Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Evaluation of the Affymetrix Brassica Exon 1.0 ST array

ABSTRACT: The aim of the experiment was to evaluate the performance of the Affymetrix Brassica Exon 1.0 ST array. Root and leaf samples from Brassica rapa line R-O-18 were compared. The same RNA samples were hybridised to the Agilent Brassica array, to compare the performance of the two arrays. 6 samples were hybridised to each array. Triplicate samples of 11-day-old roots and 2 semi-expanded leaves from 23-day-old Brassica rapoa R-O-18 plants.

ORGANISM(S): Brassica rapa

SUBMITTER: Chris Love

PROVIDER: E-GEOD-23141 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

A Brassica exon array for whole-transcript gene expression profiling.

Love Christopher G CG Graham Neil S NS O Lochlainn Seosamh S Bowen Helen C HC May Sean T ST White Philip J PJ Broadley Martin R MR Hammond John P JP King Graham J GJ

PloS one 20100916 9

Affymetrix GeneChip® arrays are used widely to study transcriptional changes in response to developmental and environmental stimuli. GeneChip® arrays comprise multiple 25-mer oligonucleotide probes per gene and retain certain advantages over direct sequencing. For plants, there are several public GeneChip® arrays whose probes are localised primarily in 3' exons. Plant whole-transcript (WT) GeneChip® arrays are not yet publicly available, although WT resolution is needed to study complex crop gen ...[more]

PMID: 20862292

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Project description:The aim of this study was to identify eQTL in Brassica rapa grown under altered soil phosphorus (P) supply, to understand better the genetic architecture of P-use efficiency (PUE) in plants. Recombinant inbred lines (RILs) of the BraIRRI mapping population were grown at adequate and growth-limiting soil P. Variation in leaf gene expression was quantified using an Agilent Brassica 95k oligonucleotide array. Informative gene expression markers (GEMs) were used to map eQTL and PUE-related QTL. Gene expression was highly dependent on soil P supply. However, the altered expression of many genes, including known P-responsive genes, was highly heritable. Interval mapping using P supply as a covariate revealed 18,876 eQTL, representing 15,912 unique probes. Notable trans-eQTL hotspots occurred on chromosomes A06 and A01; these were enriched with protein modification and phosphorus metabolism-related (A06), as well as chloroplast and photosynthesis-related (A01) transcripts. Regulatory loci and genes associated with P-use efficiency identified through eQTL analysis are potential targets for further characterisation and may have potential for crop improvement. Availability of the annotated B. rapa genome sequence will facilitate their study, including the separation of cis- and trans- effects. The experiment was designed to identify expression QTL associated with availability of phosphorus in Brassica rapa. Seventy-eight informative lines from the “BraIRRI” mapping population of Brassica rapa L. (2n = 2x = 10; A-genome) and the two parent lines (IMB211, female; R500, male) were selected for study. The establishment of the BraIRRI population is described by Iniguez-Luy et al. (2009). Plants were grown from seed in compost, under two [P]ext treatments of 9 mg L-1 (low) or 30 mg L-1 (optimal) Olsen extractable P. RNA was extracted from leaf samples from one experimental run (78 lines at low and optimal [P]ext, with one line duplicated i.e. 158 samples), and from leaf samples from the parent lines at low and optimal P in all three experimental runs (12 samples) using a modified TRIzol extraction method (Hammond et al., 2006).

Dataset Information

Evaluation of the Affymetrix Brassica Exon 1.0 ST array

Publications

A Brassica exon array for whole-transcript gene expression profiling.

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