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

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

doi:10.1105/tpc.113.115352

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.

Highlights

The regulation of gene expression is of fundamental importance to biology (Wray et al, 2003; Stern and Orgogozo, 2008; Whittkop and Kalay, 2012; Gerstein, 2012; Jones et al, 2012)
We examined whether the following genome features are predictive of genes responding to the environment (E) and/or for genes with local main-effect expression quantitative trait locus (eQTL) (G)
We found that genomic features were predictive of eQTL occurrence in the same way across these three mapping populations as they were for the TsuKas recombinant inbred line (RIL) (Table 4)

Summary

Introduction

The regulation of gene expression is of fundamental importance to biology (Wray et al, 2003; Stern and Orgogozo, 2008; Whittkop and Kalay, 2012; Gerstein, 2012; Jones et al, 2012). Many genes alter their level expression in response to environmental changes (E). We demonstrated that there are numerous genotype 3 environment (GxE) interactions for gene expression in response to progressive soil drying (Des Marais et al, 2012). We explore the genetic architecture underlying expression responses to soil drying using eQTL methods and associate this natural variation in expression with species-wide patterns of nucleotide polymorphism and features of the genome

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Conclusion