Dataset Information

Probing the endosperm gene expression landscape in Brassica napus.

ABSTRACT: BACKGROUND: In species with exalbuminous seeds, the endosperm is eventually consumed and its space occupied by the embryo during seed development. However, the main constituent of the early developing seed is the liquid endosperm, and a significant portion of the carbon resources for the ensuing stages of seed development arrive at the embryo through the endosperm. In contrast to the extensive study of species with persistent endosperm, little is known about the global gene expression pattern in the endosperm of exalbuminous seed species such as crucifer oilseeds. RESULTS: We took a multiparallel approach that combines ESTs, protein profiling and microarray analyses to look into the gene expression landscape in the endosperm of the oilseed crop Brassica napus. An EST collection of over 30,000 entries allowed us to detect close to 10,000 unisequences expressed in the endosperm. A protein profile analysis of more than 800 proteins corroborated several signature pathways uncovered by abundant ESTs. Using microarray analyses, we identified genes that are differentially or highly expressed across all developmental stages. These complementary analyses provided insight on several prominent metabolic pathways in the endosperm. We also discovered that a transcription factor LEAFY COTYLEDON (LEC1) was highly expressed in the endosperm and that the regulatory cascade downstream of LEC1 operates in the endosperm. CONCLUSION: The endosperm EST collection and the microarray dataset provide a basic genomic resource for dissecting metabolic and developmental events important for oilseed improvement. Our findings on the featured metabolic processes and the LEC1 regulatory cascade offer new angles for investigation on the integration of endosperm gene expression with embryo development and storage product deposition in seed development.

SUBMITTER: Huang Y

PROVIDER: S-EPMC2702316 | biostudies-literature | 2009

REPOSITORIES: biostudies-literature

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Probing the endosperm gene expression landscape in Brassica napus.

Huang Yi Y Chen Liang L Wang Liping L Vijayan Kannan K Phan Sieu S Liu Ziying Z Wan Lianglu L Ross Andrew A Xiang Daoquan D Datla Raju R Pan Youlian Y Zou Jitao J

BMC genomics 20090602

<h4>Background</h4>In species with exalbuminous seeds, the endosperm is eventually consumed and its space occupied by the embryo during seed development. However, the main constituent of the early developing seed is the liquid endosperm, and a significant portion of the carbon resources for the ensuing stages of seed development arrive at the embryo through the endosperm. In contrast to the extensive study of species with persistent endosperm, little is known about the global gene expression pat ...[more]

PMID: 19490642

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Project description:In species with exalbuminous seeds such as crucifer oilseeds and legumes, the endosperm is eventually consumed and its space occupied by the embryo during seed development. However, the main constituent of the early developing seed is the liquid endosperm, and most of the carbon resources for the ensuing stages of seed development arrive at the embryo through the endosperm. In contrast to the extensive study of species with persistent endosperm, little is known about the global gene expression pattern in the endosperm of exalbuminous seed species. We took a multiparallel approach that combines ESTs, protein profiling and microarray analyses to look into the gene expression landscape in the endosperm of the oilseed crop Brassica napus. An EST collection of over 30,000 entries allowed us to detect close to 10,000 unisequences expressed in the endosperm. A protein profile analysis of more than 800 proteins corroborated several signature pathways uncovered by abundant ESTs. Using microarray analyses, we identified genes that are differentially or highly expressed across all developmental stages. These complementary analyses provided insight on several prominent metabolic pathways in the endosperm. We also discovered that LEC1 was highly expressed in the endosperm and that the regulatory cascade downstream of LEC1 operates in the endosperm. The endosperm EST collection and the microarray dataset provide a basic genomic resource for dissecting metabolic and developmental events important for oilseed improvement. Our findings on the featured metabolic processes and the LEC1 regulatory cascade offer new angles for investigation on the integration of endosperm gene expression with embryo development and storage product deposition in seed development. Keywords: seed development We defined the developmental phase of the endosperm based on the stages of the embedded embryos. Under our growth conditions, the globular-shape embryo stage is reached approximately six days after flowering (DAF), the heart-shape embryo stage is reached after eight days, and by day 14 the seed enters the cotyledon stage. The collected tissues allowed the construction of two cDNA libraries: one derived from endosperm of heart-shape embryo developing stage seeds and the other from endosperm of a mix of globular-shape embryo and cotyledon stage developing seeds. Heart-shaped-embryo endosperm is also ready for protein profiling analysis. For microarray analysis, endosperms were harvested from young seeds at the globular-shape embryo, heart-shape embryo and cotyledon stages, respectively. Two biological duplicates were set up, including four technological repeats in each duplicate. A dye-swap hybridization experiment was performed for each pair of target RNA comparisons. We performed four independent aRNA labelings for each tissue pair. For example, we used globular-shape embryo stage endosperm RNA coupled with Cy5 dye vs. heart-shape embryo stage endosperm RNA coupled with Cy3 dye, and the dye-swap experiment was with globular-shape embryo stage endosperm RNA with Cy3 dye vs. the heart-shape embryo stage endosperm RNA with Cy5 dye. Each tissue pair experiment was done with four repeats, using a total of 24 microarrays for the whole experiment.

Project description:BackgroundStudies in resynthesized Brassica napus allopolyploids indicate that homoeologous chromosome exchanges in advanced generations (S(5ratio6)) alter gene expression through the loss and doubling of homoeologous genes within the rearrangements. Rearrangements may also indirectly affect global gene expression if homoeologous copies of gene regulators within rearrangements have differential affects on the transcription of genes in networks.Methodology/principal findingsWe utilized Arabidopsis 70mer oligonucleotide microarrays for exploring gene expression in three resynthesized B. napus lineages at the S(0ratio1) and S(5ratio6) generations as well as their diploid progenitors B. rapa and B. oleracea. Differential gene expression between the progenitors and additive (midparent) expression in the allopolyploids were tested. The S(5ratio6) lines differed in the number of genetic rearrangements, allowing us to test if the number of genes displaying nonadditive expression was related to the number of rearrangements. Estimates using per-gene and common variance ANOVA models indicated that 6-15% of 26,107 genes were differentially expressed between the progenitors. Individual allopolyploids showed nonadditive expression for 1.6-32% of all genes. Less than 0.3% of genes displayed nonadditive expression in all S(0ratio1) lines and 0.1-0.2% were nonadditive among all S(5ratio6) lines. Differentially expressed genes in the polyploids were over-represented by genes differential between the progenitors. The total number of differentially expressed genes was correlated with the number of genetic changes in S(5ratio6) lines under the common variance model; however, there was no relationship using a per-gene variance model, and many genes showed nonadditive expression in S(0ratio1) lines.Conclusions/significanceFew genes reproducibly demonstrated nonadditive expression among lineages, suggesting few changes resulted from a general response to polyploidization. Furthermore, our microarray analysis did not provide strong evidence that homoeologous rearrangements were a determinant of genome-wide nonadditive gene expression. In light of the inherent limitations of the Arabidopsis microarray to measure gene expression in polyploid Brassicas, further studies are warranted.

Dataset Information

Probing the endosperm gene expression landscape in Brassica napus.

Publications

Probing the endosperm gene expression landscape in Brassica napus.

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