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Agronomy

Agronomy is an international, peer-reviewed, open access journal on agronomy and agroecology published monthly online by MDPI. 
The Spanish Society of Plant Biology (SEBP) is affiliated with Agronomy and their members receive discounts on the article processing charges.
Quartile Ranking JCR - Q1 (Agronomy | Plant Sciences)

All Articles (18,305)

Reverse transcription quantitative PCR (RT-qPCR) is extensively used to quantify gene expression under drought conditions; however, its reliability depends on the validation of the reference genes under specific conditions. In cucumber, reference genes have rarely been validated under drought conditions. This study identified stable housekeeping genes for RT-qPCR normalization in the leaves of two inbred lines with contrasting drought responses. Plants underwent a 7-day drought period, with leaf samples collected at multiple points along with watered controls. The expression stability of 13 candidate genes was evaluated using four algorithms: geNorm, NormFinder, BestKeeper, and the comparative ΔCt method, with the results integrated using RefFinder. Ten genes producing specific and efficient amplicons were analyzed for stability. CACS and UBI-1 consistently ranked among the most stable genes, with TIP41-like as an additional reliable option, whereas GAPDH and HEL were unstable. GeNorm pairwise variation analysis showed that the two reference genes were sufficient for accurate normalization. Functional validation with three drought-responsive targets (LOX, HsfC1, and CYP72A219) and comparison with RNA sequencing (RNA-seq) fold changes confirmed that normalization using CACS and UBI-1 yielded the most biologically credible expression profiles. These reference genes will facilitate robust RT-qPCR analyses of drought response in cucumber leaves and provide a starting point for validating suitable normalizers in other cucumber organs and related cucurbits.

6 December 2025

Primer specificity of candidate reference genes (HKGs) in cucumber leaves under drought stress. (A) Analysis of PCR-generated amplicons on agarose gel; M, GeneRuler 100 bp DNA Ladder (Thermo Fisher Scientific, Waltham, MA, USA; fragment sizes 100–1000 bp). (B) High-resolution melting (HRM) derivative curves for the same HKGs across all samples, showing single, sharp melting peaks and no evidence of primer–dimer formation or nonspecific products, thereby confirming assay specificity.

Nitrous oxide (N2O), as one of the important greenhouse gases in the atmosphere, has a significant impact on global climate change. Its emissions are significantly regulated by land use changes, especially in ecologically fragile semi-arid areas. However, there is still a lack of systematic analysis on the key biotic and abiotic factors through which different land use patterns affect N2O emissions. Therefore, this study focuses on four typical land use types in the Loess Plateau of central Gansu: Picea asperata (PA), Medicago sativa (MS), Abandoned land (AL), and Wheat field (WF). Static box gas chromatography was used to monitor soil N2O flux in situ, and multidimensional analysis was conducted based on soil physicochemical properties, microbial community structure, and nitrogen cycling functional genes. Based on the observational data from the 2024 growing season (April to October), Research findings show that the cumulative emissions of N2O from wheat fields increased significantly by 26.4%, 19.4%, and 39.8% compared to medicago sativa, abandoned land, and picea asperata, respectively. Mechanism analysis reveals that picea asperata promote nitrogen fixation and absorption in soil through higher soil water content and organic carbon content, as well as enrichment of Proteobacteria and high expression of nrfA and napA genes, thereby inhibiting N2O production and emissions. The wheat fields, on the other hand, have significantly increased N2O emissions due to the increased abundance of amoA_B, nxrB, and nirK functional genes and enhanced urease activity, which promote nitrification and denitrification processes. The Partial Least Squares Path Model (PLS-PM) further confirmed that nitrification functional genes are key driving factors for N2O emissions. This study systematically reveals the microbial and biochemical pathways involved in regulating N2O emissions through land use in semi-arid regions, providing a theoretical basis for regional nitrogen cycle management and climate mitigation.

6 December 2025

Melanin Found in Wheat Spike Husks

  • Mikhail S. Bazhenov,
  • Dmitry Y. Litvinov and
  • Tatiana A. Feodorova
  • + 1 author

Melanin is the dark polymer pigment found in all kingdoms of life. Plant allomelanin, formed through the oxidation and polymerization of phenolic compounds, does not contain nitrogen; however, it possesses similar properties to melanin of animal, fungal, or bacterial origin. The black coloration of awns, spike husk edges, and even complete spikes is well-known in wheat and occurs frequently in wild, but rarely in cultivated, wheat species. Previously, anthocyanins were considered the only pigments responsible for the black coloration of wheat ears. Recently, it has been shown that the black coloration of the husks in other cereals can be attributed to melanin or anthocyanins, or both of these pigments. In this study, using standard procedures for chemical extraction of anthocyanins and melanin, ultraviolet–visible–near-infrared spectroscopy, and hyperspectral imaging, we examined the pigment in Persian wheat (Triticum carthlicum Line 5999) black-colored spikes and found that it exhibits properties characteristic of melanin rather than anthocyanins. Also, using microscopy, we show that the dark pigment in the husks and awns of mature spikes is located mainly in the dead protoplasts of epiderma and sub-epidermal sclerenchyma cells. The localization of the pigment suggests that melanin may perform some protective or sunlight-to-heat transforming function.

6 December 2025

Mounting labor shortages and rising operational costs are threatening the sustainability of mechanized rice production in Southern China, underscoring the urgent need for innovations that reduce labor inputs during nursery preparation and transplanting. To address these challenges, this study developed an innovative double-blanket seedling tray measuring 120 cm in length—twice that of a conventional tray. Based on this design, experiments were conducted to identify suitable lightweight substrates capable of producing cohesive and structurally stable double-blanket rice seedling mats. Two lightweight substrates—crop straw boards and matrix cotton—were evaluated in comparison to traditional nursery soil. Results demonstrated that, when combined with the nutrient solution “Miao Zhuang Feng”, both lightweight substrates significantly improved seedling quality, transplanting performance, and final yield. Notably, the fresh weight of double-blanket seedlings grown on lightweight substrates was comparable to single-blanket seedlings cultivated in soil while being 47.46% lighter than double-blanket seedlings raised with soil. To optimize double-blanket seedling mat formation and transplanting quality, five seeding densities (300, 360, 420, 480, and 540 g/tray) and four seedling ages (10, 15, 20, and 25 d) were tested using crop straw board as the substrate. The results revealed that optimal combinations varied by condition: 480 and 540 g/tray were suitable for 15-day-old seedlings, 420 g/tray for 20-day-old seedlings, 360 g/tray for 20~25-day-old seedlings, and 300 g/tray for 25-day-old seedlings. Compared with single-blanket seedlings, the double-blanket approach reduced the number of trays required per hectare and the total seedling cultivation and transportation cost by 57.97% and 16.67%. Furthermore, increasing the seeding density from 300 to 360, 420, 480, and 540 g/tray led to additional reductions of 16.31%, 26.24%, 34.75%, and 41.13%, respectively—substantially lowering labor requirements for tray handling and seedling feeding during transplanting.

6 December 2025

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Agronomy - ISSN 2073-4395