Expression quantitative trait locus mapping across water availability environments reveals contrasting associations with genomic features in Arabidopsis

David B. Lowry, Tierney L. Logan, Luca Santuari, Christian S. Hardtke, James H. Richards, Leah J. DeRose-Wilson, John K. McKay, Saunak Sen, Thomas E. Juenger

Research output: Contribution to journalArticle

33 Citations (Scopus)

Abstract

The regulation of gene expression is crucial for an organism's development and response to stress, and an understanding of the evolution of gene expression is of fundamental importance to basic and applied biology. To improve this understanding, we conducted expression quantitative trait locus (eQTL) mapping in the Tsu-1 (Tsushima, Japan) × Kas-1 (Kashmir, India) recombinant inbred line population of Arabidopsis thaliana across soil drying treatments. We then used genome resequencing data to evaluate whether genomic features (promoter polymorphism, recombination rate, gene length, and gene density) are associated with genes responding to the environment (E) or with genes with genetic variation (G) in gene expression in the form of eQTLs. We identified thousands of genes that responded to soil drying and hundreds of main-effect eQTLs. However, we identified very few statistically significant eQTLs that interacted with the soil drying treatment (GxE eQTL). Analysis of genome resequencing data revealed associations of several genomic features with G and E genes. In general, E genes had lower promoter diversity and local recombination rates. By contrast, genes with eQTLs (G) had significantly greater promoter diversity and were located in genomic regions with higher recombination. These results suggest that genomic architecture may play an important a role in the evolution of gene expression.

Original languageEnglish (US)
Pages (from-to)3266-3279
Number of pages14
JournalPlant Cell
Volume25
Issue number9
DOIs
StatePublished - Sep 1 2013

Fingerprint

Quantitative Trait Loci
Arabidopsis
quantitative trait loci
genomics
Water
Genes
genes
water
Genetic Recombination
Soil
drying
promoter regions
Gene Expression
gene expression
Genome
India
soil
genome
gene expression regulation
Gene Expression Regulation

All Science Journal Classification (ASJC) codes

  • Plant Science
  • Cell Biology

Cite this

Lowry, D. B., Logan, T. L., Santuari, L., Hardtke, C. S., Richards, J. H., DeRose-Wilson, L. J., ... Juenger, T. E. (2013). Expression quantitative trait locus mapping across water availability environments reveals contrasting associations with genomic features in Arabidopsis. Plant Cell, 25(9), 3266-3279. https://doi.org/10.1105/tpc.113.115352

Expression quantitative trait locus mapping across water availability environments reveals contrasting associations with genomic features in Arabidopsis. / Lowry, David B.; Logan, Tierney L.; Santuari, Luca; Hardtke, Christian S.; Richards, James H.; DeRose-Wilson, Leah J.; McKay, John K.; Sen, Saunak; Juenger, Thomas E.

In: Plant Cell, Vol. 25, No. 9, 01.09.2013, p. 3266-3279.

Research output: Contribution to journalArticle

Lowry, DB, Logan, TL, Santuari, L, Hardtke, CS, Richards, JH, DeRose-Wilson, LJ, McKay, JK, Sen, S & Juenger, TE 2013, 'Expression quantitative trait locus mapping across water availability environments reveals contrasting associations with genomic features in Arabidopsis', Plant Cell, vol. 25, no. 9, pp. 3266-3279. https://doi.org/10.1105/tpc.113.115352
Lowry, David B. ; Logan, Tierney L. ; Santuari, Luca ; Hardtke, Christian S. ; Richards, James H. ; DeRose-Wilson, Leah J. ; McKay, John K. ; Sen, Saunak ; Juenger, Thomas E. / Expression quantitative trait locus mapping across water availability environments reveals contrasting associations with genomic features in Arabidopsis. In: Plant Cell. 2013 ; Vol. 25, No. 9. pp. 3266-3279.
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