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Transgressive and parental dominant gene expression and cytosine methylation during seed development in Brassica napus hybrids [RNA-seq]

ABSTRACT: To investigate the expression and methylation patterns of hybrid embryo development in Brassica napus, we performed pattern analysis on different developmental stages of parental and hybrid embryos

ORGANISM(S): Brassica napus

PROVIDER: GSE202607 | GEO | 2023/03/14

REPOSITORIES: GEO

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Transgressive and parental dominant gene expression and cytosine methylation during seed development in Brassica napus hybrids [Bisulfite-seq]

Project description:To investigate the expression and methylation patterns of hybrid embryo development in Brassica napus, we performed pattern analysis on different developmental stages of parental and hybrid embryos

2023-03-14 | GSE202609 | GEO

Transgressive and parental dominant gene expression and cytosine methylation during seed development in Brassica napus hybrids [miRNA-seq]

2023-03-14 | GSE202608 | GEO

Transgressive and parental dominant gene expression and cytosine methylation during seed development in Brassica napus hybrids

Project description:This SuperSeries is composed of the SubSeries listed below.

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Brassica napus control vs. heat stress

Project description:High temperature stress results in yield loss and alterations to seed composition during seed filling in oilseed rape (Brassica napus). However, the mechanism underlying this heat response is poorly understood. In this study, we employed a microarray analysis with silique walls and seeds from the developing siliques (20 days after flowering) of Brassica napus that had undergone heat stress.

2015-01-05 | GSE57697 | GEO

Brassica napus control vs. heat stress

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Genome-wide analysis of transcriptome and histone modifications in Brassica napus hybrids

Project description:Although utilization of heterosis has largely improved the yield of many crops worldwide, the underlying molecular mechanism of heterosis, particularly for allopolyploids, remains unclear. Here, we compared epigenome and transcriptome data of an elite hybrid and its parental lines in three assessed tissues (seedling, flower bud, and silique) to explore their contribution to heterosis in allopolyploid B. napus. Transcriptome analysis illustrated that a small proportion of non-additive genes in the hybrid compared with its parents, as well as parental expression level dominance, might have a significant effect on heterosis. We identified histone modification (H3K4me3 and H3K27me3) variation between the parents and hybrid, most of which resulted from the differences between parents. H3K4me3 variations were positively correlated with gene expression differences among the hybrid and its parents. Furthermore, H3K4me3 and H3K27me3 were rather stable in hybridization and were mainly inherited additively in the B. napus hybrid. Together, our data revealed that transcriptome reprogramming and histone modification remodeling in the hybrid could serve as valuable resources for better understanding heterosis in allopolyploid crops.

2023-07-18 | GSE218592 | GEO

Gene expression regulated by Transparent Testa16 in Brassica napus

Project description:To broadly identify genes regulated by Transparent Testa16 in Brassica napus

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Gene expression profiles during seed development and maturation in Brassica napus

Project description:Time course of gene expression profiles during seed development and maturation in Brassica napus were studied using Combimatrix Brassica microarray.

2013-03-01 | GSE43918 | GEO

Gene expression profiles during seed development and maturation in Brassica napus

Project description:Time course of gene expression profiles during seed development and maturation in Brassica napus were studied using Combimatrix Brassica microarray. The time course expression of 90K Brassica napus EST contigs were measured at 8 developing seed stages of 10, 15, 20, 25, 30, 35, 40 and 45 DAF (days after flowering) using single color microarray

2013-03-01 | E-GEOD-43918 | biostudies-arrayexpress

Subgenome-dominant expression and alternative splicing in response to pathogen stress in polyploid Brassica napus and progenitors

Project description:Polyploidy has played an extensive role in the evolution of flowering plants. Allopolyploids, with subgenomes containing duplicated gene pairs called homeologs, can show rapid transcriptome changes including novel alternative splicing (AS) patterns. The extent to which abiotic stress modulates AS of homeologs is a nascent topic in polyploidy research. We subjected both natural and resynthesized lines of polyploid Brassica napus, along with the progenitors B. rapa and B. oleracea, to infection with the fungal pathogen Sclerotinia sclerotiorum. RNA-seq analyses revealed widespread divergence between polyploid subgenomes in both gene expression and AS patterns. Resynthesized B. napus displayed significantly more A and C subgenome biased homeologs under pathogen infection than during uninfected growth. Differential AS (DAS) in response to infection was highest in natural B. napus (12,709 DAS events) and lower in resynthesized Brassica napus (8,863 DAS events). Natural B. napus had more up-regulated events and fewer down-regulated events. There was a global expression bias towards the B. oleracea-derived (C) subgenome in both resynthesized and natural B. napus, enhanced by widespread non-parental downregulation of the B. rapa-derived (A) homeolog. In the resynthesized B. napus specifically, this resulted a disproportionate C subgenome contribution to pathogen defense response, characterized by biases in both transcript expression levels and the proportion of induced genes. Our results elucidate the complex ways in which Sclerotinia infection affects expression and AS of homeologous genes in natural and resynthesized B. napus, and indicate that abiotic stress can influence the evolution of homeologous genes in polyploids.

2023-02-04 | GSE201225 | GEO

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