cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.28333909.v1
title: The impact of Ca<sup>2+</sup> on the protective mechanisms of the photosystem under drought stress

description: External calcium ions (Ca<sup>2+</sup>) play a crucial role in mitigating drought stress in plants, as revealed through physiological and transcriptomic analyses using tobacco (Nicotiana tabacum L) as a model system. Under drought stress, leaves wilted, chlorophyll content decreased. The maximum photochemical efficiency of PSII (<i>F</i><sub>v</sub>/<i>F</i><sub>m</sub>) and the photosynthetic performance index decreased, fluorescence intensities at the K and L points increased, <i>Y</i><sub>(NPQ)</sub> increased, net photosynthetic rate (<i>P</i><sub>n</sub>) decreased, and PSI activity (ΔI/Io) was reduced. Upon application of external calcium under drought conditions, leaf wilting was reduced, chlorophyll content increased, <i>F</i><sub>v</sub>/<i>F</i><sub>m</sub>, PIabs, and PItotal improved, fluorescence intensities at the K and L points as well as <i>Y</i><sub>(NPQ)</sub> decreased, cyclic electron transport and <i>P</i><sub>n</sub> were enhanced, stomatal aperture increased, and Δ<i>I</i>/<i>I</i>o improved. Transcriptomic analysis revealed a significant reduction in the expression of genes related to the PSI and PSII reaction centers, ATP synthesis, electron transport, and antenna proteins under drought stress. The application of calcium significantly alleviated the drought-induced downregulation of these genes. In summary, Ca<sup>2+</sup> reduces water loss in plants, increases chlorophyll content in leaves, restores PSII reaction center activity, ensures efficient photosynthetic electron transport, maintains thylakoid membrane stability, enhances cyclic electron transport, and reduces damage to the photosystem.
DOI: 10.6084/m9.figshare.29562462
title: Addressing variability and advancing methodological clarity in plant-soil feedback experiments

description: Plant-soil feedbacks (PSFs) are essential for understanding plant community dynamics and ecosystem restoration. Glasshouse experiments provide controlled environments to study PSFs, but isolating biotic and abiotic influences remains challenging. Soil sterilization removes biotic components, with biotic effects restored via live inoculum. However, inconsistencies in sterilization methods, inoculum ratios, and storage practices complicate reproducibility. This literature review synthesizes 184 PSF studies from the past 24 years, to document methodological variation and reporting inconsistencies that influence experimental design, interpretation, and cross-study comparability, specifically highlighting variability in sterilization parameters and live inoculum application. Many studies overlooked nutrient flushes and persistent microbial activity post-sterilization. No consensus exists on live inoculum ratios, and storage practices remain poorly reported, limiting cross-study comparability. Reproducibility and realism in PSF estimates may be strengthened through measures including, but not limited to: (1) improved methodological reporting of core parameters, (2) validation of sterilization success, and (3) empirically determined inoculum ratios.
DOI: 10.6084/m9.figshare.29562462.v1
title: Addressing variability and advancing methodological clarity in plant-soil feedback experiments

description: Plant-soil feedbacks (PSFs) are essential for understanding plant community dynamics and ecosystem restoration. Glasshouse experiments provide controlled environments to study PSFs, but isolating biotic and abiotic influences remains challenging. Soil sterilization removes biotic components, with biotic effects restored via live inoculum. However, inconsistencies in sterilization methods, inoculum ratios, and storage practices complicate reproducibility. This literature review synthesizes 184 PSF studies from the past 24 years, to document methodological variation and reporting inconsistencies that influence experimental design, interpretation, and cross-study comparability, specifically highlighting variability in sterilization parameters and live inoculum application. Many studies overlooked nutrient flushes and persistent microbial activity post-sterilization. No consensus exists on live inoculum ratios, and storage practices remain poorly reported, limiting cross-study comparability. Reproducibility and realism in PSF estimates may be strengthened through measures including, but not limited to: (1) improved methodological reporting of core parameters, (2) validation of sterilization success, and (3) empirically determined inoculum ratios.
DOI: 10.6084/m9.figshare.28267832
title: The Populus MYB transcription factor <i>PSAR1</i> negatively regulates salt stress and is a repressor of ABA signaling

description: Plant transcription factors and their associations with ABA (abscisic acid) are critical for development and adaptation to environments. Here, we report that the Populus MYB transcription factor Salt stress – and ABA signaling-Repressor 1 (<i>PSAR1</i>) combines with ABA signaling to negatively regulate salt stress responses. A markedly diminished tolerance to salt stress was observed in the engineered Arabidopsis overexpressing <i>PSAR1</i> (OeLAs) compared with Wt (wild-type) plants. OeLAs seed germination to ABA (1.0 μM) was less sensitive. Whereas by higher ABA (5.0 μM) treatment a delayed blooming was viewed in the OeLAs seedlings. And the endogenous ABA level steadily decreased. Furthermore, 486 DEGs (differentially expressed genes) were identified in OeLA1 by RNA-seq, including the genes encoding the Highly ABA-Induced protein phosphatases HAI1 and HAI2. A similar expression pattern of the genes was also confirmed by qRT-PCR. Overall, these results illuminate the Populus <i>PSAR1</i> mediates environmental conditions, gene expression, and physiological ABA status.
DOI: 10.6084/m9.figshare.28267832.v1
title: The Populus MYB transcription factor <i>PSAR1</i> negatively regulates salt stress and is a repressor of ABA signaling

description: Plant transcription factors and their associations with ABA (abscisic acid) are critical for development and adaptation to environments. Here, we report that the Populus MYB transcription factor Salt stress – and ABA signaling-Repressor 1 (<i>PSAR1</i>) combines with ABA signaling to negatively regulate salt stress responses. A markedly diminished tolerance to salt stress was observed in the engineered Arabidopsis overexpressing <i>PSAR1</i> (OeLAs) compared with Wt (wild-type) plants. OeLAs seed germination to ABA (1.0 μM) was less sensitive. Whereas by higher ABA (5.0 μM) treatment a delayed blooming was viewed in the OeLAs seedlings. And the endogenous ABA level steadily decreased. Furthermore, 486 DEGs (differentially expressed genes) were identified in OeLA1 by RNA-seq, including the genes encoding the Highly ABA-Induced protein phosphatases HAI1 and HAI2. A similar expression pattern of the genes was also confirmed by qRT-PCR. Overall, these results illuminate the Populus <i>PSAR1</i> mediates environmental conditions, gene expression, and physiological ABA status.
DOI: 10.15468/dl.artjas
title: Occurrence Download

description: A dataset containing 746 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Tracheophyta",
 "DecimalLatitude is greater than or equal to 70.0",
 "DecimalLatitude is less than or equal to 75.0",
 "DecimalLongitude is greater than or equal to -115.0",
 "DecimalLongitude is less than or equal to -110.0",
 "HasCoordinate is TRUE",
 "HasGeospatialIssue is FALSE"
 ]
}

 The dataset includes 746 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0058654-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ang4tf
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{"type":"and","predicates":[{"type":"equals","key":"GADM_LEVEL_0_GID","value":"ARG","matchCase":false},{"type":"equals","key":"GADM_LEVEL_1_GID","value":"ARG.3_1","matchCase":false},{"type":"equals","key":"GADM_LEVEL_2_GID","value":"ARG.3.3_1","matchCase":false},{"type":"equals","key":"CLASS_KEY","value":"212","matchCase":false},{"type":"greaterThanOrEquals","key":"YEAR","value":"2015","matchCase":false},{"type":"not","predicate":{"type":"in","key":"BASIS_OF_RECORD","values":["MATERIAL_CITATION","MATERIAL_SAMPLE","PRESERVED_SPECIMEN"],"matchCase":false}},{"type":"lessThanOrEquals","key":"COORDINATE_UNCERTAINTY_IN_METERS","value":"10000","matchCase":false},{"type":"equals","key":"LICENSE","value":"CC BY 4.0","matchCase":false}]}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0058655-251120083545085/datasets/export for details.
DOI: 10.6084/m9.figshare.30242375
title: Insights into plant-microbe interactions in urban rhizosphere: feedback from <i>Quercus cerris</i> L. root morphology, soil zymography, and microbial community composition in rhizobox system

description: Urbanization can have a substantial impact on rhizosphere activity by generating a hostile environment that hinders plant resource uptake. To study the effects of urbanization on plant-microbe interactions, <i>Quercus cerris</i> L. seedlings were cultivated in rhizoboxes with soil collected from non-urban, peri-urban, and urban forest sites in Campobasso, Italy. Urban and peri-urban soils showed higher enzyme activity, attributable to their nutrient content, that also caused root structural changes, modeling microbial communities. In particular, an increase in root diameter was found in urban and peri-urban soils while plants developed a root system ideal for exploring and/or exploiting the non-urban soil. Microbial community analysis revealed a higher number of phyla associated with cellular processes in non-urban soils while peri-urban and urban soils were dominated by phyla involved in metabolic pathways. This approach provides a framework for studying plant-microbe interactions, offering valuable insights to enhance urban area health and resilience.
DOI: 10.6084/m9.figshare.30242375.v1
title: Insights into plant-microbe interactions in urban rhizosphere: feedback from <i>Quercus cerris</i> L. root morphology, soil zymography, and microbial community composition in rhizobox system

description: Urbanization can have a substantial impact on rhizosphere activity by generating a hostile environment that hinders plant resource uptake. To study the effects of urbanization on plant-microbe interactions, <i>Quercus cerris</i> L. seedlings were cultivated in rhizoboxes with soil collected from non-urban, peri-urban, and urban forest sites in Campobasso, Italy. Urban and peri-urban soils showed higher enzyme activity, attributable to their nutrient content, that also caused root structural changes, modeling microbial communities. In particular, an increase in root diameter was found in urban and peri-urban soils while plants developed a root system ideal for exploring and/or exploiting the non-urban soil. Microbial community analysis revealed a higher number of phyla associated with cellular processes in non-urban soils while peri-urban and urban soils were dominated by phyla involved in metabolic pathways. This approach provides a framework for studying plant-microbe interactions, offering valuable insights to enhance urban area health and resilience.
DOI: 10.6084/m9.figshare.30717923
title: <b>Assessing salt tolerance, phenotypic traits and genetic diversity in chickpea (</b><i><b>Cicer arietinum L.</b></i><b>) accessions using SSR markers</b>

description: Soil salinity is a major abiotic stress that severely limits chickpea (<i>Cicer arietinum</i> L.) productivity, especially in semi-arid regions such as Uzbekistan. This study evaluated 50 chickpea accessions under optimal and naturally saline field conditions, combining phenotypic analysis with SSR marker-based genetic diversity and <i>in silico</i> mapping to identify tolerant germplasm. Significant phenotypic variation was observed and several genotypes (e.g., ‘Malxotra’, ‘Guliston’, ‘Lazzat’, ‘Iftikhor’, ‘SSA−2’, ‘SSA−10’) were identified as highly salt-tolerant. Under salinity stress, seed weight per plant showed strong positive correlations with pod number (r = 0.63***) and seed number (r = 0.69***). Genetic diversity assessed using 37 polymorphic SSR markers revealed 148 alleles, averaging 3.8 alleles per locus. The mean polymorphism information content (PIC) was 0.37 (ranging from 0.21 to 0.63), with the highest expected heterozygosity (He = 0.69) detected for markers H1C22, STMS22, and TR20. <i>In silico</i> analysis localized these markers to salt-tolerance associated regions on chromosomes, identifying candidate genes encoding LEA proteins, ion transporters, kinases, and redox regulators. These fundings, particularly the identified tolerant genotypes and associated markers, provide a valuable foundation for marker-assisted selection and the development of salt-tolerant chickpea cultivars.
DOI: 10.6084/m9.figshare.30717923.v1
title: <b>Assessing salt tolerance, phenotypic traits and genetic diversity in chickpea (</b><i><b>Cicer arietinum L.</b></i><b>) accessions using SSR markers</b>

description: Soil salinity is a major abiotic stress that severely limits chickpea (<i>Cicer arietinum</i> L.) productivity, especially in semi-arid regions such as Uzbekistan. This study evaluated 50 chickpea accessions under optimal and naturally saline field conditions, combining phenotypic analysis with SSR marker-based genetic diversity and <i>in silico</i> mapping to identify tolerant germplasm. Significant phenotypic variation was observed and several genotypes (e.g., ‘Malxotra’, ‘Guliston’, ‘Lazzat’, ‘Iftikhor’, ‘SSA−2’, ‘SSA−10’) were identified as highly salt-tolerant. Under salinity stress, seed weight per plant showed strong positive correlations with pod number (r = 0.63***) and seed number (r = 0.69***). Genetic diversity assessed using 37 polymorphic SSR markers revealed 148 alleles, averaging 3.8 alleles per locus. The mean polymorphism information content (PIC) was 0.37 (ranging from 0.21 to 0.63), with the highest expected heterozygosity (He = 0.69) detected for markers H1C22, STMS22, and TR20. <i>In silico</i> analysis localized these markers to salt-tolerance associated regions on chromosomes, identifying candidate genes encoding LEA proteins, ion transporters, kinases, and redox regulators. These fundings, particularly the identified tolerant genotypes and associated markers, provide a valuable foundation for marker-assisted selection and the development of salt-tolerant chickpea cultivars.
DOI: 10.6084/m9.figshare.28595418
title: Metabolomics analysis to characterize the effects of flavonoids on tobacco seedlings under cold and hypoxia stress

description: Cold and hypoxia (CH) stress, a common combined stress during floating system, inhibits growth of tobacco and seriously affects the quality. Exogenous substances can regulate plant growth and respond to environmental stress. However, there are few studies focusing on tobacco responses to CH stress and the effects of exogenous substances on tobacco seedlings under CH stress are not fully understood. In this study, metabolomics analysis was performed on two tobacco varieties with contrasting CH responses, i.e. K326 (CH-sensitive) and Honghua (CH-tolerant). The results showed that flavonoids were crucial for tobacco seedlings to resist CH stress. Furthermore, exogenous anthocyanidin, flavone and quercetin significantly increased the root length, relative chlorophyll content, SP content, SOD, POD, CAT and APX activities of tobacco under CH stress, while reducing MDA content. Overall, our study highlighted the potential of flavonoids to improve CH tolerance of tobacco which could become a useful tool to resist stress during tobacco floating system.
DOI: 10.6084/m9.figshare.28595418.v1
title: Metabolomics analysis to characterize the effects of flavonoids on tobacco seedlings under cold and hypoxia stress

description: Cold and hypoxia (CH) stress, a common combined stress during floating system, inhibits growth of tobacco and seriously affects the quality. Exogenous substances can regulate plant growth and respond to environmental stress. However, there are few studies focusing on tobacco responses to CH stress and the effects of exogenous substances on tobacco seedlings under CH stress are not fully understood. In this study, metabolomics analysis was performed on two tobacco varieties with contrasting CH responses, i.e. K326 (CH-sensitive) and Honghua (CH-tolerant). The results showed that flavonoids were crucial for tobacco seedlings to resist CH stress. Furthermore, exogenous anthocyanidin, flavone and quercetin significantly increased the root length, relative chlorophyll content, SP content, SOD, POD, CAT and APX activities of tobacco under CH stress, while reducing MDA content. Overall, our study highlighted the potential of flavonoids to improve CH tolerance of tobacco which could become a useful tool to resist stress during tobacco floating system.
DOI: 10.6084/m9.figshare.30187626
title: Transcriptomic insights into <i>Piriformospora indica</i>-mediated regulation enhancing tobacco seed germination

description: Seed germination is vital for crop emergence and yield. Seed biopriming with beneficial microbes like <i>Piriformospora indica</i> has gained attention for promoting plant growth and stress tolerance. This study used tobacco as a model to explore <i>P. indica</i>’s germination-enhancing mechanisms through physiological and transcriptomic analyses via RNA-Seq under controlled laboratory conditions. Results showed P<i>. indica</i> enhanced lipid and starch degradation, upregulated related genes, and optimized sugar metabolism networks. In energy metabolism, <i>P. indica</i> reprogrammed genes in glycolysis, pyruvate metabolism, and the TCA cycle, forming an efficient energy-generating network. <i>P. indica</i> also activated phenylpropanoid biosynthesis genes and antioxidant enzyme activity, reducing oxidative stress. In summary, <i>P. indica</i> likely improves tobacco seed germination via metabolic remodeling, energy optimization, and oxidative defense. These findings offer insights into <i>P. indica</i>’s role in seed germination and hold promise for seed coating and early-stage biostimulant formulations in crops.
DOI: 10.6084/m9.figshare.30187626.v1
title: Transcriptomic insights into <i>Piriformospora indica</i>-mediated regulation enhancing tobacco seed germination

description: Seed germination is vital for crop emergence and yield. Seed biopriming with beneficial microbes like <i>Piriformospora indica</i> has gained attention for promoting plant growth and stress tolerance. This study used tobacco as a model to explore <i>P. indica</i>’s germination-enhancing mechanisms through physiological and transcriptomic analyses via RNA-Seq under controlled laboratory conditions. Results showed P<i>. indica</i> enhanced lipid and starch degradation, upregulated related genes, and optimized sugar metabolism networks. In energy metabolism, <i>P. indica</i> reprogrammed genes in glycolysis, pyruvate metabolism, and the TCA cycle, forming an efficient energy-generating network. <i>P. indica</i> also activated phenylpropanoid biosynthesis genes and antioxidant enzyme activity, reducing oxidative stress. In summary, <i>P. indica</i> likely improves tobacco seed germination via metabolic remodeling, energy optimization, and oxidative defense. These findings offer insights into <i>P. indica</i>’s role in seed germination and hold promise for seed coating and early-stage biostimulant formulations in crops.
DOI: 10.6084/m9.figshare.30665137.v1
title: <b>Genetic analysis of fusarium wilt resistance in Upland cotton germplasm (</b><i><b>Gossypium hirsutum</b></i><b>L.)</b>

description: Fusarium wilt (FW), caused by the soil-borne pathogen <i>Fusarium oxysporum</i> f. sp. <i>vasinfectum</i> (FOV), is an economically serious disease-causing significant damage to cotton crops worldwide, including in Uzbekistan. This study evaluated the resistance of Upland cotton (<i>Gossypium hirsutum</i> L.) germplasm from Uzbekistan against FOV race 4 under controlled phytotron conditions. Fifteen cotton accessions were phenotypically assessed for disease symptoms and genotypically screened with 118 simple sequence repeat (SSR) markers to identify genetic polymorphisms. Several cotton lines, including Rex, PD−648, Mebane B−1, Las Brenas−347, and DPZ−554085, exhibited high resistance to FW. A total of 40 SSR markers were polymorphic, producing 165 alleles. The identification of resistant lines possessing specific resistance-associated marker alleles provides valuable genetic resources. These findings can be effectively utilized in marker-assisted selection (MAS) to accelerate the development of high-yielding, wilt-resistant cotton cultivars. Uzbekistan's primary commercial cotton variety, Bukhara−6, is highly susceptible to the destructive Fusarium wilt pathogen (FOV4), risking national cotton production. Policy should promote the prompt development and distribution of resistant cultivars to prevent significant economic losses. This study identifies several highly resistant cotton lines, including Rex, PD−648, and Mebane B−1, within the national germplasm. These lines represent valuable genetic resources that should be quickly integrated into public breeding programs to enhance the resilience of the national cotton crop. Validated DNA markers associated with FOV4 resistance can now support marker-assisted selection (MAS). This advanced breeding technology will speed up the development of high-yielding, resistant varieties, ensuring a sustainable and profitable future for Uzbekistan's essential cotton industry.
DOI: 10.6084/m9.figshare.30665137
title: <b>Genetic analysis of fusarium wilt resistance in Upland cotton germplasm (</b><i><b>Gossypium hirsutum</b></i><b>L.)</b>

description: Fusarium wilt (FW), caused by the soil-borne pathogen <i>Fusarium oxysporum</i> f. sp. <i>vasinfectum</i> (FOV), is an economically serious disease-causing significant damage to cotton crops worldwide, including in Uzbekistan. This study evaluated the resistance of Upland cotton (<i>Gossypium hirsutum</i> L.) germplasm from Uzbekistan against FOV race 4 under controlled phytotron conditions. Fifteen cotton accessions were phenotypically assessed for disease symptoms and genotypically screened with 118 simple sequence repeat (SSR) markers to identify genetic polymorphisms. Several cotton lines, including Rex, PD−648, Mebane B−1, Las Brenas−347, and DPZ−554085, exhibited high resistance to FW. A total of 40 SSR markers were polymorphic, producing 165 alleles. The identification of resistant lines possessing specific resistance-associated marker alleles provides valuable genetic resources. These findings can be effectively utilized in marker-assisted selection (MAS) to accelerate the development of high-yielding, wilt-resistant cotton cultivars. Uzbekistan's primary commercial cotton variety, Bukhara−6, is highly susceptible to the destructive Fusarium wilt pathogen (FOV4), risking national cotton production. Policy should promote the prompt development and distribution of resistant cultivars to prevent significant economic losses. This study identifies several highly resistant cotton lines, including Rex, PD−648, and Mebane B−1, within the national germplasm. These lines represent valuable genetic resources that should be quickly integrated into public breeding programs to enhance the resilience of the national cotton crop. Validated DNA markers associated with FOV4 resistance can now support marker-assisted selection (MAS). This advanced breeding technology will speed up the development of high-yielding, resistant varieties, ensuring a sustainable and profitable future for Uzbekistan's essential cotton industry.