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Genetic analysis of variation in gene expression in Arabidopsis thaliana

Marnik Vuylsteke UGent, Fred van Eeuwijk, Paul Van Hummelen, Martin Kuiper UGent and Marc Zabeau (2005) GENETICS. 171(3). p.1267-1275
abstract
In Arabidopsis thaliana, significant efforts to determine the extent of genomic variation between phenotypically divergent accessions are under way, but virtually nothing is known about variation at the transcription level. We used microarrays to examine variation in transcript abundance among three inbred lines and two pairs of reciprocal F, hybrids of the highly self-fertilizing species Arabidopsis. Composite additive genetic effects for gene expression were estimated from pairwise comparisons of the three accessions Columbia (Col), Landsberg erecta (Ler), and Cape Verde Islands (Cvi). For the pair Col and Ler 27.0% of the 4876 genes exhibited additive genetic effects in their expression (alpha = 0.001) vs. 32.2 and 37.5% for Cvi with Lerand Col, respectively. Significant differential expression ranged from 32.45 down to 1.10 in fold change and typically differed by a factor of 1.56. Maternal or paternal transmission affected only a few genes, suggesting that the reciprocal effects observed in the two crosses analyzed were minimal. Dominance effects were estimated from the comparisons of hybrids with the corresponding midparent value. The percentage of genes showing dominance at the expression level in the F, hybrids ranged from 6.4 to 21.1 % (alpha. = 0.001). Breakdown of these numbers of genes according to the magnitude of the dominance ratio revealed heterosis for expression for on average 9% of the genes. Further advances in the genetic analysis of gene expression variation may contribute to a better understanding of its role in affecting quantitative trait variation at the phenotypic level.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
DROSOPHILA-MELANOGASTER, SEX, MAIZE, TRANSCRIPTOME, MICROARRAYS, POPULATION, HETEROSIS, PATTERNS, HYBRIDS
journal title
GENETICS
Genetics
volume
171
issue
3
pages
1267 - 1275
Web of Science type
Article
Web of Science id
000233967200033
JCR category
GENETICS & HEREDITY
JCR impact factor
4.289 (2005)
JCR rank
26/119 (2005)
JCR quartile
1 (2005)
ISSN
0016-6731
DOI
10.1534/genetics.105.041509
language
English
UGent publication?
yes
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
331298
handle
http://hdl.handle.net/1854/LU-331298
date created
2006-04-14 13:26:00
date last changed
2016-12-19 15:41:44
@article{331298,
  abstract     = {In Arabidopsis thaliana, significant efforts to determine the extent of genomic variation between phenotypically divergent accessions are under way, but virtually nothing is known about variation at the transcription level. We used microarrays to examine variation in transcript abundance among three inbred lines and two pairs of reciprocal F, hybrids of the highly self-fertilizing species Arabidopsis. Composite additive genetic effects for gene expression were estimated from pairwise comparisons of the three accessions Columbia (Col), Landsberg erecta (Ler), and Cape Verde Islands (Cvi). For the pair Col and Ler 27.0\% of the 4876 genes exhibited additive genetic effects in their expression (alpha = 0.001) vs. 32.2 and 37.5\% for Cvi with Lerand Col, respectively. Significant differential expression ranged from 32.45 down to 1.10 in fold change and typically differed by a factor of 1.56. Maternal or paternal transmission affected only a few genes, suggesting that the reciprocal effects observed in the two crosses analyzed were minimal. Dominance effects were estimated from the comparisons of hybrids with the corresponding midparent value. The percentage of genes showing dominance at the expression level in the F, hybrids ranged from 6.4 to 21.1 \% (alpha. = 0.001). Breakdown of these numbers of genes according to the magnitude of the dominance ratio revealed heterosis for expression for on average 9\% of the genes. Further advances in the genetic analysis of gene expression variation may contribute to a better understanding of its role in affecting quantitative trait variation at the phenotypic level.},
  author       = {Vuylsteke, Marnik and van Eeuwijk, Fred and Van Hummelen, Paul and Kuiper, Martin and Zabeau, Marc},
  issn         = {0016-6731},
  journal      = {GENETICS},
  keyword      = {DROSOPHILA-MELANOGASTER,SEX,MAIZE,TRANSCRIPTOME,MICROARRAYS,POPULATION,HETEROSIS,PATTERNS,HYBRIDS},
  language     = {eng},
  number       = {3},
  pages        = {1267--1275},
  title        = {Genetic analysis of variation in gene expression in Arabidopsis thaliana},
  url          = {http://dx.doi.org/10.1534/genetics.105.041509},
  volume       = {171},
  year         = {2005},
}

Chicago
Vuylsteke, Marnik, Fred van Eeuwijk, Paul Van Hummelen, Martin Kuiper, and Marc Zabeau. 2005. “Genetic Analysis of Variation in Gene Expression in Arabidopsis Thaliana.” Genetics 171 (3): 1267–1275.
APA
Vuylsteke, Marnik, van Eeuwijk, F., Van Hummelen, P., Kuiper, M., & Zabeau, M. (2005). Genetic analysis of variation in gene expression in Arabidopsis thaliana. GENETICS, 171(3), 1267–1275.
Vancouver
1.
Vuylsteke M, van Eeuwijk F, Van Hummelen P, Kuiper M, Zabeau M. Genetic analysis of variation in gene expression in Arabidopsis thaliana. GENETICS. 2005;171(3):1267–75.
MLA
Vuylsteke, Marnik, Fred van Eeuwijk, Paul Van Hummelen, et al. “Genetic Analysis of Variation in Gene Expression in Arabidopsis Thaliana.” GENETICS 171.3 (2005): 1267–1275. Print.