and the contents of the leaf mid-vein, N, P, K, and Ca. In contrast, the levels of free proline, total phenolic content, Na, Cu, Ni, Mn, Zn, Pb, and antioxidant activity increased. Additionally, GB significantly improved all parameters, while reducing the contents of Na, Cu, Ni, Mn, Zn, and Pb in the leaves.

Conclusions: Irrigation of Kapok seedlings with TSW or ADW mixed with NIW at 25% and 50% resulted in better performance, similar to irrigation with NIW alone for most parameters. Combining GB and water treatments by mixing TSW or ADW with NIW at a 50:50 ratio and spraying with 50 mM GB produced better results than control seedlings irrigated with 100% NIW. Antioxidants also play a defensive role in plants against various stress factors. Therefore, GB may have a protective effect on peroxidation-linked membrane deterioration, scavenge free radicals, and provide osmotic protection.

How To Cite this Article

© The Author(s) 2025. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

Research Article

ArticleID :JASHC/2025/11/02/01

Chromium (VI) accumulation in different plant organs of Lacy Phacelia (Phacelia tanacetifolia Benth.): Implications for phytoremediation

Issue No. 02 (Apr-June)

Authors: Hava Seyma INCI

Lacy Phacelia (Phacelia tanacetifolia Benth.) is a very beneficial nectar source for honeybees, contributing to their foraging activities and honey production. Chromium (Cr) is a toxic metal that may be taken up by plants through roots and accumulates in different organs. The accumulation of Cr in nectars can affect nectar production and subsequently bee health. This study investigated whether Lacy Phacelia accumulates Cr in different plant organs. A pot experiment was conducted under controlled conditions with five different Cr concentrations (0, 5, 10, 20 and 40 mg kg− 1). The plants were grown for 110 days, and Cr, manganese (Mn) and iron (Fe) contents accumulated in different plant organs (root, leaf, stem, flower and stamen) were examined. Similalry, the impact of different Cr concentrations on plant height, stem diameter, and dry weights of root, stem, leaf, and flower was also recorded. The highest and lowest Cr(VI) accumulation was recorded in roots and flowers respectively. The mean Cr concentration in different organs was, i.e., root (7.13 mg kg− 1) > leaf (3.25 mg kg− 1) > stem (2.53 mg kg− 1) > flower (1.62 mg kg− 1) = stamen (1.54 mg kg− 1). Translocation factor was < 1 in all Cr concentrations, indicating that it is not a suitable candidate for phytoremediaiton. The Mn concentration in different organs generally increased with increasing Cr concentrations, while Fe concentration, plant height, and dry weights of root, stem, and f lower decreased. Lacy Phacelia should not be grown on Cr-contaminated soils for agricultural purposes or phytoremediation. The accumulation of Cr in the stamens may possibily contaminate bee products obtained through the bees collecting nectar from Lacy Phacelia grown on Cr-contaminated soils. The transfer of Cr from Lacy Phacelia plants grown on Cr-contaminated soils to honeybee and honey products should be investigated in future studies to safeguard honeybee health.

How To Cite this Article

© The Author(s) 2025. Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/.         

Research Article

ArticleID :JASHC/2025/11/02/02

Integrated transcriptome and metabolome analysis provides insights into anthocyanin biosynthesis in Cichorium intybus L.

Issue No. 02 (Apr-June)

Authors: Mingzhao Zhu, Ran Zhao, Hanying Wu, Baohai Zhang, Bin Zhang and Xiangyang Han

Background: Chicory is a unique and nutritious vegetable crop. However, the molecular mechanisms underlying anthocyanin biosynthesis in chicory remain poorly understood. We combined transcriptomics and metabolomics analyses to explore the molecular basis of anthocyanin biosynthesis in red-budded (Z1) and yellow-budded (Z7) chicory.

Results: Integrated transcriptomics and metabolomics analyses were performed to investigate the molecular basis of anthocyanin biosynthesis in chicory. A total of 26 key structural genes, including F3’H, DFR, CHS, and ANS, were identified and enriched in pathways such as flavonoid and anthocyanin biosynthesis. Additionally, 29 transcription factors were identified, including 11 MYB, five bHLH, and two WD40 transcription factors, with seven MYB genes upregulated and four genes downregulated, indicating their roles in regulating anthocyanin biosynthesis. Notably, the MYB transcription factor, CI35997, which is homologous to RLL2A in lettuce, was predicted to positively regulate anthocyanin biosynthesis. Other transcription factors, such as AP2/ERF, bZIP, NAC, and Trihelix, have also been implicated. Metabolomics analysis revealed that cyanidin derivatives were the main contributors to the red coloration of chicory buds, with cyanidin-3-O-(6-O-malonyl)-glucoside being the most abundant. Furthermore, a competitive relationship between lignin and anthocyanin biosynthesis was observed, wherein the downregulation of lignin related genes enhanced anthocyanin accumulation.

Conclusions: This study identified key structural genes and transcription factors that offer molecular-level insights into anthocyanin biosynthesis in chicory. These findings provide valuable guidance for genetic improvement of chicory and other crops with high anthocyanin content.

How To Cite this Article

© The Author(s) 2025. Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/.

Research Article

ArticleID :JASHC/2025/11/02/03

Diurnal dynamics of different circadian transcription modules in Chinese pine needles and roots during dormancy induction

Issue No. 02 (Apr-June)

Authors: Junhe Yang, Kai Qu, Huili Wang, Yousry A. El-Kassaby and Wei Li

Winter dormancy ensures that trees in temperate zones respond appropriately to environmental variations, thereby enhancing their adaptability and resilience. In the northern hemisphere, the dormancy of conifers is induced by short-day and cold temperature. Previous studies have revealed that TFL2 is a key regulator involved in conifers’ bud set and growth cessation during the dormancy-induced phase. Based on the annual expression profile analysis of PtTFL2 in Chinese pine (Pinus tabuliformis Carr.), we identified key time nodes for dormancy initiation in autumn. To provide insight of the diurnal transcriptome dynamic in needles and roots during dormancy introduction, RNA seq was performed at 12 consecutive time points in 24 h under natural environment in P. tabuliformis. Interestingly, we found that both needles and roots have rhythmic oscillatory genes, even though the roots could not receive light signals directly. We applied weighted gene co-expression network analysis (WGCNA) to integrate differentially expressed genes between needles and roots at different time points into highly correlated gene modules. Although the two modules are subject to different transcriptional controls during dormancy, both contain 35 identical transcriptional regulators. Some transcriptional factors with functional similarities and synergistic effects were found to play a role in the regulatory pathway, which provided some data support for mining gene functions and analyzing related regulatory pathways. Our results provide new insights into the molecular regulatory mechanisms involved in pine dormancy.

How To Cite this Article

© The Author(s) 2025. Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/.

Research Article

ArticleID :JASHC/2025/11/02/04

Genome-wide identification of the AcBAM family in kiwifruit (Actinidia chinensis cv. Hongyang) and the expression profiling analysis of AcBAMs reveal their role in starch metabolism

Issue No. 02 (Apr-June)

Authors: Xuchen Gong, Mengfei Lin, Jie Song, Jipeng Mao, Dongliang Yao, Zhu Gao and Xiaoling Wang

After analyzing a high-quality ‘Hongyang’ genome, we identified 17 AcBAMs. Comprehensive bioinformatics were performed to elucidate the properties and evolutionary relationships of these genes. Our analysis revealed that most AcBAMs retained conserved active sites (e.g., Glu186 and Glu380) and exhibited similar structural properties. Phylogenetic and collinearity analyses grouped the genes into three main clusters, with segmental and tandem duplications contributing to their expansion. Expression profiling showed that AcBAM5 and AcBAM13 were most highly expressed during postharvest storage and were strongly induced by ABA signal. Silencing these genes led to a significant increase in starch content, suggesting their key role in starch degradation. Promoter analysis identified cis-elements related to ABA signal and cold response in the AcBAM family, and the expression of AcBAM genes was influenced by ABA and low-temperature treatments, with specific genes showing significant responsiveness.

Background: Kiwifruit (Actinidia chinensis cv. Hongyang) is a perennial woody fruit tree highly valued for its rich nutritional profile and high vitamin C content. The postharvest ripening process, characterized by starch degradation into soluble sugars, significantly influences the fruit’s flavor and texture. β-amylase (BAM) has been proven to be one of the key enzymes catalyzing starch degradation, but which BAM genes are involved and how to participate in this process in kiwifruit still need to be clarified.

Conclusion: In the study, we identified a total of 17 AcBAM genes. The expansion of AcBAMs in kiwifruit was mainly due to segmental duplication events, and some of their catalytic residues were mutated, potentially leading to a loss of biological activity. The expression patterns of AcBAMs, along with VIGS data, suggest that AcBAM5 and AcBAM13 respond to ABA signals and promote starch degradation. Our findings provide valuable insights into the regulatory mechanisms of BAM genes in kiwifruit and highlight their importance in starch metabolism and fruit ripening.

How To Cite this Article

© The Author(s) 2025. Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/.

Research Article

ArticleID :JASHC/2025/11/02/05

Plant ubiquitin E2 enzymes UBC32, UBC33, and UBC34 are involved in ERAD and function in host stress tolerance

Issue No. 02 (Apr-June)

Authors: Chaofeng Wang, Bangjun Zhou, Yi Zhang and Lirong Zeng

Background: Endoplasmic reticulum (ER)-associated protein degradation (ERAD) is a critical component of the ER-mediated protein quality control (ERQC) system and plays a vital role in plant stress responses. However, the ubiquitination machinery underlying plant ERAD—particularly the ubiquitin-conjugating enzymes (E2s)—and their contributions to stress tolerance remain poorly understood.

Results: In this study, we identified UBC32, UBC33, and UBC34 as ER-localized ubiquitin E2 enzymes involved in ERAD and demonstrated their roles in biotic and abiotic stress tolerance in tomato (Solanum lycopersicum) and Arabidopsis (Arabidopsis thaliana). In response to biotic stress, UBC33 and UBC34 collectively contribute more substantially than UBC32 to plant immunity against Pseudomonas syringae pv. tomato (Pst). Under abiotic stress and ER stress induced by tunicamycin (TM), all three E2s play important roles. Notably, mutation of UBC32 enhances tolerance to TM-induced ER stress, whereas the loss of function in UBC33 or UBC34 suppresses this response. Additionally, UBC32, UBC33, and UBC34 act synergistically in Arabidopsis seed germination under salt stress and abscisic acid (ABA) treatment. While the single mutants atubc32, atubc33, and atubc34 exhibit germination rates comparable to Col-0 under salt stress or ABA treatment, the double mutants atubc32/33, atubc32/34, and atubc33/34 show a significantly greater reduction in germination rate. Interestingly, the atubc32/33/34 triple mutant exhibits a seed germination rate under salt stress and ABA treatment, as well as a level of host immunity to Pst, comparable to that of the atubc33/34 and atubc32/34 double mutants.

Conclusions: Our findings establish UBC32, UBC33, and UBC34 as key components of the plant ERAD machinery, contributing to plant tolerance to both abiotic and biotic stress. Despite their close phylogenetic relationship, these E2 enzymes exhibit redundant, synergistic, or antagonistic roles depending on the specific stress response pathway, underscoring the complexity of their functional interactions.

How To Cite this Article

© The Author(s) 2025. Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/.

Research Article

ArticleID :JASHC/2025/11/03/01

Quantitative analysis of ethylene precursor ACC in plant samples by liquid chromatography-tandem mass spectrometry

Issue No. 03 (July-Sept)

Authors: Jianhua Tong, Wenkui Zhao, Keming Wang, Feiying Zhu, Danyi Deng and Langtao Xiao

Background: Ethylene (C2H4) is a gaseous phytohormone that regulates various plant physiological processes and mediates the responses of the plants to various environmental stresses. 1-Aminocyclopropane-1-carboxylic acid (ACC) is the direct precursor of the phytohormone ethylene, and is also considered as a plant growth regulator. Accurate quantification of ACC is critically important in investigating its function. However, it remains challenging to accurately quantify ACC in plant tissues because it is a small, electroneutral molecule with very low concentrations.

Methods: An easy, cost-saving, and highly efficient quantitative method for ACC in plant tissues was set up by liquid liquid micro-extraction (LLME) purification with green solvent ethyl-acetate, and the precise control of the mobile phase entering into the mass spectrometer combined with the ultra-high performance liquid chromatography electrospray ionization-triple quadrupole mass spectrometer (UHPLC-ESI-MS/MS).

Results:  The contents of ACC in 10 mg of different fresh fruits were detected. The established method had limit of detection (LOD) (2.5 pg), matrix effect (ME) (92.6%), good precision (3.54%), recovery rate (95.82%), and a good linear relationship within the range of 0.5 to 1500 ng.mL−1 (R2 = 0.9998).

Conclusion: We have developed an easy, sensitive, and cost-saving quantitative method for ACC in plant tissues without derivatization which is useful for the precise quantification of ACC in plant tissues.

How To Cite this Article

Research Article

ArticleID :JASHC/2025/11/03/02

Antecedent moderate nitrogen fertilization alleviated the effects of drought on growth and leaf photosynthesis of Schima Superba seedlings

Issue No. 03 (July-Sept)

Authors: Defu Wang, Honglang Duan, Yongju Zhao, Wanbin Qiu, Xiaorong Liu, Jianping Wu, Guomin Huang and Wenfei Liu

Background: Drought and nitrogen deposition are the major global change factors that alter forest dynamics by affecting tree growth and physiology. However, the impacts of increased nitrogen availability at pre-drought on trees remains poorly understood, and it remains unclear how these responses are coordinated. In this study, we conducted the fertilization-drought microcosm experiment using a widely distributed evergreen broadleaf tree species seedlings (Schima superba) in southern China. The experiment was conducted at 3 stages. First, four levels of N fertilization treatments (without N fertilization-NF, low N fertilization-LF, moderate N fertilization-MF, high N fertilization-HF) were applied for 60 days. Second, all seedlings were allowed to grow under four levels of N fertilization treatments for another 60 days to ensure that the N was absorbed by seedlings. Third, all seedling were subjected to three levels of sustained drought treatments for further 60 days. Traits related to growth and physiology were monitored.

Results: Our findings indicate that drought alone inhibited the growth and leaf photosynthetic rate of S. superba, while N fertilization alone stimulated the growth and leaf photosynthetic rate. Antecedent N fertilization alleviated the drought limitation on growth, due to the increased leaf photosynthetic rate (Asat) and instantaneous water use efficiency. Moderate N fertilization mitigated the negative effects of drought on Asat due to improved performance in stomatal conductance, leaf water potential and cell membrane permeability. Additionally, moderate N fertilization increased activities of antioxidant enzymes and osmoprotectants concentration under drought condition.

Conclusions:  Overall, our findings suggest that increased N fertilization prior to drought can alleviate the negative effects of drought on growth and physiology, which is dependent on the magnitude of N fertilization and drought stress

How To Cite this Article

Wang, D., Duan, H., Zhao, Y. et al. Antecedent moderate nitrogen fertilization alleviated the effects of drought on growth and leaf photosynthesis of Schima Superba seedlings. BMC Plant Biol 25, 917 (2025). https://doi.org/10.1186/s12870-025-06952-6

Research Article

ArticleID :JASHC/2025/11/03/03

Assembly and comparative analysis of the complete mitochondrial genome of the spice plant Cinnamomum longepaniculatum

Issue No. 03 (July-Sept)

Authors: Yanling Fan, Linxin Tan, Ruizhang Feng, Xin Zhao and Xiangdong Xu

Background:  Cinnamomum longepaniculatum(Gamble) N. Chao ex H. W. Li (C. longepaniculatum), a species renowned for its leaves and twigs yielding essential oils, is extensively utilized as a vital raw material in traditional Chinese medicine, spice, and daily chemical products, and thus possesses both high economic value and significant scientific research value. However, to date, no detailed information on the mitochondrial genome (mitogenome) has been reported.

Results:  The mitogenome of C. longepaniculatum was characterized by a linear structure, spanning 870,686 bp with 46.94% GC content. It encompassed 44 protein-coding genes (PCGs), 28 tRNAs, and 3 rRNAs. Numerous repetitive sequences were observed, including 317 simple sequence repeats (SSRs), 52 tandem repeats and 874 pairs of dispersed repeats. Phylogenetic analysis based on the 41 conserved mitochondrial PCGs of C. longepaniculatum reflected its close evolutionary affinity to C. camphora, followed by C. chekiangense and C. insularimontanum. Furthermore, dot-plot analysis revealed diverse homologous collinear regions between C. longepaniculatum and other species belonging to the Laurales. Specifically, the largest collinear blocks, spanning over 861 kb, accounted for 95.59% of the total proportion between C. longepaniculatum and Cinnamomum camphora, indicating a high degree of conservation and similarity in their mitogenome structures.

Conclusions: This study presents the initial assembly and annotation of C. longepaniculatum mitogenome, thereby enriching the limited repository of mitogenome sequences available for Laurales plants. These findings provide crucial molecular evidence for further studies on the evolutionary relationships and genomic evolution within the Laurales.

How To Cite this Article

Fan, Y., Tan, L., Feng, R. et al. Assembly and comparative analysis of the complete mitochondrial genome of the spice plant Cinnamomum longepaniculatum. BMC Plant Biol 25, 916 (2025). https://doi.org/10.1186/s12870-025-06839-6

Research Article

ArticleID :JAHSC/2025/11/03/04

A data-driven approach to forest health assessment through multivariate analysis and machine learning techniques

Issue No. 03 (July-Sept)

Authors: Raja Waqar Ahmed Khan, Hamayun Shaheen, Muhammad Ejaz Ul Islam Dar, Tariq Habib, Muhammad Manzoor, Syed Waseem Gillani, et.al.,

Background: Himalayan forests are fragile, rich in biodiversity, and face increasing threats from anthropogenic pressures and climate change. Assessing their health is critical for sustainable forest management. This study integrated ecological indicators (tree density, size, regeneration, deforestation, slope, grazing, and erosion) with machine learning (ML) to classify forest health and identify key drivers across 37 Western Himalayan sites. Principal component analysis (PCA) reduced data dimensionality, highlighting major ecological gradients. K-means clustering was used to group forests into three distinct classes based on ecological characteristics, due to its efficiency in identifying natural patterns within multivariate data. ML models, including Decision Tree (DT), Random Forest (RF), and Support Vector Machine (SVM) were trained and validated using an 80:20 train-test split and 5-fold cross-validation.

Results: PCA revealed that elevation, disturbance, and regeneration explained 74.3% variance. Forest health varied across sites, with 10 categorized as healthy, 19 as moderate, and 8 as unhealthy. Forest regeneration was highly skewed (2.67) and leptokurtic (9.8), with few sites showing high seedling abundance, while deforestation (mean = 294 stumps ha−1) indicated uneven human impact. Among ML models, RF showed the best performance with a mean accuracy of 0.83, Kappa 0.87, and balanced accuracy 0.88. SVM followed with 0.75 accuracy, Kappa 0.70, and balanced accuracy 0.81. DT performed lowest with 0.66 accuracy and Kappa 0.45. Cross-validation confirmed RF’s highest mean accuracy (90.3%), followed by SVM (88.1%) and DT (65.1%). RF-based feature importance analysis showed tree DBH, height, regeneration rate, soil erosion, and tree density as key ecological drivers of forest health.

Conclusions: This study highlights ML-driven classification as a precise, scalable, and objective tool for large-scale forest health assessments. Conservation efforts should prioritize degraded forests through afforestation, slope stabilization, controlled grazing, erosion management, and continuous ecosystem monitoring. Future studies should integrate high-resolution remote sensing (e.g., Landsat, Sentinel-2) and climate datasets (e.g., temperature, precipitation, and drought indices) to enhance predictive capabilities and support long-term forest management planning. The findings underscore the value of data-driven approaches, establishing machine learning as an effective

How To Cite this Article

Khan, R.W.A., Shaheen, H., Islam Dar, M.E. et al. A data-driven approach to forest health assessment through multivariate analysis and machine learning techniques. BMC Plant Biol 25, 915 (2025). https://doi.org/10.1186/s12870-025-06937-5

Research Article

ArticleID :JASHC/2025/11/03/05

Teasing apart the sources of phylogenetic tree discordance across three genomes in the oak family (Fagaceae)

Issue No. 03 (July-Sept)

Authors: Zhao Shen, Biao-Feng Zhou, Yi-Ye Liang, Jing-Shu Wang, Run-Xian Yu, Yong Shi, Shao-Jun Ling, Wen-Ji Luo, Qiong-Qiong Lin, Jing-Wei Niu, et.al.,

Background:  Gene tree incongruence is a well-documented, but the biological and analytical factors driving phylogenetic discordance remains incompletely understood. In this study, we investigated how different factors contribute to incongruence among gene trees in Fagaceae.

Results: Each dataset produced highly supported topologies, with Fagus and Trigonobalanus consistently placed as early-diverging lineages within the Fagaceae family. However, the cpDNA and mtDNA divided the remaining Fagaceae species into New World and Old World clades, a pattern that sharply contrasted with the phylogenetic relationships inferred from nuclear genome data. These discrepancies between the cytoplasmic and nuclear gene trees likely result from ancient interspecific hybridization within Fagaceae. The decomposition analyses revealed that gene tree estimation error, incomplete lineage sorting, and gene flow accounted for 21.19%, 9.84%, and 7.76% of gene tree variation, respectively. We further revealed that 58.1–59.5% of genes exhibited consistent phylogenetic signals (“consistent genes”), while 40.5–41.9% of genes displayed conflicting signals (“inconsistent genes”). Consistent genes showed stronger phylogenetic signals and were more likely to recover the species tree topology than inconsistent genes. However, consistent and inconsistent genes did not significantly differ in terms of sequence- and tree-based characteristics. By excluding a subset of inconsistent genes, the study significantly reduced inconsistencies between concatenation- and coalescent-based approaches.

Conclusions: This study illustrates how diverse factors contribute to gene tree incongruence, offering new insights into the evolutionary history of Fagaceae.

How To Cite this Article

Shen, Z., Zhou, BF., Liang, YY. et al. Teasing apart the sources of phylogenetic tree discordance across three genomes in the oak family (Fagaceae). BMC Plant Biol 25, 919 (2025). https://doi.org/10.1186/s12870-025-06963-3

Research Article

ArticleID :JASHC/2025/11/04/01

Assembly and comparative analysis of four complete mitochondrial genomes of Pulsatilla species

Issue No. 04 (Oct-Dec)

Authors: Yanping Xing, Che Bian, Jie Wu, Hefei Xue, Wenxiao Men, Wenjuan Hou, Yutong Huang, Yanchang Huang, Han Zheng, Jianhua Wang, Tingguo Kang, Yanyun Yang and Liang Xu

Background: Pulsatilla species, which belong to the Ranunculaceae family, have garnered significant attention due to their remarkable medicinal attributes and ornamental value. In the present study, four mitochondrial genomes (mitogenomes) of Pulsatilla species were assembled and analyzed. The aim was to lay a research foundation for unraveling the genetic interrelationships among these species and the identification of Traditional Chinese Medicine from Pulsatilla species.

Results: The mitogenomes of P. chinensis, P. chinensis var. kissii, P. cernua, and P. dahurica were assembled into single circular DNA molecules, with lengths of 878,988 bp, 684,203 bp, 747,621 bp, and 824,625 bp, encoding 53, 40, 40, and 49 protein-coding genes, 13, 14, 20, and 33 transfer RNA genes, and 3, 3, 4, and 3 ribosomal RNA genes, respectively. Repeat sequence analysis found a large number of simple sequence repeats (SSRs) and long repeat sequences (LRSs) in four mitogenomes. P. chinensis, P. chinensis var. kissii, P. cernua and P. dahurica had 43, 4, 6, 3 LRSs longer than 1 kb, respectively. Codon bias and RNA editing sites in the protein-coding genes of the four mitogenomes were similar. Furthermore, numerous collinear sequences were identified among the four mitogenomes, and homologous fragments were found by comparing them with their plastome sequences. Based on the phylogenetic trees of mitochondrial PCGs, P. chinensis, P. chinensis var. kissii, P. cernua, and P. dahurica clustered into a common subclade.

Conclusions: The comprehensive analysis of the four Pulsatilla mitogenomes revealed that the genome size, gene composition, and distribution of repeat sequences display variability. This finding offers novel perspectives into the evolution of related species, thereby enriching our understanding of their genetic underpinnings and potential for further exploration in diverse fields.

How To Cite this Article

Xing, Y., Bian, C., Wu, J. et al. Assembly and comparative analysis of four complete mitochondrial genomes of Pulsatilla species. BMC Plant Biol 25, 1450 (2025). https://doi.org/10.1186/s12870-025-07527-1

Research Article

ArticleID :JASHC/2025/11/04/02

Molecular cloning and the expression profile of two calnexin genes – CNX1 and CNX2 – during pollen development and pollen tube growth in Petunia

Issue No. 04 (Oct-Dec)

Authors: Anna Suwińska, Piotr Wasąg, Marta Lenartowska, Jarosław Tyburski and Robert Lenartowski

Background: Calnexin (CNX) is a crucial chaperone of the endoplasmic reticulum (ER) that participates in the folding and quality control of glycoproteins. In plants, CNX contributes to multiple physiological processes, including growth, development, and adaptation to abiotic stresses. Nevertheless, its specific function in male gametophyte development and pollen tube growth remains poorly understood. In this work, we report for the first time the molecular cloning of two Petunia hybrida CNX homologs, PhCNX1 and PhCNX2, examine their expression profiles during pollen development, germination, and tube elongation, and discuss their potential functional involvement in these processes.

Results: We successfully cloned and characterized full-length cDNAs of PhCNX1 and PhCNX2, which encode proteins containing conserved motifs typical of the CNX/CRT family. Through a combination of qRT-PCR, western blotting, fluorescence in situ hybridization (FISH), and immunocytochemistry, we show that both genes are expressed in Petunia anthers, germinating pollen grains, and elongating tubes. During male gametophyte development, PhCNX1 shows peak expression at the microspore stage, whereas PhCNX2 reaches its highest transcript levels in mature pollen grains. Notably, in dry pollen, both genes exhibit a marked decrease in transcript abundance. FISH analysis indicates that PhCNX mRNAs are detected in both somatic and germline tissues but are predominantly localized to the cytoplasm of tapetal cells from the microsporocyte to microspore stages. Moreover, western blot analysis reveals a progressive increase in CNX protein levels throughout anther development and its accumulation in dry pollen. Immunocytochemical staining confirms CNX localization in all anther cell types, with notable enrichment in tapetal cells and the cytoplasm of pollen grains prior to anther dehiscence; this is further supported by immunogold labeling indicating CNX localization within the ER. In germinating pollen and elongating tubes, PhCNX transcripts accumulate in the cytoplasm near the apertures and along the tube (except the clear zone), whereas CNX protein is concentrated in the ER-dense subapical region 

Conclusion: Our findings reveal that PhCNX1 and PhCNX2 are dynamically regulated throughout the course of pollen development within the anther, as well as during pollen germination and tube growth. This spatiotemporal

How To Cite this Article

Suwińska, A., Wasąg, P., Lenartowska, M. et al. Molecular cloning and the expression profile of two calnexin genes – CNX1 and CNX2 – during pollen development and pollen tube growth in Petunia. BMC Plant Biol 25, 1449 (2025). https://doi.org/10.1186/s12870-025-07186-2

Research Article

ArticleID :JASHC/2025/11/04/03

Multivariate screening of upland cotton genotypes reveals key traits for salt tolerance at the seedling stage

Issue No. 04 (Oct-Dec)

Authors: Zunaira Anwar, Allah Ditta and Muhammad Kashif Riaz Khan

Background: Soil salinity poses a serious threat to cotton production worldwide by impairing growth, yield, and fiber quality. Salt stress disrupts key morphological, physiological, and biochemical processes in cotton plants, leading to considerable reductions in productivity. Therefore, identifying salt-tolerant cotton genotypes is essential for improving crop performance in saline environments.

Methods: In this study, fifty-one cotton genotypes were evaluated for their response to salinity stress at the seedling stage. Plants were grown in hydroponic culture under controlled glasshouse conditions and subjected to 200 mM NaCl to simulate salt stress. The experiment followed a completely randomized design (CRD) with three replications, and data were analyzed using two-way analysis of variance (ANOVA) and multivariate approaches, including principal component analysis (PCA), heatmap analysis, and the multi-trait genotype-ideotype distance index (MGIDI).

Results: ANOVA showed significant variation among genotypes for all traits. Salt stress caused significant reductions in growth traits, including shoot and root length, fresh and dry biomass, water relation traits, gaseous exchange traits and photosynthetic pigments. In contrast, excised leaf water loss (ELWL), sodium (Na+ )accumulation in roots and shoots, oxidative stress markers like hydrogen peroxide (H₂O₂) and malondialdehyde (MDA), osmolytes including proline, glycine betaine (GB), and saponin, and antioxidant enzyme activities like superoxide dismutase (SOD), peroxidase (POD), catalase (CAT) increased, while potassium contents (K+) and sodium to potassium ratio (K⁺/Na+) decreased. Under control conditions, PCA showed little variation, whereas under salt stress, it explained 64.8% of the variance and separated growth- from stress-related traits. Heatmap analysis confirmed these patterns and grouped genotypes into three clusters based on ion homeostasis and oxidative stress traits. MGIDI index integrated all traits into a single score and identified superior genotypes like G2 (NIAB-868), G22 (NIA-Noori), G32 (FH-530), G3 (NIAB-878-B), G49 (FH-911), G28 (FH-416), G33 (FH-534), and G39 (FH-546).

Conclusion: These findings suggest that multivariate and multi-trait screening at the seedling stage is a useful method for identifying cotton germplasm with salt tolerance, providing a foundation for breeding programs and further field evaluation that may contribute to stable yields under saline conditions.

How To Cite this Article

Anwar, Z., Ditta, A. & Riaz Khan, M. Multivariate screening of upland cotton genotypes reveals key traits for salt tolerance at the seedling stage. BMC Plant Biol 25, 1448 (2025). https://doi.org/10.1186/s12870-025-07354-4

Research Article

ArticleID :JASHC/2025/11/014/04

Evolutionary and functional insights into HSF gene family underpin thermal adaptation in the plateau plant Anisodus tanguticus

Issue No. 04 (Oct-Dec)

Authors: Zihan Li, Qi zheng, Liqi Feng, Fengqi Lv, Yang Xiao, Zhiqi Liu, Feng Wan, Tao Zhou, Yuntong Ma and Binjie Xu

Background: Anisodus tanguticus, a plateau-dwelling medicinal plant endemic to high-altitude regions, synthesizes pharmaceutically critical tropane alkaloids but faces escalating threats from climate warming. While its unique thermal adaptation mechanisms remain enigmatic, heat shock transcription factors (HSFs) are hypothesized to orchestrate stress resilience in this species.

Results: Here, we present a genome-wide evolutionary and functional dissection of the HSF gene family in A. tanguticus, identifying 20 HSF members (AntHSFs) with distinct structural and regulatory features. Phylogenetic reconstruction classified AntHSFs into three canonical subfamilies, revealing lineage-specific diversification patterns shaped by tandem and segmental duplication events. Conserved motif architectures and DNA-binding domains underscored functional divergence, while synteny analysis highlighted evolutionary constraints and adaptive innovations compared to model species. The transcript dynamics analysis under heat treatment revealed the dynamic changes in enzyme activity and gene expression of the MDA, GSTT, GSTF, and Cu/ZnSOD genes under different heat-treated times. The AntHSF gene exhibited stage-specific expression patterns consistent with antioxidant enzyme activity, indicating that the AntHSF family plays a critical role in coordinating the antioxidant gene response through temporal regulation networks. Notably, evolutionary analysis and sub-cellular localization revealed that AntHSF7 and AntHSF9 were potentially linked to plateau-specific adaptation.

Conclusion: This study deciphers the evolutionary drivers and functional specialization of HSF genes in A. tanguticus, providing mechanistic insights into its thermal resilience and a genetic roadmap for conserving and improving this climate-vulnerable medicinal species.

How To Cite this Article

Li, Z., zheng, Q., Feng, L. et al. Evolutionary and functional insights into HSF gene family underpin thermal adaptation in the plateau plant Anisodus tanguticus. BMC Plant Biol 25, 1452 (2025). https://doi.org/10.1186/s12870-025-07443-4