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Transcriptome and DNA methylation variations between six sugar beet genotypes with distinct bolting tolerance levels

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Beta vulgaris Beta vulgaris subsp. vulgaris

PROVIDER: GSE56415 | GEO | 2014/12/31

SECONDARY ACCESSION(S): PRJNA243267

REPOSITORIES: GEO

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DNA methylation variations between six sugar beet genotypes with distinct bolting tolerance levels

Project description:The aim of this study was to explore epigenetic variations between sugar beet genotypes with distinct bolting tolerance levels and to identify genes that could be involved in sugar beet bolting tolerance. We focused on shoot apical meristem, the site of floral transition, from six sugar beet genotypes that were submitted to 9 weeks of vernalization treatment. This duration of cold exposure allowed bolting in the 3 sensitive genotypes but not in the 3 resistant ones. Single-copy sequences of DNA, potentially enriched in coding sequences, were isolated by Cot analysis and sequenced using Roche's GS-FLX sequencing technology in order to complete public sugar beet databases. Oligonucleotide arrays based on our single-copy sequences (about 42 000 predicted Open Reading Frames (ORFs)) and public database sequences (30 235 ESTs) were designed and used for transcriptomic and methylation analyses. We identified 1580 differentially expressed sequences (DES) and 1526 differentially methylated sequences (DMS) between bolting resistant and bolting sensitive genotypes. Using higher stringency criteria, we focused on 169 DES (with 87 up-regulated in R genotypes and 82 up-regulated in S ones) and 111 DMS (all hyper-methylated in S genotypes). In addition, 14 sequences were found to be both differentially methylated and differentially expressed, exhibiting negative correlation between their methylation and expression. We showed that bolting tolerance involved an integrated network of genes from environment perception, phytohormone signaling to flowering induction.

2014-12-31 | GSE56413 | GEO

Transcriptomic analysis of bolting tolerance in six sugar beet genotypes

Project description:The aim of this study was to identify genes that could be involved in sugar beet bolting tolerance. We focused on shoot apical meristem, the site of floral transition, from six sugar beet genotypes that were submitted to 9 weeks of vernalization treatment. This duration of cold exposure allowed bolting in the 3 sensitive genotypes but not in the 3 resistant ones. Single-copy sequences of DNA, potentially enriched in coding sequences, were isolated by Cot analysis and sequenced using Roche's GS-FLX sequencing technology in order to complete public sugar beet databases. Oligonucleotide arrays based on our single-copy sequences (about 42 000 predicted Open Reading Frames (ORFs)) and public database sequences (30 235 ESTs) were designed and used for transcriptomic and methylation analyses. We identified 1580 differentially expressed sequences (DES) and 1526 differentially methylated sequences (DMS) between bolting resistant and bolting sensitive genotypes. Using higher stringency criteria, we focused on 169 DES (with 87 up-regulated in R genotypes and 82 up-regulated in S ones) and 111 DMS (all hyper-methylated in S genotypes). In addition, 14 sequences were found to be both differentially methylated and differentially expressed, exhibiting negative correlation between their methylation and expression. We showed that bolting tolerance involved an integrated network of genes from environment perception, phytohormone signaling to flowering induction.

2014-12-31 | GSE55951 | GEO

Epigenomics and bolting tolerance in sugar beet genotypes.

Project description: Not available

| S-EPMC4682430 | biostudies-literature