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Identification of Scarlet Runner Bean WOX9-like binding sites in Scarlet Runner Bean seeds during seed development

ABSTRACT: 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

ORGANISM(S): Phaseolus coccineus

PROVIDER: GSE153644 | GEO | 2020/07/13

REPOSITORIES: GEO

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Identification of Scarlet Runner Bean WOX9-like binding sites in Scarlet Runner Bean seeds during seed development

Project description:Identification of Scarlet Runner Bean WOX9-like binding sites in Scarlet Runner Bean seeds during seed development

| PRJNA643538 | ENA

Transcript Profiling of Scarlet Runner Bean Embryo Regions at Globular Stage Using Laser Capture Microdissection Coupled with RNA-Seq

Project description:We used laser capture microdissection (LCM) to capture globular scarlet runner bean embryo propers and suspensors, and profiled the transcriptomes of these two embryo regions using next-generation sequencing. Our long-term goal is to understand the region-specific differentiation processes that occur during early embryo development and how genes are activated specifically in the suspensor and embryo proper. Illumina sequencing of transcripts from laser-captured embryo proper and suspensor regions of scarlet runner bean globular stage embryos. Two biological replicates were collected for each embryo region.

2014-05-10 | E-GEOD-57536 | biostudies-arrayexpress

Identification of soybean YAB1-like binding sites in soybean seeds during seed development

Project description:To dissect the gene regulatory networks operating during soybean seed development, we identified the binding sites genome-wide for transcription factor in soybean seeds during seed development using ChIP-seq

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Identification of Soybean WOX9-like binding sites in soybean seeds during seed development

2019-08-02 | GSE135267 | GEO

Identification of Soybean AGL62-like binding sites in soybean seeds during seed development

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Transcript Profiling of Scarlet Runner Bean Embryo Regions at Globular Stage Using Laser Capture Microdissection Coupled with RNA-Seq

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Profiling of transcripts in developing seeds of common bean (Phaseolus vulgaris) lines differing in major storage proteins

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:Scarlet runner bean RAD sequencing

| PRJNA783867 | ENA

Profiling of transcripts in developing seeds of common bean (Phaseolus vulgaris) lines differing in major storage proteins

2012-11-06 | GSE34233 | GEO

Transcriptome Characterization of developing bean (Phaseolus vulgaris L.) pods from two genotypes with contrasting seed zinc concentrations.

Project description:Dry bean (Phaseolus vulgaris L.) seeds are a rich source of dietary zinc, especially for people consuming plant-based diets. Within P. vulgaris there is at least two-fold variation in seed Zn concentration. Genetic studies have revealed seed Zn differences to be controlled by a single gene in two closely related navy bean genotypes, Albion and Voyager. In this study, these two genotypes were grown under controlled fertilization conditions and the Zn concentration of various plant parts were determined. The two genotypes had similar levels of Zn in their leaves and pods but Voyager had 52% more Zn in its seeds than Albion. RNA was sequence from developing pods of both genotypes. Transcriptome analysis of these genotypes identified 27,198 genes in the developing bean pods, representing 86% of the genes in the P. vulgaris genome (v 1.0 DOE-JGI and USDA-NIFA). Expression was detected in 18,438 genes. A relatively small number of genes (381) were differentially expressed between Albion and Voyager. Differentially expressed genes included three genes potentially involved in Zn transport, including zinc-regulated transporter, iron regulated transporter like (ZIP), zinc-induced facilitator (ZIF) and heavy metal associated (HMA) family genes. In addition 12,118 SNPs were identified between the two genotypes. Of the gene families related to Zn and/or Fe transport, eleven genes were found to contain SNPs between Albion and Voyager.

2015-03-24 | GSE67121 | GEO

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