Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Dormancy of green-cotyledon Col seeds matured at 20°C vs 15°C

ABSTRACT: To determine genes involved in induction of dormancy in response to reduced maturation temperatures, RNA sequencing was performed on developing seeds matured at 20°C, where low dormancy is observed, and compared to seeds matured at 15°C where high dormancy is observed. Col green cotyledon seeds matured at 20°C and 15°C were dissected from siliques between five to seven hours after dawn and frozen in liquid nitrogen. RNA was extracted as described previously (Penfield et al., 2005).

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Dana MacGregor

PROVIDER: E-GEOD-61061 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Seed production temperature regulation of primary dormancy occurs through control of seed coat phenylpropanoid metabolism.

MacGregor Dana R DR Kendall Sarah L SL Florance Hannah H Fedi Fabio F Moore Karen K Paszkiewicz Konrad K Smirnoff Nicholas N Penfield Steven S

The New phytologist 20141120 2

Environmental changes during seed production are important drivers of lot-to-lot variation in seed behaviour and enable wild species to time their life history with seasonal cues. Temperature during seed set is the dominant environmental signal determining the depth of primary dormancy, although the mechanisms though which temperature changes impart changes in dormancy state are still only partly understood. We used molecular, genetic and biochemical techniques to examine the mechanism through w ...[more]

PMID: 25412428

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Project description:To understand gene expression networks leading to functional properties and compositional traits of the soybean seed, we have undertaken a detailed examination of soybean seed development from a few days post-fertilization to the mature seed using Illumina high-throughput transcriptome sequencing (RNA-Seq). RNA was sequenced from seven different stages of seed development, yielding between 12 million and 78 million sequenced transcripts. These have been aligned to the 79,000 gene models predicted from the soybean genome recently sequenced by the Department of Energy Joint Genome Institute. Over one hundred gene models were identified with high expression exclusively in young seed stages, starting at just four days after fertilization. These were annotated as being related to many basic components and processes such as histones and proline-rich proteins. Genes involved with some storage proteins such as glycinin and beta-conglycinin had their highest expression levels at the stages of largest fresh weight, confirming previous knowledge that these storage products are being rapidly accumulated before the seed begins the desiccation process. Other gene models showed high expression in the dry, mature seeds, perhaps indicating the preparation of pathways needed later, in the early stages of imbibition. Many highly-expressed gene models at the dry seed stage are, as expected, annotated as hydrophilic proteins associated with low water conditions, such as late embryogenesis abundant (LEA) proteins and dehydrins, which help preserve the cellular structures and nutrients within the seed during desiccation. Hundreds of transcription factors with notable expression in at least one stage of seed development were also identified and examined. Results from a second biological replicate demonstrate high reproducibility of these data. High-throughput sequencing using Illumina Genome Analyzer II and Illumina HiSeq 2000 (RNA-Seq) was performed on seven stages of soybean seeds, with two biological replicates per stage.

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Dataset Information

Dormancy of green-cotyledon Col seeds matured at 20°C vs 15°C

Publications

Seed production temperature regulation of primary dormancy occurs through control of seed coat phenylpropanoid metabolism.

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