Dataset Information

AVATARS - Tissue-specific multi-omics analyses in developing Brassica napus seeds [proteomics]

ABSTRACT: Seeds of the German winter-type oilseed rape cultivar Express 617 were sampled and analysed at five key stages of seed development. Express 617 is a high oil yield cultivar with double-zero quality (low erucic acid and low glucosinolate content), which has been widely used in breeding programs and as parent for the creation of genetic mapping populations. Plants were grown under controlled, field-like conditions in the container-based system of the IPK PhenoSphere (Heuermann et al., 2023). The weather regime of the cultivation (2021/2021) was based on twelve years of hourly records of the weather station in Gatersleben and was designed to be as representative as possible of a typical growth season. Avoiding stressful weather extremes, the cultivation regime was considered to be favourable for plant growth and seed formation. Siliques were sampled at five key stages of seed development, as outlined by Borisjuk et al. (2013), covering the development from the pre-storage stage to seed maturation. To provide spatial information, seeds were manually dissected into four organs/tissues: the seed coat (SC), the inner (IC) and outer cotyledon (OC), and the radicle (RA). Aliquots of the pooled materials were subjected to mRNA-Sequencing and spectrometry–based proteomic analyses. Samples were prepared via the SP3 protocol and peptides were analysed on a timsTOF Pro mass spectrometer.

INSTRUMENT(S): timsTOF Pro

ORGANISM(S): Brassica Napus (rape)

TISSUE(S): Plant Cell, Seed

SUBMITTER: Nils Rugen

LAB HEAD: Hans-Peter Braun

PROVIDER: PXD053532 | Pride | 2025-03-19

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	Brassica_napus_Darmor-bzh_v10_2021_11_08.zip	Other
	L401HPKH21P01S1WS.d.zip	Other
	L401HPKH21P01S2IC.d.zip	Other
	L401HPKH21P01S2OC.d.zip	Other
	L401HPKH21P01S2RA.d.zip	Other

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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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AVATARS - Tissue-specific multi-omics analyses in developing Brassica napus seeds [proteomics]

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