Mountain View
biomedical and healthCAre Data Discovery Index Ecosystem
help Advanced Search
Title: Defense mechanisms against herbivory: expression regulation of spruce gene family members representative of the phenylpropanoid pathway      
dateReleased:
01-01-2011
description:
A 21.8k spruce EST-spotted microarray was utilized to examine the genetic basis of constitutive defenses against herbivory. From twelve-year-old trees originating from partial diallel pedigree that segregates for resistance against Pissodes strobi, bark tissue of apical leaders was harvested at the onset of seasonal growth and natural weevil activity in the field. Our experimental design is based on a priori known genotype. We identified cross 26 from ♀PG87*♂PG165, cross 27 from ♀PG87*♂PG117, cross 29 from ♀PG21*♂PG165 and cross 32 from ♀PG21*♂PG117, respectively, forming a factorial diallel which showed widest segregation, based on a higher number of segregating SNP loci with genotypes significantly different between the most extreme resistance categories. The distant pair design introduced by ({Fu, 2006}) was modified for outbreds and maximized direct comparisons between different alleles at each locus. Our design resulted in 94 hybridisations profiling 48 individuals in cross 26, 36 in cross 27, and 50 in cross 29 as well as 54 individuals in cross 32. One criterion for identifying positional candidate genes involved that any association between trait variation and genotype variation had to be detected within 10 cM map distances; positional candidate genes for the studied phenotypic trait were then identified by strong collocations of transcript abundance variation and overlap of at least 40% of their expression quantitative trait loci (eQTLs) with phenotypic trait QTLs. 10,000 randomizations were run (p < 0.05). The experimental design optimized genetic distances between probe pairs on 94 two-color microarrays to profile 188 interior spruce F1-hybrids, independently grown and harvested.
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-22116
refinement:
raw
alternateIdentifiers:
22116
keywords:
functional genomics
dateModified:
05-02-2014
availability:
available
types:
gene expression
name:
Picea engelmannii x Picea glauca
ID:
A-GEOD-5423
name:
Treenomix spruce 21.8K cDNA microarray
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-22116/E-GEOD-22116.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-22116/E-GEOD-22116.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE22116
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress

Feedback?

If you are having problems using our tools, or if you would just like to send us some feedback, please post your questions on GitHub.