Crop Design最新文献

{"title":"Evaluation of different sesame varieties cultivated under saline conditions in the southwestern coastal region of Bangladesh","authors":"Md Shihab Uddine Khan ,&nbsp;Md Moshiur Rahman ,&nbsp;Arup Ratan Basak ,&nbsp;Prodipto Bishnu Angon ,&nbsp;Sadia Afroz Ritu ,&nbsp;Milon Kobir ,&nbsp;Md Riazul Islam","doi":"10.1016/j.cropd.2024.100093","DOIUrl":"10.1016/j.cropd.2024.100093","url":null,"abstract":"<div><div>Sesame (<em>Sesamum indicum</em> L.) is widely used in many cooking techniques worldwide, and it is known as the \"queen of oilseeds\" because it contains polyunsaturated lipids that prevent oxidative rancidity and carry oil content up to 60%. The salty portions of the country have much lower agricultural yields, cropping intensities, and productivity than the rest of the country. In this paper, we compared the variations of yield performance and salinity torelance between modern and local sesame varieties to select the best-performing varieties under saline conditions in the southwestern coastal region of Bangladesh. The field experiment had been performed during the Kharif-1 season (mid-March to mid-July) of 2022 ​at the BINA (Bangladesh Institute of Nuclear Agriculture) substation farm, Satkhira. Four BINA varieties and two BARI (Bangladesh Agricultural Research Institute) varieties developed sesame varieties, and one local variety, viz. Binatil-1, Binatil-2, Binatil-3, Binatil-4, BARI Til-3, BARI Til-4 and Lal Til (Batiaghata local) were tested under saline conditions. A randomized complete block design was utilized, with three replications of each variety across the experimental field. The greatest plant height (92.00 ​cm) was found in BARI Til-3, whereas the lowest was observed in Binatil-3. BARI Til-4 had the highest number of branches per plant (4.55), whereas the lowest was found in Binatil-1. The highest number of capsules (22.22) was shown in Binatil-3, and the lowest was found in Binatil-1. The maximum number of seeds in capsule^-1 (72.55) was demonstrated by Lal Til, and the minimum was observed in BARI Til-4. The Lal Til variety presented the highest seed yield (1.25 ​ha^-1), whereas the Binatil-1 variety presented the lowest seed yield. These results indicate that the Lal Til variety performed better in yield. It may be cultivated in the Satkhira region under saline circumstances and used as breeding material for future breeding programs. These findings are highly important for the future of sesame cultivation in Bangladesh and other saline-prone areas.</div></div>","PeriodicalId":100341,"journal":{"name":"Crop Design","volume":"4 1","pages":"Article 100093"},"PeriodicalIF":0.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143105204","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":"Analysis of CYP701A1 genes in gossypium species and functional characterization through gene silencing","authors":"Zhao Liang ,&nbsp;Di Jiachun ,&nbsp;Guo Qi ,&nbsp;Xu Zhenzhen ,&nbsp;Zhao Jun ,&nbsp;Xu Peng ,&nbsp;Xu Jianwen ,&nbsp;Liu Jianguang ,&nbsp;Shen Xinlian ,&nbsp;Chen Xusheng","doi":"10.1016/j.cropd.2024.100081","DOIUrl":"10.1016/j.cropd.2024.100081","url":null,"abstract":"<div><div>Gibberellins (GA) are known to play crucial roles in various aspects of plant growth and development. The cytochrome P450 enzyme family is recognized for its significance in plant metabolic processes. Specifically, CYP701s, a subgroup of CYP71, encode <em>ent</em>-kaurene oxidase in the gibberellin synthesis pathway. In this study, we analyzed genomic data from 30 <em>Gossypium</em> species, including nine allotetraploid genomes (AD1-AD7, with two each for AD1 and AD2), 21 diploid genomes (A-G, K, with two A-genomes and 12 D-genomes), and <em>Gossypioides kirkii</em> genome as an outgroup for evolutionary analysis, totaling 31 genomes. Subsequently, 40 <em>CYP701A1</em> genes were identified from various genomes and conducted a comprehensive analysis of their structure and evolution. Virus-induced gene silencing (VIGS) technology was utilized to knock out the <em>GhCYP701A1</em> gene in <em>Gossypium hirsutum</em> ac TM-1. Subsequent analysis revealed changes in hormone content, with decreased gibberellin levels and notable increases in auxin, cytokinin, and jasmonic acid contents. Conversely, salicylic acid content decreased, while the precursor for ethylene synthesis, 1-aminocyclopropane-1-carboxylic acid (ACC), remained relatively stable. Transcriptome analysis of the gene silencing plants identified 15,962 differentially expressed genes, including 8376 upregulated and 7586 downregulated genes. Enrichment analysis through KEGG pathway highlighted ‘Plant hormone signal transduction’ as a prominent pathway with 234 differentially expressed genes. The study provided insights into the function and regulatory network of the gene.</div></div>","PeriodicalId":100341,"journal":{"name":"Crop Design","volume":"4 1","pages":"Article 100081"},"PeriodicalIF":0.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143105207","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":"Advance technologies for DNA-protein interactions and future research prospect","authors":"Chengyi Qu ,&nbsp;Hao Du","doi":"10.1016/j.cropd.2024.100082","DOIUrl":"10.1016/j.cropd.2024.100082","url":null,"abstract":"<div><div>DNA-protein interactions (DPIs) are essential for genome functioning, with billions of years of evolution shaping specific patterns of protein-DNA interactions to regulate gene networks in response to various stimuli. Over the years, scientists have developed numerous techniques to study these interactions. This review provides a historical overview of these methods, highlighting their advantages and disadvantages and offering the examples of recent applications. Our aim is to help researchers select the most appropriate technique on the basis of their working goals and capabilities. For the experimental design of DPIs assays, several kinds of techniques are relatively quicker or/and simpler, the precision and accuracy of these methods must be carefully considered to verify the DNA-protein interaction. The review also discusses the recent advances in the computational approaches for predicting DNA-protein bindings and diverse reporting systems.</div></div>","PeriodicalId":100341,"journal":{"name":"Crop Design","volume":"4 1","pages":"Article 100082"},"PeriodicalIF":0.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143135730","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":"Genome-wide association study and candidate gene identification for the cold tolerance at the seedling stage of rapeseed (Brassica napus L.)","authors":"Guangyu Wu,&nbsp;Yanda Zhou,&nbsp;Jingyi Zhang,&nbsp;Mengjie Gong,&nbsp;Lixi Jiang,&nbsp;Yang Zhu","doi":"10.1016/j.cropd.2024.100083","DOIUrl":"10.1016/j.cropd.2024.100083","url":null,"abstract":"<div><div>Rapeseed (<em>Brassica napus</em> L.) is an important overwintering oilseed crop and suffers from severe cold stress during the seedling stage, due to the increasingly delayed sowing in the Yangtze river basin. However, the genetic basis underlying cold tolerance in rapeseed seedlings is not well understood. In this study, we observed the cold tolerance of 217 rapeseed accessions in the field and found a significant negative correlation between cold tolerance grades and malondialdehyde (MDA) content. A genome-wide association study (GWAS) of cold tolerance grades identified four significant loci in the genomic region of one MYB transcription factor <em>BnaA8.MYB60</em>. Furthermore, field accessions with <em>BnaA8.MYB60</em> ^Hap1 exhibited significantly higher cold tolerance and lower expression of <em>BnaA8.MYB60</em> compared to the majority of accessions with <em>BnaA8.MYB60</em> ^Hap2. These results suggested that variation in the genomic sequences of <em>BnaA8.MYB60</em> caused the divergence of gene expression levels and functions on cold tolerance in rapeseed seedlings. This study could provide the theoretical guidance for the breeding of cold-tolerant rapeseed varieties.</div></div>","PeriodicalId":100341,"journal":{"name":"Crop Design","volume":"4 1","pages":"Article 100083"},"PeriodicalIF":0.0,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143105206","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":"Genome-wide association study identifies loci and candidate genes for root traits in rice grown in Brazil","authors":"Gabriel Brandão das Chagas ,&nbsp;Latóia Eduarda Maltzahn ,&nbsp;Josiane Vargas de Oliveira Maximino ,&nbsp;Viviane Kopp da Luz ,&nbsp;Ariano Martins de Magalhães Junior ,&nbsp;Antonio Costa de Oliveira ,&nbsp;Luciano Carlos da Maia ,&nbsp;Camila Pegoraro","doi":"10.1016/j.cropd.2025.100095","DOIUrl":"10.1016/j.cropd.2025.100095","url":null,"abstract":"<div><div>Rice is a staple food for more than half of the world's population. In Brazil, this crop plays an important role in consumption, production and economy. Root system is a key trait for rice yield, as it is responsible for water uptake, absorption, transportation of nutrients from soil, and other vital functions. Root dry weight (RDW) and root length (RL) are related to crop yields. Understanding molecular basis of rice root traits is a strategy to help breeders develop genotypes with higheryield. However, few studies using Brazilian germplasm have been developed. Therefore, the objective of this research was to map genome regions responsible for root dry weight and length in adult rice plants grown in Southern of Brazil. Genome-wide association study (GWAS) was applied using 7098 single nucleotide polymorphism (SNPs) markers and a collection of 188 rice genotypes. Seven SNP markers for root length and four markers for root dry weight were detected. Genes encoding myeloblastosis (MYB) transcription factor, cinnamyl alcohol dehydrogenase, cyclin-dependent protein kinase (Cdk)-activating kinase were associated with root length. Amidst the genes related to root dry weight, those encoding cellulose synthase, lipid transfer protein, Receptor-like cytoplasmic kinase and CCCH-type zinc finger protein associated with drought tolerance were identified. This study provides insights of genetic control of rice root traits considering as a panel composed mainly of Brazilian genotypes. The rice breeders can apply this knowledge to guide for further research and develop new cultivars in Brazil.</div></div>","PeriodicalId":100341,"journal":{"name":"Crop Design","volume":"4 2","pages":"Article 100095"},"PeriodicalIF":0.0,"publicationDate":"2025-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143855205","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":"Comparative interactomics build the bridges from micromolecules to biological behaviour and morphology","authors":"Jinwen Chen","doi":"10.1016/j.cropd.2024.100078","DOIUrl":"10.1016/j.cropd.2024.100078","url":null,"abstract":"<div><div>Behaviour, morphology and responses to stimuli in biological systems are determined by the genetic information of different types of biomolecules and the interactions between them. Comparative interactomics, the discipline devoted in comparing two or more interaction networks that happen in different species or under different cellular conditions, is a powerful tool for understanding systems evolution and the complex relationships that control cellular processes. This review provides an overview of data sources and research methods for comparative interactomics and the current directions in the application of comparative interactomics are summarised in brief. We also highlight the potential challenges of comparative interactomics in terms of interaction detection, noise delineation, alignment algorithms and quantitative network upgrading. We provide insights for future studies of network evolution using more accurate experimental and informative methodologies, with the hope that comparative interactomics to be further developed and build the study bridges from micromolecules to biological phenotypes.</div></div>","PeriodicalId":100341,"journal":{"name":"Crop Design","volume":"3 4","pages":"Article 100078"},"PeriodicalIF":0.0,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142592937","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":"Strategizing pigeonpea for enhancing health-benefitting traits: A path to nutritional advancements","authors":"Jwala Pranati ,&nbsp;Vaishnavi Chilakamarri ,&nbsp;Ashwini Kalyan ,&nbsp;H.B. Shruthi ,&nbsp;Naresh Bomma ,&nbsp;Kalenahalli Yogendra ,&nbsp;Prakash Gangashetty","doi":"10.1016/j.cropd.2024.100068","DOIUrl":"10.1016/j.cropd.2024.100068","url":null,"abstract":"<div><div>Nutritional security is the key objective of India's 2030 Vision and UN Sustainable Development Goal 3. Although the world has made progress towards food security, there is still work to be done in assuring nutrition for all. While millions of people worldwide suffer from protein energy malnutrition and micronutrient deficiencies, providing nutrient-rich foods offers a long-term solution. Pigeonpea is a major daily diet of developing and undeveloped nations covering Asian and African households and increasing its protein and micronutrient (iron and zinc content) is a feasible approach. Thus, this review focusses on strategizing how pigeonpea could provide nutritional assurance in the coming decade. It primarily summarizes the dietary profile, health advantages, and anti-nutritional factors that hinder pigeonpea. Furthermore, it delineates the current progress through conventional breeding and molecular tools, while providing strategies to amalgamate advances in transgenics, omics and rapid generation advancement platforms to enhance health-benefitting traits and tackling the anti-nutritional factors contributing potentially towards the nutritional security.</div></div>","PeriodicalId":100341,"journal":{"name":"Crop Design","volume":"3 4","pages":"Article 100068"},"PeriodicalIF":0.0,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141851295","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":"Genetic improvement of medicinal and aromatic plant species: Breeding techniques, conservative practices and future prospects","authors":"Nazarul Hasan ,&nbsp;Rafiul Amin Laskar ,&nbsp;Shahabab Ahmad Farooqui ,&nbsp;Neha Naaz ,&nbsp;Nidhi Sharma ,&nbsp;Megha Budakoti ,&nbsp;Dinesh Chandra Joshi ,&nbsp;Sana Choudhary ,&nbsp;Mahendar Singh Bhinda","doi":"10.1016/j.cropd.2024.100080","DOIUrl":"10.1016/j.cropd.2024.100080","url":null,"abstract":"<div><div>Throughout history, herbal medicine has played a vital role in understanding and treating various ailments in humans and animals. The medicinal aromatic plant species, with their chemical compounds, offer potential solutions for addressing numerous diseases. Enhancing the genetic makeup of these plant species for both medicinal and economic purposes is now imperative. Mutation breeding is a significant strategy, having led to the development of nearly 3500 plant species. Polyploidy induction, doubling chromosomes, can result in larger and more valuable plant parts with medicinal and economic value. Plant tissue culture (PTC) is a crucial breeding technique, allowing for artificial polyploidy and Agrobacterium-mediated gene transformation to manipulate medicinal plant genomes, producing pharmaceutical secondary metabolites. The introduction of the third-generation clustered regularly interspaced short repeats (CRISPR)-Cas9 gene editing system has enabled the correction of defects seen in the first- and second-generation gene editing technologies, which relied on synthetic endonucleases like zinc finger endonuclease (ZFN) and transcription activator-like receptor nuclease (TALEN). These gene editing methods facilitate the manipulation of secondary metabolite pathways in medicinal plants. Virus-induced gene silencing (VIGS) based on short interfering RNA-mediated RNA silencing provides a rapid alternative for knocking out gene expression in medicinal and aromatic plant species that may not easily undergo stable genetic transformation. This article offers an overview of global trends, advancements, and prospects in conserving and breeding of medicinal aromatic plants, and helping as a valuable reference for sustainable resource utilization.</div></div>","PeriodicalId":100341,"journal":{"name":"Crop Design","volume":"3 4","pages":"Article 100080"},"PeriodicalIF":0.0,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142586629","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":"Smart farming: Leveraging IoT and deep learning for sustainable tomato cultivation and pest management","authors":"Md Rakibul Hasan ,&nbsp;Md. Mahbubur Rahman ,&nbsp;Fahim Shahriar ,&nbsp;Md. Saikat Islam Khan ,&nbsp;Khandaker Mohammad Mohi Uddin ,&nbsp;Md. Mosaddik Hasan","doi":"10.1016/j.cropd.2024.100079","DOIUrl":"10.1016/j.cropd.2024.100079","url":null,"abstract":"<div><p>Since the world's population is rising continuously, more cultivable land is being utilized for their dwellings. As a result, the amount of food supply is decreasing day by day. In order to address the food shortage, a proper plan and technological breakthroughs is must. Tomato is a kind of vegetable which has the healthy ingredients and essential for our daily food list. The proposed system suggests an IoT based tomato cultivation and pest management system, with the help of deep learning methods. In the IoT implementation, camera module and moisture sensor are used to collect images of tomato plant, soil condition respectively. Based on the moisture content, the water pump will supply the water when it necessary. Besides, the real-time images of tomato leaf will be sent to the server to identify and classify natural enemies like various insect species. In the proposed system seven types of pests are identified with the help of ten deep learning models like InceptionV3, Xception, InceptionResNetV2, MobileNet, MobileNetV2, MobileNetV3Large, MobileNetV3Small, DenseNet121, DenseNet169, DenseNet201. This study has trained with leaves and insects separately to identify whether an image from a tomato plant is insectoid or not. 458 images of pests and 912 images of leaves are utilized in the proposed architecture. The accuracy of classifying insects or leaves using DenseNet201 is 100 ​%. The highest accuracy of 94 ​% is obtained to classify the different insects using the DenseNet201 model.</p></div>","PeriodicalId":100341,"journal":{"name":"Crop Design","volume":"3 4","pages":"Article 100079"},"PeriodicalIF":0.0,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2772899424000284/pdfft?md5=ab87dbf1526aea0dc25c64f64cff8542&pid=1-s2.0-S2772899424000284-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142243238","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":"A novel multi trait genotype ideotype distance index (MGIDI) for genotype selection in plant breeding: Application, prospects, and limitations","authors":"Pinki Debnath ,&nbsp;Kakon Chakma ,&nbsp;M. Shafi Ullah Bhuiyan ,&nbsp;Reshma Thapa ,&nbsp;Ronghui Pan ,&nbsp;Delara Akhter","doi":"10.1016/j.cropd.2024.100074","DOIUrl":"10.1016/j.cropd.2024.100074","url":null,"abstract":"<div><p>The Multitrait Genotype Ideotype Distance Index (MGIDI) is a strong and adaptable technique for choosing superior genotypes of diverse crops based on numerous attributes. It is a multivariate selection indicator that incorporates different characteristic information into a single value and ranks genotypes based on their distance from an ideal genotype. Breeders can use variable selection criteria including weighting traits and assessing genetic strengths and weaknesses. It organizes attributes into components and chooses optimal genotypes based on many traits using principal component analysis. This review covered the available information regarding the background, applications, prospects, and limitations of MGIDI for crop improvement and breeding in this research. We discussed the significant discoveries and consequences of several studies that used MGIDI to enhance the productivity, excellence, and flexibility of numerous crops, such as bush yam, barley, cassava, cucumber, guar, lentil, maize, rice, bean, soybean, wheat, etc. Additionally, we talked about some of the potential applications of MGIDI for breeding and crop improvement, such as tolerance to salinity, stability analysis, tolerance to waterlogging, mechanism of drought response, performance in agronomy and tuber quality, nutritional value and productivity, adaptability, increased yield, early maturity, and stress resistance etc. Following the upward trend, MGIDI can be considered as a valuable index technique for selection of crop genotypes that can address food security, climate change, and nutritional quality problems worldwide. We expect that this study will spark more research and use of MGIDI in different crops characteristics, contributing to the improvement of plant breeding science.</p></div>","PeriodicalId":100341,"journal":{"name":"Crop Design","volume":"3 4","pages":"Article 100074"},"PeriodicalIF":0.0,"publicationDate":"2024-09-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2772899424000235/pdfft?md5=738e11c856be8307a5041292adf13221&pid=1-s2.0-S2772899424000235-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142232458","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}