Ontology highlight
ABSTRACT:
PROVIDER: PRJEB61198 | ENA |
REPOSITORIES: ENA
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Project description:Drought is a major limiting constraint to faba bean production worldwide, including Tunisia. However, molecular mechanisms underlying faba bean responses to drought stress are not well understood. In this context, transcriptome analysis by RNA-seq was performed to investigate drought-related genes and construct a network of faba bean drought stress response and tolerance. De novo assembly of the transcriptome generated 26,728 differentially expressed genes (DEGs). Of these, 13,920 were up-regulated and 12,808 down-regulated in faba bean drought-stressed leaves. Moreover, a total of 10,800 simple sequence repeats (SSRs) and 2130 transcription factors involved in major metabolic pathways including abscisic acid (ABA)-dependent and -independent signaling pathway were identified. GO, KOG and KEGG enrichment analyses revealed that these DEGs were involved in several important processes including photosynthesis, flavonoid biosynthesis, response to stimulus and abiotic stress, reactive oxygen species (ROS) scavengers, signal transduction, biosynthesis of secondary metabolites and transporters, suggesting the involvement of these important pathways in faba bean response to water deficit. Various stress proteins such as late embryogenesis abundant proteins (LEA), dehydrins (DHNs) and heat shock proteins (HSPs) have been identified and their expression was robustly upregulated in drought-stressed leaves, indicating their key contribution to drought response and adaptation by conferring protection and providing stability to faba bean plant cellular processes under water deficit. The reliability of the RNA-seq results was confirmed by the analysis of 10 randomly selected genes using qRT-PCR. Taken together, these findings help advancing our knowledge and can guide breeding programs aimed at improving the tolerance of faba bean to drought stress.
2025-03-31 | GSE292422 | GEO
Project description:Vicia faba panel EUCLEG yield related traits
| PRJNA1037350 | ENA
Project description:Low-pass sequencing (sequencing a genome to an average depth less than 1× coverage) combined with genotype imputation has been proposed as an alternative to genotyping arrays for trait mapping and calculation of polygenic scores. To empirically assess the relative performance of these technologies for different applications, we performed low-pass sequencing (targeting coverage levels of 0.5× and 1×) and array genotyping (using the Illumina Global Screening Array (GSA)) on 120 DNA samples derived from African and European-ancestry individuals that are part of the 1000 Genomes Project. We then imputed both the sequencing data and the genotyping array data to the 1000 Genomes Phase 3 haplotype reference panel using a leave- one-out design. We evaluated overall imputation accuracy from these different assays as well as overall power for GWAS from imputed data, and computed polygenic risk scores for coronary artery disease and breast cancer using previously derived weights. We conclude that low-pass sequencing plus imputation, in addition to providing a substantial increase in statistical power for genome wide association studies, provides increased accuracy for polygenic risk prediction at effective coverages of ∼ 0.5× and higher compared to the Illumina GSA.
2021-01-31 | GSE165845 | GEO
Project description:Here we present genome-wide high-coverage genotyping data on a panel of 75 human samples from Western Balkan region, Europe, that are used in addition to public data in studing the genetic variation of Southern Europe that was sequenced to the avwerage depth of 1X.
2014-08-22 | GSE59032 | GEO