Crop Design最新文献

{"title":"Transposable elements in plants: Silencing, activation and roles","authors":"Yanling Wen ,&nbsp;Xiaojiang Wu ,&nbsp;Haodan Zeng ,&nbsp;Jianhong Xu ,&nbsp;Zhen Liu","doi":"10.1016/j.cropd.2026.100132","DOIUrl":"10.1016/j.cropd.2026.100132","url":null,"abstract":"<div><div>Transposable elements (TEs) are mobile genetic elements that are widespread in nearly all eukaryotic genomes,often constituting a substantial portion of the DNA sequence. However, due to mutation accumulation and epigenetic control, the vast majority of TEs have either permanently lost their ability to transpose or remain dormant for extended periods, with only a small fraction retaining activity in contemporary genomes. Active TEs can introduce novel insertions into the genome, serving as a crucial source of genetic variation. They not only influence plant growth and development but also enhance the adaptability of plants to adverse environments. Moreover, TEs have valuable applications in various aspects of genetic research. Studies have demonstrated that external factors such as biotic stress, abiotic stress, tissue culture, and hybridization can activate their mobility. This paper summarizes current research progress on TE activity,with a focus on the regulatory mechanisms governing their mobilization, the diverse impacts of active TEs on plants, their utility in genetic research, and the primary methodologies used to investigate TE activity. By synthesizing these aspects, we aim to deepen the understanding of TE–host genome interactions, offer an integrated perspective on genome dynamics and evolution, and facilitate broader application of TEs in genetic research.</div></div>","PeriodicalId":100341,"journal":{"name":"Crop Design","volume":"5 1","pages":"Article 100132"},"PeriodicalIF":0.0,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146173908","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Recent progress and perspective of peroxisome-targeted bioengineering in plant chassis","authors":"Xinyu Wang ,&nbsp;Shuyan Song ,&nbsp;Ci Kong ,&nbsp;Qianwen Deng ,&nbsp;Xiaowen Wang ,&nbsp;Ronghui Pan ,&nbsp;Huaxin Dai","doi":"10.1016/j.cropd.2025.100128","DOIUrl":"10.1016/j.cropd.2025.100128","url":null,"abstract":"<div><div>In plant chassis, peroxisomes, as key hubs of metabolism, play important roles in fatty acid β-oxidation, reactive oxygen species (ROS) metabolism and photorespiration. Fatty acid β-oxidation breaks down fatty acids through a multi-step enzymatic reaction, providing precursors for energy metabolism and phytohormone synthesis; ROS metabolism maintains redox balance through the antioxidant system and enhances plant resilience; and photorespiration relies on the synergistic action of peroxisomes with other organelles to optimize the efficiency of carbon and nitrogen utilization. Notably, peroxisomes possess a clear and simple targeting signaling system and a flexible abundance regulation mechanism, which provide unique advantages for their metabolic engineering. Recent studies have achieved effective control of fatty acid accumulation and promoted crop lipid yield by modulating the activity and transport mechanism of specific enzymes within the peroxisome. Furthermore, by reconfiguring the metabolic pathways in peroxisomes, researchers successfully optimized the photorespiratory pathway, which significantly improved the energy utilization efficiency and enhanced the stress tolerance of crops. Meanwhile, the modification of ROS metabolism have also demonstrated potential to enhance the antioxidant capacity and environmental adaptability of plants. These advances not only deepen our understanding of the peroxisome functions, but also provide new strategies and technical tools for crop breeding improvement and efficient secondary metabolite synthesis, which are expected to have broader application prospects in agricultural biotechnology and natural product biosynthesis in the future.</div></div>","PeriodicalId":100341,"journal":{"name":"Crop Design","volume":"5 1","pages":"Article 100128"},"PeriodicalIF":0.0,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146173128","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"CropSynergy: Harnessing IoT solutions for smart and efficient crop management","authors":"Md Sanzid Hossain Eyasin,&nbsp;Mahbub E Sobhani,&nbsp;Shamima Nasrin,&nbsp;Abu Sadat Al Rafi,&nbsp;A.K.M. Muzahidul Islam","doi":"10.1016/j.cropd.2025.100127","DOIUrl":"10.1016/j.cropd.2025.100127","url":null,"abstract":"<div><div>Agriculture has been a cornerstone of human civilization and continues evolving to meet the growing global population's demands. In an era of rapid technological advancement, the integration of smart agriculture, also known as smart farming or precision farming, has become essential for sustainable agricultural practices. This approach uses the Internet of Things (IoT) and Artificial Intelligence (AI) to improve data collection and analysis, facilitating real-time monitoring of crop health, soil conditions, irrigation, and comprehensive farm management. By incorporating IoT, farmers can make informed decisions, optimize resource use, and improve crop yields. This study explores the scope of integrating IoT into crop management to optimize traditional crop-related issues and to improve the quality, production, and marketing process. Our in-depth analysis illustrates the IoT architecture, the IoT in smart farming, and how IoT sensors and devices collect real-time data on soil moisture, temperature, humidity, and other environmental factors, which are then processed using cloud computing platforms and stored accordingly. After conducting an exhaustive search with sorted keywords aligned with our research interests, we have identified more than a thousand research articles. A further filtering approach is applied based on inclusion and exclusion criteria to select a significant number of well-suited articles, which are thoroughly analyzed in the development of this systematic review paper. The growing number of literature in this field has created a vast area for exploration. In response, we have thoroughly studied all the aspects of IoT and have proposed a novel taxonomy for IoT to systematically classify and analyze key aspects like Sensors, Actuators, Development Board, and Communication. We examine the application of IoT in crop management, emphasizing its benefits, challenges, and future potential. In addition, we analyze key IoT components, such as sensors, data analytics, and decision-making tools, and explore their role in enhancing agricultural sustainability, economic viability, and food security. Finally, we concluded our study by addressing the challenges and outlining future directions for further advancement.</div></div>","PeriodicalId":100341,"journal":{"name":"Crop Design","volume":"5 1","pages":"Article 100127"},"PeriodicalIF":0.0,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146173127","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Salinity stress in rice: Physiological and molecular mechanisms with a focus on the role of the hst1 gene and OsRR22 in enhancing salt tolerance","authors":"Murat Aycan,&nbsp;Toshiaki Mitsui","doi":"10.1016/j.cropd.2025.100129","DOIUrl":"10.1016/j.cropd.2025.100129","url":null,"abstract":"<div><div>Salinity is a major abiotic stress that threatens global food security, particularly in arid and semi-arid regions. Rice (<em>Oryza sativa</em> L.) is a stable food for over half of the world's population. Rising soil salinity, driven by climate change and unsustainable irrigation practices, is expected to affect nearly half of the world's arable lands by 2050. This review focuses on the role of the <em>hst1</em> gene, a mutant form of <em>OsRR22</em>, in enhancing salinity tolerance in rice. The <em>hst1</em> gene plays a crucial role in maintaining ion homeostasis, scavenging reactive oxygen species (ROS), and regulating stress-responsive signaling pathways, all of which are critical for mitigating salt-induced damage in rice. Under salt stress, the <em>hst1</em> mutation enables rice plants to accumulate less sodium (Na⁺) and more potassium (K⁺), thus preserving cellular function and enhancing photosynthetic efficiency. Additionally, <em>hst1</em> activates antioxidant enzymes such as superoxide dismutase (SOD), catalase (CAT), and glutathione reductase (GR), which protect cells from oxidative damage caused by ROS. The gene also modulates transcription factors that regulate downstream stress-response genes, contributing to improved growth and yield under saline conditions. By understanding the physiological and molecular mechanisms underlying <em>hst1</em>-mediated salt tolerance, this review provides insights into breeding strategies for developing salt-tolerant rice varieties. Such advancements are essential for sustaining rice production in saline-affected regions and ensuring global food security in the face of climate change and population growth.</div></div>","PeriodicalId":100341,"journal":{"name":"Crop Design","volume":"5 1","pages":"Article 100129"},"PeriodicalIF":0.0,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146173842","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic dissection and identification of blast resistance genes in an elite broad-spectrum resistance rice variety Xiushui114","authors":"Yihan Gao ,&nbsp;Shasha Liu ,&nbsp;Qingshuo Gu ,&nbsp;Haoyan Wang ,&nbsp;Xin Wang ,&nbsp;Qun Li ,&nbsp;Zuhua He ,&nbsp;Yiwen Deng","doi":"10.1016/j.cropd.2025.100130","DOIUrl":"10.1016/j.cropd.2025.100130","url":null,"abstract":"<div><div>Rice blast, caused by <em>Magnaporthe oryzae</em> (<em>M</em>. <em>oryzae</em>), is one of the most destructive diseases of rice and poses a critical threat to global food security. Breeding rice varieties with broad-spectrum and durable resistance through the deployment of resistance (<em>R</em>) genes remains the most effective and economical control strategy. In this study, we identified a highly blast-resistant rice variety, Xiushui114 (XS), by screening diverse rice accessions across three blast nurseries from 2016 to 2019. Pathogenicity assays demonstrated that XS exhibits resistance to more than 16 <em>M. oryzae</em> strains collected from major rice-growing regions, indicating a broad-spectrum resistance phenotype. Genetic analyses revealed that XS carries multiple R genes. Using a map-based cloning approach and sequence analysis further confirmed the presence of several known blast <em>R</em> genes, including <em>Pizh</em>, <em>Pik-KA</em>, <em>Pita</em>, and <em>Pib</em>, in XS. Resistance-spectrum evaluation indicated that <em>Pizh</em> contributes predominantly to the strong resistance observed in XS. Together, these findings establish XS as a valuable germplasm resource for improving rice blast resistance and provide new insights for breeding programs aiming to develop durable, broad-spectrum blast-resistant cultivars.</div></div>","PeriodicalId":100341,"journal":{"name":"Crop Design","volume":"5 1","pages":"Article 100130"},"PeriodicalIF":0.0,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145908860","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The pentose phosphate pathway influences maize radicle growth through regulating reactive oxygen species levels","authors":"Zhenlong Zhang ,&nbsp;Zhibo Li ,&nbsp;Fuchao Jiao,&nbsp;Haiyan Zhang,&nbsp;Jingtang Chen,&nbsp;Ming Wang","doi":"10.1016/j.cropd.2025.100131","DOIUrl":"10.1016/j.cropd.2025.100131","url":null,"abstract":"<div><div>The radicle of maize (<em>Zea mays</em> L.) is the first nutritional organ to emerge during seedling growth. However, the regulatory mechanisms underlying the pentose phosphate pathway (PPP) in radicle growth remain poorly understood. In this study, we investigated the effects of PPP inhibition on maize radicle development by treating maize seeds with the PPP inhibitor (6-amino nicotinamide, 6-AN). We evaluated radicle phenotypes and key energy and redox indicators, and performed integrated transcriptomic and metabolomic analyses to identify differentially expressed genes, metabolites, and affected pathways. Our results showed that 6-AN treatment significantly reduced radicle length and altered the NADPH/NADP⁺ and NADH/NAD⁺ ratios, with a marked decrease in reactive oxygen species (ROS) levels, total antioxidant capacity (T-AOC), and activities of SnRK1 and NADPH oxidase (NOX). These findings suggest that PPP inhibition leads to a significant reduction in energy and redox status. Additionally, transcriptomic and metabolomic analyses revealed that redox-related pathways were significantly affected. Notably, ROS levels in the radicle were restored to some extent by the addition of H₂O₂ and NADPH, confirming that PPP regulates radicle growth by modulating ROS homeostasis through NADPH. This study highlights the critical role of the PPP in regulating radicle development via ROS balance.</div></div>","PeriodicalId":100341,"journal":{"name":"Crop Design","volume":"5 1","pages":"Article 100131"},"PeriodicalIF":0.0,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146173129","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unlocking higher productivity and nutrient use efficiency in cereals through nano-fertilizers","authors":"Shivani Ranjan ,&nbsp;Sumit Sow ,&nbsp;Souvik Sadhu ,&nbsp;Ritwik Sahoo ,&nbsp;Dibyajyoti Nath ,&nbsp;Dinabandhu Samanta ,&nbsp;Muhammad Nazim ,&nbsp;Navnit Kumar ,&nbsp;Lalita Rana","doi":"10.1016/j.cropd.2025.100119","DOIUrl":"10.1016/j.cropd.2025.100119","url":null,"abstract":"<div><div>The rapid increase in global demand for cereals has led to excessive use of conventional fertilizers. While these fertilizers enhance crop yields, they are also associated with environmental degradation, soil and water pollution, and health concerns. In response to these issues, nanotechnology has been introduced as a revolutionary approach in agriculture, offering improvements through advanced practices. Nano-fertilizers, including nano NPK, nano iron, HAP-modified urea nanoparticles, and nano zeolite composite fertilizers, have been studied for their potential benefits. This review examines the application of these nano-fertilizers in three major cereal crops—wheat, maize, and rice. The comparative studies reveal that the biological yield of wheat can be increased by 20–55 ​%, maize by 20–40 ​%, and rice by 13–25 ​% with the use of nano-fertilizers. Furthermore, the overall grain yield of wheat has been found to increase by 20–55 ​%, maize by 22–50 ​%, and rice by 30–40 ​%. It is emphasized that careful management of nano-fertilizer concentrations is essential to avoid any adverse effects on plant health. The review highlights the significant improvements in cereal productivity and nutrient use efficiency offered by nano-fertilizers as a sustainable alternative to conventional methods along with limitations and way forward.</div></div>","PeriodicalId":100341,"journal":{"name":"Crop Design","volume":"4 4","pages":"Article 100119"},"PeriodicalIF":0.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145222062","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"CropARNet: A deep learning framework for crop genomic prediction with attention and residual modules","authors":"Shuchang Zhou ,&nbsp;Ke Cheng ,&nbsp;Lei Lv ,&nbsp;Jiamei Jiang ,&nbsp;Shusheng Zhou ,&nbsp;Yanda Zhou ,&nbsp;Zhitao Xu ,&nbsp;Qixiang Huang ,&nbsp;Huankun Yang ,&nbsp;Lingxi Chen ,&nbsp;Yuzhe Xu ,&nbsp;Zhangliang Yao ,&nbsp;Ting Zhao","doi":"10.1016/j.cropd.2025.100118","DOIUrl":"10.1016/j.cropd.2025.100118","url":null,"abstract":"<div><div>Genomic selection (GS) utilizes genome-wide markers to predict complex traits, thereby enhancing crop breeding efficiency. Recently, deep learning has emerged as a promising approach to improve prediction accuracy in GS. This study introduces CropARNet, a novel deep learning framework for GS that integrates a self-attention mechanism with a deep residual network. We systematically evaluated CropARNet's performance on 53 key agronomic traits across four major crops: rice, maize, cotton, and millet. When benchmarked against established models including GBLUP, DNNGP, XGBoost, and CropFormer, CropARNet ranked first in prediction accuracy for 29 of the 53 traits and consistently placed among the top performers for the remainder. Furthermore, CropARNet can successfully predict phenotypes using transcriptomic data. In summary, CropARNet represents a robust, accurate, and powerful tool for advancing the molecular breeding of complex traits in crops. The CropARNet software and illustrative examples are publicly available for download at: <span><span>https://github.com/Zhoushuchang-lab/CropARNet</span><svg><path></path></svg></span>.</div></div>","PeriodicalId":100341,"journal":{"name":"Crop Design","volume":"4 4","pages":"Article 100118"},"PeriodicalIF":0.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145050537","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Nickel stress modulates growth dynamics, disrupts redox homeostasis, and induces ultrastructural damage in maize","authors":"Muhammad Rehman ,&nbsp;Bahar Ali ,&nbsp;Abdul Salam ,&nbsp;Madiha Zaynab ,&nbsp;Zulqarnain Haider ,&nbsp;Muhammad Umair Yasin ,&nbsp;Irshan Ahmad ,&nbsp;Chunyan Yang ,&nbsp;Muhammad Haseeb Javaid ,&nbsp;Yinbo Gan","doi":"10.1016/j.cropd.2025.100122","DOIUrl":"10.1016/j.cropd.2025.100122","url":null,"abstract":"<div><div>Heavy metal (HMs) contamination is becoming increasingly critical due to rapid urbanization and unregulated industrialization. Nickel (Ni), although an essential trace element for plants, becomes toxic at high concentration, where it can accumulate to phytotoxic levels and make plants highly susceptible to its adverse effects. This study investigated the impact of variable Ni concentrations on maize seedlings by analyzing physiological, biochemical, ultrastructural, and molecular responses to understand the stress adaptation mechanisms. The results showed that Ni exposure suppressed plant growth and development by inducing oxidative stress, limiting nutrient uptake, and reducing photosynthetic efficiency. Higher Ni concentrations led to excessive reactive oxygen species (ROS) production in roots and shoots, resulting in oxidative damage as indicated by elevated malondialdehyde (MDA) content and ultrastructural disruptions. In vivo ROS detection using Dichloro-dihydro-fluorescein diacetate (H₂DCFDA) and dihydroethidium (DHE) staining further confirmed ROS overaccumulation under stress. Antioxidant enzyme activities initially increased with Ni levels, but declined sharply at the highest concentration, while ROS levels continued to rise, suggesting a breakdown in redox homeostasis. Furthermore, qPCR analysis revealed changes in the expression of antioxidant-related genes under Ni stress. In summary, Ni exposure disrupted redox balance, triggered oxidative damage, and activated defense responses in maize seedlings.</div></div>","PeriodicalId":100341,"journal":{"name":"Crop Design","volume":"4 4","pages":"Article 100122"},"PeriodicalIF":0.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145363987","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic manipulation of BnCOP1 genes enhances multiple agronomic traits in rapeseed","authors":"Yanjing Xu ,&nbsp;Yue Cao ,&nbsp;Rui Sun ,&nbsp;Baogang Lin ,&nbsp;Jie Dong","doi":"10.1016/j.cropd.2025.100117","DOIUrl":"10.1016/j.cropd.2025.100117","url":null,"abstract":"","PeriodicalId":100341,"journal":{"name":"Crop Design","volume":"4 4","pages":"Article 100117"},"PeriodicalIF":0.0,"publicationDate":"2025-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145363988","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}