Current Plant Biology最新文献_第9页

Heritable variation in root emergence during post-drought recovery reveals potential links to seedling drought recovery in rice 干旱后恢复期间根系出苗的遗传变异揭示了水稻幼苗干旱恢复的潜在联系

IF 5.4 Q1 PLANT SCIENCES

Current Plant Biology

Pub Date : 2025-06-16 DOI: 10.1016/j.cpb.2025.100509

Lukas Krusenbaum , Matthias Wissuwa , Lam Thi Dinh

Drought stress is a significant factor limiting rice yields worldwide. Effective drought tolerance involves both the ability of a plant to withstand water-limited conditions and the capacity to recover after rehydration. As rainfall patterns shift due to climate change, adaptation to variations in water availability during the growth period becomes increasingly important. Given the critical role of crown root number and length in drought response, understanding these traits is crucial. In this study, we evaluated the ability of rice genotypes to produce new crown roots following drought stress, using both a QTL mapping population and a diverse set of 3K-Rice Genomes Project accessions. Our results revealed high heritability (H² = 0.65) for new root number (NRN), as well as significant genotypic variation in NRN and new root length (NRL) during recovery. They are independent of general root vigor or drought tolerance under stress. A newly developed, simple screening method was validated in greenhouse and field trials, showing consistent genotype-specific responses, with a significant correlation (R = 0.73, p = 0.007). Varieties such as DJ123 and CHILE BORO maintained high NRN values under both water bath and soil-based recovery conditions, whereas IR64, despite producing many roots, showed limited recovery potential. Candidate loci associated with recovery-related root traits partially overlapped with known QTL for rooting ability and drought response, indicating both novel and previously characterized genomic regions. Our findings demonstrate that new root development during recovery is a distinct and heritable trait with potential for use in breeding programs.

干旱胁迫是世界范围内限制水稻产量的重要因素。有效的抗旱性既包括植物对水限制条件的承受能力，也包括补液后的恢复能力。由于气候变化导致降雨模式发生变化，适应生长期水分供应的变化变得越来越重要。考虑到冠根数和长度在干旱响应中的关键作用，了解这些性状是至关重要的。在这项研究中，我们利用一个QTL定位群体和一组不同的3k -水稻基因组计划资料，评估了水稻基因型在干旱胁迫下产生新冠根的能力。结果表明，新根数遗传力高（H²= 0.65），新根数和新根长在恢复过程中存在显著的基因型变异。它们在逆境下不受根系活力或抗旱性的影响。在温室和田间试验中验证了一种新开发的简单筛选方法，显示出一致的基因型特异性反应，相关性显著（R = 0.73, p = 0.007）。DJ123和智利BORO等品种在水浴和土基恢复条件下均保持较高的NRN值，而IR64虽然根系数量多，但恢复潜力有限。与恢复相关的根系性状相关的候选位点与已知的生根能力和干旱响应QTL部分重叠，表明这是新的和先前表征的基因组区域。我们的研究结果表明，在恢复过程中新根的发育是一种独特的可遗传性状，具有潜在的育种应用潜力。

{"title":"Heritable variation in root emergence during post-drought recovery reveals potential links to seedling drought recovery in rice","authors":"Lukas Krusenbaum , Matthias Wissuwa , Lam Thi Dinh","doi":"10.1016/j.cpb.2025.100509","DOIUrl":"10.1016/j.cpb.2025.100509","url":null,"abstract":"<div><div>Drought stress is a significant factor limiting rice yields worldwide. Effective drought tolerance involves both the ability of a plant to withstand water-limited conditions and the capacity to recover after rehydration. As rainfall patterns shift due to climate change, adaptation to variations in water availability during the growth period becomes increasingly important. Given the critical role of crown root number and length in drought response, understanding these traits is crucial. In this study, we evaluated the ability of rice genotypes to produce new crown roots following drought stress, using both a QTL mapping population and a diverse set of 3K-Rice Genomes Project accessions. Our results revealed high heritability (H² = 0.65) for new root number (NRN), as well as significant genotypic variation in NRN and new root length (NRL) during recovery. They are independent of general root vigor or drought tolerance under stress. A newly developed, simple screening method was validated in greenhouse and field trials, showing consistent genotype-specific responses, with a significant correlation (R = 0.73, p = 0.007). Varieties such as DJ123 and CHILE BORO maintained high NRN values under both water bath and soil-based recovery conditions, whereas IR64, despite producing many roots, showed limited recovery potential. Candidate loci associated with recovery-related root traits partially overlapped with known QTL for rooting ability and drought response, indicating both novel and previously characterized genomic regions. Our findings demonstrate that new root development during recovery is a distinct and heritable trait with potential for use in breeding programs.</div></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"43 ","pages":"Article 100509"},"PeriodicalIF":5.4,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144306293","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}

引用次数: 0

Sodium nitroprusside as a priming agent induces drought stress tolerance in Citrus 硝普钠诱导柑橘抗旱性

IF 5.4 Q1 PLANT SCIENCES

Current Plant Biology

Pub Date : 2025-06-09 DOI: 10.1016/j.cpb.2025.100508

Emanuele Scialò , Angelo Sicilia , Angela Roberta Lo Piero

Priming is a process whereby exposure to a mild stress or specific chemical stimulus enhances plants' resilience to future biotic and abiotic stresses. Signalling molecules such as hydrogen peroxide (H₂O₂) and nitric oxide (NO) function as priming agents. In this study, Bitters (C22) citrus rootstock was treated with the NO donor sodium nitroprusside (SNP) and subjected to drought stress. Malondialdehyde (MDA) and H₂O₂ levels were measured to assess oxidative stress. Primed plants showed significantly higher tolerance to water scarcity than non-primed ones. RNA-seq analysis revealed that priming, followed by drought stress, regulated a broad spectrum of stress responses, enhancing the expression of genes involved in photosynthetic efficiency and antioxidant activity, reallocating energy, and reinforcing external barriers and xylem vessels. As concerns phytohormones, analysis of gene expression clearly indicated that auxin biosynthesis and signalling were activated, whereas those involving ethylene were repressed. Moreover, the application of weighted gene co-expression network analysis (WGCNA) enabled the identification of genes whose expression showed positive or negative correlations with the levels of MDA and/or H₂O₂. This study provides insights into the role of priming in improving Citrus adaptability to water scarcity and identifying molecular strategies and candidate genes to enhance drought tolerance. To our knowledge, this is the first study correlating transcriptomic data with priming-induced drought tolerance in Citrus.

启动是一个过程，暴露于温和的压力或特定的化学刺激，以提高植物对未来的生物和非生物压力的恢复能力。过氧化氢（H2O2）和一氧化氮（NO）等信号分子起着引发剂的作用。本研究采用NO供体硝普钠（SNP）处理Bitters （C22）柑橘砧木，进行干旱胁迫。测定丙二醛（MDA）和H2O2水平以评估氧化应激。处理过的植株对缺水的耐受性显著高于未处理过的植株。RNA-seq分析显示，干旱胁迫后的启动调控了广泛的胁迫反应，增强了参与光合效率和抗氧化活性、能量重新分配、强化外部屏障和木质部导管的基因的表达。在植物激素方面，基因表达分析清楚地表明生长素的生物合成和信号传导被激活，而涉及乙烯的基因则被抑制。此外，应用加权基因共表达网络分析（weighted gene co-expression network analysis， WGCNA），可以鉴定出表达与MDA和/或H2O2水平呈正相关或负相关的基因。本研究揭示了启动在提高柑橘对缺水的适应性、确定提高柑橘抗旱性的分子策略和候选基因中的作用。据我们所知，这是第一个将转录组学数据与柑桔引物诱导的耐旱性联系起来的研究。

{"title":"Sodium nitroprusside as a priming agent induces drought stress tolerance in Citrus","authors":"Emanuele Scialò , Angelo Sicilia , Angela Roberta Lo Piero","doi":"10.1016/j.cpb.2025.100508","DOIUrl":"10.1016/j.cpb.2025.100508","url":null,"abstract":"<div><div>Priming is a process whereby exposure to a mild stress or specific chemical stimulus enhances plants' resilience to future biotic and abiotic stresses. Signalling molecules such as hydrogen peroxide (H<sub>2</sub>O<sub>2</sub>) and nitric oxide (NO) function as priming agents. In this study, Bitters (C22) citrus rootstock was treated with the NO donor sodium nitroprusside (SNP) and subjected to drought stress. Malondialdehyde (MDA) and H<sub>2</sub>O<sub>2</sub> levels were measured to assess oxidative stress. Primed plants showed significantly higher tolerance to water scarcity than non-primed ones. RNA-seq analysis revealed that priming, followed by drought stress, regulated a broad spectrum of stress responses, enhancing the expression of genes involved in photosynthetic efficiency and antioxidant activity, reallocating energy, and reinforcing external barriers and xylem vessels. As concerns phytohormones, analysis of gene expression clearly indicated that auxin biosynthesis and signalling were activated, whereas those involving ethylene were repressed. Moreover, the application of weighted gene co-expression network analysis (WGCNA) enabled the identification of genes whose expression showed positive or negative correlations with the levels of MDA and/or H<sub>2</sub>O<sub>2</sub>. This study provides insights into the role of priming in improving <em>Citrus</em> adaptability to water scarcity and identifying molecular strategies and candidate genes to enhance drought tolerance. To our knowledge, this is the first study correlating transcriptomic data with priming-induced drought tolerance in <em>Citrus</em>.</div></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"43 ","pages":"Article 100508"},"PeriodicalIF":5.4,"publicationDate":"2025-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144272489","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}

引用次数: 0

Endophytic microbes enhance sugarcane defense against Sporisorium scitamineum by activating calcium signaling and stress-responsive traits 内生微生物通过激活钙信号和胁迫响应特性增强甘蔗对甘蔗孢杆菌的防御能力

IF 5.4 Q1 PLANT SCIENCES

Current Plant Biology

Pub Date : 2025-06-06 DOI: 10.1016/j.cpb.2025.100506

Faisal Mehdi , Yuanli Wu , Yimei Gan , Zhengying Cao , Shuting Jiang , Limei Zan , Shuzhen Zhang , Benpeng Yang

Sugarcane, a widely grown crop, faces many challenges from pests, diseases, and environmental stresses. One of the most serious threats is smut disease, caused by the fungus Sporisorium scitamineum (SS). Although there are methods to control it, managing this disease effectively is still a big challenge. This study evaluates the synergistic application of endophytic bacteria Bacillus sp. QN2MO-1 (BS) and Pseudomonas chlororaphis (PS) as a biocontrol approach to combat smut disease. Two sugarcane cultivars, ROC22 and Zhongtang 3, were initially grown in pots and later relocated to field conditions. Endophyte applications and SS infection were validated using qRT-PCR. A detailed assessment was conducted on physiological and morphological parameters, antioxidant enzyme activities, stress indicators, and the expression of stress-responsive genes. Results demonstrated that BS and PS, either individually or combined, effectively suppressed smut disease. Enhanced expression of defense-related genes (ScCAT1, SOD1 and PR1.04). Increased antioxidant enzyme activities (SOD, CAT, POD) were observed, particularly in the resistant cultivar Zhongtang 3. Elevated levels of salicylic acid (SA) and jasmonic acid (JA) indicated the activation of stress-related pathways, enhancing defense mechanisms. Endophyte-treated plants exhibited maximum growth and photosynthetic rates. Conversely, reduced malondialdehyde (MDA) and hydrogen peroxide (H₂O₂) levels suggested mitigation of oxidative stress. In the case of CAMTAs genes expression profiling, SsnpCAMTA5 upregulated in both cultivars, SsnpCAMTA7, SsnpCAMTA8 upregulated in Zhongtang 3. SsnpCAMTA12 downregulated in only Zhongtang 3 both time points (30 and 60 dpi). This result suggest that the bacterial endophytes triggered the pathogens related genes. These findings emphasize the potential of BS and PS as a sustainable, innovative biocontrol strategy, offering a promising solution to enhance sugarcane resilience and mitigate smut disease through integrated biological approaches.

甘蔗是一种广泛种植的作物，面临着病虫害和环境压力等诸多挑战。最严重的威胁之一是黑穗病，由真菌孢子菌（Sporisorium schitamineum， SS）引起。尽管有控制该病的方法，但有效管理该病仍然是一个巨大的挑战。本研究评价了内生细菌Bacillus sp. QN2MO-1 （BS）和绿假单胞菌（Pseudomonas chlororaphis， PS）协同防治黑穗病的效果。两个甘蔗品种ROC22和中糖3号最初在盆栽中种植，后来转移到田间条件下。利用qRT-PCR验证内生菌应用和SS感染。对其生理形态参数、抗氧化酶活性、胁迫指标及应激反应基因表达进行了详细评价。结果表明，BS和PS单独或联合施用均能有效抑制黑穗病的发生。防御相关基因（ScCAT1、SOD1和PR1.04）表达增强。抗氧化酶（SOD、CAT、POD）活性明显升高，其中以抗性品种中唐3号表现最为明显。水杨酸（SA）和茉莉酸（JA）水平的升高表明应激相关通路的激活，增强了防御机制。内生菌处理的植株生长和光合速率最高。相反，降低丙二醛（MDA）和过氧化氢（H₂O₂）水平表明氧化应激减轻。在CAMTAs基因表达谱分析中，SsnpCAMTA5在两个品种中均上调，SsnpCAMTA7、SsnpCAMTA8在中唐3中上调。SsnpCAMTA12仅在中唐3号（30和60 dpi）两个时间点下调。这说明细菌内生菌触发了病原菌相关基因。这些发现强调了BS和PS作为一种可持续的、创新的生物防治策略的潜力，为通过综合生物学方法提高甘蔗抗灾能力和减轻黑穗病提供了一种有希望的解决方案。

{"title":"Endophytic microbes enhance sugarcane defense against Sporisorium scitamineum by activating calcium signaling and stress-responsive traits","authors":"Faisal Mehdi , Yuanli Wu , Yimei Gan , Zhengying Cao , Shuting Jiang , Limei Zan , Shuzhen Zhang , Benpeng Yang","doi":"10.1016/j.cpb.2025.100506","DOIUrl":"10.1016/j.cpb.2025.100506","url":null,"abstract":"<div><div>Sugarcane, a widely grown crop, faces many challenges from pests, diseases, and environmental stresses. One of the most serious threats is smut disease, caused by the fungus <em>Sporisorium scitamineum</em> (SS). Although there are methods to control it, managing this disease effectively is still a big challenge. This study evaluates the synergistic application of endophytic bacteria <em>Bacillus sp. QN2MO-1</em> (BS) and <em>Pseudomonas chlororaphis</em> (PS) as a biocontrol approach to combat smut disease. Two sugarcane cultivars, ROC22 and Zhongtang 3, were initially grown in pots and later relocated to field conditions. Endophyte applications and SS infection were validated using qRT-PCR. A detailed assessment was conducted on physiological and morphological parameters, antioxidant enzyme activities, stress indicators, and the expression of stress-responsive genes. Results demonstrated that BS and PS, either individually or combined, effectively suppressed smut disease. Enhanced expression of defense-related genes (<em>ScCAT1, SOD1</em> and <em>PR1.04)</em>. Increased antioxidant enzyme activities (SOD, CAT, POD) were observed, particularly in the resistant cultivar Zhongtang 3. Elevated levels of salicylic acid (SA) and jasmonic acid (JA) indicated the activation of stress-related pathways, enhancing defense mechanisms. Endophyte-treated plants exhibited maximum growth and photosynthetic rates. Conversely, reduced malondialdehyde (MDA) and hydrogen peroxide (H₂O₂) levels suggested mitigation of oxidative stress. In the case of CAMTAs genes expression profiling, <em>SsnpCAMTA5</em> upregulated in both cultivars, <em>SsnpCAMTA7, SsnpCAMTA8 upregulated in</em> Zhongtang 3. <em>SsnpCAMTA12</em> downregulated in only Zhongtang 3 both time points (30 and 60 dpi). This result suggest that the bacterial endophytes triggered the pathogens related genes. These findings emphasize the potential of BS and PS as a sustainable, innovative biocontrol strategy, offering a promising solution to enhance sugarcane resilience and mitigate smut disease through integrated biological approaches.</div></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"43 ","pages":"Article 100506"},"PeriodicalIF":5.4,"publicationDate":"2025-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144261521","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}

引用次数: 0

Intra- and inter-population variation in Spinacia turkestanica: Implications for spinach genetic resources sampling 土耳其菠菜居群内和居群间变异：菠菜遗传资源取样的意义

IF 5.4 Q1 PLANT SCIENCES

Current Plant Biology

Pub Date : 2025-06-06 DOI: 10.1016/j.cpb.2025.100507

Rob van Treuren , Magdalena Krysiak , Jan-Kees Goud , Ryo Kimura , Chris Kik

Spinacia turkestanica Iljin is closely related to cultivated spinach (S. oleracea L.) and therefore of interest to genebank curators and plant breeders. In 2008 an expedition was carried out in Tajikistan and Uzbekistan to collect seed samples of S. turkestanica. Eighteen of these accessions and two additional accessions from Turkmenistan were characterized for 21 phenotypic traits and 50 SNP markers to study the distribution of variation within and between populations. Six varieties of cultivated spinach were included in the study as references. In general, S. turkestanica was clearly distinct from the reference varieties for phenotypic and molecular diversity. The main part of the observed diversity in S. turkestanica was distributed within rather than between populations. The populations from Tajikistan and Uzbekistan showed a positive correlation between phenotypic and genotypic distance (r = 0.458, p < 0.001) and between geographic distance and genotypic distance (r = 0.515, p < 0.001). Genetic differentiation was largest between populations from Tajikistan and populations from Uzbekistan, which are separated by the Zarafshan mountains. A resampling study showed that sampling 30–50 plants from each of 5–6 geographically widespread populations is sufficient to capture more than 98 % of the observed SNP alleles and more than 99 % of the observed phenotypic variation within the targeted area in Tajikistan and Uzbekistan. Whether this recommendation also holds for adaptive variation, such as resistance to biotic and abiotic stress, is subject of further study.

turkestanica Iljin与栽培菠菜（S. oleracea L.）密切相关，因此对基因库管理员和植物育种者感兴趣。2008年，在塔吉克斯坦和乌兹别克斯坦进行了一次考察，以收集S. turkestanica的种子样本。其中18份材料和另外2份来自土库曼斯坦的材料被鉴定为21个表型性状和50个SNP标记，以研究群体内和群体间的变异分布。6个栽培菠菜品种被纳入研究作为参考。总体而言，土耳其斯坦树在表型和分子多样性上与参考品种明显不同。观察到的土耳其南枝多样性主要分布于居群内而非居群间。塔吉克斯坦和乌兹别克斯坦人群表型与基因型距离呈正相关（r = 0.458,p <； 0.001），地理距离与基因型距离呈正相关（r = 0.515,p <； 0.001）。来自塔吉克斯坦的种群和来自乌兹别克斯坦的种群之间的遗传分化最大，这两个种群被Zarafshan山脉隔开。一项重新采样研究表明，在塔吉克斯坦和乌兹别克斯坦的目标区域内，从5-6个地理上广泛分布的种群中每个种群取样30-50株植物，就足以捕获观察到的SNP等位基因的98% %以上和观察到的表型变异的99% %以上。这一建议是否也适用于适应性变异，如对生物和非生物胁迫的抗性，还有待进一步研究。

{"title":"Intra- and inter-population variation in Spinacia turkestanica: Implications for spinach genetic resources sampling","authors":"Rob van Treuren , Magdalena Krysiak , Jan-Kees Goud , Ryo Kimura , Chris Kik","doi":"10.1016/j.cpb.2025.100507","DOIUrl":"10.1016/j.cpb.2025.100507","url":null,"abstract":"<div><div><em>Spinacia turkestanica</em> Iljin is closely related to cultivated spinach (<em>S. oleracea</em> L.) and therefore of interest to genebank curators and plant breeders. In 2008 an expedition was carried out in Tajikistan and Uzbekistan to collect seed samples of <em>S. turkestanica</em>. Eighteen of these accessions and two additional accessions from Turkmenistan were characterized for 21 phenotypic traits and 50 SNP markers to study the distribution of variation within and between populations. Six varieties of cultivated spinach were included in the study as references. In general, <em>S. turkestanica</em> was clearly distinct from the reference varieties for phenotypic and molecular diversity. The main part of the observed diversity in <em>S. turkestanica</em> was distributed within rather than between populations. The populations from Tajikistan and Uzbekistan showed a positive correlation between phenotypic and genotypic distance (r = 0.458, p < 0.001) and between geographic distance and genotypic distance (r = 0.515, p < 0.001). Genetic differentiation was largest between populations from Tajikistan and populations from Uzbekistan, which are separated by the Zarafshan mountains. A resampling study showed that sampling 30–50 plants from each of 5–6 geographically widespread populations is sufficient to capture more than 98 % of the observed SNP alleles and more than 99 % of the observed phenotypic variation within the targeted area in Tajikistan and Uzbekistan. Whether this recommendation also holds for adaptive variation, such as resistance to biotic and abiotic stress, is subject of further study.</div></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"43 ","pages":"Article 100507"},"PeriodicalIF":5.4,"publicationDate":"2025-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144280375","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}

引用次数: 0

Drought mitigation in plants through root exudate-mediated rhizosphere interactions: Opportunities for future research 通过根分泌物介导的根际相互作用缓解植物干旱：未来研究的机会

IF 5.4 Q1 PLANT SCIENCES

Current Plant Biology

Pub Date : 2025-06-04 DOI: 10.1016/j.cpb.2025.100504

Salam Suresh Singh, Ngangbam Somen Singh, Emilynruwaka Lamare, Ningthoujam Ranjana Devi, Shadokpam Anjali Devi, Remei Kaguijenliu, Biki Takum, Keshav Kumar Upadhyay, Shri Kant Tripathi

Drought is among the most significant environmental factors that frequently limits the growth and productivity of terrestrial plants, making them susceptible to various diseases and resulting in the death of many species each year. Because the plants could not relocate to avoid environmental stresses (i.e., drought, cold temperatures, and high salinity), they developed specific adaptive mechanisms at the root-soil interface to cope with these stresses, especially drought. For instance, under drought conditions, plants change the composition of root exudates by increasing the concentrations of abscisic acid (ABA). This hormone is transported through the xylem transport system to plant leaves, signalling the leaf stomata to regulate stomatal activity. It reduces water loss in plants and enhances their resistance to drought conditions. This review examines the role of soil-root-microbe interactions under drought stress and highlights how this interaction influences nutrient cycling, osmotic pressure adjustment, signalling pathways, and microbial recruitment to enhance plant resilience under drought stress. Furthermore, the mechanisms by which root exudates enhance plant resilience through nitrogen and phosphorus cycling, detoxification of aluminium toxicity, and regulation of stomatal activity are discussed. Understanding these processes and mechanisms provides new insights into developing sustainable forest and agricultural management practices that enhance plant productivity under drought conditions by increasing their resilience in a changing environment.

干旱是最重要的环境因素之一，经常限制陆生植物的生长和生产力，使它们容易受到各种疾病的影响，并导致每年许多物种死亡。由于植物不能迁移以避免环境胁迫（如干旱、低温和高盐度），因此它们在根-土壤界面发展了特定的适应机制来应对这些胁迫，特别是干旱。例如，在干旱条件下，植物通过增加脱落酸（ABA）的浓度来改变根分泌物的组成。这种激素通过木质部运输系统输送到植物叶片，向叶片气孔发出信号，调节气孔活动。它减少了植物的水分流失，增强了它们对干旱条件的抵抗力。本文综述了干旱胁迫下土壤-根-微生物相互作用的作用，并强调了这种相互作用如何影响养分循环、渗透压调节、信号通路和微生物招募，以增强植物在干旱胁迫下的抗逆性。此外，还讨论了根系分泌物通过氮磷循环、铝毒解毒和调节气孔活性等途径增强植物抗逆性的机制。了解这些过程和机制为制定可持续森林和农业管理实践提供了新的见解，这些实践可通过提高植物在不断变化的环境中的适应能力来提高干旱条件下的植物生产力。

{"title":"Drought mitigation in plants through root exudate-mediated rhizosphere interactions: Opportunities for future research","authors":"Salam Suresh Singh, Ngangbam Somen Singh, Emilynruwaka Lamare, Ningthoujam Ranjana Devi, Shadokpam Anjali Devi, Remei Kaguijenliu, Biki Takum, Keshav Kumar Upadhyay, Shri Kant Tripathi","doi":"10.1016/j.cpb.2025.100504","DOIUrl":"10.1016/j.cpb.2025.100504","url":null,"abstract":"<div><div>Drought is among the most significant environmental factors that frequently limits the growth and productivity of terrestrial plants, making them susceptible to various diseases and resulting in the death of many species each year. Because the plants could not relocate to avoid environmental stresses (i.e., drought, cold temperatures, and high salinity), they developed specific adaptive mechanisms at the root-soil interface to cope with these stresses, especially drought. For instance, under drought conditions, plants change the composition of root exudates by increasing the concentrations of abscisic acid (ABA). This hormone is transported through the xylem transport system to plant leaves, signalling the leaf stomata to regulate stomatal activity. It reduces water loss in plants and enhances their resistance to drought conditions. This review examines the role of soil-root-microbe interactions under drought stress and highlights how this interaction influences nutrient cycling, osmotic pressure adjustment, signalling pathways, and microbial recruitment to enhance plant resilience under drought stress. Furthermore, the mechanisms by which root exudates enhance plant resilience through nitrogen and phosphorus cycling, detoxification of aluminium toxicity, and regulation of stomatal activity are discussed. Understanding these processes and mechanisms provides new insights into developing sustainable forest and agricultural management practices that enhance plant productivity under drought conditions by increasing their resilience in a changing environment.</div></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"43 ","pages":"Article 100504"},"PeriodicalIF":5.4,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144229910","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}

引用次数: 0

Integrative multi-omics analysis of rice grown continuously under P-starvation stress unravels Pup1-mediated regulatory complex for resilience to phosphorus deficiency 水稻在缺磷胁迫下连续生长的综合多组学分析揭示了pup1介导的缺磷恢复调节复合物

IF 5.4 Q1 PLANT SCIENCES

Current Plant Biology

Pub Date : 2025-06-03 DOI: 10.1016/j.cpb.2025.100505

S. Tamil Selvan , Pallavi , Karishma Seem , Venkata Y. Amara , V. Prathap , K.K. Vinod , Archana Singh , Trilochan Mohapatra , Suresh Kumar

Phosphorus (P) is a vital macronutrient for various physiological/biochemical activities like ATP production through respiration/photosynthesis, carbohydrate metabolism, nucleic acid/membrane synthesis, intracellular signalling, and functioning of enzymes. To deal with P-starvation/deficiency, plant modulates gene expression for adjusting metabolic/signaling pathways. For P homeostasis, metabolic activities are reoriented by transcriptional as well as post-transcriptional/post-translational modulations to integrate physio-biochemical, (epi)genomic, proteomic, and metabolomic processes. Despite the advances in understanding P-starvation/deficiency responses of plants, the genes/regulatory processes for resilience to low-P stress in plants remain enigmatic. To unravel the genes/pathways and regulatory actions of Pup1 QTL on P-starvation in rice, integrative multi-omics analysis of a near-isogenic line-23 (NIL-23, harboring Pup1) and its parental high-yielding rice variety was performed. The multi-omics analysis indicated adoption of multifaceted tolerance mechanisms, integrated nutrient acquisition/transport, hormone signaling, cell wall modification, metabolic modulations, and epigenetic modifications, controlled by Pup1 in NIL-23. Transcriptomic and proteomic analyses highlighted up-regulation of genes/proteins involved in starch/sucrose/nucleotide-sugars metabolism, biosynthesis of secondary metabolites, energy metabolism, and phytohormone signaling in NIL-23. As Pup1 does not carry many protein-coding genes, regulatory functions of the QTL through transcriptomic/epigenetic cascades (via key regulators like transcription factors, chromatin remodelers, and epigenetic factors) modulate gene expression on P-starvation. These affect crucial processes like adaptive changes in plant’s morphology, nutrient acquisition, and metabolic reprogramming in NIL-23. The present study provides a better understanding on Pup1-mediated regulatory complex for resilience to nutrient/phosphorus deficiency, which might help improving P utilization efficiency of crop plants for enhanced productivity in P-scarce soils.

磷(P)是各种生理/生化活动的重要常量营养素，如通过呼吸/光合作用产生ATP、碳水化合物代谢、核酸/膜合成、细胞内信号传导和酶的功能。为了应对磷饥饿/缺乏，植物通过调节基因表达来调节代谢/信号通路。对于磷稳态，代谢活动通过转录以及转录后/翻译后调节重新定向，以整合生理生化、（epi）基因组、蛋白质组学和代谢组学过程。尽管对植物缺磷/缺磷反应的了解有所进展，但植物抗低磷胁迫的基因/调控过程仍然是一个谜。为了揭示Pup1 QTL在水稻缺磷过程中的基因通路和调控作用，对一个近等基因系23 （nil23，携带Pup1）及其亲本高产水稻品种进行了综合多组学分析。多组学分析表明，NIL-23的多种耐受机制，包括营养获取/转运、激素信号、细胞壁修饰、代谢调节和表观遗传修饰，均由Pup1控制。转录组学和蛋白质组学分析强调了NIL-23中参与淀粉/蔗糖/核苷酸-糖代谢、次生代谢物生物合成、能量代谢和植物激素信号传导的基因/蛋白质的上调。由于Pup1不携带许多蛋白质编码基因，QTL通过转录组/表观遗传级联（通过转录因子、染色质重塑因子和表观遗传因子等关键调节因子）调节p -饥饿的基因表达。这些影响了植物形态的适应性变化、营养获取和NIL-23的代谢重编程等关键过程。本研究为进一步了解pup1介导的养分/磷缺乏弹性调控复合体提供了理论依据，有助于提高作物对磷的利用效率，提高缺磷土壤的生产力。

{"title":"Integrative multi-omics analysis of rice grown continuously under P-starvation stress unravels Pup1-mediated regulatory complex for resilience to phosphorus deficiency","authors":"S. Tamil Selvan , Pallavi , Karishma Seem , Venkata Y. Amara , V. Prathap , K.K. Vinod , Archana Singh , Trilochan Mohapatra , Suresh Kumar","doi":"10.1016/j.cpb.2025.100505","DOIUrl":"10.1016/j.cpb.2025.100505","url":null,"abstract":"<div><div>Phosphorus (P) is a vital macronutrient for various physiological/biochemical activities like ATP production through respiration/photosynthesis, carbohydrate metabolism, nucleic acid/membrane synthesis, intracellular signalling, and functioning of enzymes. To deal with P-starvation/deficiency, plant modulates gene expression for adjusting metabolic/signaling pathways. For P homeostasis, metabolic activities are reoriented by transcriptional as well as post-transcriptional/post-translational modulations to integrate physio-biochemical, (epi)genomic, proteomic, and metabolomic processes. Despite the advances in understanding P-starvation/deficiency responses of plants, the genes/regulatory processes for resilience to low-P stress in plants remain enigmatic. To unravel the genes/pathways and regulatory actions of <em>Pup1</em> QTL on P-starvation in rice, integrative multi-omics analysis of a near-isogenic line-23 (NIL-23, harboring <em>Pup1</em>) and its parental high-yielding rice variety was performed. The multi-omics analysis indicated adoption of multifaceted tolerance mechanisms, integrated nutrient acquisition/transport, hormone signaling, cell wall modification, metabolic modulations, and epigenetic modifications, controlled by <em>Pup1</em> in NIL-23. Transcriptomic and proteomic analyses highlighted up-regulation of genes/proteins involved in starch/sucrose/nucleotide-sugars metabolism, biosynthesis of secondary metabolites, energy metabolism, and phytohormone signaling in NIL-23. As <em>Pup1</em> does not carry many protein-coding genes, regulatory functions of the QTL through transcriptomic/epigenetic cascades (via key regulators like transcription factors, chromatin remodelers, and epigenetic factors) modulate gene expression on P-starvation. These affect crucial processes like adaptive changes in plant’s morphology, nutrient acquisition, and metabolic reprogramming in NIL-23. The present study provides a better understanding on <em>Pup1</em>-mediated regulatory complex for resilience to nutrient/phosphorus deficiency, which might help improving P utilization efficiency of crop plants for enhanced productivity in P-scarce soils.</div></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"43 ","pages":"Article 100505"},"PeriodicalIF":5.4,"publicationDate":"2025-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144261520","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}

引用次数: 0

Decoding core molecular mechanisms related to multiple abiotic stress adaptation in cotton: Insights from RNA-seq data meta-analysis in combination with machine learning approach 解码棉花多重非生物胁迫适应相关的核心分子机制：结合机器学习方法的RNA-seq数据元分析见解

IF 5.4 Q1 PLANT SCIENCES

Current Plant Biology

Pub Date : 2025-06-01 DOI: 10.1016/j.cpb.2025.100503

Bahman Panahi , Rasmieh Hamid

Drought, salinity and alkaline conditions are the major constraints to cotton (Gossypium spp.) productivity and require the development of genotypes with increased resilience for sustainable cultivation. Abiotic stress tolerance in cotton involves complex gene networks and regulatory pathways. Transcriptome meta-analysis provides a robust approach to elucidate these mechanisms by integrating diverse data sets and identifying consistently responding genes. In this study, RNA-seq meta-analysis using p-value combination approach was harnessed to elucidate the core molecular mechanisms involved in adaptation to drought, salinity and alkaline stress in root and leaf tissues. Moreover, functional analysis of identified core genes were performed using GO and KEGG enrichment and protein-protein interaction network analysis. Prioritization of core genes was further performed using topological analysis of core gene networks and machine learning approach. Key genes identified as central regulatory hubs, such as Gh_A01G1844.1 (aquaporin PIP2–2), Gh_D03G1591.1 (ethylene-responsive transcription factor 5) and Gh_A05G1554.1 (dehydrin COR47), play a central role in adaptive responses, including osmotic adjustment, oxidative stress management and tissue-specific functionality. Enrichment analysis revealed that critical processes such as transcriptional regulation, macromolecular metabolism and cellular signaling pathways are crucial for stress resilience. In addition, the prediction of transcription factor (TF) networks identified the major TF families bHLH, WRKY, NAC, ERF and MYB, which integrate different regulatory mechanisms. In addition, the network analysis revealed important signaling pathways such as ethylene and nodulation, with genes such as Dehydration-Responsive Element 1 D (DRE1D) and Cycling DOF Factor 1 (CDF1) contributing to adaptive responses. This study provides a valuable resource for breeding programs aimed at improving abiotic stress tolerance in cotton and offers insights into the genetic and functional basis of adaptation in different environmental contexts.

干旱、盐碱和碱性条件是制约棉花生产力的主要因素，因此需要开发抗灾能力强的基因型，以实现可持续种植。棉花的非生物抗逆性涉及复杂的基因网络和调控途径。转录组荟萃分析通过整合不同的数据集和识别一致的应答基因，为阐明这些机制提供了一种强有力的方法。本研究利用RNA-seq荟萃分析，利用p值组合方法阐明了根和叶组织适应干旱、盐度和碱性胁迫的核心分子机制。此外，利用GO和KEGG富集和蛋白相互作用网络分析对鉴定的核心基因进行功能分析。利用核心基因网络的拓扑分析和机器学习方法进一步进行核心基因的优先级排序。作为中心调控枢纽的关键基因，如Gh_A01G1844.1（水通道蛋白PIP2-2）、Gh_D03G1591.1（乙烯应答转录因子5）和Gh_A05G1554.1（脱氢蛋白COR47），在适应性反应中发挥核心作用，包括渗透调节、氧化应激管理和组织特异性功能。富集分析表明，转录调控、大分子代谢和细胞信号通路等关键过程对应激恢复至关重要。此外，转录因子（TF）网络预测确定了主要的TF家族bHLH、WRKY、NAC、ERF和MYB，它们整合了不同的调控机制。此外，网络分析揭示了乙烯和结瘤等重要信号通路，脱水响应元件1d （DRE1D）和循环DOF因子1 （CDF1）等基因参与了适应性反应。该研究为提高棉花的非生物抗逆性育种计划提供了宝贵的资源，并提供了对不同环境下适应的遗传和功能基础的见解。

{"title":"Decoding core molecular mechanisms related to multiple abiotic stress adaptation in cotton: Insights from RNA-seq data meta-analysis in combination with machine learning approach","authors":"Bahman Panahi , Rasmieh Hamid","doi":"10.1016/j.cpb.2025.100503","DOIUrl":"10.1016/j.cpb.2025.100503","url":null,"abstract":"<div><div>Drought, salinity and alkaline conditions are the major constraints to cotton (Gossypium spp.) productivity and require the development of genotypes with increased resilience for sustainable cultivation. Abiotic stress tolerance in cotton involves complex gene networks and regulatory pathways. Transcriptome meta-analysis provides a robust approach to elucidate these mechanisms by integrating diverse data sets and identifying consistently responding genes. In this study, RNA-seq meta-analysis using p-value combination approach was harnessed to elucidate the core molecular mechanisms involved in adaptation to drought, salinity and alkaline stress in root and leaf tissues. Moreover, functional analysis of identified core genes were performed using GO and KEGG enrichment and protein-protein interaction network analysis. Prioritization of core genes was further performed using topological analysis of core gene networks and machine learning approach. Key genes identified as central regulatory hubs, such as <em>Gh_A01G1844.1</em> (aquaporin PIP2–2), <em>Gh_D03G1591.1</em> (ethylene-responsive transcription factor 5) and <em>Gh_A05G1554.1</em> (dehydrin COR47), play a central role in adaptive responses, including osmotic adjustment, oxidative stress management and tissue-specific functionality. Enrichment analysis revealed that critical processes such as transcriptional regulation, macromolecular metabolism and cellular signaling pathways are crucial for stress resilience. In addition, the prediction of transcription factor (TF) networks identified the major TF families bHLH, WRKY, NAC, ERF and MYB, which integrate different regulatory mechanisms. In addition, the network analysis revealed important signaling pathways such as ethylene and nodulation, with genes such as Dehydration-Responsive Element 1 D (DRE1D) and Cycling DOF Factor 1 (CDF1) contributing to adaptive responses. This study provides a valuable resource for breeding programs aimed at improving abiotic stress tolerance in cotton and offers insights into the genetic and functional basis of adaptation in different environmental contexts.</div></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"43 ","pages":"Article 100503"},"PeriodicalIF":5.4,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144205752","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}

引用次数: 0

The “Ataulfo” mango (Mangifera indica L.) maintains its L- ascorbic acid content during fruit ripening: Insights into synthesis and recycling pathways “Ataulfo”芒果（Mangifera indica L.）在果实成熟过程中保持其L-抗坏血酸含量：合成和循环途径的见解

IF 5.4 Q1 PLANT SCIENCES

Current Plant Biology

Pub Date : 2025-05-29 DOI: 10.1016/j.cpb.2025.100502

Armida A. Gil-Salido , Carmen A. Contreras-Vergara , Ana Paulina Sortillón-Sortillón , Mitzuko Dautt-Castro , Agustín Rascón-Chu , Miguel A. Martínez-Téllez , Adriana Sañudo-Barajas , Sergio Casas-Flores , Rosalba Contreras-Martínez , Rosabel Velez-de la Rocha , Manuel A. Báez-Sañudo , Jugpreet Singh , María A. Islas-Osuna

Mango is consumed worldwide for its sweet flavor, pleasant aroma, high commercial value, and rich source of L-ascorbic acid (AA), an essential human micronutrient. AA is primarily synthesized in plants via the Smirnoff-Wheeler (SW) pathway. Alternative routes for AA synthesis, such as gulose, myo-inositol, and galacturonic acid, are proposed in some species alongside a recycling pathway that helps maintain AA homeostasis in plant cells. However, a formal genetic demonstration of the alternative routes for AA synthesis and recycling in mangoes remains. In this study, 165 genes associated with AA metabolism were identified in the “Tommy Atkins” mango genome; some of them were previously identified in mango “Ataulfo” and “Kent” transcriptomes. Physical-chemical parameters, AA content, and carbohydrate levels were measured in collected “Ataulfo” mangoes. The expression of SW key genes involved in AA synthesis from alternative and recycling pathways, was evaluated during postharvest ripening, and promoter regions of these genes were analyzed in silico for the presence of regulatory cis-elements. During ripening, transcript accumulation of MiGME-3, MiGGP-1, MiGalLDH, MiGALUR-1, MiPME-1, MIMDHAR-4, and MiAPX-4 from the SW, alternative and recycling pathways showed a significant increase of 3- to 10-fold. However, AA content remained relatively stable throughout ripening, averaging 124 mg/100 g fresh weight, suggesting additional regulatory factors that may counterbalance the increased synthesis. Promoter analysis revealed the presence of seven cis-elements associated with stress and ripening regulation, indicating potential regulatory mechanisms for the identified genes. More than one route could be active in mango fruits, contributing to AA biosynthesis and maintenance during ripening.

芒果因其甜美的风味、宜人的香气、高商业价值和丰富的人体必需微量营养素l -抗坏血酸（AA）来源而被全世界消费。AA主要通过Smirnoff-Wheeler （SW）途径在植物体内合成。在一些物种中，氨基酸合成的替代途径，如糖、肌醇和半乳糖醛酸，被认为是一个有助于维持植物细胞中AA稳态的循环途径。然而，芒果中AA合成和再循环途径的正式遗传证明仍然存在。在本研究中，在“Tommy Atkins”芒果基因组中鉴定了165个与AA代谢相关的基因；其中一些先前在芒果的“Ataulfo”和“Kent”转录组中被鉴定出来。测定了所采集的“Ataulfo”芒果的理化参数、AA含量和碳水化合物水平。在采后成熟过程中，研究人员评估了从替代途径和循环途径合成AA的SW关键基因的表达，并分析了这些基因的启动子区域是否存在调节顺式元件。在成熟过程中，MiGME-3、MiGGP-1、MiGalLDH、MiGALUR-1、MiPME-1、mimhar -4和MiAPX-4转录物从SW、替代途径和循环途径积累的量显著增加了3- 10倍。然而，在整个成熟过程中，AA含量保持相对稳定，平均为124 mg/100 g鲜重，这表明其他调节因素可能抵消了增加的合成。启动子分析揭示了7个与胁迫和成熟调控相关的顺式元件的存在，提示了所鉴定基因的潜在调控机制。芒果果实中可能有多种途径具有活性，有助于成熟过程中AA的生物合成和维持。

{"title":"The “Ataulfo” mango (Mangifera indica L.) maintains its L- ascorbic acid content during fruit ripening: Insights into synthesis and recycling pathways","authors":"Armida A. Gil-Salido , Carmen A. Contreras-Vergara , Ana Paulina Sortillón-Sortillón , Mitzuko Dautt-Castro , Agustín Rascón-Chu , Miguel A. Martínez-Téllez , Adriana Sañudo-Barajas , Sergio Casas-Flores , Rosalba Contreras-Martínez , Rosabel Velez-de la Rocha , Manuel A. Báez-Sañudo , Jugpreet Singh , María A. Islas-Osuna","doi":"10.1016/j.cpb.2025.100502","DOIUrl":"10.1016/j.cpb.2025.100502","url":null,"abstract":"<div><div>Mango is consumed worldwide for its sweet flavor, pleasant aroma, high commercial value, and rich source of L-ascorbic acid (AA), an essential human micronutrient. AA is primarily synthesized in plants via the Smirnoff-Wheeler (SW) pathway. Alternative routes for AA synthesis, such as gulose, myo-inositol, and galacturonic acid, are proposed in some species alongside a recycling pathway that helps maintain AA homeostasis in plant cells. However, a formal genetic demonstration of the alternative routes for AA synthesis and recycling in mangoes remains. In this study, 165 genes associated with AA metabolism were identified in the “Tommy Atkins” mango genome; some of them were previously identified in mango “Ataulfo” and “Kent” transcriptomes. Physical-chemical parameters, AA content, and carbohydrate levels were measured in collected “Ataulfo” mangoes. The expression of SW key genes involved in AA synthesis from alternative and recycling pathways, was evaluated during postharvest ripening, and promoter regions of these genes were analyzed <em>in silico</em> for the presence of regulatory <em>cis</em>-elements. During ripening, transcript accumulation of <em>MiGME-3, MiGGP-1, MiGalLDH, MiGALUR-1, MiPME-1, MIMDHAR-4,</em> and <em>MiAPX-4</em> from the SW, alternative and recycling pathways showed a significant increase of 3- to 10-fold. However, AA content remained relatively stable throughout ripening, averaging 124 mg/100 g fresh weight, suggesting additional regulatory factors that may counterbalance the increased synthesis. Promoter analysis revealed the presence of seven <em>cis</em>-elements associated with stress and ripening regulation, indicating potential regulatory mechanisms for the identified genes. More than one route could be active in mango fruits, contributing to AA biosynthesis and maintenance during ripening.</div></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"43 ","pages":"Article 100502"},"PeriodicalIF":5.4,"publicationDate":"2025-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144196045","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}

引用次数: 0

Improving EfficientNet_b0 for distinguishing rice from different origins: A deep learning method for geographical traceability in precision agriculture 改进用于区分不同产地水稻的EfficientNet_b0：精准农业中地理可追溯性的深度学习方法

IF 5.4 Q1 PLANT SCIENCES

Current Plant Biology

Pub Date : 2025-05-26 DOI: 10.1016/j.cpb.2025.100501

Helong Yu , Zhenyang Chen , Xiaoyan Liu , Shaozhong Song , Mojun Chen

Rice is one of the important crops for food supply, and there are multiple differences in the quality of rice grown in different geographic environments, which have an important impact on subsequent yield, economic efficiency, and food processing. Most of the current computer vision-based rice kernel classification focuses only on different varieties. In this study, we propose a method based on deep learning and image processing to recognize rice from different origins. First, Ji-Japonica 830 rice was collected from ten different regions, and a total of 30,000 images were obtained through image segmentation and data enhancement to participate in the training and testing of the model. Four lightweight networks and four classical networks were compared and tested in the pre-training phase, where EfficientNet_b0 obtained the highest accuracy of 93.38 %, and then EfficientNet_b0 was improved by introducing a dynamic adjustment strategy for the learning rate, removing the Dropout layer, and introducing a grouped convolution, which resulted in 96.80 % accuracy. The experimental results show that the method performs well in terms of classification accuracy, parameters, time, and robustness, and can effectively distinguish rice kernels from different geographic environments.

水稻是重要的粮食供应作物之一，不同地理环境下种植的水稻品质存在多重差异，这对后续产量、经济效益和食品加工都有重要影响。目前大多数基于计算机视觉的水稻籽粒分类只关注不同品种。在这项研究中，我们提出了一种基于深度学习和图像处理的方法来识别不同产地的大米。首先，采集10个不同地区的Ji-Japonica 830水稻，通过图像分割和数据增强，共获得3万张图像，参与模型的训练和测试。在预训练阶段对四种轻量级网络和四种经典网络进行了比较和测试，其中效率net_b0的准确率最高，达到93.38 %，然后通过引入学习率动态调整策略、去除Dropout层、引入分组卷积对效率net_b0进行了改进，准确率达到96.80 %。实验结果表明，该方法在分类精度、参数、时间和鲁棒性等方面都有较好的表现，能够有效区分不同地理环境下的米粒。

{"title":"Improving EfficientNet_b0 for distinguishing rice from different origins: A deep learning method for geographical traceability in precision agriculture","authors":"Helong Yu , Zhenyang Chen , Xiaoyan Liu , Shaozhong Song , Mojun Chen","doi":"10.1016/j.cpb.2025.100501","DOIUrl":"10.1016/j.cpb.2025.100501","url":null,"abstract":"<div><div>Rice is one of the important crops for food supply, and there are multiple differences in the quality of rice grown in different geographic environments, which have an important impact on subsequent yield, economic efficiency, and food processing. Most of the current computer vision-based rice kernel classification focuses only on different varieties. In this study, we propose a method based on deep learning and image processing to recognize rice from different origins. First, Ji-Japonica 830 rice was collected from ten different regions, and a total of 30,000 images were obtained through image segmentation and data enhancement to participate in the training and testing of the model. Four lightweight networks and four classical networks were compared and tested in the pre-training phase, where EfficientNet_b0 obtained the highest accuracy of 93.38 %, and then EfficientNet_b0 was improved by introducing a dynamic adjustment strategy for the learning rate, removing the Dropout layer, and introducing a grouped convolution, which resulted in 96.80 % accuracy. The experimental results show that the method performs well in terms of classification accuracy, parameters, time, and robustness, and can effectively distinguish rice kernels from different geographic environments.</div></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"43 ","pages":"Article 100501"},"PeriodicalIF":5.4,"publicationDate":"2025-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144196046","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}

引用次数: 0

Integrated QTL mapping and transcriptomic profiling elucidate molecular determinants of sucrose accumulation in apricot (Prunus armeniaca L) 综合QTL定位和转录组学分析阐明杏（Prunus armeniaca L）蔗糖积累的分子决定因素

IF 5.4 Q1 PLANT SCIENCES

Current Plant Biology

Pub Date : 2025-05-23 DOI: 10.1016/j.cpb.2025.100500

Fengchao Jiang , Li Yang , Junhuan Zhang , Meiling Zhang , Wenjian Yu , Haoyuan Sun

Apricot is a commercially vital stone fruit prized for its distinctive organoleptic characteristics and nutritional value. We developed an F1 population from ‘Chuanzhihong’ × ‘Luotuohuang’ to investigate the genetic basis of sugar metabolism. Whole-genome resequencing identified 63,162 high-quality InDel markers, while metabolomic profiling quantified soluble sugars (sucrose, glucose, fructose) across fruit developmental stages. Continuous variation in sugar accumulation patterns indicated polygenic inheritance. A high-density genetic map (601.5 cM, 0.44 cM average interval) revealed 20 stable QTLs across 8 linkage groups, explaining 8.0–16.2 % phenotypic variance for individual and total sugars. WGCNA identified sugar component-specific modules showing strong correlations (r = 0.57–0.95). Integrative analysis prioritized PA08G27233 as a hub gene within QTL intervals, encoding a SWEET transporter (designated PaSWEET1) with evolutionary conservation to AtSWEET1. This study elucidates molecular mechanisms of photoassimilate partitioning in apricot and provides genomic resources (high-resolution map, candidate genes) for marker-assisted breeding. The findings advance functional characterization of sugar metabolism pathways in Prunus species.

杏是一种商业上重要的核果，因其独特的感官特征和营养价值而受到珍视。为研究糖代谢的遗传基础，以‘川致红’× ‘骆驼黄’为材料，选育了一个F1群体。全基因组重测序鉴定出63,162个高质量InDel标记，代谢组学分析量化了果实发育阶段的可溶性糖（蔗糖、葡萄糖、果糖）。糖积累模式的持续变化表明多基因遗传。高密度遗传图谱（601.5 cM， 0.44 cM平均间隔）揭示了8个连锁群中的20个稳定qtl，解释了个体糖和总糖的8.0 - 16.2% %表型变异。WGCNA鉴定出糖组分特异性模块具有很强的相关性（r = 0.57-0.95）。整合分析将PA08G27233作为QTL区间内的枢纽基因，编码一个SWEET转运体（命名为PaSWEET1），并具有进化保守性。本研究阐明了杏光同化物质分配的分子机制，为标记辅助育种提供了基因组资源（高分辨率图谱、候选基因）。研究结果为李属植物糖代谢途径的功能表征提供了新的思路。

{"title":"Integrated QTL mapping and transcriptomic profiling elucidate molecular determinants of sucrose accumulation in apricot (Prunus armeniaca L)","authors":"Fengchao Jiang , Li Yang , Junhuan Zhang , Meiling Zhang , Wenjian Yu , Haoyuan Sun","doi":"10.1016/j.cpb.2025.100500","DOIUrl":"10.1016/j.cpb.2025.100500","url":null,"abstract":"<div><div>Apricot is a commercially vital stone fruit prized for its distinctive organoleptic characteristics and nutritional value. We developed an F1 population from ‘Chuanzhihong’ × ‘Luotuohuang’ to investigate the genetic basis of sugar metabolism. Whole-genome resequencing identified 63,162 high-quality InDel markers, while metabolomic profiling quantified soluble sugars (sucrose, glucose, fructose) across fruit developmental stages. Continuous variation in sugar accumulation patterns indicated polygenic inheritance. A high-density genetic map (601.5 cM, 0.44 cM average interval) revealed 20 stable QTLs across 8 linkage groups, explaining 8.0–16.2 % phenotypic variance for individual and total sugars. WGCNA identified sugar component-specific modules showing strong correlations (r = 0.57–0.95). Integrative analysis prioritized <em>PA08G27233</em> as a hub gene within QTL intervals, encoding a SWEET transporter (designated <em>PaSWEET1</em>) with evolutionary conservation to AtSWEET1. This study elucidates molecular mechanisms of photoassimilate partitioning in apricot and provides genomic resources (high-resolution map, candidate genes) for marker-assisted breeding. The findings advance functional characterization of sugar metabolism pathways in <em>Prunus</em> species.</div></div>","PeriodicalId":38090,"journal":{"name":"Current Plant Biology","volume":"43 ","pages":"Article 100500"},"PeriodicalIF":5.4,"publicationDate":"2025-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144168295","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}

引用次数: 0