Journal Detail

Research Article

ArticleID :JTAM/2025/11/01/01

Nutrient uptake and rhizosphere microbial community as related to yield advantage in broomcorn millet‒alfalfa intercropping under different row configurations

Issue No. 01 (Jan-Mar)

Authors: Shengzhican Li, Ashanjiang Yiminijiang, Ruoxuan Li, Mandi Wu, Mingxiu Long, Peizhi Yang and Shubin He

To investigate the effects of row ratio configurations on intercropping advantages and related rhizosphere microbial communities, a field experiment involving five treatments of different rows of broomcorn millet, i.e., P1M1 (1 row of broomcorn millet intercropped with 1 row of alfalfa), P2M3, P1M2, P1M3 and broomcorn millet alone (SP), was conducted on the Loess Plateau of China. We analyzed the yield, nutritional content of broomcorn millet, the soil nutrient availability and the diversity and community composition of AMF (arbuscular mycorrhizal fungi) and diazotrophs in the rhizosphere of broomcorn millet. The results showed that compared with monocultures, alfalfamillet intercropping system under different row ratio configurations significantly increased the yield of broomcorn millet and the absorption of PTP and PTK (total phosphorus and potassium of broomcorn millet). In addition, the broomcorn millet-alfalfa intercropping system also improved soil nutrition, with the decrease of the row ratio of broomcorn millet, the changes of TN, NH4 +-N and microbial biomass in the rhizosphere of broomcorn millet were consistent, which was opposite to NO3 −-N. Moreover, co-occurrence network and PLS-PM (partial least squares path modelling) analysis showed alfalfa-broomcorn millet intercropping system changed the community diversity and composition of soil microorganisms, increased the improvement of soil nutrition (TN, NH4 +-N and microbial biomass), and promoted the absorption of different nutrients by plants (N, P and K) mainly through the negative regulation of AMF and the synergistic effect of AMF on diazotrophs, and finally increased crop yield. This shows that broomcorn millet-alfalfa intercropping can increase plant nutrient content by adjusting soil nutrients and soil microbial activities, thereby increasing yield. Furthermore, we found that 1P2M was the best ratio of alfalfa-millet intercropping system, which may provide reliable suggestions and selection basis for future agricultural production practices.

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 :JTAM/2025/11/01/02

Integration of transcriptome and metabolome reveals key regulatory defense pathways associated with high temperature stress in cucumber (Cucumis sativus L.)

Issue No. 01 (Jan-Mar)

Authors: Yong Yuan, Xiao Ma, Chuang Li, Xitong Zhong, Yuyan Li, Jianyu Zhao, Xiaolan Zhang and Zhaoyang Zhou

High temperature stress seriously affects the quality and yield of vegetable crops, especially cucumber (Cucumis sativus L.). However, the metabolic dynamics and gene regulatory network of cucumber in response to high temperature stress remain poorly studied. In this study, we identified a heat-tolerant cucumber Gy14 and a heat-sensitive cucumber 32X. RNA-seq analysis of Gy14 and 32X under high temperature stress showed that some differentially expressed genes (DEGs) were related to the biosynthesis of secondary metabolites. Metabolomic analysis revealed that there were more phenylpropanoids and their downstream derivatives in Gy14 compared to that in 32X under Re_2d condition (2 normal days recovery after heat). Integrated analysis of transcriptome and metabolome revealed that these upregulated genes played a pivotal role in flavonoid biosynthesis. Moreover, high temperature stress significantly induced the expression of the gibberellin (GA) biosynthesis genes and exogenous application of GA3 alleviated the damage of high temperature to cucumber seedlings. Together, these findings provided new insights into the transcriptome response and metabolomic reprogramming of cucumber against high temperature stress.

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 :JTAM/2025/11/01/03

OrchidBase 6.0: increasing the number of Cymbidium (Orchidaceae) genomes and new bioinformatic tools for orchid genome analysis

Issue No. 01 (Jan-Mar)

Authors: You-Yi Chen, Ye Sun, Chung-I Li, Shao-Ting Lin, Hao-Chen Zheng, Zhe-Bin Zhang, Bing-Ru Lee, Chun-Lin Hsieh, et.al.,

Background: Orchids are well-known for their rich diversity of species as well as wide range habitats. Their floral structures are so unique in angiosperms that many of orchids are economically and culturally important in human society. Orchids pollination strategy and evolutionary trajectory are also fantastic human for centuries. Previously, OrchidBase was created not only for storage and management of orchid genomic and transcriptomic information including Apostasia shenzhenica, Dendrobium catenatum, Phalaenopsis equestris, and two species of Platanthera that belong to three different subfamilies of Orchidaceae, but explored orchid genetic sequences for their function. The OrchidBase offers an opportunity for the plant science community to compare orchid genomes and transcriptomes, and retrieve orchid sequences for further study.

Description: Recently, three whole-genome sequences of the Epidendroideae species, Cymbidium sinense, C. ensifolium and C. goeringii, were sequenced de novo, assembled, and analyzed. In addition, the systemic transcriptomes of these three species have been established. We included these datasets to develop a new version

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 :JTAM/2025/11/01/04

Exploration of key genes and pathways in response to submergence stress in red clover (Trifolium pratense L.) by WGCNA

Issue No. 01 (Jan-Mar)

Authors: Panpan Shang, Lei Bi, Wenwen Li, Xiaoli Zhou, Yanlong Feng, Jiahai Wu and Bing Zeng

Background:  Submergence stress is a prevalent abiotic stress affecting plant growth and development and can restrict plant cultivation in areas prone to flooding. 

Research: on plant submergence stress tolerance has been essential in managing plant production under excessive rainfall. Red clover (Trifolium pratense L.), a high-quality legume forage, exhibits low tolerance to submergence, and long-term submergence can lead to root rot and death.

Results: This study assessed the microstructure, physiological indicators, and the key genes and metabolic pathways under submergence stress in the root system of red clover HL(Hong Long) and ZY(Zi You) varieties under submergence stress at 0 h, 8 h, 24 h, 3 d, and 5 d. Based on 7740 transcripts identified in the leaves at 0 h, 8 h, and 24 h submergence stress, Weighted Gene Co-expression Network Analysis (WGCNA) was performed on the differentially expressed genes (DEGs) at 8 h and 24 h. Functional annotation of the DEGs in the four key modules was obtained. Based on the results, the red clover root system exhibited epidermal cell rupture, enlargement and rupture of cortical thin-walled cells, thickening of the mid-column, and a significant increase in the number of air cavities and air cavity area of aeration tissue with the prolongation of submergence stress. The malondialdehyde content, relative conductivity, peroxidase, and superoxide dismutase initially increased and decreased as submergence stress duration increased. Four specific modules (cyan, purple, light cyan, and ivory) closely correlated with each stress were identified by WGCNA. The 14 obtained Hub genes were functionally annotated, among which six genes, including gene51878, gene11315, and gene11848, were involved in glyoxylate and dicarboxylic acid metabolism, carbon fixation in photosynthetic organisms, carbon metabolism, biosynthesis of pantothenic acid and CoA, flavonoid biosynthesis.

Conclusion: In this study, using WGCNA, the molecular response mechanisms of red clover to submergence stress was proposed, and the core genes and metabolic pathways in response to submergence stress were obtained, providing a valuable data resource at the physiological and molecular levels for subsequent studies of submergence stress tolerance in plants.

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 :JTAM/2025/11/01/05

Silicon-mediated modulation of maize growth, metabolic responses, and antioxidant mechanisms under saline conditions

Issue No. 01 (Jan-Mar)

Authors: Muhammad Saad Ullah, Athar Mahmood, Hussam F. Najeeb Alawadi, Mahmoud F. Seleiman, Bilal Ahmad Khan et.al.,

Purpose: This study explored how exogenous silicon (Si) affects growth and salt resistance in maize.

Methods: The maize was cultivated in sand-filled pots, incorporating varied silicon and salt stress (NaCl) treatments. Silicon was applied at 0, 2, 4, 6, and 8 mM, and salt stress was induced using 0, 60 and120 mM concentrations. Soil salinity triggers a range of physiochemical abnormalities, often leading to growth arrest and, eventually, the demise of susceptible plants.

Results: The salt stress significantly reduced the total chlorophyll content (12.58–33.14%), antioxidant enzymes, notably SOD (32–46%), POD (10.33–18.48%), and CAT (10.05–13.19%). In contrast, salt stress increased secondary metabolites, including total phenols (49.11–66.35%.), flavonoids (220.99–280.36%), and anthocyanin (50.04–58.6%). Adding silicon under salt stress reduced the absorption of Na+ by 6.69%, 20.7%, 41.12%, and 34.28%, respectively, compared to their respective controls. Additionally, applying Si at 8 mM significantly enhanced antioxidant enzymes such as SOD (50.57%), POD (15.58%), CAT (10.06%) and chlorophyll ratio (21.32%).

Conclusion: Silicon application positively impacted nearly all growth and physiological features, indicating it helps mitigate against salinity. This was achieved by regulating various salinity indicators, where secondary metabolites, including anthocyanin, ascorbic acid, total phenols, and flavonoids, increased.

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 :JTAM/2025/11/02/01

Turnip mosaic virus infection cleaves MEDIATOR SUBUNIT16 in plants increasing plant susceptibility to the virus and its aphid vector Myzus persicae

Issue No. 02 (Apr-June)

Authors: Swayamjit Ray, Tyseen Murad, Gabriella D. Arena, Kanza Arshad, Zebulun Arendsee, Venura Herath, Steven A. Whitham and Clare L. Casteel

Plant viruses both trigger and inhibit host plant defense responses, including defenses that target their insect vectors, such as aphids. Turnip mosaic virus (TuMV) infection and its protein, NIa-Pro (nuclear inclusion protease a), suppress aphid-induced plant defenses, however the mechanisms of this suppression are still largely unknown. In this study, we determined that NIa-Pro’s protease activity is required to increase aphid performance on host plants and that 40 transcripts with predicted NIa-Pro cleavage sequences are regulated in Arabidopsis plants challenged with aphids and/or virus compared to healthy controls. One of the candidates, MEDIATOR 16 (MED16), regulates the transcription of ethylene (ET)/jasmonic acid (JA)-dependent defense responses against necrotrophic pathogens. We show that a nuclear localization signal is removed from MED16 by specific proteolytic cleavage in virus-infected plants and in plants overexpressing NIa-Pro in the presence of aphids. Although some cleavage was occasionally detected in the absence of virus infection, it occurred at a much higher rate in plants that were virus-infected or overexpressing NIa-Pro, especially when aphids were also present. This suggests MED16 functions in the nucleus may be impacted in virus infected plants. Consistent with this, induction of the MED16-dependent transcript of PLANT DEFENSIN 1.2 (PDF1.2), was reduced in virus-infected plants and in plants expressing NIa-Pro compared to controls, but not in plants expressing NIa-Pro C151A that lacks its protease activity. Finally, we show the performance of both the virus and the aphid vector was enhanced on med16 mutant Arabidopsis compared to controls. Overall, this study demonstrates MED16 regulates defense responses against both the virus and the aphid and provides insights into the mechanism by which TuMV suppresses anti-virus and anti-herbivore defenses.

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 :JTAM/2025/11/02/02

Medicago Mting1 Mting2 double knockout mutants are extremely dwarfed and never flower implicating essential MtING functions in growth and flowering

Issue No. 02 (Apr-June)

Authors: Matthew Mayo‑Smith, Axel Poulet, Lulu Zhang, Yongyan Peng, David Goldstone and Joanna Putterill

Background: Optimal flowering time is critical to agricultural productivity. Despite this, flowering regulation in the Fabaceae (legume) family is not fully understood. For example, FLC and CO control Arabidopsis flowering, but do not regulate flowering in the temperate legume Medicago. Little is known about the genetic roles of the two plant ING genes. They encode proteins with conserved ING and PHD finger domains predicted to function as epi genetic readers. Previously, using CRISPR‑Cas9 knock outs, we reported that Medicago MtING2 promotes flowering and growth. However, surprisingly, Mting2 PHD finger mutants flowered similarly to wild type. Additionally, MtING1 did not regulate flowering because Mting1 mutants flowered like wild type. 

Methods: To further dissect the combined genetic function of MtING1 and MtING2 and their PHD fingers, we cross pollinated Mting1 and Mting2 single mutants to create two double mutants: The Mting1-7 Mting2-2 double knockout mutant and the Mting1-1 Mting2-11 double PHD finger mutant. Mutant phenotypes were assessed in floral‑inductive conditions. We used fluorescence confocal microscopy and in vitro protein biophysical analysis to investigate the sub cellular localization and oligomerization of the proteins. We carried out gene expression analysis by RNA‑seq and RT qPCR to determine how the two genes affect transcript accumulation to influence growth and flowering. 

Results: The Mting double knockout mutants displayed a striking, non‑flowering, highly dwarfed phenotype indicating overlapping and complementary functions. Conversely Mting double PHD finger mutants showed only mild dwarfing and weak delays to flowering, indicating that the PHD fingers did not have a major impact on MtING function. MtING proteins localised to the nucleus, consistent with their predicted roles as histone readers, but did not interact in solution. Large changes to gene expression were seen in the Mting2-2 single mutant and the double knockout mutant, with key flowering genes downregulated and predicted floral repressors elevated. Furthermore, the MtINGs promoted the expression of Medicago homologs of target genes of the Arabidopsis NuA4 HAT complex.

Conclusions: Our findings demonstrate the key combined function the MtING genes play in regulation of global gene expression, flowering time and wider development and implicate an important role in epigenetic regulation via HAT complexes

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 :JTAM/2025/11/02/03

Exploring genomic loci and candidate genes associated with drought tolerance indices in spring wheat evaluated under two levels of drought

Issue No. 02 (Apr-June)

Authors: Mohamed Mosalam, Rahma A. Nemr, Maha Aljabri, Alaa A. Said and Mohamed El-Soda

Background: Wheat is a major global crop, and increasing its productivity is essential to meet the growing population demand. However limited water resources is the primary constraint. This study aimed to identify genetic factors associated with drought tolerance using a diverse panel of 287 wheat genotypes evaluated under well watered and drought-stressed conditions. Water Use Efficiency (WUE) and Grain Yield (GY), along with drought tolerance indices, were assessed. A genome-wide association study (GWAS) using 26,814 high-density SNP markers identified loci linked to these traits, with 768 SNPs showing significant associations. Additionally, genomic selection (GS) was performed using the rrBLUP model to predict trait performance across environments.

Results:  Among the 768 significant SNPs associated with the measured traits at -log10 (P) ≥ 3, 81 SNPs were mapped with a higher threshold -log10 (P) ≥ 4, indicating pleiotropic and QTL-by-environment interaction effects. Several novel and known genes, previously reported to have functions related to biotic and abiotic stresses response were linked to significant SNPs. Among the drought indices evaluated, stress tolerance index (STI), geometric mean productivity (GMP), and tolerance index (TOL) were the most reliable indicators for selecting stable, high-yielding genotypes under drought and control conditions. The same three indices exhibited high prediction values under the severe drought stress (SS) condition. Five genotypes were identified as promising candidates for breeding programs based on their superior drought tolerance, high grain yield, and nutritional value.

Conclusion: This study provides valuable insights into the genetic basis of drought tolerance in wheat, highlighting key SNPs and genomic regions associated with improved water use efficiency and yield stability. The findings contribute to the development of drought-tolerant wheat varieties with optimized water utilization to achieve increased yield per unit of water at diverse water levels, ultimately contributing to sustainable agriculture and food security.

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 :JTAM/2025/11/02/04

Identification of the SWEET gene family and functional characterization of PsSWEET1a and PsSWEET17b in the regulation of sugar accumulation in ‘Fengtang’ plum (Prunus salicina Lindl.)

Issue No. 02 (Apr-June)

Authors: Shan Liu, Xiaoshuang Nie, Hong Chen and Xinjie Shen

Background: ‘Fengtang’ plum is a cultivar known for its significant sugar accumulation. Although various studies have been conducted on sugar metabolism, the specific molecular mechanisms underlying the high sugar accumulation in ‘Fengtang’ plum remain largely unexplored. Here, we present the role of the Sugars Will Eventually be Exported Transporters (SWEETs) family in regulating sugar accumulation in ‘Fengtang’ plum fruits.

Results: In this study, 18 PsSWEET genes were identified based on homology with Arabidopsis genes and the Pfam database (ID: PF03083). Alignment of multiple sequences revealed that the seven alpha-helical transmembrane regions (7-TMs) are largely conserved in the PsSWEET family. Phylogenetic analysis demonstrated that the 18 SWEET family members could be categorized into four clades. Nine predicted motifs were identified within the PsSWEET genes of plum. The PsSWEET genes were unevenly distributed across five chromosomes, and synteny analysis revealed three pairs of fragmented duplication events. PsSWEET1a and PsSWEET17b are pivotal in ‘Fengtang’ plum fruit development. Subcellular localization analyses indicated that PsSWEET1a is localized to the nucleus and cytoplasm, while PsSWEET17b is associated with the vacuolar membrane. Gene function was further validated through transient silencing and overexpression of the PsSWEET1a and PsSWEET17b genes in plum fruits, which significantly impacted their soluble sugar content. Heterologous expression of PsSWEET1a and PsSWEET17b in tomato resulted in an increase in soluble sugar content due to the modulation of sugar accumulation-related genes and enzyme activities.

Conclusion: The genes PsSWEET1a and PsSWEET17b, which regulate the content of soluble sugar in plum fruit, were successfully identified. This study provides a comprehensive insight into the SWEET gene family of plum, offering novel perspectives on the regulation of sugar accumulation in fruit and laying a critical foundation for further enhancement of plum fruit quality.

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 :JTAM/2025/11/03/01

Identification of Rcr12, a single dominant clubroot resistance gene near Rcr6 on chromosome B3 of Brassica nigra

Issue No. 03 (July-Sept)

Authors: Hao Hu, Adrian Chang, Ling Cao, Yangdou Wei and Fengqun Yu

Background: Clubroot disease, caused by the soil-borne protist Plasmodiophora brassicae, is a major threat to Brassica crops worldwide, leading to significant yield losses. Genetic resistance is the most effective and sustainable management strategy; however, the identification and characterization of clubroot resistance (CR) genes remain a challenge, particularly in Brassica nigra. Despite its abundant CR resources, only one CR gene, Rcr6, has been identified in the B genome of B. nigra, leaving much of its genetic potential unexplored. Understanding the genomic distribution and diversity of CR genes in B. nigra is crucial for expanding resistance breeding options, especially for canola (B. napus).

Results: This study identified Rcr12, a single dominant CR gene on chromosome B3 of the highly resistant B. nigra line BRA19278. Using bulked segregant RNA sequencing (BSR-seq) and fine mapping in segregating populations derived from a cross between CR2748 (a susceptible B. nigra line) and BRA19278, together with single-root protoplast-derived isolates (SPIs) of P. brassicae and comparative analysis across multiple reference genomes, we established that Rcr12 is distinct from Rcr6 despite their close physical proximity. Evidence supporting its distinctiveness includes differential resistance patterns against various SPIs, unique SNP marker associations, and pangenomic analyses. Fine mapping refined the Rcr12 locus to a 0.33 Mb region on chromosome B3, containing multiple resistance gene candidates, in contrast to the single candidate identified for Rcr6. This study is the first to report an nucleotide-binding leucine rich repeat (NLR) cluster-type CR locus near an NLR singleton in Brassica crops, underscoring the evolutionary and functional significance of this gene arrangement.

Conclusion: The discovery of Rcr12 expands our understanding of NLR gene organization and its role in host resistance evolution. Beyond advancing clubroot resistance breeding, this discovery lays the groundwork for studying functional interactions between NLR singletons and clusters in plant immunity. Additionally, the use of purified SPIs as a pathogen differentiation tool offers a novel approach to resolving ambiguities in clubroot research, addressing the complexity of host-pathogen interactions and facilitating future investigations, especially with the anticipated release of a new pathogen classification system.

How To Cite this Article

© Crown 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 :JTAM/2025/11/03/02

Identification and expression analysis of the FRK gene family in Oilseed (Brassica napus L.)

Issue No. 03 (July-Sept)

Authors: Rui Yang, Jindong Chen, Ying Huang, Lingli Xie, Jinsong Xu, Le Xu, Xuekun Zhang and Benbo Xu

Fructokinases (FRKs) are pivotal enzymes involved in sugar metabolism and plant growth regulation. In this study, a total of 38 BnFRK genes were identified in the Brassica napus genome through a comprehensive genome-wide analysis. Phylogenetic classification divided these genes into four groups, with conserved motif and gene structure analyses indicating both functional conservation and divergence. Synteny and collinearity analyses revealed extensive gene duplication events, particularly within Group IV, suggesting lineage-specific expansion after polyploidization. Promoter cis-element analysis indicated that BnFRKs are potentially involved in hormone response and abiotic stress regulation. Transcriptome data and qRT-PCR validation demonstrated that several BnFRKs, especially BnFRK12, showed significant induction under salt, alkali, low nitrogen and osmotic stress conditions, highlighting their potential roles in stress adaptation. These findings provide a foundation for further functional characterization of BnFRK genes and their application in improving stress resilience in rapeseed

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 :JTAM/2025/11/03/03

Genome identification of NAC gene family and its gene expression patterns in responding to salt and drought stresses in Rhododendron delavayi

Issue No. 03 (July-Sept)

Authors: Mengxian Cai, Chunxing Sun, Jing Ou and Tuo Zeng

Background: The NAC (NAM, ATAF1/2, and CUC2) transcription factors (TFs), which play a vital role in plant growth and development, stress response, and disease resistance, have been extensively analyzed in various plant species. However, there is limited knowledge regarding the NAC family in Rhododendron delavayi, an important ornamental f lower.

Result: In this study, a total of 102 RdNAC genes were identified from the R. delavayi genome. Phylogenetic analysis divided these genes into seven subfamilies, each characterized by similar conserved motifs. Chromosomal mapping revealed an uneven distribution of RdNACs across all 13 chromosomes, with gene family expansion driven primarily by dispersed duplication (110 gene pairs) and, to a lesser extent, tandem duplication (17 pairs). Intraspecific synteny analysis detected 26 pairs of duplicated RdNAC genes, while interspecific collinearity with Arabidopsis thaliana uncovered 83 orthologous pairs, indicating both lineage-specific diversification and conserved evolutionary relationships. Ka/Ks ratio calculations for both intra-RdNAC duplicates and RdNAC–AtNAC orthologs yielded values below 0.5, reflecting strong purifying selection. Conserved-motif and domain analyses identified ten distinct motifs and 35 structural domains, with the NAM and MIT CorA-like superfamily domains being the most prevalent. Promoter analysis of 2 kb upstream regions revealed a high abundance of abiotic stress-related cis-acting elements (e.g., ABRE, ARE, CGTCA-motif, LTR). Finally, qRT-PCR demonstrated that under drought (20% PEG) and salt (200 mM NaCl) treatments, multiple RdNACs, particularly RdNAC022 and RdNAC099, were significantly upregulated, underscoring their potential roles in stress response.

Conclusion: This study provides a comprehensive identification of the RdNAC TF family in R. delavayi, contributing to a better understanding of these transcription factors in this species. The findings also serve as a reference for analyzing stress responses, particularly concerning drought and salt stress in R. delavayi.

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 :JTAM/2025/11/03/04

The bZIP transcription factor CibZIP43 positively regulates salt and heat tolerance in pecan (Carya illinoinensis)

Issue No. 03 (July-Sept)

Authors: Linna Wang, Nianqing Jiang, Lina Zou, Jinhua He, Zixian Yao, Shunran Zhang and Yan Xiang

Pecan (Carya illinoinensis) is an economically and ecologically important tree species, but its growth is frequently challenged by salt stress and heat stress. bZIP transcription factors are key regulators of plant responses to abiotic stresses. This study aimed to functionally characterize the pecan transcription factor CibZIP43 and reveal its role in salt and heat stress tolerance. The CibZIP43 gene was overexpressed in Arabidopsis, and the results showed that CibZIP43 overexpression (OE) in Arabidopsis significantly enhanced the tolerance of transgenic plants to salt and heat stress. Physiological and biochemical analyzes showed that CibZIP43 OE lines exhibited better growth and improved physiological indices under salt and heat stress, including increased chlorophyll content, relative water content, and antioxidant enzyme activities, along with reduced membrane lipid peroxidation and proline accumulation. Moreover, CibZIP43 OE enhanced plant adaptation to salt and heat stress by regulating the expression of Na+/K+ transporter-related and heat stress-related genes. These findings uncover new molecular mechanisms and provide potential genetic resources for breeding for stress-tolerance in pecan varieties.

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 :JTAM/2025/11/03/05

Genome-Wide identification and expression profiles of the WRKY transcription factor family in Artocarpus nanchuanensis

Issue No. 03 (July-Sept)

Authors: Xiao Zhang, Changying Xia, Shiqi You, Yunli Chen, Youwei Zuo, Huan Zhang, Wenqiao Li, Zhe Zhang and Hongping Deng

Background As one of the largest families of transcription factors (TFs), the WRKY gene family plays a significant role in plant growth, development, and response to hormone and environmental stress. Currently, there is no systematic analysis of the WRKY gene family in Artocarpus nanchuanensis.

Results To explore its evolutionary mechanism and potential function, we performed a comprehensive analysis. A total of 113 AnWRKYs were identified, and 109 were mapped onto 28 chromosomes. These genes could be classified into 3 groups (Group I, Group IIa-IIe, Group III) based on phylogenetic analysis and the sequence characteristics of the AnWRKY domain. Syntenic analyses revealed 4 pairs of tandem repeats and 123 pairs of large fragment repeats. Furthermore, the expression profiles of AnWRKYs in roots, stems, and leaves showed that AnWRKYs had different spatial expression patterns. AnWRKY2, AnWRKY14, AnWRKY46, AnWRKY55, and AnWRKY105 may play important roles in the response to abiotic stress. In addition, subcellular localization analysis indicated that AnWRKY55 was localized in the nucleus.

Conclusions This study is the first to report the identification and characterization of AnWRKYs in A. nanchuanensis and provides an important basis for future comprehensive evolutionary and functional analyses of AnWRKYs in A. nanchuanensis.

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 :JTAM/2025/11/04/01

Arbuscular mycorrhizal fungi mediate leaf sugar profile in water-stressed trifoliate orange

Issue No. 04 (Oct-Dec)

Authors: Shi-Qi Pu, Feng-Ling Zheng, Qiang-Sheng Wu, Abeer Hashem, Elsayed Fathi Abd-Allah and Ying-Ning Zou

Background: Arbuscular mycorrhizal fungi (AMF) enhance plant drought tolerance partly by promoting soluble sugar accumulation, the mechanisms by which AMF colonization influences host sugar metabolism and associated gene expression under drought remain poorly understood. This study therefore examined the effects of inoculation with Funneliformis mosseae (T.H. Nicolson & Gerd.) C. Walker & A. Schüßler on the growth, water status, sugar profiles, and the expression/activity of sucrose-associated genes in the leaves of trifoliate orange (Citrus trifoliata L.) under water stress conditions.

Results: Over a 10-week water stress period, the root colonization by F. mosseae decreased by 14.36%, compared with ample water controls. Under water stress, F. mosseae inoculation significantly promoted plant growth performance (height, leaf number, and stem thickness), leaf water potential, nitrogen balance index, and chlorophyll index compared to those without inoculation. Ten sugar components (eight monosaccharides and two disaccharides) were detected. Inoculation with F. mosseae significantly elevated leaf contents of D-fructose, D-galactose, glucose, and inositol under both ample water and water stress conditions. It also increased leaf contents of D-arabinose under water stress, while decreasing the sucrose content under ample water conditions. The presence of the fungus boosted the acid invertase (AI) activity under water stress and up-regulated the relative expression of CtAI, CtNI, and CtSPS genes in leaves under both conditions. These gene expressions displayed a significantly positive correlation with root mycorrhizal colonization rate and glucose content, but a negative correlation with sucrose content.

Conclusion: F. mosseae modulated leaf sugar profiles in trifoliate orange under water stress, particularly by regulating sucrose synthesis and cleavage through modulating the expression of sucrose-associated genes. Since this study focused on a single AMF species and leaf response, further work should investigate diverse AMF species and sugar profiles in other plant tissues under water stress.

How To Cite this Article

Pu, SQ., Zheng, FL., Wu, QS. et al. Arbuscular mycorrhizal fungi mediate leaf sugar profile in water-stressed trifoliate orange. BMC Plant Biol 25, 1456 (2025). https://doi.org/10.1186/s12870-025-07139-9

Research Article

ArticleID :JTAM/2025/11/04/02

The negative responses and acclimation mechanisms of Neopyropia yezoensis conchocelis filaments to short- and long-term ocean acidification

Issue No. 04 (Oct-Dec)

Authors: Danrui Li, Li Liu, Ruowen Ding, Xianghai Tang, Yuanyuan Wang, Yan Zhao and Xuexi Tang

Background: Ocean acidification (OA) significantly alters the carbonate chemistry of seawater, leading to a decrease of seawater pH to impact the physiological and biochemical processes of those intertidal macroalgae. Previous studies have focused on the response of macroalgae to OA at thallus stage, while the effects at filamentous stage remain insufficiently explored.

Results:  This study investigated the physiological-biochemical and molecular mechanisms of the filamentous conchocelis stage (the diploid sporophyte) of Neopyropia yezoensis responding to short- (5 days) and long-term (20 days) OA (2000 ppm CO2, pH 7.53). The results showed that short-term OA rapidly inhibited the growth and photosynthesis, suppressed chlorophyll synthesis and nitrogen assimilation, and down-regulated genes associated with photosynthesis, Calvin cycle, and carbohydrate metabolism of N. yezoensis conchocelis filaments. However, N. yezoensis conchocelis filaments showed acclimation strategies under long-term OA, in terms of metabolic reorganization, prioritizing stress tolerance over growth. Further weighted gene co-expression network analysis (WGCNA) based on the metabolomic and transcriptomic results under long-term OA showed that the strategy was manifested by the accumulation of soluble sugars as osmolytes, lipid β-oxidation compensating for energy deficits, and H+ extrusion mediated via ABC transporters.

Conclusions: This study suggested time-depended responses of N. yezoensis conchocelis filaments to OA, proving the pronounced negative effects of OA on N. yezoensis conchocelis filaments, revealing N. yezoensis conchocelis f ilaments could acclimate to long-term OA by resource reallocation. These findings provide new insight into the survival of N. yezoensis conchocelis filaments under OA, and facilitate the development of technologies and breeding strategies for improved acidification tolerance in N. yezoensis.

How To Cite this Article

Li, D., Liu, L., Ding, R. et al. The negative responses and acclimation mechanisms of Neopyropia yezoensis conchocelis filaments to short- and long-term ocean acidification. BMC Plant Biol 25, 1457 (2025). https://doi.org/10.1186/s12870-025-07432-7

Research Article

ArticleID :JTAM/2025/11/04/03

From genome to gene expression: the genomic landscape of a hybrid species of Eucalyptus urophylla × Eucalyptus grandis and its divergence from parental species hybrid

Issue No. 04 (Oct-Dec)

Authors: Guo Liu, Jianzhong Luo, Wanhong Lu, Yan Lin, Lei Zhang, Jingyi Pan, Jiangbo Zhai and Anying Huang

Background: Eucalyptus urophylla × Eucalyptus grandis (E. urograndis) is a globally significant forest tree species renowned for its rapid growth, high yield, and exceptional wood production efficiency. A comparative analysis of its parental genomes, coupled with an in-depth investigation of the expression patterns of wood-related genes, will provide critical genomic resources to enhance research and utilization of this superior eucalypt hybrid species.

Results: In this study, we present a draft genome assembly consisting of 592.09 Mb of data, with 99.91% anchored to 11 pseudochromosomes. The assembly achieved a contig N50 of up to 3.73 Mb and a scaffold N50 of up to 58.62 Mb. Gene annotation and evaluation revealed that the E. urograndis genome contains 32,151 genes, of which 93.50% were fully annotated using Benchmarking Universal Single-Copy Orthologs (BUSCOs). Based on evolutionary analysis, E. grandis and E. urograndis are estimated to have diverged approximately 2.90 million years ago (Mya). Additionally, 131 gene families were found to be significantly expanded, and 475 positively selected genes (PSGs) were identified in the E. urograndis genome. Furthermore, RNA sequencing (RNA-seq) technology was employed to analyze allele-specific expression patterns of key enzymes involved in cellulose, xylan, and lignin biosynthesis. Several allele-specific expression genes (ASEGs) were identified, potentially associated with heterosis in E. urograndis.

Conclusions: The chromosomal-level genome assembly of E. urograndis presented in this study serves as a valuable genomic resource for eucalyptus molecular breeding, provides novel insights into its evolution, wood formation improvement, and adaptability, and enhances our understanding of genetic and molecular mechanisms underlying heterosis in Eucalyptus hybrids.

How To Cite this Article

Liu, G., Luo, J., Lu, W. et al. From genome to gene expression: the genomic landscape of a hybrid species of Eucalyptus urophylla × Eucalyptus grandis and its divergence from parental species hybrid. BMC Plant Biol 25, 1458 (2025). https://doi.org/10.1186/s12870-025-07371-3

Research Article

ArticleID :JTAM/2025/11/04/04

Mitigation of alkaline stress and iron deficiency in Petunia hybrida through resveratrol-induced physiological and nutrient responses

Issue No. 04 (Oct-Dec)

Authors: Ahmad Nadhir Hussein, Zohreh Jabbarzadeh, Javad Reazpour-Fard, Reza Darvishzadeh and Jafar Amiri

Soil alkalinity is a major abiotic stress limiting plant growth and nutrient uptake, particularly in calcareous soils where iron availability is severely restricted. Although various strategies have been explored to mitigate alkaline stress and iron deficiency in crops, the role of resveratrol—a non-flavonoid polyphenolic phytoalexin known for its potent antioxidant and signaling properties—has not been thoroughly investigated in ornamental species under such stress conditions. This study aimed to evaluate the physiological, biochemical and nutrient-modulating effects of foliar-applied resveratrol on Petunia hybrida cv. Supercascade Rose subjected to combined alkaline and iron-deficiency stress. A greenhouse factorial experiment was conducted with nutrient solutions at two pH levels (6.0 ± 0.2 and 8.3 ± 0.2) and two iron concentrations (15 and 1.5 mg L⁻¹ Fe), along with three resveratrol treatments (0, 100, and 200 µM) applied biweekly. Under alkaline and low-iron conditions, plant biomass was reduced by approximately 49–52%, total chlorophyll content declined by nearly 80%, and oxidative stress markers including electrolyte leakage, hydrogen peroxide (H₂O₂), glycine betaine (GB), and malondialdehyde (MDA) increased significantly. Resveratrol application, particularly at 100 µM, significantly alleviated these adverse effects by enhancing biomass by 63.5%, increasing chlorophyll content by 148%, and reducing oxidative damage markers by approximately 15%, compared to untreated stressed plants. Furthermore, resveratrol boosted ferric chelate reductase (FCR) activity, promoted macro- and micronutrient accumulation in roots and leaves, and preserved water status and membrane integrity. This study provides the first comprehensive evidence demonstrating that exogenous resveratrol effectively mitigates the detrimental impacts of alkaline and iron-deficiency stresses in an important ornamental species. The findings underscore resveratrol’s potential as an eco-friendly, cost-effective biostimulant to enhance nutrient use efficiency, oxidative stress tolerance, and overall resilience of floricultural crops grown in suboptimal soil environments.

How To Cite this Article

Hussein, A.N., Jabbarzadeh, Z., Reazpour-Fard, J. et al. Mitigation of alkaline stress and iron deficiency in Petunia hybrida through resveratrol-induced physiological and nutrient responses. BMC Plant Biol 25, 1455 (2025). https://doi.org/10.1186/s12870-025-07388-8