E-MTAB-1899 - Transcription profiling by array of switchgrass lines NL94-298 (low tillering) and NL94-145 (high tillering) to identify genes associated with high tillering trait

Status
Released on 14 January 2014, last updated on 2 May 2014
Organism
Panicum virgaturm
Samples (8)
Array (1)
Protocols (6)
Description
The most effective method of micro-propagation for clonal replicates for switchgrass seed production is from the axillary buds of the lower nodes. We hypothesized that buds and nodes from low and high tillering lines from an inbred population will aid in identifying genes important for the different tillering habits of these plants. Since tiller number is directly correlated with biomass yields, identifying genes associated with high tillering trait will provide valuable biomarkers for marker-assisted selection and for QTL mapping of tillering trait in switchgrass. First-generation switchgrass inbred lines derived from selfing a parental genotype ‘NL94 LYE 16x13’, which was selected from the Oklahoma State University northern lowland breeding population in 2007 was used in this study. The NL94/298 inbred line produced fewer tillers than NL94/145. Stems of the high tillering line had 2-3 phytomers, while the low tillering line had 1-2 phytomers. Eight other inbred lines from this population that showed similar phenotypes as NL94/145 or NL94/298 and similar genotypes based on 380 genomic SSR marker profiles were selected for this study. Individual stems from these nine lines each for high and low tillering habit were harvested from field growing plants in the Agronomy field plots, Stillwater. Vegetative buds from first phytomer and node regions from second phytomer were cut out using a sharp scalpel under a dissection scope and immediately frozen in liquid nitrogen for transcriptomics analysis.
Experiment types
transcription profiling by array, co-expression, genotype, replicate
Contact
Citation
Transcriptome analysis of nodes and buds from high and low tillering switchgrass inbred lines. Wang Y, Zeng X, Peal L, Tang Y, Wu Y, Mahalingam R. PLoS One 8(12):e83772 (2013), Europe PMC 24386276
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-MTAB-1899.idf.txt
Sample and data relationshipE-MTAB-1899.sdrf.txt
Raw data (1)E-MTAB-1899.raw.1.zip
Processed data (1)E-MTAB-1899.processed.1.zip
Array designA-AFFY-194.adf.txt
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