Dissection of quantitative trait nucleotides and candidate genes associated with agronomic and yield-related traits under drought stress in rapeseed varieties: integration of genome-wide association study and transcriptomic analysis

Frontiers in Plant Science, Год журнала: 2024, Номер 15

Опубликована: Март 19, 2024

Introduction An important strategy to combat yield loss challenge is the development of varieties with increased tolerance drought maintain production. Improvement crop under stress critical global food security. Methods In this study, we performed multiomics analysis in a collection 119 diverse rapeseed ( Brassica napus L.) dissect genetic control agronomic traits two watering regimes [well-watered (WW) and (DS)] for 3 years. DS treatment, irrigation continued till 50% pod stage, whereas WW condition, it was throughout whole growing season. Results The results genome-wide association study (GWAS) using 52,157 single-nucleotide polymorphisms (SNPs) revealed 1,281 SNPs associated traits. Six stable showed sequence variation flowering time between conditions across Three novel on chromosome C04 plant weight were located within tolerance-related gene ABCG16 , their pleiotropically effects seed per characterized. We identified C02 peak as signal time, harboring 52.77% SNPs. 288-kbps LD decay distance 2,232 candidate genes (CGs) CGs BIG1 - D CAND1 DRG3 PUP10 PUP21 involved phytohormone signaling pollen significant number, weight, grain conditions. By integrating GWAS RNA-seq, 215 promising developmental process, reproductive processes, cell wall organization, response stress. differentially expressed (DEGs) leaf contrasting accessions BIG1-D variation. Discussion our provide insights into improvement marker-assisted selection (MAS) breeding high-yield drought-tolerant varieties.

Язык: Английский

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Integrative Approaches to Abiotic Stress Management in Crops: Combining Bioinformatics Educational Tools and Artificial Intelligence Applications

Sustainability, Год журнала: 2024, Номер 16(17), С. 7651 - 7651

Опубликована: Сен. 3, 2024

Abiotic stresses, including drought, salinity, extreme temperatures and nutrient deficiencies, pose significant challenges to crop production global food security. To combat these challenges, the integration of bioinformatics educational tools AI applications provide a synergistic approach identify analyze stress-responsive genes, regulatory networks molecular markers associated with stress tolerance. Bioinformatics offer robust framework for data collection, storage initial analysis, while enhance pattern recognition, predictive modeling real-time processing capabilities. This review uniquely integrates applications, highlighting their combined role in managing abiotic plants crops. The novelty is demonstrated by multiomics algorithms, providing deeper insights into response pathways, biomarker discovery recognition. Key include resistance gene network inference, omics plant monitoring through fusion remote sensing AI-assisted phenomics. Challenges such as handling big data, model interpretability, overfitting experimental validation remain there, but future prospects involve developing user-friendly platforms, establishing common standards, interdisciplinary collaboration harnessing mitigation strategies Educational initiatives, collaborations trainings are essential equip next generation researchers required skills utilize advanced effectively. convergence holds vast accelerating development stress-resilient crops, optimizing agricultural practices ensuring security under increasing environmental pressures. Moreover, this integrated crucial advancing sustainable agriculture amidst growing challenges.

Язык: Английский

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Photosynthetic performance, pigments and biochemicals influence seed yield in rapeseed under water deficit conditions: MGIDI index helps screening drought-tolerant genotypes

Field Crops Research, Год журнала: 2025, Номер 322, С. 109733 - 109733

Опубликована: Янв. 9, 2025

Язык: Английский

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Rapeseed Flower Counting Method Based on GhP2-YOLO and StrongSORT Algorithm

Plants, Год журнала: 2024, Номер 13(17), С. 2388 - 2388

Опубликована: Авг. 27, 2024

Accurately quantifying flora and their respective anatomical structures within natural ecosystems is paramount for both botanical breeders agricultural cultivators. For breeders, precise plant enumeration during the flowering phase instrumental in discriminating genotypes exhibiting heightened frequencies, while growers, such data inform potential crop rotation strategies. Moreover, quantification of specific components, as flowers, can offer prognostic insights into yield variances among different genotypes, thereby facilitating informed decisions pertaining to production levels. The overarching aim present investigation explore capabilities a neural network termed GhP2-YOLO, predicated on advanced deep learning techniques multi-target tracking algorithms, specifically tailored rapeseed flower buds blossoms from recorded video frames. Building upon foundation renowned object detection model YOLO v8, this integrates specialized P2 head Ghost module augment model's capacity detecting diminutive targets with lower resolutions. This modification not only renders more adept at target identification but also it lightweight less computationally intensive. optimal iteration GhP2-YOLOm demonstrated exceptional accuracy samples, showcasing an impressive mean average precision 50% intersection over union metric surpassing 95%. Leveraging virtues StrongSORT, subsequent blossom patterns dataset was adeptly realized. By selecting 20 segments comparative analysis between manual automated counts buds, overall count, robust correlation evidenced, R-squared coefficients measuring 0.9719, 0.986, 0.9753, respectively. Conclusively, user-friendly "Rapeseed detection" system developed utilizing GUI PyQt5 interface, visualization flowers buds. holds promising utility field surveillance apparatus, enabling agriculturalists monitor developmental progress real time. innovative study introduces tallying methodologies footage, positioning convolutional networks protocols invaluable assets realms research administration.

Язык: Английский

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A simple and cost-effective SNP genotyping assay for marker-assisted selection of wilt resistance in castor breeding

Industrial Crops and Products, Год журнала: 2025, Номер 226, С. 120693 - 120693

Опубликована: Фев. 18, 2025

Язык: Английский

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Genome-wide analysis of CHYR gene family and BnA03.CHYR.1 functional verification under salt stress in Brassica napus L.

BMC Plant Biology, Год журнала: 2025, Номер 25(1)

Опубликована: Март 20, 2025

Abstract Brassica napus , an allotetraploid used as oilseed crop, vegetable, or feed possesses significant economic and medicinal value. Although the CHYR gene family has been functionally characterised in various aspects of plant growth, development, stress responses, its systematic investigation B. is lacking. In contrast to seven genes ( AtCHYR1-AtCHYR7 ) identified Arabidopsis thaliana nine orthologues were detected rapa oleracea while 24 found . This discrepancy consistent with established triplication events that occurred during Brassicaceae evolution. Phylogenetic analysis indicated CHYRs could be categorised into three distinct groups. Among these, BnCHYRs contained conserved domains, including CHY-zinc finger, C3H2C3-type RING finger zinc ribbon domains. Group III members featured additional one hemerythrin domains their N-terminal regions. Each BnCHYR group shared similar patterns distribution Our results revealed selected eight up-regulated following heat treatment, exhibiting varying expression response salt, cold, drought seedling stage. Expression several significantly induced by more abiotic stressors. BnA03.CHYR.1 was salt repressed polyethylene glycol treatment. localised nucleus cytoplasm, overexpression A. enhanced tolerance stress. provide a comprehensive elucidating biological role adaptive responses plants

Язык: Английский

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Agro-physiological and transcriptome profiling reveal key genes associated with potato tuberization under different nitrogen regimes in aeroponics

PLoS ONE, Год журнала: 2025, Номер 20(3), С. e0320313 - e0320313

Опубликована: Март 28, 2025

Nitrogen (N) is a crucial nutrient for the growth and development of potatoes. However, excessive use nitrogen fertilizers can have detrimental effects on human health, aquatic ecosystems, environment. Therefore, understanding genes involved in metabolism essential developing future strategies to improve efficiency (NUE) plants. This study aimed identify associated with high tuber yield two contrasting potato varieties Kufri Jyoti (N inefficient) Pukhraj efficient) grown under low regimes using an aeroponics system. Both were doses (low N: 0.5 mM N; 5 N) completely randomized design (CRD) three replications over years. The phenotypic results confirmed that was more efficient compared Jyoti, particularly conditions. Additionally, transcriptome analysis produced high-quality data ( ≥ Q20), ranging from 4.35 5.46 Gb per sample. Statistically significant p ≤ 0.05) identified based reference genome. Differentially expressed (DEGs) categorized as either up-regulated or down-regulated leaf tissues. Transcriptome profiling both tissues revealed traits contributing DEGs further characterized through gene ontology (GO) annotation KEGG pathway analysis. Selected validated real-time quantitative polymerase chain reaction (RT-qPCR) In summary, several being component potatoes different These included glutaredoxin, transcription factors (BTB/POZ, AP2/ERF, MYB), nitrate transporter, aquaporin TIP1;3, glutamine synthetase, aminotransferase, GDSL esterase/lipase, sucrose synthase, UDP-glycosyltransferases, osmotin, xyloglucan endotransglucosylase/hydrolase, laccases. we overexpressed including cysteine protease inhibitor 1, miraculin, sterol desaturase, pectinesterase N stress. Our highlights these genes’ roles enhancing cultivated aeroponics.

Язык: Английский

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Exploring genomic loci and candidate genes associated with drought tolerance indices in spring wheat evaluated under two levels of drought

BMC Plant Biology, Год журнала: 2025, Номер 25(1)

Опубликована: Апрель 1, 2025

Wheat is a major global crop, and increasing its productivity essential to meet the growing population demand. However limited water resources primary constraint. This study aimed identify genetic factors associated with drought tolerance using diverse panel of 287 wheat genotypes evaluated under well-watered drought-stressed conditions. Water Use Efficiency (WUE) Grain Yield (GY), along indices, were assessed. A genome-wide association (GWAS) 26,814 high-density SNP markers identified loci linked these traits, 768 SNPs showing significant associations. Additionally, genomic selection (GS) was performed rrBLUP model predict trait performance across environments. Among measured traits at -log10 (P) ≥ 3, 81 mapped higher threshold 4, indicating pleiotropic QTL-by-environment interaction effects. Several novel known genes, previously reported have functions related biotic abiotic stresses response SNPs. indices evaluated, stress index (STI), geometric mean (GMP), (TOL) most reliable indicators for selecting stable, high-yielding control The same three exhibited high prediction values severe (SS) condition. Five as promising candidates breeding programs based on their superior tolerance, grain yield, nutritional value. provides valuable insights into basis in wheat, highlighting key regions improved use efficiency yield stability. findings contribute development drought-tolerant varieties optimized utilization achieve increased per unit levels, ultimately contributing sustainable agriculture food security.

Язык: Английский

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Elicitor-induced stilbene production and lignin reduction in peanut hairy roots: Insights from transcriptomic and metabolomic analysis

Plant Stress, Год журнала: 2025, Номер 16, С. 100823 - 100823

Опубликована: Апрель 1, 2025

Язык: Английский

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Basidiomycetes Polysaccharides Regulate Growth and Antioxidant Defense System in Wheat

International Journal of Molecular Sciences, Год журнала: 2024, Номер 25(13), С. 6877 - 6877

Опубликована: Июнь 22, 2024

Higher-fungi xylotrophic basidiomycetes are known to be the reservoirs of bioactive metabolites. Currently, a great deal attention has been paid exploitation mycelial fungi products as an innovative alternative in crop protection. No data exist on mechanisms behind interaction between mushrooms’ glycopolymeric substances and plants. In this study, effects basidiomycete metabolites morphophysiological biochemical variables wheat plants have explored. Wheat (Triticum aestivum L. cv. Saratovskaya 29) seedlings were treated with extracellular polysaccharides (EPSs) isolated from submerged cultures twenty strains assigned 13 species 8 genera. The EPS solutions at final concentrations 15, 40, 80 mg/L applied followed by their growth for 10 days. plant samples, biomass, length coleoptile, shoot root, root number, rate lipid peroxidation malondialdehyde concentration, content hydrogen peroxide, total phenols measured. peroxidase superoxide dismutase activity defined. Most preparations improved biomass yields, well morphological parameters examined. application enhanced activities antioxidant enzymes decreased oxidative damage lipids. Judging its overall effect indices redox system plants, concentration 40 shown most beneficial compared other concentrations. This study proves that novel bioformulations based mushroom EPSs can developed effective antioxidative response. Phytostimulating properties found give grounds consider produced active component capable inducing responses stress.

Язык: Английский

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