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Keywords = plant domestication

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17 pages, 1325 KB  
Article
Shifts in Composition, Origin, and Distribution of Invasive Alien Plants in Guangxi, China, over 50 Years
by Jia Kong, Cong Hu, Yadong Qie, Chaohao Xu, Aihua Wang, Zhonghua Zhang and Gang Hu
Diversity 2026, 18(1), 44; https://doi.org/10.3390/d18010044 - 14 Jan 2026
Viewed by 24
Abstract
Invasions by alien plants are major global drivers of ecosystem changes and loss of biodiversity. Guangxi is an ecological barrier in southern China that is increasingly being affected by invasive alien plant species. We comprehensively reviewed the literature, compiling and analyzing the long-term [...] Read more.
Invasions by alien plants are major global drivers of ecosystem changes and loss of biodiversity. Guangxi is an ecological barrier in southern China that is increasingly being affected by invasive alien plant species. We comprehensively reviewed the literature, compiling and analyzing the long-term changes in species composition, native range, life forms, municipal-scale patterns, and correlates of invasive alien plant richness in Guangxi at three time points (1973, 2010, and 2023). Over the 50-year period, the number of invasive alien plant species markedly increased from 31 species in 1973 to 84 in 2010 and 158 in 2023; the number of families, genera, and species increased 2.05-, 3.75-, and 5.10-fold, respectively. Species native to North America consistently dominated the invasive flora, followed by those native to Africa. The number of species native to South America and Asia increased in the records from 2010 to 2023. Annual herbaceous plants accounted for the largest proportion of invasive species throughout the study period and showed the largest absolute increase in species number. However, no substantial temporal shifts in the overall life-form composition were detected. At the municipal scale, the invasive alien plant richness exhibited pronounced spatial heterogeneity. The invasive alien plant richness was highest in Guilin and Baise in 1973, in Guilin in 2023, followed by Nanning and Baise. Correlation analyses based on 2023 data revealed a significant positive association between invasive alien plant richness and tourism intensity, whereas relationships between population size, gross domestic product, and climatic variables were weak or nonsignificant. Overall, our results document the continued expansion and the spatial differentiation of invasive alien plants in Guangxi over the 50-year period of 1973–2023. These patterns primarily reflect the accumulation in the number of recorded invasive species under a consistent classification framework and should be interpreted with caution given the potential variation in survey effort among periods and cities. The results provide a descriptive baseline for the provincial-scale monitoring, risk assessment, and management of invasive alien plants. Full article
(This article belongs to the Special Issue Ecology, Distribution, Impacts, and Management of Invasive Plants)
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18 pages, 3261 KB  
Article
In Vitro Leaf-Based Method for Agrobacterium-Mediated Genetic Transformation of Sugar Beet
by Dmitry N. Miroshnichenko, Anna Klementyeva, Lilia Mourenets, Alexander S. Pushin, Aleksey P. Firsov and Sergey V. Dolgov
Crops 2026, 6(1), 12; https://doi.org/10.3390/crops6010012 - 13 Jan 2026
Viewed by 55
Abstract
Sugar beet, one of the most important natural sources of sugars in the world, is well known as a recalcitrant crop for genetic transformation. In the present study, several key components of Agrobacterium-mediated transformation of sugar beet have been studied. The correct [...] Read more.
Sugar beet, one of the most important natural sources of sugars in the world, is well known as a recalcitrant crop for genetic transformation. In the present study, several key components of Agrobacterium-mediated transformation of sugar beet have been studied. The correct choice of explant and plant regeneration potential of domestic breeding lines was evaluated; however, most attention was paid to the search for the most efficient selectable marker gene and selection agents. To produce transgenic plants, we applied a method based on the agrobacterial inoculation of wounded morphogenic structures previously initiated on in vitro cultivated leaves. Four selective marker genes conferring antibiotic or herbicide resistance were evaluated. In the case of selection using kanamycin or G418 (nptII gene controlled by the nos promoter), no transgenic plants were obtained, while the addition of the aminoglycoside antibiotic hygromycin (hpt gene, driven by the nos promoter) to the medium ensured the successful production of transgenic plants from three breeding lines with a frequency ranging from 1.5 to 5.1%. The selection of transgenic tissues using herbicides such as phosphinothricin and glyphosate after transformation with the bar and cp4-epsps genes (both controlled by the CaMV 35S promoter) also ensured the obtaining of transgenic plants, but the transformation efficiency was significantly low, reaching only 1.0 and 0.4%, respectively. Primary transgenic sugar beet plants grown in the greenhouse demonstrated enhanced resistance to herbicides in dosages commonly used in the field. In addition, after self-pollination of the primary T0 transgenic lines, homozygous T2 offspring were successfully selected, which demonstrated stable resistance to glyphosate due to the constitutive expression of the introduced cp4-epsps gene. Full article
(This article belongs to the Topic Genetic Engineering in Agriculture, 2nd Edition)
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17 pages, 4129 KB  
Article
Development and Comparison of Visual Colorimetric Endpoint LAMP and Real-Time LAMP-SYBR Green I Assays for Alternaria alternata (Fr.) Keissl in European Plum
by Hongyue Li, Canpeng Fu, Pan Xie, Wenwen Gao, Zhiqiang Mu, Lingkai Xu, Qiuyan Han and Shuaishuai Sha
J. Fungi 2026, 12(1), 56; https://doi.org/10.3390/jof12010056 - 12 Jan 2026
Viewed by 198
Abstract
European plum (Prunus domestica L.) is widely cultivated worldwide, with China producing 6.8 million t annually (55% of the global total output). However, the Kashgar region of Xinjiang, China’s primary production area, has experienced outbreaks of brown spot disease caused by Alternaria [...] Read more.
European plum (Prunus domestica L.) is widely cultivated worldwide, with China producing 6.8 million t annually (55% of the global total output). However, the Kashgar region of Xinjiang, China’s primary production area, has experienced outbreaks of brown spot disease caused by Alternaria alternata (Fr.) Keissl. Outbreaks of this disease severely hinder both domestic and global development of the European plum industry. Because this pathogen has a strong latent infection capability during the early stages of disease development, its early detection is important. We develop two detection methods targeting the ITS sequence of A. alternata: LAMP-Cresol Red chromogenic visible endpoint detection and LAMP-SYBR Green I real-time fluorescent detection. Both methods demonstrate high specificity for A. alternata, enabling stable detection of the pathogen in various plant samples; detection limits reach the femtogram (fg) level, significantly surpassing conventional PCR detection capabilities. Development of these highly efficient and precise early detection methods provides a solid foundation for sustainable development of China as a global hub of the European plum industry, and contributes significantly to global disease prevention, control, and industrial stability for this crop. Full article
(This article belongs to the Section Fungal Genomics, Genetics and Molecular Biology)
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25 pages, 1850 KB  
Article
Recovery, Identification, and Presumptive Agricultural Application of Soil Bacteria
by Guadalupe Steele, Andrew K. Rindsberg and Hung King Tiong
Appl. Microbiol. 2026, 6(1), 11; https://doi.org/10.3390/applmicrobiol6010011 - 9 Jan 2026
Viewed by 157
Abstract
Conventional and organic agriculture can both cause soil microbial community structure (SMCS) destruction, infertility, and abandonment. The application of soil productivity-improving biofertilizers is a sustainable practice that requires holistic knowledge, including complex biointeractions, diverse microbial metabolism, and culture requirements, the last of which [...] Read more.
Conventional and organic agriculture can both cause soil microbial community structure (SMCS) destruction, infertility, and abandonment. The application of soil productivity-improving biofertilizers is a sustainable practice that requires holistic knowledge, including complex biointeractions, diverse microbial metabolism, and culture requirements, the last of which rely on methodology and technology. In this study, a holistic culture-based and meta-analysis approach was employed to explore pristine and domesticated soils for presumptive plant growth-promoting (PGP) bacteria. Various soil samples were logistically acquired and processed using enrichment and heat alternatives. Morphologically diverse isolates were streak-purified and analyzed for 16S rRNA bacterial identification. Meta-analysis of PGP bacteria in domesticated environments was conducted using Google Search and NCBI PubMed. Soil fertility was analyzed for the pH and nitrogen/phosphorus/potassium (NPK) contents using biochemical tests. Notably, 7 genera and 15 species were differentially recovered, with Bacillus being the most prevalent and diverse in species. Conversely, Aeromonas, Lactobacillus, Lelliottia, Pseudomonas, and Staphylococcus were found only in pristine soil. While soil pH was consistent in all pristine soil samples, NPK contents ranged widely across the pristine (i.e., P/K) and domesticated samples (i.e., N/P/K). These findings could enhance biofertilizer SMCS, function, and effectiveness in the agricultural productivity needed to feed the expanding population. Full article
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19 pages, 976 KB  
Article
Production and Quality of ‘Smooth Cayenne’ Pineapple as Affected by Nitrogen Fertilization and Types of Plantlets in the Northern Region of Rio de Janeiro State, Brazil
by Denilson Coelho De Faria, Rômulo André Beltrame, Jéssica Morais Cunha, Stella Arndt, Simone de Paiva Caetano Bucker Moraes, Paulo Cesar Dos Santos, Marta Simone Mendonça Freitas, Moises Zucoloto, Silvio de Jesus Freitas, Willian Bucker Moraes, Marlene Evangelista Vieira and Almy Junior Cordeiro de Carvalho
Agronomy 2026, 16(2), 153; https://doi.org/10.3390/agronomy16020153 - 7 Jan 2026
Viewed by 236
Abstract
This study evaluated the effects of nitrogen fertilization and different types of planting material on the yield and fruit quality of pineapple (Ananas comosus var. comosus) cv. Smooth Cayenne under the edaphoclimatic conditions of the Northern region of Rio de Janeiro [...] Read more.
This study evaluated the effects of nitrogen fertilization and different types of planting material on the yield and fruit quality of pineapple (Ananas comosus var. comosus) cv. Smooth Cayenne under the edaphoclimatic conditions of the Northern region of Rio de Janeiro State, Brazil. The experiment was conducted in a randomized block design, arranged in a factorial scheme with four nitrogen rates, six types of planting material, and two harvest seasons (winter and summer). Based on the results, it can be inferred that slips provided higher yields and heavier fruits, whereas plants derived from crowns and suckers showed lower productivity. Increasing nitrogen rates promoted greater fruit mass and length, higher pulp percentage, and increased production of vegetative propagules. Fruits harvested in the summer showed higher soluble solids content (15.5 °Brix), greater pulp and juice percentages, and lower titratable acidity, which are desirable characteristics for fresh consumption. Despite the seasonal differences, fruit mass ranging from 1.5 to 2.0 kg met commercial standards for both processing and domestic markets. The soluble solids/titratable acidity ratio (15.8) was below the ideal range for fresh consumption. The combination of appropriate planting material and nitrogen fertilization contributes to higher production efficiency, cost reduction, and improved fruit quality. Full article
(This article belongs to the Section Horticultural and Floricultural Crops)
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17 pages, 9949 KB  
Article
Aluminum Alleviation of Iron Deficiency Chlorosis Is Conserved in Wild Rice Relative Oryza rufipogon and in Maize
by Jover da Silva Alves, Yugo Lima-Melo, Andriele Wairich, Vic Martini Sasso, Vitor L. Nascimento, Raul Antonio Sperotto, Luciane Almeri Tabaldi, Gustavo Brunetto and Felipe Klein Ricachenevsky
Plants 2026, 15(1), 159; https://doi.org/10.3390/plants15010159 - 5 Jan 2026
Viewed by 192
Abstract
Aluminum (Al), an element that has no biological function described in plants, is commonly found in acidic soils, reducing plant growth, despite some beneficial effects reported in the literature. Iron (Fe) is an essential nutrient for plants, and Fe deficiency causes leaf interveinal [...] Read more.
Aluminum (Al), an element that has no biological function described in plants, is commonly found in acidic soils, reducing plant growth, despite some beneficial effects reported in the literature. Iron (Fe) is an essential nutrient for plants, and Fe deficiency causes leaf interveinal chlorosis. Remarkably, rice (Oryza sativa), a C3 crop considered tolerant to Al, shows alleviation of Fe deficiency chlorosis when exposed to Al, suggesting that Al can positively impact Fe homeostasis. However, whether this effect is observed only in rice or is common to other plant species is unknown. The rice wild progenitor Oryza rufipogon is closely related to the domesticated species, sharing several traits such as a semi-aquatic habit and use of the combined strategy for Fe uptake. Maize (Zea mays), on the other hand, is a C4 plant, adapted to well-aerated soils, and uses a classic chelation-based strategy for Fe uptake. Here we used these two Poaceae representatives to determine whether Al excess could alleviate Fe deficiency chlorosis in species other than rice. Although Al caused toxicity irrespective of Fe levels, its addition essentially abolished chlorosis in Fe-deficient plants. The expression of Fe deficiency-induced marker genes was reduced to control levels in both species, suggesting that the Al alleviation effect leads to systemic signaling and down-regulation of Fe uptake mechanisms. Al alleviation partially rescued photosynthetic machinery inhibited by Fe deficiency, suggesting that leaves are maintaining photosynthetic activity when Al is present even under low Fe conditions. Taken together, our data show that the Al alleviation effect is shared by two other Poaceae species in addition to O. sativa and suggest that it might not be directly linked to domestication, changes in C3/C4 metabolism, or Al tolerance levels found in different species. Full article
(This article belongs to the Special Issue Molecular Regulation of Plant Stress Responses)
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16 pages, 1763 KB  
Article
Adsorption of Phosphonates to Iron- or Aluminum-Based Flocculants in Wastewater Treatment
by Konrad Malk, Ramona Riedel, Christoph Hinz, Thomas Fischer and Marion Martienssen
Water 2026, 18(1), 116; https://doi.org/10.3390/w18010116 - 3 Jan 2026
Viewed by 286
Abstract
In this study, we investigated the impact of varying iron (Fe) and aluminum (Al) contents on the adsorption of phosphonates to activated sludge. Phosphonates originating from household applications account for up to 40% of the non-reactive dissolved phosphorus in domestic sewage treatment plants [...] Read more.
In this study, we investigated the impact of varying iron (Fe) and aluminum (Al) contents on the adsorption of phosphonates to activated sludge. Phosphonates originating from household applications account for up to 40% of the non-reactive dissolved phosphorus in domestic sewage treatment plants and thus can contribute to the eutrophication of water bodies. Although these substances are not readily degradable, substantial quantities, ranging from 40% to more than 90%, are removed by sludge adsorption. The results demonstrate a strong correlation between the adsorption of aminophosphonates and the Fe3+ content of the sludge. The maximum phosphonate loadings were 5.94 mmol g−1 Fe3+ for ATMP, 4.94 mmol g−1 Fe3+ for EDTMP, 4.74 mmol g−1 Fe3+ for DTPMP, and 2.25 mmol g−1 Fe3+ for glyphosate. In contrast to pure ferric hydride flocs, the adsorption of phosphonates was approximately threefold higher when the hydroxides were located within activated sludge flocs. It is concluded that native sludge flocs provide larger iron surfaces than ferric hydroxide alone. Based on the weight of the adsorbents, aluminum salts were four times less efficient than ferric salts. In sludge without ferric or aluminum hydroxides, phosphonate adsorption was negligible. Full article
(This article belongs to the Section Wastewater Treatment and Reuse)
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17 pages, 10821 KB  
Article
Sustainability Assessment of a Novel Modified Sequencing Batch Reactor (MSBR) Using a Multi-Criteria Decision Analysis and the SPeARTM Framework
by Hanaa A. Muhammad, Bakhtyar A. Othman and Galawezh B. Bapeer
Nitrogen 2026, 7(1), 6; https://doi.org/10.3390/nitrogen7010006 - 31 Dec 2025
Viewed by 245
Abstract
Freshwater resources are on the verge of depletion due to the rapid increase in population, lifestyle changes, and especially during climate change in Iraq. Therefore, treating domestic wastewater correctly will significantly contribute to keeping the balance of water purity and its usage. To [...] Read more.
Freshwater resources are on the verge of depletion due to the rapid increase in population, lifestyle changes, and especially during climate change in Iraq. Therefore, treating domestic wastewater correctly will significantly contribute to keeping the balance of water purity and its usage. To fulfil this, the Sustainable Project Appraisal Routine (SPeARTM) program, which leverages Multi-Criteria Decision Analysis with operational sustainability indicators, is used to compare the relative sustainability performance of the novel Modified Sequencing Batch Reactor by visualising the results of the degree of its sustainability compared to the Moving Bed Biofilm Reactor and the conventional Sequencing Batch Reactor system. Although selecting the most sustainable treatment depends on specific treatment goals, available resources, site conditions, and stakeholder preferences, this study considers the equal weighting of sustainability assessment across environmental, social, and economic indices to inform sustainable decision making. The results show that integrating both conventional treatment plants into the novel modified treatment plant demonstrates a comparatively more balanced and stable sustainability performance under the assessed operational conditions. As at a design capacity of 100 m3·day−1, the MSBR achieved a higher organic and nutrient removal efficiencies relative to the conventional SBR and MBBR systems while operating at an intermediate energy demand (187.7 kWh·day−1) compared with the SBR (121.7 kWh·day−1) and the MBBR (211.8 kWh·day−1). Thus, it can compensate for the weaknesses and combines the strengths of the sustainability indices of the two systems, which supports the Modified Sequencing Batch Reactor as a comparatively favourable option for wastewater treatment within the assessed sustainability framework. Full article
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14 pages, 1471 KB  
Article
Energy Transformation Towards Climate Neutrality by 2050: The Case of Poland Based on CO2 Emission Reduction in the Public Power Generation Sector
by Przemysław Kaszyński, Marcin Malec, Michał Fijołek and Jacek Kamiński
Energies 2026, 19(1), 118; https://doi.org/10.3390/en19010118 - 25 Dec 2025
Viewed by 284
Abstract
The European Union’s energy transition is based on three fundamental pillars, the realisation of which is intended to achieve climate neutrality by 2050. These pillars comprise the decarbonization of the economy, the development of renewable energy sources (RES), and the improvement of energy [...] Read more.
The European Union’s energy transition is based on three fundamental pillars, the realisation of which is intended to achieve climate neutrality by 2050. These pillars comprise the decarbonization of the economy, the development of renewable energy sources (RES), and the improvement of energy efficiency. The prevailing decarbonization trend involves a systematic reduction in the use of fossil fuels across the economy and their replacement with energy derived from low-emission and renewable sources. These objectives pose a significant challenge, particularly for countries such as Poland, where electricity generation remains predominantly reliant on hard coal and lignite. In recent years, a substantial reduction in CO2 emissions has been observed in the energy sector, primarily due to the increasing share of renewables in the electricity generation mix. The main energy companies, most of which are majority-owned by the State Treasury, have developed specific strategies to meet these targets. This article analyses the strategic documents of domestic energy companies together with other publicly available sources. Based on these documents, projections have been developed regarding the decommissioning of individual generating units in public power plants and combined heat and power facilities fuelled by hard coal and lignite. Scenario-based analyses were then conducted, drawing on these projections and assumptions, to assess the potential scale of CO2 emission reductions from the domestic energy sector through to 2050. Full article
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24 pages, 4390 KB  
Article
Growth and Hormonal Responses to Salicylic Acid and Calcium Chloride Seed Priming in Domestic and Wild Salt-Tolerant Barley Species Under Saline Conditions
by Rim Ben Youssef, Nahida Jelali, Purificación Andrea Martínez-Melgarejo, Alfonso Albacete, Chedly Abdelly, Francisco Pérez-Alfocea and Cristina Martínez-Andújar
Plants 2026, 15(1), 64; https://doi.org/10.3390/plants15010064 - 25 Dec 2025
Viewed by 319
Abstract
Salinity is among the main abiotic constraints limiting crop productivity worldwide. Salt tolerance can be improved by introducing adaptive traits from wild species and enhancing pre-existing salt-adaptive mechanisms through priming. This study evaluated the beneficial effect of salicylic acid (SA, 1.25 mM) and [...] Read more.
Salinity is among the main abiotic constraints limiting crop productivity worldwide. Salt tolerance can be improved by introducing adaptive traits from wild species and enhancing pre-existing salt-adaptive mechanisms through priming. This study evaluated the beneficial effect of salicylic acid (SA, 1.25 mM) and calcium chloride (CaCl2, 5 mM) seed priming on plant growth under salinity in the domestic barley Hordeum vulgare (Hv) and the wild, salt-adapted Hordeum maritimum (Hm). Primed plants were grown under control, 100 and 200 mM sodium chloride (NaCl) for two weeks. Growth and hormone profiling were performed. Hv showed higher growth inhibition than Hm but was more responsive to stress alleviation by priming, particularly with SA, which increased biomass by up to 47% at 200 mM NaCl. The contrasting responses of both species reflected distinct hormonal strategies. The intrinsic salt tolerance of Hm appears linked to high constitutive levels of stress- and growth-related hormones. In Hv, growth recovery under salinity following priming was associated with hormonal reprogramming, involving reduced abscisic acid (ABA) accumulation and enhanced levels of growth-promoting hormones (indole-3-acetic acid (IAA), trans-zeatin (tZ), and isopentenyl adenine (iP)), especially in roots. Hormonal changes mediated by priming are analyzed in relation to adaptive growth responses and species’ ecological origins. Full article
(This article belongs to the Special Issue Plant Hormones in Growth, Development, and Regeneration)
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27 pages, 7997 KB  
Article
Glyco-Architectural Remodelling of the Feline Heart: Age- and HCM-Related Insights from Lectin Histochemistry
by Irina Constantin, Romelia Pop, Andrada Negoescu, Dragoș Hodor, Mara Georgiana Haralambie, Raluca Marica and Flaviu-Alexandru Tăbăran
Life 2026, 16(1), 20; https://doi.org/10.3390/life16010020 - 22 Dec 2025
Viewed by 319
Abstract
Glycosylation plays a critical role in maintaining cardiac structure and function, yet its modulation during aging and hypertrophic cardiomyopathy (HCM) in feline hearts remains uncharacterized. This study provides a systematic analysis of lectin-binding patterns in feline myocardium across different age groups and disease [...] Read more.
Glycosylation plays a critical role in maintaining cardiac structure and function, yet its modulation during aging and hypertrophic cardiomyopathy (HCM) in feline hearts remains uncharacterized. This study provides a systematic analysis of lectin-binding patterns in feline myocardium across different age groups and disease states. Post-mortem feline hearts (n = 64), classified by age (newborn to senior) and diagnostic status (healthy vs. HCM-affected), were evaluated using tissue microarrays stained with five plant-derived lectins—Concanavalin A (ConA), Wheat Germ Agglutinin (WGA), RCA (Ricinus communis Agglutinin I), Tomato (Lycopersicon esculentum Agglutinin), and Griffonia (Bandeiraea) simplicifolia Lectin I (BS)—alongside Draq5 nuclear counterstaining. Lectin histochemistry revealed distinct, region-specific glycosylation patterns, with notable remodelling in both aged and HCM-affected hearts. These glycan alterations reflect underlying molecular and structural changes associated with cardiac aging and pathology. Although lectin histochemistry has been used to examine cardiac glycosylation in species such as mice, rats, zebrafish, and humans, comparable data for felines have been lacking, even if domestic cat represents a spontaneous model for human HCM. This study provides the first essential step in characterizing the feline cardiac glycosylation. The observed shifts in lectin-binding profiles reveal specific remodelling associated with aging and HCM in cats. These results provide a foundation for future studies assessing the utility of glycan motifs as potential post-mortem markers of disease progression in felines. Full article
(This article belongs to the Special Issue Veterinary Pathology and Veterinary Anatomy: 3rd Edition)
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19 pages, 8323 KB  
Article
High-Copy SINE Transposons Facilitate Broad Ecological Adaptation in White Clover (Trifolium repens)
by Wei Hong, Meng Wang, Jun Tian, Xiaoyue Zhu, Ruixin Zhang, Changhong Guo and Yongjun Shu
Horticulturae 2026, 12(1), 6; https://doi.org/10.3390/horticulturae12010006 - 19 Dec 2025
Viewed by 301
Abstract
Recent advances in plant genomics have characterized transposable elements (TEs) as key contributors to genome structure and gene regulation. This study focuses on the remarkably high abundance of short interspersed nuclear elements (SINEs) in the genus Trifolium. Using the allotetraploid horticultural plant [...] Read more.
Recent advances in plant genomics have characterized transposable elements (TEs) as key contributors to genome structure and gene regulation. This study focuses on the remarkably high abundance of short interspersed nuclear elements (SINEs) in the genus Trifolium. Using the allotetraploid horticultural plant white clover (Trifolium repens L.) as the study organism, we systematically investigate lineage-specific SINE amplification, genomic distribution, insertional preferences, and their regulatory effects on gene expression. Our analyses reveal that SINEs are significantly more abundant in Trifolium than in other angiosperms. Comparative genomic analyses further indicate that SINE accumulation is closely associated with polyploidization and domestication. Gene Ontology (GO) enrichment analyses demonstrate that SINEs are preferentially enriched in stress responsive genes. Expression analyses further showed that, within duplicated gene pairs, genes with SINE insertions in their upstream promoter regions exhibit significantly higher transcript levels compared with genes without such insertions. Under drought, cold, and cadmium stress, these SINE-associated genes exhibit upregulation, and our data analysis shows a strong correlation between the presence of SINE insertions and stress-induced upregulation of gene expression. This study demonstrates that SINE insertions in upstream promoter regions modulate transcriptional regulatory networks involved in stress responses, contributing to broad ecological adaptation in white clover. Full article
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26 pages, 1758 KB  
Review
More than Heat: The Complex Nature of Pungent Capsicum spp.
by Filomena Monica Vella, Domenico Cautela and Bruna Laratta
Compounds 2025, 5(4), 61; https://doi.org/10.3390/compounds5040061 - 18 Dec 2025
Viewed by 402
Abstract
For centuries, people have used herbs, plants, and spices as remedies for health problems or simply to ameliorate body energy or vitality because of the bioactive compounds they contain. The Capsicum genus, which includes the chili pepper, is one of the oldest crops [...] Read more.
For centuries, people have used herbs, plants, and spices as remedies for health problems or simply to ameliorate body energy or vitality because of the bioactive compounds they contain. The Capsicum genus, which includes the chili pepper, is one of the oldest crops to be domesticated and used. It is characterized by three qualities: pungency/flavor, color, and aroma. Capsaicinoids are responsible for the pungent flavor. Carotenoids and flavonoids determine the remarkable and colorful tones of chili peppers. Volatile compounds provide their characteristic aroma. This prompts consumers to purchase and utilize the numerous varieties of chili peppers, whether fresh or dried. The presence of these bioactive compounds gives chili peppers functional attributes that promote health. This paper reviews the scientific research carried out over the last 25 years on these attributes. This paper also looks at how Capsicum fruits could be used as a valuable source of nutrients from plants that have beneficial biological properties. Full article
(This article belongs to the Special Issue Compounds–Derived from Nature)
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17 pages, 8326 KB  
Article
Pangenome-Wide Identification, Evolutionary Analysis of Maize ZmPLD Gene Family, and Functional Validation of ZmPLD15 in Cold Stress Tolerance
by Si-Nan Li, Yun-Long Li, Ming-Hao Sun, Yan Sun, Xin Li, Quan Cai, Yunpeng Wang and Jian-Guo Zhang
Plants 2025, 14(24), 3858; https://doi.org/10.3390/plants14243858 - 18 Dec 2025
Viewed by 492
Abstract
Phospholipase D (PLD) genes play key roles in plant abiotic stress responses, but the systematic identification of the maize (Zea mays) PLD family and its cold tolerance mechanism remain unclear. Using 26 maize genomes (pangenome), we identified 21 ZmPLD members via [...] Read more.
Phospholipase D (PLD) genes play key roles in plant abiotic stress responses, but the systematic identification of the maize (Zea mays) PLD family and its cold tolerance mechanism remain unclear. Using 26 maize genomes (pangenome), we identified 21 ZmPLD members via Hidden Markov Model (HMM) search (Pfam domain PF00614), including five private genes—avoiding gene omission from single reference genomes. Phylogenetic analysis showed ZmPLD conservation with Arabidopsis and rice PLDs; Ka/Ks analysis revealed most ZmPLDs under purifying selection, while three genes (including ZmPLD15) had positive selection signals, suggesting roles in maize adaptive domestication. For ZmPLD15, five shared structural variations (SVs) were found in its promoter; some contained ERF/bHLH binding sites, and SVs in Region1/5 significantly regulated ZmPLD15 expression. Protein structure prediction and molecular docking showed conserved ZmPLD15 structure and substrate (1,2-diacyl-sn-glycero-3-phosphocholine) binding energy across germplasms. Transgenic maize (B73 background) overexpressing ZmPLD15 was generated. Cold stress (8–10 °C, 6 h) and recovery (24 h) on three-leaf seedlings showed transgenic plants had better leaf cell integrity than wild type (WT). Transgenic plants retained 45.8% net photosynthetic rate (Pn), 47.9% stomatal conductance (Gs), and 55.8% transpiration rate (Tr) versus 7.6%, 21.3%, 13.8% in WT; intercellular CO2 concentration (Ci) was maintained properly. This confirms ZmPLD15 enhances maize cold tolerance by protecting photosynthetic systems, providing a framework for ZmPLD research and a key gene for cold-tolerant maize breeding. Full article
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18 pages, 2520 KB  
Article
Reproductive and Vegetative Yield Component Trade-Offs in Selection of Thinopyrum Intermedium
by Andrés Locatelli, Valentín D. Picasso, Pablo R. Speranza and Lucía Gutiérrez
Agronomy 2025, 15(12), 2895; https://doi.org/10.3390/agronomy15122895 - 16 Dec 2025
Viewed by 356
Abstract
Integrating perennial grain crops into agricultural systems can become a key milestone for increasing the provision of ecosystem services of food production systems. Intermediate wheatgrass is a novel perennial grain and forage crop that is undergoing domestication. Potential trade-offs between resource allocation and [...] Read more.
Integrating perennial grain crops into agricultural systems can become a key milestone for increasing the provision of ecosystem services of food production systems. Intermediate wheatgrass is a novel perennial grain and forage crop that is undergoing domestication. Potential trade-offs between resource allocation and reproductive and vegetative plant structures can challenge the response to selection for both grain and forage production under dual-purpose use. Our goal was to understand the genetic relationship between grain and forage yield components, quantify potential trade-offs between vegetative and reproductive allocation, and optimize the response to selection under dual-purpose management. Phenological, grain, and forage traits were evaluated in 30 half-sib families across two field experiments conducted over three years. No trade-offs were detected between grain and forage yield traits, indicating that the simultaneous improvement of both traits is feasible. Grain yield per spike and spikes per plant are promising secondary traits for indirect selection, given their moderate-to-high heritability (h2 = 0.58 and 0.41) and strong Pearson correlation coefficients with grain yield per plant (0.68 and 0.82). These traits could be assessed in the first year, increasing genetic gain per unit time. Intermediate wheatgrass germplasm could therefore be efficiently developed by shortening the time to first evaluation, using secondary traits, and performing selection under dual-purpose management. Full article
(This article belongs to the Special Issue The Revision of Production Potentials and Yield Gaps in Field Crops)
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