Ontology highlight
ABSTRACT:
PROVIDER: PRJEB96000 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Lettuce (Lactuca sativa L.) is a highly perishable horticultural crop with a relatively short shelf life due to leaf senescence that limits its commercial value and contributes to food waste. Postharvest senescence varies with influences of both environmental and genetic factors. Preharvest genetic factors can be indicative of postharvest quality. Discovery of additional preharvest markers to assess lettuce shelf life is an important step towards increasing the efficiency of lettuce breeding efforts for improved shelf life. We selected and evaluated three romaine lettuces with variable shelf lives with the aim of identifying preharvest markers of lettuce postharvest shelf life. We evaluated leaf morphological characteristics for each of the three cultivars. To assess molecular indicators of shelf life, we used an RNA sequencing approach to construct transcriptomic profiles of two of the cultivars, a short shelf life (SSL) breeding line 60184 and a long shelf life (LSL) cultivar ‘Okeechobee’ at maturity. We identified 552 upregulated and 315 downregulated differentially expressed (DE) genes between the genotypes. We found that 27 % of the DE lettuce genes had an Arabidopsis thaliana ortholog characterized as senescence-associated, indicating that variable expression of senescence-associated genes (SAGs) could serve as a tool for preharvest markers of postharvest shelf life. Notably, we identified several SAGs and functional groupings with highly differential expression between the cultivars. This includes several jasmonate ZIM-domain (JAZ), jasmonic acid (JA) signaling genes, chlorophyll a-b binding (CAB) chloroplast-associated genes, and cell wall modification genes including pectate lyases (PL) and expansins (EXP). This study presented an innovative approach for identifying molecular markers for preharvest factors linked to postharvest traits for prolonged shelf. These genes could potentially be developed further as preharvest predictors of shelf life for lettuce breeding
2024-02-27 | GSE226302 | GEO
Project description:Artichokes provide a wide range of health-promoting nutrients and produce ornamental flowers with pleasant sensory appeal. However, their high photosynthetic activity, respiration rate, and sensitivity to mechanical injuries makes them highly perishable. Using the high-throughput RNA-seq and metabolomics analysis, we identified significant variations in the expression levels of differentially expressed genes (DEGs) and metabolites between ‘Green Queen’ (GQ) and ‘Imperial Star’ (IS) cultivars, relating to their shelf-life. The DEGs were categorized into pathways involved in hormone signaling, cell wall metabolism, stress response, organ development, and health beneficial compounds with expression varying across storage intervals. Notably, genes and transcription factors (TFs) involved in plant hormone signaling pathways and senescence were primarily upregulated in IS, explicating its shorter shelf life. Genes such as b -carotene 3-hydroxylase (BHY) and 11-beta-hydroxysteroid dehydrogenase-like 4A (HSD4), upregulated in both cultivars during storage, facilitate the production of metabolites with reported anti-aging, anti-inflammatory, diabetic resistance, and cardiovascular benefits. Metabolomics analysis unveils an accumulation of phenols, flavonoids, vitamins and breakdown of inulin, which remain stable in GQ and occur in a time-dependent manner in IS during storage. These findings elucidate the genotypic effect on the shelf-life of artichoke stored under same conditions and provide valuable insights for improving postharvest shelf life and nutritional quality through gene editing techniques.
2026-07-01 | GSE286173 | GEO
Project description:Fertility is a multifactorial trait and a key determinant of productivity and sustainability in beef cattle production. Identifying molecular mechanisms and biomarkers associated with fertility could improve the prediction of reproductive potential in beef heifers. Herein, using transcriptomic data from peripheral white blood cells (PWBCs) collected before the time of artificial insemination (AI), we investigated molecular differences between fertile and subfertile beef heifers (n = 6 per group) classified based on their reproductive outcomes. RNA-Sequencing identified 230 differentially expressed genes (DEGs; P ≤ 0.05 and |log2FC| > 0.5) between groups. Over-representation analyses revealed that these molecules were associated with cell cycle regulation, metabolism, and immune-related pathways, including chemokine and JAK-STAT signaling.
2026-04-30 | GSE325134 | GEO
Project description:Microbial community of ground beef Targeted Locus (Loci)
| PRJNA279329 | ENA
Project description:Melon is a globally commercialized fruit, and Fusarium rot disease poses a significant threat to post-harvest losses. The conventional use of fungicides raises concerns about chemical residues, prompting exploration into alternative technologies such as Pulsed Light (PL). While PL has been effective in controlling infections in various fruits and vegetables, the precise physiological responses and molecular mechanisms in melon fruits remain incompletely understood. In this study, melon fruits infected with the Fusarium pallidoroseum were treated with different doses of PL (0, 6, 9, and 12 J cm-2), and the impact on both fungal control and fruit shelf life extension was investigated. The 9 J cm-2 dose emerged as the most effective in controlling fungal growth without causing damage, inducing beneficial responses. This optimal PL dose upregulated genes in the lignan biosynthesis pathway and the infection upregulated genes involved with systemic acquired resistance, triggered by the pipecolic acid. In this way, the PL treatment and the infection trigger a double mechanism of resistance in melon fruits. A second and third experiment focused on evaluating the extension of melon fruit shelf life and the safe manipulation window post-PL treatment. The results revealed an average shelf life extension of six days and a safe manipulation period of 24 hours. The extension in shelf life was associated with a deviation in information flux from the ethylene biosynthesis to upregulation of the polyamine biosynthesis pathway, which produces nitric oxide, a product that can inhibit ethylene biosynthesis and its action. Furthermore, the observed 24-hour safety period against fungal infection post-PL treatment was characterized as a memory response resistance caused by the upregulation of lignan biosynthesis, which is a potential and efficient alternative to chemical products like fungicides. Overall, this study provides insights into the transcriptional molecular mechanisms through which PL promotes systemic acquired resistance and extends the shelf life of melon fruits.
2024-02-25 | GSE256527 | GEO
Project description:The aim of the overall study was to investigate the development of immune competence in artificially reared dairy calves and in two breeds of naturally suckled beef calves over the first 168h of life. Dairy calves were fed 5% total body weight of colostrum, with beef calves monitored to ensure natural ingestion of colostrum. Blood samples were taken from all calves at 24h 48h 72h and 168h, and analysed for alterations to immunes genes.
2018-10-29 | GSE114432 | GEO