Ontology highlight
ABSTRACT:
PROVIDER: PRJNA819666 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Root is of vital important in acquiring nutrients and water from soils. Uncovering the regulatory mechanism of wheat root growth is of great help for genetic improvement of roots traits. A comparative proteomic analysis was performed. Expressed proteins were identified under CK and LN conditions. Protein expression profiles in different genetic varieties were obtained.
2018-03-19 | PXD008793 |
Project description:Elevated growth temperatures are negatively affecting crop productivity and increasing yield losses. Root traits associated with improved adaptation to rising temperatures are a promising approach to generate new varieties better suited to face the environmental constrains caused by climate change. In this study, we identified various Brassica napus roots traits altered in response to warm temperature. Thus, different combination of changes in specific root traits results in an extended and deeper root system. This overall root growth expansion facilitates root adaptation by maximizing root-soil surface interaction and increasing its ability to explore extended soil areas. We associated these traits to coordinated cellular events, including changes in cell division and elongation rates, that drive the increase in root growth triggered by warm temperature. Comparative genome wide transcriptomic analysis revealed the main genetic determinants of these RSA changes and uncovered the necessity of a tight regulation of the heat shock stress response to adjust root growth to warm temperature. Our work provides a phenotypic, cellular and genetic framework of root response to warming temperatures that will help to harness root adaptation mechanisms for crop yield improvement under the future climatic scenario.
2023-01-25 | GSE173272 | GEO
Project description:Background: Most skin-related traits have been studied in Caucasian genetic backgrounds. A comprehensive study on skin-associated genetic effects on underrepresented populations such as Vietnam is needed to fill the gaps in the field. Objectives: We aimed to develop a computational pipeline to predict the effect of genetic factors on skin traits using public data (GWAS catalogs and whole-genome sequencing (WGS) data from the 1000 Genomes Project-1KGP) and in-house Vietnamese data (WGS and genotyping by SNP array). Also, we compared the genetic predispositions of 25 skin-related traits of Vietnamese population to others to acquire population-specific insights regarding skin health. Results: The skin-related genetic profile of Vietnamese cohorts was similar at most to East Asian cohorts (JPT: Fst=0.036, CHB: Fst=0.031, CHS: Fst=0.027, CDX: Fst=0.025) in the population study. In addition, we identified pairs of skin traits at high risk of frequent co-occurrence (such as skin aging and wrinkles (r = 0.45, p =1.50e-5) or collagen degradation and moisturizing (r = 0.35, p = 1.1e-3)).
2023-11-26 | GSE248483 | GEO
Project description:Root traits are significant targets for breeding stress-resilient and high-yielding wheat genotypes under climatic fluctuations. However, root transcriptome analysis is usually obscured due to challenges in root research. We performed transcriptome analysis of thirty bread wheat cultivars using RNA-seq to investigate the diversity and expression of root system architecture (RSA) related transcripts. We examined the expression patterns of these transcripts in both root and leaf tissues and found that various transcripts are root-specific which could be manipulated for desirable root traits.The presented RNA-seq datasets provide valueable source for identification of genes involved in various biological processes under varying climatic conditions.
2023-06-29 | GSE235844 | GEO
Project description:Genomic diversity is a source of transcriptomic and phenotypic diversities. Although genomic variations in rice (Oryza sativa) accessions have been extensively analyzed, information of transcriptomic and phenotypic variations, especially for below-ground variations, are limited. Here, we report the diversities of above- and below-ground traits and transcriptomes in highly diversified 61 rice accessions grown in the upland-field. We found that phenotypic variations were explained by four principal components and that tiller numbers and crown root diameters could summarize admixture groups. Transcriptome analysis revealed that admixture-group-associated differentially expressed genes were enriched with stress response related genes, suggesting that admixture groups have distinct stress response mechanisms. Root growth was negatively correlated with auxin inducible genes, suggesting the association between auxin signaling and mild drought stress. Negative correlation between crown root diameters and stress response related genes suggested that thicker crown root diameter is associated with mild drought stress tolerance. Finally co-expression network analysis implemented with DAP-seq analysis identified phytohormone signaling network and key transcription factors negatively regulating crown root diameters. Our datasets would serve as an important resource for understanding genomic and transcriptomic basis of phenotypic variations under the upland-field condition.
2021-03-07 | GSE162312 | GEO
Project description:The aim of the present study was to globally survey the transcriptome of the two inbred lines B73 and Mo17 in comparison to their reciprocal F1-progeny in an unbiased approach via RNA-seq using four biological replicates to increase the power for detecting differential expression while maintaining a low false discovery rate (FDR). For this purpose, primary roots of 3.5-d-old seedlings were surveyed, as young primary roots display a very simple structure. This stage was previously demonstrated to precede the first detectable developmental changes between inbred lines and hybrids during heterosis manifestation for numerous root-related traits (Hoecker et al. 2006). By choosing this particular stage, we intended to identify transcriptional patterns and regulators possibly determining the processes leading to heterosis for these early root system traits.
2012-06-27 | E-MTAB-4345 | biostudies-arrayexpress
Project description:Ramie is an important industrial fiber crop, and the fiber yield and its related traits are the most valuable traits in ramie production. However, the genetic basis for these traits is still poorly understood. Herein, a high-density genetic map with 1085 markers spanning 2,118.8 cM was constructed using a population derived from two parents, cultivated ramie Zhongsizhu 1 (ZSZ1) and its wild progenitor B. nivea var. tenacissima (BNT). The fiber yield (FY) and its four related traits—stem diameter (SD) and length (SL), stem bark weight (BW) and thickness (BT)—were performed for quantitative trait locus (QTL) analysis, resulting in eight, six, six, three, and ten QTLs for SD, SL, BW, BD and FY traits, respectively. These 33 QTLs were mapped into 11 genomic regions, thus forming 11 QTL clusters; there were 11 QTLs identified their beneficial alleles from the wild species BNT. Interestingly, all QTLs in Cluster 8 and Cluster 10 displayed overdominance, indicating that these two regions were likely heterotic loci. In addition, there were five fiber yield-related genes identified to undergo positive selection in previous study, and they were found to locate into the genomic region near to the QTLs of this study. The genetic dissection for FY and its related traits improved our understanding to the genetic basis of these traits, as well to their domestication in ramie. The identification of many QTLs and the discovery of beneficial alleles from wild species provided a basis for the improvement of yield traits in ramie breeding.
2019-01-31 | GSE125891 | GEO
Project description:<p>Plant monocultures growing for extended periods face severe losses of productivity. This phenomenon, known as 'yield decline', is often caused by the accumulation of above- and below-ground plant antagonists. The effectiveness of plant defences against antagonists might help explain differences in yield decline among species. Using a trait-based approach, we studied the role of 20 physical and chemical defence traits of leaves and fine roots on yield decline of 4- and 18-year-old monocultures of 27 grassland species. We hypothesized that yield decline is lower for species with high defences, that root defences are better predictors of yield decline than leaf defences, and that in roots, physical defences better predict yield decline than chemical defences, while the reverse is true for leaves. We additionally hypothesized that the relationship between defences and yield decline increase with time and that species increasing the expression of defence traits after long-term monoculture growth would suffer less yield decline. We summarized leaf and fine root defence traits using principal component analysis and analysed the relationship between the most informative components as well as their temporal changes and monoculture yield decline. The significant predictors of yield decline were traits related to the so-called collaboration gradient of the root economics space (specific root length and root diameter) as well as their temporal changes and traits related to the leaf physical vs chemical defence trade-off (leaf dry matter, silicon and cellulose content, toughness and phytochemical diversity). We were unable to unequivocally identify the mechanisms relating the effect of those traits to yield decline as they could mediate plant responses to several stressor such as antagonist nutrient depletion and drought. Further studies are needed to differentiate between these alternative mechanisms and gain a comprehensive understanding of the drivers behind the impact of root and leaf defence traits on yield decline.</p>
2023-11-03 | MTBLS4286 | MetaboLights