Crop Design最新文献

{"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":"2025-09-12","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":"2025-08-30","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":"Rhizosphere microbial communities of bacteria and fungi responding to cadmium stress in wheat","authors":"Yunfeng Xu ,&nbsp;Ling Shen ,&nbsp;Mingjiong Chen ,&nbsp;Haoran Sun ,&nbsp;Liangbo Fu ,&nbsp;Guoping Zhang ,&nbsp;Qiufang Shen","doi":"10.1016/j.cropd.2025.100112","DOIUrl":"10.1016/j.cropd.2025.100112","url":null,"abstract":"<div><div>Cadmium (Cd) contamination in soil poses a threat to crop production and food safety. Rhizosphere microorganisms are crucial for crop growth and production. However, sufficient evidence regarding Cd-responsive bacteria and fungi within crop rhizosphere remains largely unknown. Here, we investigated the impacts of Cd on soil microbial communities in wheat rhizosphere by performing 16S and ITS sequencing under normal (CK) and Cd (10 μM) conditions. We found that the lower concentration of Cd significantly increased Cd concentration in wheat grains (nearly 0.2 mg ​kg⁻¹), but it had no obvious growth inhibition. Interestingly, bacterial abundance and diversity were significantly decreased in soil rhizosphere when exposed to Cd, whereas little changes were observed in fungi. A total of 259 CK-specific and 45 Cd-specific operational taxonomic units (OTUs) in bacteria, as well as 3 CK-specific and 2 Cd-specific OTUs in fungi were identified. The function of identified bacteria were enriched in human diseases, organismal systems, metabolism, genetic information processing and environmental information processing. We also revealed a complicated bacterial co-occurrence network responding to Cd, including the core bacteria of <em>Acidobacteria</em>, <em>Nitrospirae</em> and <em>Chloroflexi</em> phylums. This study revealed Cd-responding bacteria and fungi communities in wheat rhizosphere, which may provide new insights into beneficial microorganisms for food safety.</div></div>","PeriodicalId":100341,"journal":{"name":"Crop Design","volume":"4 3","pages":"Article 100112"},"PeriodicalIF":0.0,"publicationDate":"2025-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144656528","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":"Advances and applications of the fungal bioluminescence pathway","authors":"Yuhao Li ,&nbsp;Dang Xu ,&nbsp;Hao Du","doi":"10.1016/j.cropd.2025.100111","DOIUrl":"10.1016/j.cropd.2025.100111","url":null,"abstract":"<div><div>Bioluminescence has emerged as a valuable resource for developing novel biological tools and engineered luminescent organisms. The fungal bioluminescence pathway (FBP) represents a particularly promising system, employing endogenous, non-toxic substrates to enable sustained light emission in autoluminescent plants. Recent progress in substrate optimization, enzyme engineering, and metabolic pathway enhancement has significantly improved the system's robustness, facilitating commercial applications. Beyond plant illumination, FBP has proven effective as a biological reporter for quantitative measurements in research settings. This review comprehensively examines the FBP system, detailing its progress, challenges, and multidisciplinary applications. As an innovative biotechnology system, the FBP system paves the way for a future illuminated by living organisms.</div></div>","PeriodicalId":100341,"journal":{"name":"Crop Design","volume":"4 3","pages":"Article 100111"},"PeriodicalIF":0.0,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144656533","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":"Heterosis estimation and heterotic grouping of sorghum [Sorghum bicolor (L) moench] inbred lines in dryland environments","authors":"Temesgen Begna ,&nbsp;Techale Birhan ,&nbsp;Taye Tadesse","doi":"10.1016/j.cropd.2025.100110","DOIUrl":"10.1016/j.cropd.2025.100110","url":null,"abstract":"<div><div>Sorghum is one of the most vital cereal crops well adapted to arid and semi-arid regions. However, its productivity remains low compared to its potential, primarily due to severe and recurrent drought stress. To develop climate-resilient sorghum hybrids, it is essential to understand the extent of heterosis and identify heterotic groups comprising drought-tolerant inbred lines. Therefore, this study was conducted to quantify the magnitude of heterosis and to classify sorghum inbred lines into heterotic groups using specific combining ability (SCA) and general combining ability (GCA) across multiple traits. A total of 42 sorghum genotypes were evaluated using an alpha lattice design with two replications across two environments during the 2019 cropping season. Significant genetic differences among genotypes were observed for the traits studied across locations. Several top-performing and well-adapted hybrids P-9534 ​× ​Melkam (6.32 ​t ​ha⁻¹), B6 ​× ​ICRS-14 (5.92 ​t ​ha⁻¹), TX-623 ​× ​ICRS-14 (5.88 ​t ​ha⁻¹), P9511 ​× ​Melkam (5.78 ​t ​ha⁻¹), and P-850341 ​× ​ICRS-14 (5.57 ​t ​ha⁻¹) were identified as promising for moisture-stressed environments. Among these, B6 ​× ​ICRS-14 exhibited the highest mid-parent heterosis (112.41 ​%), TX-623 ​× ​ICRS-14 showed the highest better-parent heterosis (68.71 ​%), and P-9534 ​× ​Melkam recorded the highest standard heterosis (30.71 ​%) for grain yield. Heterotic grouping based on specific combining ability (SCA) classified the sorghum inbred lines into two distinct groups, while the general combining ability of multiple traits (HGCAMT) method identified three heterotic groups for the development of superior hybrid varieties. Combining ability-based heterotic grouping is a critical approach for identifying the most suitable parental lines for creating new, agronomically superior hybrids. Overall, several sorghum hybrids demonstrated superiority over their mid-parents, better-parents, and the standard check in terms of grain yield and key agronomic traits. Therefore, the hybrids P-9534 ​× ​Melkam, B6 ​× ​ICRS-14, TX-623 ​× ​ICRS-14, MARC3 ​× ​Melkam, MARC3 ​× ​ICRS-14, P-9511 ​× ​Melkam, and P-850341 ​× ​ICRS-14 were identified as superior performers with the potential to significantly increase sorghum productivity per unit area.</div></div>","PeriodicalId":100341,"journal":{"name":"Crop Design","volume":"4 3","pages":"Article 100110"},"PeriodicalIF":0.0,"publicationDate":"2025-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144679316","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 heat shock transcription factors regulate response mechanisms to abiotic stresses in plants","authors":"Yu-Xiao Wang ,&nbsp;Jian-Hong Xu","doi":"10.1016/j.cropd.2025.100109","DOIUrl":"10.1016/j.cropd.2025.100109","url":null,"abstract":"<div><div>Plants frequently encounter diverse abiotic stresses, including high temperature, low temperature, drought, salinity, and heavy metal contamination during their growth and development. These environmental challenges disrupt cellular homeostasis, impacting cell membrane stability, osmotic regulation, ionic composition, thereby leading to protein misfolding and the over-accumulation of reactive oxygen species (ROS). Heat shock transcription factors (HSFs) play a crucial role in plant stress response and adaptation by regulating the transcription of heat shock protein (HSP) genes and other stress-inducible genes. This process is integral to plant resilience against adverse conditions and other physiological functions. This review synthesizes the structure features, classification, regulatory mechanisms, and functional roles of plant HSFs in response to abiotic stresses such as high and low temperature, drought and salinity. Furthermore, we discuss future research directions, aiming to provide a theoretical guidance and genetic resources for enhancing crop stress tolerance through genetic improvement.</div></div>","PeriodicalId":100341,"journal":{"name":"Crop Design","volume":"4 3","pages":"Article 100109"},"PeriodicalIF":0.0,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144656532","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":"Qualitative and quantitative characterization of mutations and genetic diversity analysis in M2 populations of chilli (Capsicum annuum L.)","authors":"Nazarul Hasan ,&nbsp;Sana Choudhary ,&nbsp;Neha Naaz ,&nbsp;Nidhi Sharma ,&nbsp;Megha Budakoti ,&nbsp;Dinesh Chandra Joshi ,&nbsp;Mahendar Singh Bhinda ,&nbsp;Rafiul Amin Laskar","doi":"10.1016/j.cropd.2025.100108","DOIUrl":"10.1016/j.cropd.2025.100108","url":null,"abstract":"<div><div>Mutations were induced through chemical mutagens to increase the genetic variability for the development of various mutants in M₂ generation from genetic background of <em>Capsicum annuum</em> L. Main objective of this study was to identify mutants and to assess the genetic diversity in EMS, MMS, Cd(NO₃)₂ and Pb(NO₃)₂ induced M₂ populations of <em>Capsicum annuum</em> L. Mutant phenotypes were categorized into sub-categories on the basis of their plant growth and morphological ​appearance, including plant habit, leaf, flower, fruit, and root. Mean value and genetic parameters such as genetic coefficient of variance, heritability and genetic gain were evaluated in quantitative traits. Inter-population differences were also carried out through analysis of variance. Enhanced heritability and genetic advance with high genetic coefficient variation in yield attributing traits provide an opportunity for the improvement of <em>Capsicum annuum</em> L. through phenotypic selection. In the present result, enhanced mean value at lower concentrations of mutagens in quantitative traits could endorse the improvement of mutant lines over their parental lines. Numbers of fruit per plant and 1000-seed weight were main priority traits in selection of high-yielding mutants and have a strong association with yield. The cluster analysis revealed that three divergent groups of <em>Capsicum annuum</em> L. with parent genotypes in an independent group showed high efficacy of mutagens. Genetic divergence among the cluster populations provides more opportunities to use chemical mutagens for inducing heritable changes in genetic material of <em>Capsicum annuum</em> L. and for further improvement of desirable traits. Mutants selected from treatments, including EMS1, EMS2, EMS3, MMS1 and MMS2, and Pb1, Pb2, and Cd1 could be used to develop an efficient and fast crop variety with desirable traits, and the mutagen EMS and MMS are more effective than Cd(NO₃)₂ and Pb(NO₃)₂.</div></div>","PeriodicalId":100341,"journal":{"name":"Crop Design","volume":"4 3","pages":"Article 100108"},"PeriodicalIF":0.0,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144656531","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":"NLRs in plant immunity: Structural insights and molecular mechanisms","authors":"Qingshuo Gu ,&nbsp;Shasha Liu ,&nbsp;Zuhua He ,&nbsp;Xiangzong Meng ,&nbsp;Yiwen Deng","doi":"10.1016/j.cropd.2025.100103","DOIUrl":"10.1016/j.cropd.2025.100103","url":null,"abstract":"<div><div>Plants defend against pathogens by employing intracellular NLR (nucleotide-binding leucine-rich repeat) receptors to detect pathogen effectors and initiate immune responses. While some NLRs function independently, increasing evidence reveals that many NLRs act in single, pairs or within immune networks, involving cooperative or antagonistic interactions mediated by domains such as TIR, CC, or integrated decoy domains. Recent structural breakthroughs have shown how NLRs assemble into oligomeric resistosomes, such as ZAR1 and Sr35 forming Ca²⁺-permeable channels, and TNL resistosomes acting as NADases to generate signaling molecules. These molecules are sensed by EDS1–PAD4 or EDS1–SAG101 complexes, which subsequently activate helper NLRs like ADR1s and NRG1s to mediate defense signaling and cell death. Moreover, novel regulatory mechanisms and negative regulators are being uncovered. These advances offer mechanistic insights into the NLR immune network and provide valuable insight into novel <em>R</em> gene design and molecular breeding for crop disease resistance.</div></div>","PeriodicalId":100341,"journal":{"name":"Crop Design","volume":"4 2","pages":"Article 100103"},"PeriodicalIF":0.0,"publicationDate":"2025-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143855206","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":"Control of seed weight by a DNA demethylase in soybean","authors":"Mengzhu Zhang ,&nbsp;Wu Jiao ,&nbsp;Xinyu Jiang ,&nbsp;Jinhui Wang ,&nbsp;Longfei Wang ,&nbsp;Wenxue Ye ,&nbsp;Yue Wang ,&nbsp;Qingshan Chen ,&nbsp;Dawei Xin ,&nbsp;Qingxin Song","doi":"10.1016/j.cropd.2025.100102","DOIUrl":"10.1016/j.cropd.2025.100102","url":null,"abstract":"<div><div>Soybean seeds are a major source of protein and oil for human and animal nutrition. The molecular mechanisms underlying seed weight regulation, especially through epigenetic processes, are still poorly understood in soybean. Here, we reveal that a DNA demethylase gene, <em>GmDMEa</em>, underlies a genetic locus controlling seed weight through genome-wide association studies of 316 soybean accessions. Disruption of <em>GmDMEa</em> by CRISPR/Cas9 significantly increases seed weight and yield per plant accompanied with increased DNA methylation levels in the specific genomic regions which are demethylated in endosperm relative to embryo. <em>GmDMEa</em> is involved in activation of the endosperm-preferred genes that are negatively correlated with seed weight. Furthermore, DNA methylation variations induce significant changes of chromatin accessibility in endosperm. Notably, allelic variations of <em>GmDMEa</em> were artificially selected during soybean domestication. These findings reveal the role of dynamic DNA methylation in regulation of seed weight and provide a valuable gene resource for soybean breeding.</div></div>","PeriodicalId":100341,"journal":{"name":"Crop Design","volume":"4 2","pages":"Article 100102"},"PeriodicalIF":0.0,"publicationDate":"2025-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143859235","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":"Heterologous expression of a chloride transporter gene AoCLCf from Avicennia officinalis enhances salt tolerance of Arabidopsis plants","authors":"Sivamathini Rajappa ,&nbsp;Prakash Kumar","doi":"10.1016/j.cropd.2025.100101","DOIUrl":"10.1016/j.cropd.2025.100101","url":null,"abstract":"<div><div>Plant chloride transporters are pivotal for preserving turgor pressure, pH, and cellular ion balance while adapting to salinity stress. We identified a salt-responsive gene, <em>AoCLCf</em> from <em>Avicennia officinalis</em>, which belongs to the chloride channel (CLC) family, and it shares significant sequence similarity with its <em>Arabidopsis</em> counterpart, <em>AtCLCf</em>. Through functional characterization in yeast mutants and <em>Arabidopsis</em> plants, we found that <em>AoCLCf</em> expression was induced primarily in roots under salt stress. Subcellular localization revealed a salt-induced translocation of GFP-AoCLCf from the Golgi apparatus to the plasma membrane. Expression of <em>AoCLCf</em> in the <em>Saccharomyces cerevisiae</em> mutant strain <em>Δgef1</em> helped to rescue the growth of the mutant at high NaCl concentrations (up to 1.25M). Moreover, constitutive expression of <em>AoCLCf</em> in wild-type <em>Arabidopsis</em> significantly enhanced salt tolerance, as evidenced by increased seed germination rates, and improved seedling growth (greater root and shoot length) under 150 ​mM NaCl treatment. Spectrofluorimetric assays using liposomes embedded with recombinant AoCLCf protein showed that it functions as a chloride channel. These findings underscore the pivotal role of AoCLCf in improving salt stress tolerance through the maintenance of cellular ion homeostasis.</div></div>","PeriodicalId":100341,"journal":{"name":"Crop Design","volume":"4 2","pages":"Article 100101"},"PeriodicalIF":0.0,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143859234","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}