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Genome-wide gene expression disturbance by single a A1/C1 chromosome substitution line in Brassica rapa restituted from natural B. napus

ABSTRACT: Genome-wide gene expression disturbance by single a A1/C1 chromosome substitution line in Brassica rapa restituted from natural B. napus

PROVIDER: PRJNA422522 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6378390_1.fastq.gz	Fastqsanger.gz
	SRR6378390_2.fastq.gz	Fastqsanger.gz
	SRR6378391_1.fastq.gz	Fastqsanger.gz
	SRR6378391_2.fastq.gz	Fastqsanger.gz
	SRR6378392_1.fastq.gz	Fastqsanger.gz

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Genome-wide gene expression disturbance by single a A1/C1 chromosome substitution line in Brassica rapa restituted from natural B. napus

Project description:Alien chromosome substitution lines are vital germplasm for breeding and genetic mapping. Previously, a whole set of nine Brassica rapa-oleracea monosonic alien addition lines (MAALs, C1-C9) was established in the background of natural B. napus genotype “Oro”, after the restituted B. rapa (RBR) for Oro was realized. Herein, a monosomic substitution line with one alien C1 chromosome (Cs1) in the RBR complement was selected in the progenies of MAAL C1 and RBR, by the PCR amplification of specific gene markers and fluorescence in situ hybridization. Cs1 exhibited the whole plant morphology similar to RBR except for the defective stamens without fertile pollen grains, but it produced some seeds and progeny plants carrying the C1 chromosome at high rate besides those without the alien chromosome after pollination by RBR. The viability of the substitution and its progeny for the restituted B. rapa diploid further elucidated the functional compensation between the chromosome pairs with high homoeology. To reveal the impact of such aneuploidy on genome-wide gene expression, the transcriptomes of MAAL C1, Cs1 and euploid RBR were analyzed. Compared to RBR, Cs1 had sharply reduced gene expression level across chromosome A1, demonstrating the loss of one copy of A1 chromosome. Both additional chromosome C1 in MAAL and substitutional chromosome C1 in Cs1 caused not only cis-effect but also prevalent trans-effect differentially expressed genes. A dominant gene dosage effects prevailed among low expressed genes across chromosome A1 in Cs1, and moreover, dosage effects for some genes potentially contributed to the phenotype deviations. Our results provided novel insights into the transcriptomic perturbation and gene dosage effects on phenotype in chromosome substitution related to one naturally evolved allopolyploid.

2018-04-09 | GSE108122 | GEO

A1 B1 C1

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Genome-Wide Gene Expression Disturbance by Single A1/C1 Chromosome Substitution in Brassica rapa Restituted From Natural B. napus.

Project description:Alien chromosome substitution (CS) lines are treated as vital germplasms for breeding and genetic mapping. Previously, a whole set of nine Brassica rapa-oleracea monosonic alien addition lines (MAALs, C1-C9) was established in the background of natural B. napus genotype "Oro," after the restituted B. rapa (RBR) for Oro was realized. Herein, a monosomic substitution line with one alien C1 chromosome (Cs1) in the RBR complement was selected in the progenies of MAAL C1 and RBR, by the PCR amplification of specific gene markers and fluorescence in situ hybridization. Cs1 exhibited the whole plant morphology similar to RBR except for the defective stamens without fertile pollen grains, but it produced some seeds and progeny plants carrying the C1 chromosome at high rate besides those without the alien chromosome after pollinated by RBR. The viability of the substitution and its progeny for the RBR diploid further elucidated the functional compensation between the chromosome pairs with high homoeology. To reveal the impact of such aneuploidy on genome-wide gene expression, the transcriptomes of MAAL C1, Cs1 and euploid RBR were analyzed. Compared to RBR, Cs1 had sharply reduced gene expression level across chromosome A1, demonstrating the loss of one copy of A1 chromosome. Both additional chromosome C1 in MAAL and substitutional chromosome C1 in Cs1 caused not only cis-effect but also prevalent trans-effect differentially expressed genes. A dominant gene dosage effects prevailed among low expressed genes across chromosome A1 in Cs1, and moreover, dosage effects for some genes potentially contributed to the phenotype deviations. Our results provided novel insights into the transcriptomic perturbation and gene dosage effects on phenotype in CS related to one naturally evolved allopolyploid.

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Drosophila melanogaster 2nd chromosome substitution lines

Project description:Transcriptional profiling of Drosophila melanogaster 2nd chromosome substitution lines; Background chromosomes are identical across lines; 2nd chromosomes are different across line and can be homozygous or heterozygous within each line Keywords: Natural variation

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Drosophila melanosgaster 2nd chromosome substitution lines

2010-05-06 | E-GEOD-12191 | biostudies-arrayexpress

Gene expression variation in Y-chromosome substitution lines of Drosophila melanogaster

Project description:These arrays were done in the context of a study to probe gene expression variation across Y-chromosome substitution lines of Drosophila melanogaster Keywords: polymorphism, evolution, chromosome substitution

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Transcription profiling of wheat variety Chinese Spring and two derived chromosome 5A substitution lines treated with cold stress

Project description:Chromosome 5A of wheat is a major regulator of freezing tolerance. It harbours gene loci controlling freezing tolerance (Fr-A1 and Fr-A2) and vernalization requirement (Vrn-A1). The number of cold-responsive genes and their functional classification was studied by cDNA macroarray-based transcript profiling in the moderately freezing-sensitive wheat (Triticum aestivum L.) variety Chinese Spring and two derived chromosome 5A substitution lines exhibiting lower or higher levels of freezing tolerance, respectively. During 21-days of cold acclimation at 2 °C the transcript level changed significantly for 681 (6.6%) out of 10,297 studied unigenes. The freezing-tolerant substitution line exhibited about 1.5-fold higher number of differentially expressed genes compared to the sensitive one. Transcript levels of several genes were altered by cold treatment only in one of the three genotypes. For 78 genes regulation by factors hosted on chromosome 5A was determined and postulated. These genes encoded proteins involved in transcriptional regulation, defence processes and carbohydrate metabolism. Three of the chromosome 5A-affected genes, having especially strong and rapid cold-induced changes of transcript level, namely Tacr7 (Triticum aesticum cold-responsive gene 7 homolog), Cab (Ca2+-binding), and Dem (deficient embryo and meristems) were genetically mapped and characterized in further detail. Only the gene Cab was located on chromosome 5A, whereas Tacr7 and Dem resided on other chromosomes. Although chromosome 5A-affected genes are also found to be localised on the same chromosome, the present findings indicate that chromosome 5A is strongly involved in trans-regulation of genes potentially due to the presence of regulatory loci, like Fr-A2, which is harboring numerous CBF transcription factors.

2009-06-22 | E-IPKG-10 | biostudies-arrayexpress

Single Cell RNA-seq data of C1-sgControl, C1-sgEED and C1-sgKMT2D cells

Project description:Analysis of gene expression patterns at single cell level of C1-sgControl, C1-sgEED and C1-sgKMT2D cells.

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Gene expression variation in Y-chromosome substitution lines of Drosophila melanogaster

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