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Molecular and phenotypic profiling of white Guinea yam (Dioscorea rotundata) breeding lines 白色几内亚山药(Dioscorea rotundata)育种系的分子和表型分析
Pub Date : 2023-11-01 DOI: 10.3389/fhort.2023.1290521
Prince Emmanuel Norman, Asrat Asfaw, Paterne Angelot Agre, Agyemang Danquah, Pangirayi Bernard Tongoona, Eric Yirenkyi Danquah, Robert Asiedu
Phenotypic and genotypic profiling helps identify genotypes with suitable and complementary traits for genetic improvement in crops. A total of 32 traits were assessed in 36 genotypes of white Guinea yam established in a 6 × 6 triple lattice design. The objective was to evaluate an array of plant traits that define the genetic merits of breeding lines for yam improvement. Different analytical tools were used to identify and prioritize relevant traits defining the genetic merits of breeding lines in the yam improvement program. Out of the 32 traits measured, the linear combination of 14 traits that minimize within-group variance and maximize between-group variance for discriminating the genetic values of yam breeding lines were identified. When best linear unbiased prediction with genomic relationship matrix (GBLUP) was used, the accuracies of genomic breeding values were higher (r=0.87 to 0.97) for the seven traits (dry matter content, intensity of flesh oxidization of shredded tuber, pasting temperature, pasting time, tuber flesh colour, yam mosaic virus and fresh tuber yield) with high broad-sense heritability values (H 2 m >0.6). While, for the remaining seven traits with low (H 2 m <0.3) to medium (H 2 m =0.3 to 0.54) broad-sense heritability values, the accuracies of genomic estimated breeding values (GEBV) were low (r<0.4) to medium (r=0.4-0.8). The genotype–trait (GT) biplot display revealed superior clones with desirable genetic values for the key traits. These results are relevant for parental selection aimed at improving key agronomic traits in white Guinea yam.
表型和基因型分析有助于确定具有适合和互补性状的基因型,用于作物的遗传改良。采用6 × 6三重晶格设计,对36个基因型的32个性状进行了评价。目的是评价一系列确定山药改良育种系遗传优点的植物性状。在山药改良计划中,使用不同的分析工具来鉴定和排序确定选育系遗传优势的相关性状。在测定的32个性状中,鉴定出14个性状的组内方差最小和组间方差最大的线性组合,用于判别山药选系的遗传价值。采用基因组关系矩阵最佳线性无偏预测(GBLUP), 7个性状(干物质含量、肉质氧化强度、糊制温度、糊制时间、块茎肉色、山药花叶病毒和鲜块茎产量)的基因组育种精度较高(r=0.87 ~ 0.97),具有较高的广义遗传力值(H 2 m >0.6)。而其余7个广义遗传力值为低(hm =0.3)至中等(hm =0.3 ~ 0.54)的性状,其基因组育种估计值(GEBV)的精度为低(hm =0.4) ~中等(r=0.4 ~ 0.8)。基因型性状(GT)双图显示显示了具有理想遗传价值的优良克隆。这些结果与改善白几内亚山药主要农艺性状的亲本选择有关。
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引用次数: 0
New developments and opportunities for AI in viticulture, pomology, and soft-fruit research: a mini-review and invitation to contribute articles 人工智能在葡萄栽培、果学和软果研究中的新发展和机遇:一篇小型综述和投稿文章邀请
Pub Date : 2023-10-11 DOI: 10.3389/fhort.2023.1282615
Sigfredo Fuentes, Eden Tongson, Claudia Gonzalez Viejo
Climate change constraints on horticultural production and emerging consumer requirements for fresh and processed horticultural products with an increased number of quality traits have pressured the industry to increase the efficiency, sustainability, productivity, and quality of horticultural products. The implementation of Agriculture 4.0 using new and emerging digital technologies has increased the amount of data available from the soil–plant–atmosphere continuum to support decision-making in these agrosystems. However, to date, there has not been a unified effort to work with these novel digital technologies and gather data for precision farming. In general, artificial intelligence (AI), including machine/deep learning for data modeling, is considered the best approach for analyzing big data within the horticulture and agrifood sectors. Hence, the terms Agriculture/AgriFood 5.0 are starting to be used to identify the integration of digital technologies from precision agriculture and data handling and analysis using AI for automation. This mini-review focuses on the latest published work with a soil–plant–atmosphere approach, especially those published works implementing AI technologies and modeling strategies.
气候变化对园艺生产的限制,以及消费者对新鲜和加工的园艺产品质量要求的增加,迫使该行业提高园艺产品的效率、可持续性、生产力和质量。利用新兴数字技术实施的农业4.0增加了土壤-植物-大气连续体的可用数据量,以支持这些农业系统的决策。然而,到目前为止,还没有一个统一的努力来使用这些新颖的数字技术并为精准农业收集数据。一般来说,人工智能(AI),包括用于数据建模的机器/深度学习,被认为是分析园艺和农业食品部门大数据的最佳方法。因此,术语“农业/农业食品5.0”开始被用于识别来自精准农业的数字技术的集成以及使用人工智能进行自动化的数据处理和分析。这篇迷你综述的重点是最新发表的土壤-植物-大气方法的作品,特别是那些发表的实施人工智能技术和建模策略的作品。
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引用次数: 0
Monitoring oomycetes in water: combinations of methodologies used to answer key monitoring questions 监测水中卵菌:用于回答关键监测问题的方法组合
Pub Date : 2023-10-10 DOI: 10.3389/fhort.2023.1210535
Tim R. Pettitt
Monitoring oomycete populations and communities in bodies of water is vital in developing our understanding of this important group of fungus-like protists that contains many serious pathogens of both crops and wild plants. The methodologies involved in monitoring oomycetes are often presented as a developmental hierarchy, progressing from ‘traditional’ culture-based techniques through immunological techniques and basic PCR to qPCR and metagenomics. Here, techniques are assessed according to the roles they can perform in relation to four stages of the monitoring process: capture, detection and identification, viability determination, and quantification. Possible synergies are then considered for the combined use of different techniques in addressing the various needs relating to different questions asked of monitoring, with an emphasis on the continuing value of cultural and immunodiagnostic procedures. Additionally, the exciting future presented by the ongoing development and improvement of metabarcoding and the use of high throughput sequencing techniques in the measurement and monitoring of oomycete inoculum to determine and mitigate plant disease risks is addressed.
监测水体中的卵菌种群和群落对于加深我们对这种重要的真菌样原生生物的了解至关重要,这种原生生物含有许多作物和野生植物的严重病原体。监测卵菌的方法通常呈现为一个发展层次,从“传统的”基于培养的技术,到免疫学技术和基本PCR,再到qPCR和宏基因组学。在这里,技术是根据它们在监测过程的四个阶段所能发挥的作用进行评估的:捕获、检测和识别、可行性确定和量化。然后考虑可能的协同作用,以联合使用不同的技术来解决与监测提出的不同问题有关的各种需求,重点是培养和免疫诊断程序的持续价值。此外,元条形码的不断发展和改进以及在卵菌接种量的测量和监测中使用高通量测序技术来确定和减轻植物疾病风险的令人兴奋的未来也得到了解决。
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引用次数: 0
Leaf shredding as an alternative strategy for managing apple scab resistance to demethylation inhibitor fungicides 叶片切碎作为管理苹果痂对去甲基化抑制剂杀菌剂抗性的替代策略
Pub Date : 2023-10-03 DOI: 10.3389/fhort.2023.1175168
Julia C. Meitz-Hopkins, Saskia G. von Diest, Trevor A. Koopman, Kenneth R. Tobutt, Xiangming Xu, Cheryl L. Lennox
Within integrated apple scab control there is a strong focus on reduction of Venturia inaequalis primary inoculum. The hypothesis that leaf shredding as an orchard sanitation practice would reduce the effective population size of the fungus (resulting in lower genetic variation due to reduction in sexual offspring) was tested. Assuming the allele causing fungicide resistance is already present in the population, it will be widely distributed at the end of the season, since selection occurs when the demethylation inhibitor (DMI) fungicide was applied. For short-term disease management a reduction of inoculum size, (i.e. potential ascospore dose) is most important. In the long-term resistant isolates/genotypes would be less likely to survive the winter and/or to infect in the spring, if that inoculum (i.e. in fallen leaves) has been removed. To sustain the use of highly effective synthetic fungicides, such as the DMIs, fungicide resistance management practices have to be evaluated. Fungicide resistance, which negatively affects pathogen fitness, is hypothetically reversible, if the selection pressure by the fungicide is removed. This study quantified the effect of leaf shredding on changes in the pathogen’s flusilazole sensitivity and population genetic structure using SSR markers. Venturia inaequalis populations in orchard trials, where sanitation practices had been applied, were tested for flusilazole sensitivity in planta and in vitro . Significant shifts towards flusilazole resistance were identified in orchards with a history of DMI application without sanitation treatment, with a mean sensitivity of EC 50 = 0.208 ug/ml (n=49) compared to an unexposed V. inaequalis population (EC 50 = 0.104 ug/ml, n=55). However, the isolates from the same sanitation trial orchards, from leaf shredding treatment in combination with a fungicide spray programme, had a mean EC50 of 0.110 ug/ml (n=41), similar to an unexposed V. inaequalis population. Furthermore, V. inaequalis offspring after sanitation treatment, showed shifts in microsatellite allele frequency distribution patterns used as an indicator of sexual reproduction. This study concludes that sanitation treatments, i.e. leaf shredding, impact on fungicide sensitivity and therefore effectively contributes to fungicide resistance management.
在综合苹果痂病控制中,重点是减少不均等文氏菌的初级接种。假设碎叶作为果园卫生实践将减少真菌的有效种群规模(导致遗传变异降低,由于减少有性后代)进行了测试。假设导致杀菌剂抗性的等位基因已经存在于种群中,它将在季节结束时广泛分布,因为选择发生在使用去甲基化抑制剂(DMI)杀菌剂时。对于短期疾病管理,减少接种量(即潜在的子囊孢子剂量)是最重要的。从长期来看,如果接种物(即落叶中的接种物)被移除,抗性分离株/基因型将不太可能在冬季存活和/或在春季感染。为了持续使用高效合成杀菌剂,如双甲基咪唑,必须对杀菌剂耐药性管理做法进行评估。如果杀菌剂的选择压力被消除,对病原体适应性产生负面影响的杀菌剂耐药性在理论上是可逆的。本研究利用SSR标记量化了叶片切碎对病原菌氟美唑敏感性和群体遗传结构变化的影响。在采用卫生措施的果园试验中,对不均等文图里亚种群进行了植物和体外氟唑唑敏感性测试。在没有卫生处理的情况下施用DMI的果园中,发现对氟唑唑的抗性发生了显著变化,与未暴露的不等长叶枯病菌群体(EC 50 = 0.104 ug/ml, n=55)相比,EC 50 = 0.208 ug/ml (n=49)的平均敏感性。然而,来自同一卫生试验果园的分离株,在叶片切碎处理与杀菌剂喷洒方案相结合的情况下,其平均EC50为0.110 ug/ml (n=41),与未暴露的不等长叶枯病菌群体相似。此外,卫生处理后的不均等弧菌后代表现出微卫星等位基因频率分布模式的变化,这是有性生殖的一个指标。本研究的结论是,卫生处理,如叶片切碎,影响杀菌剂敏感性,因此有效地有助于杀菌剂抗性管理。
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引用次数: 1
Digging for gold: evaluating the authenticity of saffron (Crocus sativus L.) via deep learning optimization 挖掘黄金:通过深度学习优化评估藏红花(藏红花L.)的真实性
Pub Date : 2023-09-29 DOI: 10.3389/fhort.2023.1225683
Ahmed Elaraby, Hussein Ali, Bin Zhou, Jorge M. Fonseca
Introduction Saffron is one of the most coveted and one of the most tainted products in the global food market. A major challenge for the saffron industry is the difficulty to distinguish between adulterated and authentic dried saffron along the supply chain. Current approaches to analyzing the intrinsic chemical compounds (crocin, picrocrocin, and safranal) are complex, costly, and time-consuming. Computer vision improvements enabled by deep learning have emerged as a potential alternative that can serve as a practical tool to distinguish the pureness of saffron. Methods In this study, a deep learning approach for classifying the authenticity of saffron is proposed. The focus was on detecting major distinctions that help sort out fake samples from real ones using a manually collected dataset that contains an image of the two classes (saffron and non-saffron). A deep convolutional neural model MobileNetV2 and Adaptive Momentum Estimation (Adam) optimizer were trained for this purpose. Results The observed metrics of the deep learning model were: 99% accuracy, 99% recall, 97% precision, and 98% F-score, which demonstrated a very high efficiency. Discussion A discussion is provided regarding key factors identified for obtaining positive results. This novel approach is an efficient alternative to distinguish authentic from adulterated saffron products, which may be of benefit to the saffron industry from producers to consumers and could serve to develop models for other spices.
藏红花是全球食品市场上最令人垂涎和污染最严重的产品之一。藏红花行业面临的一个主要挑战是很难区分供应链上掺假和正宗的干藏红花。目前分析内在化合物(藏红花素、微藏红花素和番红花醛)的方法复杂、昂贵且耗时。通过深度学习实现的计算机视觉改进已经成为一种潜在的替代方案,可以作为区分藏红花纯度的实用工具。方法提出了一种基于深度学习的藏红花真伪鉴别方法。研究的重点是通过人工收集的包含两类(藏红花和非藏红花)图像的数据集来检测主要的区别,从而帮助从真实样本中区分出假样本。为此,训练了深度卷积神经模型MobileNetV2和自适应动量估计(Adam)优化器。结果深度学习模型的准确率为99%,查全率为99%,准确率为97%,F-score为98%,效率非常高。讨论了确定获得积极结果的关键因素。这种新颖的方法是区分真伪藏红花产品的有效替代方法,这可能有利于藏红花产业从生产者到消费者,并可以为其他香料开发模型。
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引用次数: 0
Enhancing biosecurity against virus disease threats to Australian grain crops: current situation and future prospects 加强对澳大利亚粮食作物病毒病威胁的生物安全:现状和未来展望
Pub Date : 2023-09-29 DOI: 10.3389/fhort.2023.1263604
Solomon Maina, Roger A. C. Jones
Australia is a major grain exporter, and this trade makes an important contribution to its economy. Fortunately, it remains free of many damaging virus diseases and virus vectors found elsewhere. However, its crop biosecurity is under increasing pressure from global ecological, climatic, and demographic challenges. Stringent biosecurity and plant health programs safeguard Australian grain production from damaging virus and virus vector incursions entering via different pathways. These programs formerly relied upon traditional testing procedures (indicator hosts, serology, PCRs) to intercept incoming virus-contaminated plant material. Recently, the integration of rapid genomic diagnostics innovation involving High Throughput Sequencing (HTS) smart tools into sample testing schedules is under exploration to improve virus testing accuracy, efficiency, and cost effectiveness under diverse circumstances. This process includes evaluating deployment of Illumina and Oxford Nanopore Technology shotgun sequencing. It also includes evaluating targeted viral genome HTS and virus vector metabarcoding approaches. In addition, using machine learning and deep learning capacities for big data analyses and remote sensing technologies will improve virus surveillance. Tracking damaging virus variants will be improved by surveillance networks which combine virus genomic-surveillance systems with an interoperable virus database. Sequencing Australian virus specimen collections will help ensure the accuracy of virus identifications based solely on genetic information. Enhancing routine diagnosis and data collection using these innovations will improve post entry virus interception and background virus and vector surveillance. This will help reduce the frequency of new incursions, improve virus management during eradication, containment and other plant health activities, and achieve more profitable Australian grain production.
澳大利亚是一个主要的粮食出口国,粮食贸易对其经济做出了重要贡献。幸运的是,它仍然没有在其他地方发现的许多破坏性病毒疾病和病毒载体。然而,由于全球生态、气候和人口挑战,中国作物生物安全面临越来越大的压力。严格的生物安全和植物健康计划保护澳大利亚的粮食生产免受通过不同途径进入的破坏性病毒和病毒载体的入侵。这些程序以前依赖于传统的检测程序(指示剂宿主、血清学、聚合酶链反应)来拦截传入的受病毒污染的植物材料。最近,正在探索将涉及高通量测序(HTS)智能工具的快速基因组诊断创新整合到样品检测计划中,以提高不同情况下病毒检测的准确性、效率和成本效益。这个过程包括评估Illumina和Oxford Nanopore Technology霰弹枪测序的部署。它还包括评估靶向病毒基因组HTS和病毒载体元条形码方法。此外,利用机器学习和深度学习能力进行大数据分析和遥感技术将改善病毒监测。将病毒基因组监测系统与可互操作的病毒数据库相结合的监测网络将改进对破坏性病毒变体的跟踪。对澳大利亚收集的病毒标本进行测序将有助于确保仅根据遗传信息进行病毒鉴定的准确性。利用这些创新加强常规诊断和数据收集,将改善入境后病毒拦截以及背景病毒和媒介监测。这将有助于减少新入侵的频率,在根除、遏制和其他植物卫生活动期间改善病毒管理,并使澳大利亚的粮食生产更有利可图。
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引用次数: 0
Remote detection of fungal pathogens in viticulture using laser-induced fluorescence: an experimental study on infected potted vines 利用激光诱导荧光技术远程检测葡萄栽培真菌病原菌:盆栽受感染葡萄的实验研究
Pub Date : 2023-09-15 DOI: 10.3389/fhort.2023.1185468
Christoph Kölbl, Manu Diedrich, Elias Ellingen, Frank Duschek, Moustafa Selim, Beate Berkelmann-Löhnertz
Introduction Pathogenic fungi, such as Plasmopara viticola and Erysiphe necator , severely threaten the annual yield of grapes in both quantity and quality. In contrast to other crop production systems, fungicides are intensively applied in viticulture as a countermeasure. The goal of precision viticulture is to optimize vineyard performance as well as the environmental impact by reducing fungicides and applying different techniques and combined strategies. Therefore, new emerging technologies are required, including non-invasive detection, as well as monitoring and tools for the early and in-field detection of fungal development. Methods In this study, we investigated leaves of potted vines ( Vitis vinifera cv. ‘Riesling’) and traced the development of the inoculated leaves using our new remote detection system vinoLAS ® , which is based on laser-induced fluorescence spectroscopy. We ran a measurement campaign over a period of 17 days. Results We were able to detect a leaf infection with P. viticola , the causal agent of downy mildew, between 5 and 7 days after inoculation. Our results provide evidence for a successful application of laser-based standoff detection in vineyard management in the future. Thus, the vinoLAS system can serve as a model technology for the detection of pathogenic disease symptoms and thus monitoring complete vineyard sites. This allows for early countermeasures with suitable crop protection approaches and selected hot-spot treatments. Discussion As P. viticola is considered one of the most damaging fungi in European viticulture, disease mapping via this monitoring tool will help to reduce fungicide applications, and will, therefore, support the implementation of the European Green Deal claims.
葡萄浆原菌(Plasmopara viticola)和葡萄赤霉(Erysiphe necator)等病原菌严重威胁葡萄的产量和质量。与其他作物生产系统不同,杀菌剂作为对策在葡萄栽培中大量应用。精准葡萄栽培的目标是通过减少杀菌剂和应用不同的技术和组合策略来优化葡萄园的性能和对环境的影响。因此,需要新的新兴技术,包括非侵入性检测,以及用于真菌发育早期和现场检测的监测和工具。方法对盆栽葡萄(Vitis vinifera cv.)的叶片进行研究。“雷司令”),并使用我们基于激光诱导荧光光谱的新型远程检测系统vinoLAS®跟踪接种叶片的发展。我们进行了为期17天的测量活动。结果接种后5 ~ 7天,可检测到白霜霉病病原菌白霜菌的叶片侵染。我们的研究结果为未来激光对峙检测在葡萄园管理中的成功应用提供了证据。因此,vinoLAS系统可以作为检测病原疾病症状的模型技术,从而监测整个葡萄园。这允许采用适当的作物保护方法和选定的热点处理进行早期对策。由于葡萄霉被认为是欧洲葡萄栽培中最具破坏性的真菌之一,通过这种监测工具绘制病害地图将有助于减少杀菌剂的使用,因此将支持实施欧洲绿色协议的主张。
{"title":"Remote detection of fungal pathogens in viticulture using laser-induced fluorescence: an experimental study on infected potted vines","authors":"Christoph Kölbl, Manu Diedrich, Elias Ellingen, Frank Duschek, Moustafa Selim, Beate Berkelmann-Löhnertz","doi":"10.3389/fhort.2023.1185468","DOIUrl":"https://doi.org/10.3389/fhort.2023.1185468","url":null,"abstract":"Introduction Pathogenic fungi, such as Plasmopara viticola and Erysiphe necator , severely threaten the annual yield of grapes in both quantity and quality. In contrast to other crop production systems, fungicides are intensively applied in viticulture as a countermeasure. The goal of precision viticulture is to optimize vineyard performance as well as the environmental impact by reducing fungicides and applying different techniques and combined strategies. Therefore, new emerging technologies are required, including non-invasive detection, as well as monitoring and tools for the early and in-field detection of fungal development. Methods In this study, we investigated leaves of potted vines ( Vitis vinifera cv. ‘Riesling’) and traced the development of the inoculated leaves using our new remote detection system vinoLAS ® , which is based on laser-induced fluorescence spectroscopy. We ran a measurement campaign over a period of 17 days. Results We were able to detect a leaf infection with P. viticola , the causal agent of downy mildew, between 5 and 7 days after inoculation. Our results provide evidence for a successful application of laser-based standoff detection in vineyard management in the future. Thus, the vinoLAS system can serve as a model technology for the detection of pathogenic disease symptoms and thus monitoring complete vineyard sites. This allows for early countermeasures with suitable crop protection approaches and selected hot-spot treatments. Discussion As P. viticola is considered one of the most damaging fungi in European viticulture, disease mapping via this monitoring tool will help to reduce fungicide applications, and will, therefore, support the implementation of the European Green Deal claims.","PeriodicalId":499141,"journal":{"name":"Frontiers in Horticulture","volume":"33 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135437812","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}
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Frontiers in Horticulture
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