title: Exploiting Differential Gene Expression and Epistasis to Discover Candidate Genes for Drought-Associated QTLs in Arabidopsis thaliana.
abstract: Soil water availability represents one of the most important selective agents for plants in nature and the single greatest abiotic determinant of agricultural productivity, yet the genetic bases of drought acclimation responses remain poorly understood. Here, we developed a systems-genetic approach to characterize quantitative trait loci (QTLs), physiological traits and genes that affect responses to soil moisture deficit in the TSUxKAS mapping population of Arabidopsis thaliana. To determine the effects of candidate genes underlying QTLs, we analyzed gene expression as a covariate within the QTL model in an effort to mechanistically link markers, RNA expression, and the phenotype. This strategy produced ranked lists of candidate genes for several drought-associated traits, including water use efficiency, growth, abscisic acid concentration (ABA), and proline concentration. As a proof of concept, we recovered known causal loci for several QTLs. For other traits, including ABA, we identified novel loci not previously associated with drought. Furthermore, we documented natural variation at two key steps in proline metabolism and demonstrated that the mitochondrial genome differentially affects genomic QTLs to influence proline accumulation. These findings demonstrate that linking genome, transcriptome, and phenotype data holds great promise to extend the utility of genetic mapping, even when QTL effects are modest or complex.
authors: Department of Integrative Biology, University of Texas, Austin, Texas 78712 Department of BioAgricultural Sciences and Pest Management, Colorado State University, Fort Collins, Colorado 80523 johntlovell@gmail.com.
authors: John T
authors: http://orcid.org/0000-0002-8938-1166
authors: JT
authors: Lovell
authors: Department of BioAgricultural Sciences and Pest Management, Colorado State University, Fort Collins, Colorado 80523.
authors: Jack L
authors: JL
authors: Mullen
authors: Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824.
authors: David B
authors: DB
authors: Lowry
authors: Department of BioAgricultural Sciences and Pest Management, Colorado State University, Fort Collins, Colorado 80523.
authors: Kedija
authors: K
authors: Awole
authors: Department of Land, Air, and Water Resources, University of California, Davis, California 95616.
authors: James H
authors: http://orcid.org/0000-0001-8222-7927
authors: JH
authors: Richards
authors: Department of Epidemiology and Biostatistics, University of California, San Francisco, California 94143.
authors: Saunak
authors: http://orcid.org/0000-0003-4519-6361
authors: S
authors: Sen
authors: Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115, Taiwan.
authors: Paul E
authors: PE
authors: Verslues
authors: Department of Integrative Biology, University of Texas, Austin, Texas 78712 Institute of Cellular and Molecular Biology, University of Texas, Austin, Texas 78712.
authors: Thomas E
authors: TE
authors: Juenger
authors: Department of BioAgricultural Sciences and Pest Management, Colorado State University, Fort Collins, Colorado 80523.
authors: John K
authors: JK
authors: McKay
mesh_terms: D000040:Abscisic Acid / Q000378:metabolism; D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000235:genetics*; D055864:Droughts; D004843:Epistasis, Genetic / Q000235:genetics*; D018506:Gene Expression Regulation, Plant; D040641:Quantitative Trait Loci / Q000235:genetics*
chemical_list: D029681:Arabidopsis Proteins; D000040:Abscisic Acid