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High-throughput multiparametric live-cell and immunofluorescence analyses demonstrate antifibrotic bioactivities of O. basilicum and A. membranaceus hairy roots on human hepatic stellate cells 高通量多参数活细胞和免疫荧光分析证实了basilicum和A. membranaceus毛状根对人肝星状细胞的抗纤维化生物活性
IF 5.4 Q1 PLANT SCIENCES Pub Date : 2025-05-01 DOI: 10.1016/j.cpb.2025.100484
Shannah Secret , Milena Mennecozzi , Tom Crabbe , Alessandra Devoto
Plants are a well-established source of compounds with biopharmaceutical activity, but the diversity and often low abundance of phytochemicals have hindered their medical application. Bridging this gap requires scalable growth conditions and sustainable extraction methodologies harnessed to robust and predictive assays of disease and cell toxicity. This study utilises plant hairy root biomass and constituent bioactives combined with high-throughput assays of fibrogenic progression using activated human hepatic stellate cells.
Fibrosis is a build-up of connective tissue components like collagen type I and fibronectin and is one of the underlying drivers of liver cirrhosis, a complex and often fatal condition arising from alcohol abuse, poor diet, or viral infection. New treatments are required to reverse the predicted steady increase in the global burden of this disease.
In this study, Astragalus membranaceus and Ocimum basilicum were transformed with Agrobacterium rhizogenes (Rhizobium rhizogenes) to provide reproducible and rapidly growing hairy root cultures. Titrations of methanol and pressed root extracts obtained from both species, altered selectively, the deposition of collagen type I and fibronectin, along variable effects on live readouts of stellate cells proliferation and death, distinguishing between Caspase-3/7 activation and membrane integrity maintenance. These results differ from the wider effects observed with the known anti-fibrotic compounds Nintedanib and Silymarin, which suggests that the extracts may prove to be a significant source of novel biopharmaceuticals useful in the treatment of liver cirrhosis. Remarkably, the concentrations showing activity were not toxic for primary human hepatocytes.
Moreover, the platform developed provides a novel integrated high-throughput sustainable extraction method and readout to elucidate the mechanism of action of unknown compounds with respect to previous studies.
植物是具有生物制药活性的化合物的公认来源,但植物化学物质的多样性和往往低丰度阻碍了它们的医学应用。弥合这一差距需要可扩展的生长条件和可持续的提取方法,利用强大的疾病和细胞毒性预测分析。本研究利用植物毛状根生物量和成分生物活性,结合使用活化的人肝星状细胞进行高通量纤维化进展测定。纤维化是一种结缔组织成分的积累,如I型胶原蛋白和纤维连接蛋白,是肝硬化的潜在驱动因素之一,肝硬化是一种复杂且通常致命的疾病,由酗酒、不良饮食或病毒感染引起。需要新的治疗方法来扭转这一疾病全球负担的预期稳定增长。本研究利用根生农杆菌(Rhizobium rhizogenes)对黄芪和罗勒木进行转化,获得了可繁殖且生长迅速的毛状根培养物。从这两种植物中提取的甲醇和压根提取物的滴定,选择性地改变了I型胶原和纤维连接蛋白的沉积,以及对星状细胞增殖和死亡的实时读数的可变影响,区分了Caspase-3/7激活和膜完整性维持。这些结果不同于已知的抗纤维化化合物尼达尼布和水飞蓟素所观察到的更广泛的效果,这表明提取物可能被证明是用于治疗肝硬化的新型生物药物的重要来源。值得注意的是,显示活性的浓度对原代人肝细胞没有毒性。此外,开发的平台提供了一种新的集成高通量可持续提取方法和读数,以阐明未知化合物的作用机制。
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引用次数: 0
Genome-wide association study for protein and color content in a tetraploid wheat collection 四倍体小麦蛋白质和颜色含量的全基因组关联研究
IF 5.4 Q1 PLANT SCIENCES Pub Date : 2025-05-01 DOI: 10.1016/j.cpb.2025.100483
Ilaria Marcotuli , Patricia Cabas-Lühmann , Davide Caranfa , Antonia Mores , Stefania Lucia Giove , Pasqualina Colasuonno , Sara Muciaccia , Maria Simone , Andrés R. Schwember , Agata Gadaleta
Grain protein content (GPC) and yellow index (YI) are the most important quality traits to measure the quality of tetraploid wheats that benefit the pasta consumers. The main objective of this study was to characterize GPC and YI using 144 different accessions of tetraploid wheats (Triticum turgidum L., 2 n = 4x = 28; AABB genome) constituted by several subspecies and evaluated in southern Italy for 2 years (2019 and 2022) and in central Chile during 2021 in order to identify new useful superior alleles. SNPs marker, suitable for genome-wide association study (GWAS) were 3924. GWAS was carried out using the Mixed Linear Model (Q+K) which identified 22 marker-trait associations for both traits analyzed, representing 10 and 12 regions associated with grain protein content and yellow index, respectively. QTL linked to GPC were detected on chromosomes 2 A, 3 A, 5 A, and 7 A, while QTL for YI were localized on chromosomes 1B, 2B, 3 A, 4B, 6 A, 6B, 7 A, reflecting their complex genetic nature. The phenotypic variation (R2) explained, ranking from 8.1 % to 8.6 % for GPC and from 8.2 % to 11.6 % for YI content. In addition, one gene involved in nitrogen metabolism, the glutamine synthetase 2 (GS2) on chromosome 2 A, and the main gene involved in the synthesis of carotenoid pigments, the phytoene synthase 1 (Psy-A1) on chromosome 7 A were identified as key candidate genes regulating these two quality traits. Finally, the identification of new haplotypes improves our understanding of the genetic mechanisms controlling protein and color traits in tetraploid wheat and facilitate the development of superior wheat varieties in the future.
籽粒蛋白质含量(GPC)和黄指数(YI)是衡量四倍体小麦品质的最重要品质性状,对面食消费者有利。本研究的主要目的是利用144个不同的四倍体小麦(Triticum turgidum L., 2 n = 4x = 28;AABB基因组)由几个亚种组成,并在意大利南部(2019年和2022年)和智利中部(2021年)进行了为期两年的评估,以确定新的有用的优越等位基因。适用于全基因组关联研究(GWAS)的snp标记有3924个。采用混合线性模型(Q+K)进行GWAS分析,共鉴定出22个与所分析性状相关的标记性状,分别代表10个和12个与籽粒蛋白质含量和黄指数相关的区域。与GPC相关的QTL定位在2 A、3 A、5 A和7 A染色体上,而与YI相关的QTL定位在1B、2B、3 A、4B、6 A、6B、7 A染色体上,反映了它们复杂的遗传性质。表型变异(R2)解释,GPC含量从8.1 %到8.6 %,YI含量从8.2 %到11.6 %。此外,2号染色体 A上参与氮代谢的谷氨酰胺合成酶2 (GS2)基因和7号染色体上参与类胡萝卜素色素合成的植物烯合成酶1 (Psy-A1)基因 A被确定为调控这两个品质性状的关键候选基因。最后,新单倍型的鉴定有助于我们对四倍体小麦蛋白质和颜色性状的遗传机制的理解,为今后培育优质小麦品种提供依据。
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引用次数: 0
Endophytic fungi—Big player in plant-microbe symbiosis 内生真菌——植物与微生物共生的重要参与者
IF 5.4 Q1 PLANT SCIENCES Pub Date : 2025-04-24 DOI: 10.1016/j.cpb.2025.100481
Qian-xi Li , Fu-cheng Lin , Zhen-zhu Su
Endophytic fungi are recognized as beneficial microorganisms that form symbiotic relationships with plants. These fungi enhance plant adaptability to biotic and abiotic stresses, promote plant growth through the secretion of phytohormones, and facilitate nutrient absorption, while in return, they derive nutritional benefits from their host plants. Such intricate and balanced associations hold significant promise for agriculture, particularly in improving yield stability and stress tolerance in economically important crops. Despite decades of research deepening our understanding of fungal-plant symbiosis, systematic syntheses of emerging discoveries remain scarce. This paper elucidates three key insights: (1) the historical progression of research on endophytic fungi, tracing the field from early descriptive ecology to modern molecular insights into symbiosis; (2) the molecular cross-talk underpinning symbiotic progression, from initial recognition to metabolic integration; and (3) the molecular mechanisms by which endophytic fungi confer growth promotion and disease resistance to their host plants. By bridging fundamental symbiosis mechanisms with their potential agricultural applications, we provide a conceptual framework for leveraging endophytic fungi as biocontrol agents in sustainable agriculture.
内生真菌是公认的与植物形成共生关系的有益微生物。这些真菌增强植物对生物和非生物胁迫的适应性,通过分泌植物激素促进植物生长,促进营养吸收,同时从寄主植物那里获得营养益处。这种复杂而平衡的关联对农业有着重大的前景,特别是在提高重要经济作物的产量稳定性和抗逆性方面。尽管几十年的研究加深了我们对真菌-植物共生的理解,但新兴发现的系统合成仍然很少。本文阐述了内生真菌研究的三个关键观点:(1)内生真菌研究的历史进展,从早期的描述生态学到现代对共生的分子认识;(2)支持共生进程的分子串扰,从最初的识别到代谢整合;(3)内生真菌促进寄主植物生长和抗病的分子机制。通过将基本的共生机制与其潜在的农业应用联系起来,我们为利用内生真菌作为可持续农业的生物防治剂提供了一个概念框架。
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引用次数: 0
Candidate gene discovery for nitrogen use efficiency in rice based on genome-wide association study 基于全基因组关联研究发现水稻氮素利用效率的候选基因
IF 5.4 Q1 PLANT SCIENCES Pub Date : 2025-04-08 DOI: 10.1016/j.cpb.2025.100479
Kunchi Yu , Jin Liu , Mingmao Sun , Xiaoding Ma , Bing Han , Maomao Li , Zhengwu Zhao , Longzhi Han , Di Cui
Providing reliable and sufficient food resources for a growing global population is a significant societal challenge, in particular achieving this while keeping nitrogen pollution within safe environmental limits. Therefore, it is crucial to identify nitrogen-use efficient (NUE) accessions and identify candidate genes associated with NUE for sustainable agricultural development. Here, we present analysis on the genetic diversity of 518 accessions of Chinese germplasm and performed a genome-wide association study (GWAS) on 16 traits associated with NUE and yield. We identified a total of 89 significant loci, including 47 associated with NUE and 42 with yield, of which 56 (63 %) were newly discovered. Through association and indica-japonica genetic differentiation analysis, we identified a high-confidence candidate gene - OsNPT4 - that encoding a protein from the POT family. This gene was associated with nitrogen grain production efficiency (NGPE), nitrogen harvest index (NHI), and tillering number (TN). RNA-seq results indicated that OsNPT4 may play a crucial role in effectuating the response of rice plants to nitrogen treatment. Further haplotype analysis revealed significant differences among the various haplotypes of this gene concerning NGPE, NHI, and TN, with accessions carrying Hap1 demonstrating strong NUE and increased yields. RT-qPCR results showed that OsNPT4 expression significantly increased in Hap1-carrying accessions in both leaves and roots upon treatment, while no significant differences were observed in Hap2-carrying accessions. This further confirmed OsNPT4 as a key candidate gene associated with varying NUE. Taken together, our results provide a theoretical foundation for cloning NUE genes and facilitate the design of molecular breeding strategies.
为不断增长的全球人口提供可靠和充足的粮食资源是一项重大的社会挑战,特别是在实现这一目标的同时将氮污染保持在安全的环境限制范围内。因此,鉴定氮素利用效率(NUE)和NUE相关候选基因对农业可持续发展至关重要。本文对518份中国种质资源的遗传多样性进行了分析,并对与氮肥利用效率和产量相关的16个性状进行了全基因组关联研究。共鉴定出89个显著位点,其中47个与NUE相关,42个与产量相关,其中56个(63% %)是新发现的。通过关联和籼粳遗传分化分析,我们确定了一个高置信度的候选基因- OsNPT4 -编码来自POT家族的蛋白质。该基因与氮素籽粒生产效率(NGPE)、氮素收获指数(NHI)和分蘖数(TN)相关。RNA-seq结果表明,OsNPT4可能在水稻植株对氮处理的响应中起关键作用。进一步的单倍型分析显示,该基因的不同单倍型在NGPE、NHI和TN方面存在显著差异,携带Hap1的品种表现出较高的NUE和产量。RT-qPCR结果显示,经处理后,OsNPT4在携带hap1的植株叶片和根系中表达量均显著增加,而在携带hap2的植株中表达量无显著差异。这进一步证实了OsNPT4是与不同NUE相关的关键候选基因。研究结果为NUE基因的克隆和分子育种策略的设计提供了理论基础。
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引用次数: 0
Two-year QTL dissecting of high harvest index and related traits in a novel rice variety Yuenongsimaio 水稻新品种粤农四麦高产指数及相关性状的2年QTL剖析
IF 5.4 Q1 PLANT SCIENCES Pub Date : 2025-04-05 DOI: 10.1016/j.cpb.2025.100475
Shiguang Wang , Liting Zhang , Wei Liu, Xiaofei Wang, Haoxiang Wu, Hao Chen, Tengkui Chen, Zhanhua Lu, Xiuying He
High harvest index (HI), defined as the grain yield-to-biomass ratio (≥ 0.55), reflects a well-balanced source-sink relationship. It is a key trait in rice high-HI breeding programs, which has proven to be a successful strategy for developing super high-yield rice varieties. However, its genetic basis remains elusive. This study conducted QTL analysis for HI-related traits using a recombinant inbred line (RIL) population derived from a cross between a geng/japonica cultivar, Lijiangxintuanheigu (LTH), and a high HI xian/indica variety, Yuenongsimiao (YNSM). A high‑density genetic map with 6674 bin markers identified 97 QTLs across 12 HI-related traits, forming 13 QTL clusters that affect the source-sink related traits in rice. These bin markers were converted from 1,009,324 high-quality SNPs sourced from the sequenced RIL population. Notably, qRSC1 (QTL cluster of rice source capacity 1), which included qFLL1, qSTW1, qBM1.2, and qHI1, was tightly linked to the semi-dwarf gene sd1 and collectively shaped the high HI plant architecture of YNSM. In contrast, qRSC3 (qFLL3/qFLW3/qSTW3/qBM3.1/qHI3.1) exhibited an opposite effect and positively regulated source-related traits. Among nine QTLs associated with yield per plant (YPP), only qYPP2.2, part of qRSS2 (QTL cluster of rice sink size 2), was consistently detected over two consecutive years. qRSS2 governed sink size by integrating multiple yield-related QTLs, including qYPP2.2. Overall, qRSC1, qRSC3, and qRSS2 collectively optimized source-sink balance, enabling YNSM’s high HI and high yields. These findings provide insights into the genetic basis of high HI in YNSM and may facilitate breeding high-yielding rice with superior HI.
高收获指数(High harvest index, HI)是指粮食产量与生物量的比值(≥0.55),反映了一个平衡良好的源库关系。它是水稻高hi育种计划的关键性状,已被证明是培育超高产水稻品种的成功策略。然而,其遗传基础仍然难以捉摸。本研究利用改良粳稻品种“丽江新团黑谷”(LTH)与高产籼籼品种“越农四苗”(YNSM)杂交的重组自交系(RIL)群体,进行了高HI相关性状的QTL分析。在一个包含6674个bin标记的高密度遗传图谱中,鉴定出12个与水稻高致病性相关性状的97个QTL,形成13个影响水稻源库相关性状的QTL集群。这些bin标记是由1009324个来自RIL群体的高质量snp转化而来。值得注意的是,包括qFLL1、qSTW1、qBM1.2和qHI1在内的qRSC1(水稻源容量1的QTL集群)与半矮秆基因sd1紧密相连,共同塑造了YNSM的高HI植株结构。相比之下,qRSC3 (qFLL3/qFLW3/qSTW3/qBM3.1/qHI3.1)表现出相反的作用,并正调控源相关性状。在9个与单株产量(YPP)相关的QTL中,只有qYPP2.2,即qRSS2(水稻库大小2的QTL簇)的一部分,连续两年被检测到。qRSS2通过整合多个与产量相关的qtl(包括qYPP2.2)来控制汇大小。总体而言,qRSC1、qRSC3和qRSS2共同优化了源汇平衡,实现了YNSM的高HI和高产量。这些发现为研究高HI的遗传基础提供了依据,并为培育高HI的高产水稻提供了可能。
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引用次数: 0
Meta-analysis of grapevine microbiota: Insights into the influence of cultivars, plant parts, geography, and vineyard practices on bacterial diversity 葡萄菌群的荟萃分析:葡萄品种、植物部位、地理和葡萄园实践对细菌多样性的影响
IF 5.4 Q1 PLANT SCIENCES Pub Date : 2025-04-05 DOI: 10.1016/j.cpb.2025.100478
Daniel Legesse, Yassine Bouhouch, Cédric Jacquard, Lisa Sanchez, Essaid Ait-Barka, Qassim Esmaeel
Investigating the grapevine microbiome is crucial for developing sustainable management practices in viticulture. This meta-analysis used amplicon metagenomics to analyze bacterial sequences from the Sequence Read Archive, covering 756 grapevine accessions. The dataset includes 378 paired end sequencing runs across twelve cultivars, four sample types, six origins, and two vineyard conditions. The analysis revealed significant variations in microbial communities across different grapevine cultivars and sample types, highlighting the influence of both the cultivar and ecological niche on microbial diversity. Differential abundance analyses further identified key microbial taxa driving variations across different grapevine plant parts. Furthermore, the study identified microbial taxa that consistently thrive across diverse conditions, suggesting their potential role in grapevine health and development. These findings support the possibility of utilizing specific microbial agents for biological control and sustainable vineyard management. This meta-analysis underscores the complexity of the grapevine microbiome and its pivotal role in vineyard ecosystems, providing valuable insights for future research and the advancement of sustainable viticulture practices.
研究葡萄藤微生物群对于发展葡萄栽培的可持续管理实践至关重要。这项荟萃分析使用扩增子宏基因组学分析了来自Sequence Read Archive的细菌序列,涵盖了756个葡萄藤条目。该数据集包括378对末端测序,涉及12个品种,4种样品类型,6个产地和2个葡萄园条件。结果表明,不同葡萄品种和样品类型的微生物群落存在显著差异,突出了品种和生态位对微生物多样性的影响。差异丰度分析进一步确定了驱动葡萄植株不同部位差异的关键微生物类群。此外,该研究还发现了在不同条件下持续繁殖的微生物分类群,这表明它们在葡萄藤的健康和发育中具有潜在的作用。这些发现支持了利用特定微生物制剂进行生物防治和可持续葡萄园管理的可能性。这项荟萃分析强调了葡萄微生物群的复杂性及其在葡萄园生态系统中的关键作用,为未来的研究和可持续葡萄栽培实践的进步提供了有价值的见解。
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引用次数: 0
Physiological novelties for salinity tolerance created by transgressive effects and cryptic gene functions unlocked by alien introgression from Oryza rufipogon to Oryza sativa 水稻(Oryza rufipogon)向sativa的外源入侵解锁了水稻(Oryza sativa)的隐基因功能,并通过入侵效应创造了耐盐生理上的新特性
IF 5.4 Q1 PLANT SCIENCES Pub Date : 2025-04-04 DOI: 10.1016/j.cpb.2025.100477
Swarupa Nanda Mandal , Ai Kitazumi , Coenraad R. van Beek , Isaiah C.M. Pabuayon , Jacobo Sanchez , Benildo G. de los Reyes
The inherent complexity of adaptive mechanisms to salinity stress necessitates novel approaches to plant breeding. In rice, wide introgression is an approach that is yet to be fully exploited, especially from the not-so-distant species related to cultivars. We explored the genetic combining potential of the AA-genome wild species Oryza rufipogon, the closest progenitor of cultivated Oryza sativa ssp. japonica, to uncover physiological novelties for salinity tolerance created by transgressive effects. Comprehensive evaluation of a set of chromosome segment substitution lines (CSSL) for various physiometric traits revealed the occurrence of individuals transgressing the parental phenotypic range. This indicates that introgression of alien O. rufipogon genomic segments into O. sativa genomic background can alter the overall potential of the recipient by creating novel physiological attributes better than the donor or worse than the recipient. In-depth characterization of transgressive tolerant and transgressive sensitive CSSLs showed the occurrence of novel attributes in terms of energy balance and gas exchange that positively correlated with enhanced or reduced potential for salinity tolerance. Integrated morphological, physiological, biochemical, ionomic, genomic, and transcriptomic profiling revealed five genomic regions with QTL effects, and seven genes with putative eQTL effects that explain the occurrence of transgressive phenotypes. Genes with eQTL effects are associated with the regulation of cytokinin-mediated processes, MYB transcription factors, and transmembrane transport, that positively correlated with the maintenance of shoot biomass, regulation of stomatal conductance, and modulation of cellular homeostasis. The transgressive lines had non-parental expression patterns for eleven genes that originated from O. rufipogon. These genes gained new patterns of regulation (de-regulation effects) in the genomic background of O. sativa indicating the unleashing of cryptic functions through introgression.
植物对盐胁迫的适应机制具有内在的复杂性,因此需要采用新的育种方法。在水稻中,广泛渗入是一种尚未充分利用的方法,特别是与栽培品种关系不远的物种。研究了栽培稻的最近祖先野生稻(Oryza rufipogon) aa基因组的遗传组合潜力。日本,以揭示生理上的新奇的耐盐性产生的海侵效应。对一组染色体片段代换系(CSSL)的各种生理性状进行综合评价,发现存在个体越过亲本表型范围的现象。这表明,外来的紫花苜蓿基因组片段渗入到紫花苜蓿的基因组背景中,可以通过创造比供体更好或比受体更差的新生理属性来改变受体的整体潜力。对耐海侵和敏感海侵的深入表征表明,在能量平衡和气体交换方面出现了新的属性,这些属性与耐盐潜力的增强或降低呈正相关。综合形态学、生理、生化、基因组学、基因组学和转录组学分析,揭示了5个具有QTL效应的基因组区域,以及7个具有假定的eQTL效应的基因,这些基因可以解释越界表型的发生。具有eQTL效应的基因与细胞分裂素介导的过程、MYB转录因子和跨膜运输的调控有关,与茎部生物量的维持、气孔导度的调控和细胞稳态的调节呈正相关。侵染系中有11个基因具有非亲本表达模式。这些基因在苜蓿基因组背景下获得了新的调控模式(去调控效应),表明通过基因渗入释放了隐功能。
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引用次数: 0
Genome-wide association study (GWAS) of rice (Oryza sativa L.) panicle compactness 水稻(Oryza sativa L.)圆锥花序紧凑性的全基因组关联研究(GWAS)
IF 5.4 Q1 PLANT SCIENCES Pub Date : 2025-04-02 DOI: 10.1016/j.cpb.2025.100464
Masoumeh Kordi , Naser Farrokhi , Asadollah Ahmadikhah , Pär K. Ingvarsson , Abbas Saidi , Mehdi Jahanfar
The Green Revolution altered the rice panicle by increasing grain numbers per panicle. Here, we perform a genome-wide association study to understand the molecular mechanisms determining the number of grains in a panicle in rice. Panicle image analyses were performed on 158 genetically diverse rice accessions, and GWAS was run using the FarmCPU model with 34,072 single nucleotide polymorphisms to relate genotypic variation to the corresponding phenotypes. Flanking regions of candidate SNPs were separately defined for each chromosome based on LD decay distance to identify putative-associated genes. An RNA-seq data analysis was performed between stem and panicle to emphasize the role of candidate genes in panicle compactness. The results were further confirmed by a PPI network analysis using the putative candidate genes. In total 95 significant SNPs were identified; as close SNPs were considered a QTL that resulted in 56 QTLs across the 12 rice chromosomes. We identified novel candidate genes for panicle compactness traits, such as cytochrome P450, polygalacturonase, glycosyltransferase, MADS-box, WRKY, YABBY, WUSCHEL-related homeobox, protein kinase, lipase, zinc finger transcription factor and protein phosphatase. Haplotype analysis identified haplogroups qNSSBB53, qNSSBB102, qNSSBU3, qNSSBU21, and qLS3 for three traits of NSSBB, NSSBU and LS. An analysis of epistatic interactions among candidate SNPs identified 91 significant SNP-SNP interactions.
绿色革命改变了水稻圆锥花序,增加了每粒圆锥花序的谷粒数。在此,我们进行了一项全基因组关联研究,以了解决定水稻圆锥花序粒数的分子机制。我们对 158 个不同基因的水稻品种进行了圆锥花序图像分析,并使用 FarmCPU 模型和 34,072 个单核苷酸多态性进行了 GWAS 分析,以将基因型变异与相应的表型联系起来。根据LD衰减距离,为每条染色体分别定义了候选SNP的侧翼区域,以确定推定的相关基因。对茎和圆锥花序进行了 RNA-seq 数据分析,以强调候选基因在圆锥花序紧密度中的作用。利用推定候选基因进行的 PPI 网络分析进一步证实了这一结果。共鉴定出 95 个重要的 SNPs;由于接近的 SNPs 被认为是一个 QTL,因此在 12 条水稻染色体上产生了 56 个 QTLs。我们发现了圆锥花序紧密度性状的新候选基因,如细胞色素 P450、聚半乳糖醛酸酶、糖基转移酶、MADS-box、WRKY、YABBY、WUSCHEL 相关同源框、蛋白激酶、脂肪酶、锌指转录因子和蛋白磷酸酶。单倍型分析确定了NSSBB、NSSBU和LS三个性状的单倍群qNSSBB53、qNSSBB102、qNSSBU3、qNSSBU21和qLS3。候选 SNP 之间的表观相互作用分析确定了 91 个显著的 SNP-SNP 相互作用。
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引用次数: 0
Artificial intelligence for fostering sustainable agriculture 促进可持续农业的人工智能
IF 5.4 Q1 PLANT SCIENCES Pub Date : 2025-03-25 DOI: 10.1016/j.cpb.2025.100476
Konathala Kusumavathi , Ramesh Konatala , Priyanka Lal , Smritikana Sarkar , Hirak Banerjee , Pintoo Bandopadhyay , Debadatta Sethi , Konga Upendar
Agriculture intensification has a paradoxical effect, as it increases food production and productivity by increasing farmer’s return on investment while instantaneously posing a serious threat to long-term sustainability like depletion of resources, soil degradation, water scarcity and finally environmental pollution. All these challenges have flickered concerns about the quality of life. To bash all these concerns, the precise and judicious use of agricultural inputs is necessary. Bespoke solutions (Site-Specific) tailored to specific problems can optimize resource utilization while minimizing negative impacts. Integrating advanced technologies like automation by the use of sensors, drones and robotics guarantees solutions in the context of availability and efficiency of agricultural labour decline. This technology-driven approach can reform agriculture. So, the holistic approach of using technological advancements with sustainable practices is necessary for a long-term ecological balance with enhancement in productivity. The integration of driven solutions allows farmers to obtain real-time insights into soil health, water availability and nutrient status facilitating sustainable farming practices. The main goal of this manuscript is to review the applications of AI in agriculture for crop monitoring with sustainable use of resources such as soil, water, and nutrients, as well as to elevate food production with better quality maintenance. This article scrutinizes the findings of several researchers to get a brief outline of the subject of the recent execution of automation in agriculture and compares it with conventional methods followed by the farmer.
农业集约化具有矛盾的效果,因为它通过提高农民的投资回报来增加粮食产量和生产力,同时对资源枯竭、土壤退化、水资源短缺以及最终的环境污染等长期可持续性构成严重威胁。所有这些挑战都引发了人们对生活质量的担忧。为了消除所有这些担忧,精确而明智地使用农业投入是必要的。针对特定问题定制的解决方案(特定于站点)可以优化资源利用,同时最大限度地减少负面影响。在农业劳动力可用性和效率下降的背景下,集成传感器、无人机和机器人等自动化等先进技术,确保了解决方案。这种技术驱动的方法可以改革农业。因此,利用技术进步和可持续实践的整体方法对于提高生产力的长期生态平衡是必要的。驱动解决方案的整合使农民能够实时了解土壤健康、水分供应和营养状况,促进可持续农业实践。本文的主要目的是综述人工智能在农业作物监测中的应用,实现土壤、水和养分等资源的可持续利用,以及在提高粮食产量的同时更好地保持质量。本文仔细研究了几位研究人员的发现,以简要概述最近在农业中实施自动化的主题,并将其与农民采用的传统方法进行比较。
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引用次数: 0
Enhancing wheat yellow rust detection through modified deep learning approach 改进的深度学习方法增强小麦黄锈病检测
IF 5.4 Q1 PLANT SCIENCES Pub Date : 2025-03-24 DOI: 10.1016/j.cpb.2025.100472
Shant Kumar , Rohit Singh , Sudheer Kumar , Sandeep Gupta
The study reports the effectiveness of machine learning and deep learning (ML/DL) algorithms in detecting yellow rust disease in wheat, keeping in view that early stage detection is crucial for minimizing the crop yield loss. Various traditional ML algorithms including Support Vector Machine (SVM), Decision Tree (DT), k-Nearest Neighbor KNN, Naïve Bayes (NB), Random Forest (RF) and Sequential Convolutional Neural Network (CNN) are utilized to access the plant disease detection efficiency. In contrast a modified version of CNN (MCNN), integrated with SVM principles, is proposed to enhance the performance of standard CNN. A newly established dataset named Yellow Rust 2022–2023 (YR-22/23) is used to estimate and compare the performance of considered ML/DL algorithms. Additionally, a benchmarked dataset named YellowRust-19 is considered for cross validation of ML/DL algorithms. The result indicates that the MCNN outperforms the standard algorithms (CNN) in terms of accuracy (1.2 %) metrics and is highly time efficient. Our proposed modified CNN method attained prediction accuracy of about 98 % for detection of yellow rust of wheat. Result highlights that merger of ML/DL approaches holds great promises to improve the overall efficiency of plant disease detection.
该研究报告了机器学习和深度学习(ML/DL)算法在检测小麦黄锈病方面的有效性,同时考虑到早期检测对于最大限度地减少作物产量损失至关重要。利用支持向量机(SVM)、决策树(DT)、k近邻KNN、Naïve贝叶斯(NB)、随机森林(RF)和顺序卷积神经网络(CNN)等各种传统ML算法来获取植物病害检测效率。与此相反,提出了一种改进版的CNN (MCNN),结合SVM原理,提高了标准CNN的性能。新建立的名为Yellow Rust 2022-2023 (YR-22/23)的数据集用于估计和比较所考虑的ML/DL算法的性能。此外,一个名为YellowRust-19的基准数据集被考虑用于ML/DL算法的交叉验证。结果表明,MCNN在准确率(1.2 %)指标上优于标准算法(CNN),并且具有很高的时间效率。本文提出的改进CNN方法对小麦黄锈病的预测准确率达到了98% %左右。结果表明,ML/DL方法的合并在提高植物病害检测的整体效率方面具有很大的前景。
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引用次数: 0
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Current Plant Biology
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