Crop Design最新文献

{"title":"Unveiling the potential: BZR1-mediated resistance to sheath blight and optimized agronomic traits in rice","authors":"Huan Chen , Tiange Zhou , Xinrui Li , 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}

{"title":"Understanding the molecular breeding and omics approaches for finger millet (Eleusine coracana L.) improvement towards a global sustainable nutritional security","authors":"Salma Kayastha ,&nbsp;Jyoti Prakash Sahoo ,&nbsp;Manaswini Mahapatra ,&nbsp;Narayan Panda","doi":"10.1016/j.cropd.2023.100049","DOIUrl":"10.1016/j.cropd.2023.100049","url":null,"abstract":"<div><p>Finger millet (<em>Eleusine coracana</em> L.) has gained notable interest in recent times for its capacity to tackle global challenges related to nutritional security and sustainability. This review delves into the critical issue of global nutritional security by focusing on Finger millet, as an essential staple crop known for its rich nutraceutical content. However, due to the expanding global population and the imperative for sustainable food sources, there is an urgent need to elevate the nutritional content of crops such as Finger millet. This review also utilizes molecular breeding and omics methodologies, encompassing genomics, transcriptomics, proteomics, and metabolomics, to thoroughly examine the molecular dimensions involved in enhancing the nutraceutical content and other crucial agronomic traits in Finger millet. These cutting-edge techniques provide insights into the genetic makeup and expression of key genes related to nutrient accumulation and distribution during grain development, as well as for other important agronomic traits. Moreover, this review also emphasizes the importance of sustainable agricultural practices to ensure the long-term availability of nutrient-rich crops like Finger millet. However, by harnessing the power of genetics and advanced analytical genomic tools, researchers can pave the way for the development of Finger millet varieties, contributing to a more sustainable and nutritious food security for the growing world population.</p></div>","PeriodicalId":100341,"journal":{"name":"Crop Design","volume":"3 1","pages":"Article 100049"},"PeriodicalIF":0.0,"publicationDate":"2023-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2772899423000277/pdfft?md5=ef3fc16e735afad0d2f10e2940258d96&pid=1-s2.0-S2772899423000277-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138625719","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":"Controlled Environment Ecosystem: A plant growth system to combat climate change through soilless culture","authors":"Avinash Sharma ,&nbsp;Mainu Hazarika ,&nbsp;Punabati Heisnam ,&nbsp;Himanshu Pandey ,&nbsp;V.S. Devadas ,&nbsp;Mannu Wangsu","doi":"10.1016/j.cropd.2023.100044","DOIUrl":"10.1016/j.cropd.2023.100044","url":null,"abstract":"<div><p>The variations in climatic factors can lead to morphological changes like male sterility, self-incompatibility, embryo abortions, poor seed setting, low nutrient content, growth retardation, yield loss and even crop failure of agricultural or horticultural crops under open land ecosystem. The traditional agricultural systems involve using a large quantity of water on a large arable land, along with a lot of agro chemicals, which can lead to leaching of nutrients and chemical residues into the soil and water bodies, insect competition, weed emergence, or soil erosion. The controlled environment plant growth chamber reserves 80 ​% land use, 90 ​% water use and runs off or translocates nutrients more efficiently than traditional agriculture. The controlled environment plant growth chamber utilizes standard nutrient diffusion for plant growth and regulates stable nutrient use efficiency, water use efficiency, photosynthetic assimilation product, metabolic use efficiency, climatic factors, greenhouse gases emission, carbon sequestration, carbon foot print with the mechanistic model with machine learning examines critical or non critical levels, dynamics and influences of water, climate and nutrient in controlled environment system. The controlled environment plant growth chamber enables production of outstanding physical and chemical quality enriched plants. The controlled environment witnesses the combat against climate change and the restoration or conservation of natural resources, as well as the generation of research, employment, and industrial development. More comparative investigations are required to understand and justify climate combating with major plants in controlled environment ecosystem and natural environment ecosystem with or without soil.</p></div>","PeriodicalId":100341,"journal":{"name":"Crop Design","volume":"3 1","pages":"Article 100044"},"PeriodicalIF":0.0,"publicationDate":"2023-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2772899423000228/pdfft?md5=b9597ed4041e88364ab3fb2038fa6c73&pid=1-s2.0-S2772899423000228-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139291324","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}