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ABSTRACT:
PROVIDER: PRJNA666967 | ENA |
REPOSITORIES: ENA
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Project description:Common bean (Phaseolus vulgaris L.) is the most consumed grain legume in developing countries in Latin America and Sub-Saharan Africa1. Like other legumes, common bean seeds are rich in protein, carbohydrates, fibers and other health-promoting phenolic compounds thus being vital for food security and income source for local small farmers2. Seed quality traits depend on accumulation of various storage molecules during the seed development (SD) process and influenced by the genotype and adaptive changes to environment3. Concerning common bean, there is still a lack of a deeper molecular knowledge of SD that is hampering the development of new biotech approaches for seed trait modulation and could timely address challenges of agriculture or industry. Our present work aims to unravel the molecular mechanisms underlying SD using a proteomic approach. To achieve this goal, we characterized SD in terms biomass, seed length and weight in the genotype SER16, one of the most promissory drought-resistant release of the CIAT-CGIAR. Seed samples were collected at the 4 main SD stages: Late-Embryogenesis (10 days after anthesis, d.a.a.), Early (20 d.a.a.) and Late Maturation (30 d.a.a.) and Desiccation (40 d.a.a.). The analysis of bean proteome was conducted using a gel-free proteomic analysis (LC-MS/MS) under the scope of EU-FP7-PRIME-XS project. A total of 410 unique proteins were differentially expressed throughout the 4 major seed development stages, in which most of the identified proteins belong in the ‘protein metabolism’ (31,98%) functional category, that includes synthesis, regulation, folding. Other functional categories are represented such as carbohydrate and lipid metabolism (11,26%) and stress/defense and redox metabolism (11,04%). We identified 93 proteins were unique to the first (10-20 d.a.a.), 22 to the second (20-30 d.a.a.) and 40 to the last (30-40 d.a.a.) phase transition, reflecting the major biological processes occurring at this specific seed developmental stage. This study will contribute to reveal key metabolic pathways and mechanisms with potential role in modulating common bean seed development and quality traits.
2018-01-05 | PXD002254 | Pride
Project description:To dissect the gene regulatory networks operating during Scarlet Runner Bean seed development, we identified the binding sites genome-wide for transcription factor in Scarlet Runner Bean seeds during seed development using ChIP-seq
2020-07-13 | GSE153644 | GEO
Project description:Light inhibits the seed germination in the Cypriot accession (CYP) of Aethionema arabicum. Extended light illumination also induces a secondary seed dormancy that inhibits the germination even if the seeds were transferred back to darkness. A forward genetic screen identified rgl2 mutant, that show light inhibited germination, but fails to re-enter the secondary dormancy. This analysis aims to compare the seed transcriptome before or after the dormancy was established by light illumination (100 µmol/m2s; white light). One day light treatment (1dL) inhibits the germination but the seeds are not yet dormant. Seven day (7dL) long light treatment induces dormancy in the WT but not in the rgl2 mutant.
2023-09-01 | GSE237220 | GEO
Project description:Seed maturation, dormancy and germination are distinct physiological processes. Transition from maturation to dormancy, and from dormancy into germination are not only critical developmental phases in the plant life cycle but are also important agricultural traits. These developmental processes and their phase transitions are fine determined and coordinately regulated by genetic makeup and environmental cues. SCARECROW-LIKE15 (SCL15) has been demonstrated to be essential for repressing the seed maturation programme in vegetative tissues (Gao et al., Nat Commun, 2015, 6:7243). Here we report that SCL15 is also important for seed dormancy maintenance, germination timing and seed vigor performance based on the effects of SCL15 mutation on plant germination, growth and reproduction when compared with wild type Arabidopsis and over-expression lines 35S:SCL15 and Napin:SCL15. Seed dormancy is enhanced by the mutation of SCL15 in a GA signaling dependent way, indicating that SCL15 plays a negative role for primary dormancy release. Seed germination is positively regulated by SCL15 through interaction with ABA, GA and auxin signaling. SCL15 acts as positive regulator of seed vigor and effect of SCL15 mRNA abundance on seed reserve accumulation and seed development during late embryogenesis may contribute to the seed vigor performance.
2020-11-04 | GSE160707 | GEO
Project description:Transcriptomic analysis of maintenance of dormancy induced by seed development temperature We used Affymetrix GeneChip Wheat Genome Array to detail transcriptional programs underlying maintenance of dormancy induced by seed development tempearture in imbibing seeds of wheat
2021-06-30 | GSE153527 | GEO
Project description:To understand the molecular basis for differences of common bean wild-type and mutant in sulphur amino acid content, transcripts were profiled at four developmental stages of seeds from wild-type SARC1 and major seed storage protein-deficient line SMARC1N-PN1 using a CustomArray 90K array. Microarray data confirmed that transcripts of storage and sulphur-rich proteins and sulphur-metabolism related genes were differentially expressed between the lines. The common bean (Phaseolus vulgaris) mutant line, SMARC1N-PN1 and its wild type, SARC1 used in the microarray experiment were grown in the field in London, ON, in 2009. Four developmental stages of seeds, based on fresh seed weight, were harvested. The stages of seeds used are Stage IV M-bM-^@M-^S cotyledon, 25 mg seed weight; Stage V M-bM-^@M-^S cotyledon, 50 mg seed weight; Stage VI M-bM-^@M-^S maturation, 150 mg seed weight, corresponding to the most active phase of reserve accumulation; and Stage VIII M-bM-^@M-^S maturation, 380 mg seed weight, corresponding to the onset of desiccation, were harvested for total RNA extraction. Four biological replicates for Stage IV and V and 3 biological replicates for Stage VI and VIII.
2012-11-06 | E-GEOD-34233 | biostudies-arrayexpress
Project description:Abscisic acid (ABA) regulates seed and bud dormancy. We show by forward and reverse genetic analysis that the tomato transcription factor SlZFP2 is required for release of bud and seed dormancy through negative regulation of ABA biosynthesis. We also demonstrated that ABA promotes growth and represses flowering in tomato both through transcriptional control on the florigen-encoding gene SINGLE FLOWER TRUSS (SFT) in tomato. To gain further insight on transcriptome changes by overexpresion of HA-SlZFP2, we sequenced two lines of p35S:HA-SlZFP2 in LA1589 background and their nontransgenic siblings on Illumina Hiseq2000 platform.
2014-04-01 | GSE45243 | GEO
Project description:Purpose: The goal of our study is to compare two different ecotypes of Oryza sativa L., PHS-susceptible rice trait and PHS-resistant rice trait under three different maturation stages in rice seed embryo with profile of miRNA-seq. Methods: Oryza sativa. L miRNA profiles of two different ecotypes with 3 different maturation stages of rice seed embryo were generated by NGS, in duplicate, following Illumina NGS workflow. Results: We found the differentially expressed microRNAs between PHS-susceptible rice trait and PHS-resistant rice trait according to the three different seed maturation stages. Target transcripts of differentially expressed microRNAs have been predicted via psRNATarget web server, and a part of those target genes are likely to be regulated by microRNAs, affecting overall responses to heat stress and the regulation of seed dormancy during maturation. Conclusions: Our study represents the analysis of rice seed small RNAs, specifically microRNAs, under two different ecotypes, three different seed maturation stages in rice seed embryo. Our results show that microRNAs are involved in response to heat stress and the regulation of seed dormancy. This study will provide a foundation for understanding dynamics of seed dormancy during the seed development and overcoming pre-harvest sprouting.
2021-07-04 | GSE175561 | GEO
Project description:Light inhibits the seed germination in the Cypriot accession (CYP) of Aethionema arabicum. Extended light illumination also induces a secondary seed dormancy that inhibits the germination even if the seeds were transferred back to darkness. This analysis aims to compare the seed transcriptome before or after the dormancy was established by light illumination (100 µmol/m2s; white light). One day light treatment (1dL) inhibits the germination but the seeds are not yet dormant. Seven day (7dL) or 14-day (14dL) long light treatment induces dormancy, and the seeds stay dormant after 7 dal-light plus 7 day-dark (7dL7dD) treatment. To understand the dormancy establishment, transcriptome was compared between non-dormant (1dL) and dormant (7dL, 14dL, 7dL7dD) seed samples.
2023-09-01 | GSE237127 | GEO