Crop Design最新文献

{"title":"Enhancing rangeland weed detection through convolutional neural networks and transfer learning","authors":"","doi":"10.1016/j.cropd.2024.100060","DOIUrl":"10.1016/j.cropd.2024.100060","url":null,"abstract":"<div><p>The detection of weed species in rangeland environments is a challenging task due to various factors such as dense, variable species vegetation, ocular occlusion, and a wide variety of plant morphology. Most research in weed detection, however, focuses on croplands. This research addresses the need for accurate rangeland weed detection models by leveraging convolutional neural network (CNN) models enhanced with transfer learning applied to the DeepWeeds data set taken in situ in regional North Eastern Australia. It investigates the effectiveness of transfer learning across seven popular models, utilizing data augmentation and fine-tuning. The performance of these models was evaluated using accuracy metrics and compared against each other. The results demonstrated that transfer learning, coupled with fine tuning, could be a viable solution for generating efficient weed plant detection models with lower demands on computational resources and smaller datasets, despite the challenging conditions of rangeland environments. EfficientNetV2B1 had the highest classification accuracy of 94.2 ​%, and lowest training times. Moreover, high levels of accuracy were also achieved using InceptionV3, VGG16, and Densenet121, albeit with a training time penalty. This research provides insights into the performance of CNN models in challenging rangeland environments, demonstrates the potential of using transfer learning to enhance weed detection models, and underscores the significance of model selection in agricultural applications of CNNs.</p></div>","PeriodicalId":100341,"journal":{"name":"Crop Design","volume":"3 3","pages":"Article 100060"},"PeriodicalIF":0.0,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2772899424000090/pdfft?md5=b5ed423e593946c009845b48ef4441bf&pid=1-s2.0-S2772899424000090-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141414283","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Modeling reveals synergies among root traits for phosphorus acquisition in pearl millet","authors":"","doi":"10.1016/j.cropd.2024.100059","DOIUrl":"10.1016/j.cropd.2024.100059","url":null,"abstract":"<div><p>Pearl millet is a key food security grain crop in the world's drylands due to its tolerance to abiotic stresses. However, its yield remains low and is negatively impacted by climate change. Root phenes are potential targets to improve crop productivity and resilience to environmental stress. However, the sheer number of combinations resulting from interactions of multiple phenes is a challenge for empirical research. <em>In silico</em> approaches are a plausible alternative to assess the utility of different phene combinations in varying states over diverse environmental contexts. Here, we developed an implementation of the functional-structural plant/soil model – OpenSimRoot, for pearl millet in typical sub-Sahelian soil and environmental conditions. Root architectural, anatomical, and physiological parameters were measured using a popular pearl millet variety (Souna 3) and implemented in the model. The above-ground biomass and root length density predicted by the model were similar to data from field trials. The utility of different root phenes was then evaluated for improved phosphorus uptake and plant growth in P deficient soils. Doubled root hair length and density, shallower root angle (−15°) and doubled long lateral root density were found to improve plant growth by 76 ​%, 33 ​% and 33 ​% respectively under low P conditions. Moreover, these phenes showed synergism when combined <em>in silico</em> and led to optimal biomass production in low P supply conditions that resulted in a 75 ​% loss of biomass in the reference variety. Our study suggests that these phenotypes could be targeted to improve biomass production in pearl millet and consequently its yield in low-P availability conditions.</p></div>","PeriodicalId":100341,"journal":{"name":"Crop Design","volume":"3 3","pages":"Article 100059"},"PeriodicalIF":0.0,"publicationDate":"2024-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2772899424000089/pdfft?md5=5549435158853fc7a243a39138f2ab18&pid=1-s2.0-S2772899424000089-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141394433","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unveiling the potential: BZR1-mediated resistance to sheath blight and optimized agronomic traits in rice","authors":"Huan Chen ,&nbsp;Tiange Zhou ,&nbsp;Xinrui Li ,&nbsp;Yuan Hu Xuan","doi":"10.1016/j.cropd.2024.100061","DOIUrl":"10.1016/j.cropd.2024.100061","url":null,"abstract":"","PeriodicalId":100341,"journal":{"name":"Crop Design","volume":"3 3","pages":"Article 100061"},"PeriodicalIF":0.0,"publicationDate":"2024-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2772899424000107/pdfft?md5=83a156156b495e953da9549242e1864f&pid=1-s2.0-S2772899424000107-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141390469","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The pentatricopeptide repeat protein TCD6 functions RNA editing and cleavage of ndhA and is required for chloroplast development in early rice seedlings","authors":"Yunguang Sun ,&nbsp;Licheng Kuang ,&nbsp;Jinglin Wang ,&nbsp;Mengshuang Gu ,&nbsp;Yu Chen ,&nbsp;Xiaobiao Pan ,&nbsp;Dongzhi Lin ,&nbsp;Yanjun Dong","doi":"10.1016/j.cropd.2024.100063","DOIUrl":"10.1016/j.cropd.2024.100063","url":null,"abstract":"<div><p>Pentatricopeptide repeat (PPR) proteins compose one of the largest protein families in higher plants and play a role in regulating organellar gene expression. In this study, we discovered that a new rice mutant <em>tcd6</em> exhibited albino phenotype and aberrant chloroplast before the three-leaf (autotrophic) seedling stage. Through Map-based cloning and complementation tests, it was shown that <em>TCD6</em> encodes a chloroplast-located PPR protein, with 14 PPR motifs and an atypical DYW-like motif. In addition, the disruption of <em>TCD6</em> hindered the nuclear-encoded polymerase (NEP)-dependent transcript levels for plastid genes and led to defects in the cleavage and editing of <em>ndhA</em> (encoding NDH subunit<em>)</em> in early <em>tcd6</em> mutant seedlings. Taken together, our results indicate that <em>TCD6</em> is indispensable for chloroplast development and involves in RNA editing and cleavage of <em>ndhA</em> during early seedling (autotrophic) growth of rice.</p></div>","PeriodicalId":100341,"journal":{"name":"Crop Design","volume":"3 3","pages":"Article 100063"},"PeriodicalIF":0.0,"publicationDate":"2024-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2772899424000120/pdfft?md5=cd0814ee0897a0f12002e6c622df607b&pid=1-s2.0-S2772899424000120-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141407249","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development and application of transcriptomics technologies in plant science","authors":"Han Wang ,&nbsp;Yueting Xu ,&nbsp;Zhizhong Zhang ,&nbsp;Guoping Zhang ,&nbsp;Cong Tan ,&nbsp;Lingzhen Ye","doi":"10.1016/j.cropd.2024.100057","DOIUrl":"10.1016/j.cropd.2024.100057","url":null,"abstract":"<div><p>Over the past decade, bulk RNA sequencing (RNA-seq) has become an indispensable tool in molecular biology, and have made the novel development, with two innovative methodologies being developed, single-cell RNA sequencing (scRNA-seq) technology and spatial transcriptome (ST) technology. The scRNA-seq technology allows researchers to analyze gene expression in individual cells, providing more detailed information relative to the past technologies. Meanwhile, ST technology overcomes the limitations of single-cell sequencing in terms of loss of spatial information, enabling scientists to better understand the spatial distribution of gene expression within tissues. These advancements of transcriptomics technologies revolutionize the field of genomics and have been widely used in disease diagnosis and medicine. However, they are less utilized in plant research. This review describes the development, advantage and limitations of three transcriptomics technologies, and presents their applications in plant sciences.</p></div>","PeriodicalId":100341,"journal":{"name":"Crop Design","volume":"3 2","pages":"Article 100057"},"PeriodicalIF":0.0,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2772899424000065/pdfft?md5=268790ea3d3b1417800694d53dc269d9&pid=1-s2.0-S2772899424000065-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140463519","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Balancing disease resistance and yield Stability: BGL overexpression in rice for resistance against sheath blight and rice blast","authors":"Jingmiao Liu ,&nbsp;Yuan Hu Xuan ,&nbsp;Tiange Zhou","doi":"10.1016/j.cropd.2024.100062","DOIUrl":"https://doi.org/10.1016/j.cropd.2024.100062","url":null,"abstract":"<div><p>Diseases in rice is a major factor that affects both the yield and quality of the crop. ​The central focus of our study is the investigation of overexpression of BGLs in rice and its remarkable impact on resistance against two prevalent and destructive diseases in rice, namely, sheath blight and rice blast. The overexpression of BGLs exhibited resistance against both these diseases, addressing a critical concern in rice production. Additionally, despite increased resistance, rice yields remained stable, indicating that BGL overexpression may offer a practical solution for integrated disease management without compromising productivity.</p></div>","PeriodicalId":100341,"journal":{"name":"Crop Design","volume":"3 2","pages":"Article 100062"},"PeriodicalIF":0.0,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2772899424000119/pdfft?md5=e5b99a9957c6f4d082117e0494222c91&pid=1-s2.0-S2772899424000119-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141328874","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bacteria manipulate autophagy through acetylation in both fungi and plants","authors":"Sung Un Huh","doi":"10.1016/j.cropd.2024.100058","DOIUrl":"10.1016/j.cropd.2024.100058","url":null,"abstract":"","PeriodicalId":100341,"journal":{"name":"Crop Design","volume":"3 2","pages":"Article 100058"},"PeriodicalIF":0.0,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2772899424000077/pdfft?md5=f6a88ea83126eb85bccd1b3cd4518685&pid=1-s2.0-S2772899424000077-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140275957","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"OMICS strategies: Revealing the enigma of salinity tolerance in mangroves","authors":"K. Henna Parveen,&nbsp;Jumana Muhammed,&nbsp;V.K. Sneha,&nbsp;P. Busheera,&nbsp;Anu Augustine","doi":"10.1016/j.cropd.2024.100052","DOIUrl":"10.1016/j.cropd.2024.100052","url":null,"abstract":"<div><p>Salinity is a significant challenge for agriculture, negatively impacting soil health and crop yields worldwide. Coping with salinity stress is intricate due to its multifaceted nature, making it challenging to fully grasp. Mangroves, recognized for their salt tolerance, thrive in diverse salinity levels, spanning from freshwater to seawater. They play a vital role in coastal ecosystems, thriving in areas where many other plants struggle. For a thorough knowledge of the salinity stress signaling and tolerance mechanism in mangroves, a variety of “omics” techniques have been explored. Recent research has illuminated crucial pathways, transcription factors, microRNAs, and signaling components in mangroves exposed to salty conditions. This knowledge holds promise for developing salt-tolerant crop plants through genetic modification techniques, which can help address the increasing issue of soil salinity. Our review encompasses genomics and transcriptomics studies that identify crucial genes and pathways in mangroves' response to salinity. Since the transcriptome lacks a direct correlation with the protein expression dynamics, we have also emphasized mangrove proteomics and metabolomics studies. The review also outlines the different strategies that can be used to enhance the salinity tolerance of crops using mangroves as models.</p></div>","PeriodicalId":100341,"journal":{"name":"Crop Design","volume":"3 2","pages":"Article 100052"},"PeriodicalIF":0.0,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2772899424000016/pdfft?md5=22d6ee653fdea040d2e86568bf24bab8&pid=1-s2.0-S2772899424000016-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140468290","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular docking insights into nuclear factor Y (NF-Y) transcription factor and pyrabactin resistance 1 (PYL) receptor proteins reveal abiotic stress regulation in finger millet","authors":"Varsha Rani ,&nbsp;Vinay Kumar Singh ,&nbsp;D.C. Joshi ,&nbsp;Rajesh Singh ,&nbsp;Dinesh Yadav","doi":"10.1016/j.cropd.2023.100051","DOIUrl":"10.1016/j.cropd.2023.100051","url":null,"abstract":"<div><p>Finger Millet (<em>Eleusine coracana -</em> (L.) Gaertn), is an important nutraceutical crop with the potential for imparting food and nutritional security. These plants have a comparatively higher tolerance for several abiotic stresses like drought, salinity, and heat. Several players including Transcription Factor (TF) like Nuclear Factor Y (NF-Y) might be associated with this enhanced level of tolerance. Further, it is unclear how phytohormones like Abscisic acid (ABA) regulate the expression of NF-Y, whether in ABA-dependent or ABA-Independent pathway. The interaction of PYL (Pyrabactin resistance1-like) receptor proteins with Nuclear Factor Y (NF-Y) Transcription Factor in the presence of phytohormones like abscisic acid (ABA) provides one insight related to the enhanced tolerance towards abiotic stresses under ABA-dependent signaling in finger millet crop. A total of three PYL receptors of finger millet designated as EcPYL1, EcPYL5, and EcPYL9 were retrieved in the finger millet genome. These receptors were modeled through the SWISS-MODEL using templates 5gwo and 3wg8 and docked with ABA. The best-docked protein-ligand complex PYL5-ABA (binding energy ΔG ​= ​-8.8 kcal mol^-1) was found to be most stable at the 50ns MD simulation study. Further protein-protein interaction between PYL5 and NF-YA2/B3/C1 sub-family members showed a good interaction. This clearly indicates the possibility of the NF-Y-PYL module in the ABA transduction pathway, which performs a crucial role in the expression of stress-responsive genes. These studies reveal the intricate relationship between the ABA, PYL receptors of finger millet, and NF-Y transcription factor in regulating the stress-responsive genes and provide an insight into the abiotic stress tolerance mechanisms, which can be targeted for crop improvement.</p></div>","PeriodicalId":100341,"journal":{"name":"Crop Design","volume":"3 1","pages":"Article 100051"},"PeriodicalIF":0.0,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2772899423000290/pdfft?md5=377fe0f6fe5b520a892715bbc5d32b47&pid=1-s2.0-S2772899423000290-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139127488","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic exploration and functional insights into the diversification of the Snf2 gene family in subgenomes of Triticum aestivum","authors":"Muhammad Fahad ,&nbsp;Chuanjia Liu ,&nbsp;Yuxin Shen ,&nbsp;Muhammad Sajid ,&nbsp;Liang Wu","doi":"10.1016/j.cropd.2023.100050","DOIUrl":"10.1016/j.cropd.2023.100050","url":null,"abstract":"<div><p>Sucrose nonfermenting 2 (Snf2) family proteins function as the ATP-dependent catalytic engines of chromatin remodeling complexes, which harness ATP hydrolysis energy to alter chromatin structure and nucleosome positioning, enabling regulatory factor access to DNA. Plant genomes contain numerous Snf2 family proteins, several of which have been demonstrated to act as key developmental regulators at different stages in model plants like Arabidopsis and rice. Despite their vital roles, the <em>Snf2</em> genes in <em>Triticum aestivum</em> remain largely uncharacterized. Here, we report the identification of 112 wheat <em>Snf2</em> genes that were unevenly distributed across the 21 chromosomes, with 40 genes on the A subgenome, 33 on the B subgenome, and 39 on the D subgenome, and phylogenetically classified these <em>Snf2</em> genes into 18 subfamilies related to the 6 Snf2 groups in Arabidopsis. Evolutionary analysis revealed that purifying selection has largely driven the evolution of <em>Snf2</em> genes, acting as the primary selective force shaping the <em>Snf2</em> gene family in wheat, while segmental duplications have served as the main mechanism for expanding the gene family. All identified Snf2 proteins contained at least one Helicase_C and SNF2_N domain among 10 conserved domains, and their gene structures consisted of 3–38 exons. Tissue-specific expression analysis uncovered distinct expression patterns among <em>Snf2</em> gene family members, including some with enhanced reproductive tissue expression, while analysis under various abiotic and biotic stresses revealed differential regulation of specific family members in response to these conditions. Overall, these systematic analyses including identification, evolutionary relationships, and expression profiling provide valuable insights into the wheat Snf2 family while establishing a genomic framework to elucidate Snf2 functional roles in wheat growth, development, and stress responses.</p></div>","PeriodicalId":100341,"journal":{"name":"Crop Design","volume":"3 1","pages":"Article 100050"},"PeriodicalIF":0.0,"publicationDate":"2023-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2772899423000289/pdfft?md5=4b4ddd09e117ea839bd12764824bf75f&pid=1-s2.0-S2772899423000289-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139018768","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}