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Genetic analysis of variation in gene expression in Arabidopsis thaliana

(2005) GENETICS. 171(3). p.1267-1275
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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.
Keywords
DROSOPHILA-MELANOGASTER, SEX, MAIZE, TRANSCRIPTOME, MICROARRAYS, POPULATION, HETEROSIS, PATTERNS, HYBRIDS

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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.
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.
Chicago author-date
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.
Chicago author-date (all authors)
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.
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.
IEEE
[1]
M. Vuylsteke, F. van Eeuwijk, P. Van Hummelen, M. Kuiper, and M. Zabeau, “Genetic analysis of variation in gene expression in Arabidopsis thaliana,” GENETICS, vol. 171, no. 3, pp. 1267–1275, 2005.
@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},
  keywords     = {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},
}

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