title: Association genetics of the loblolly pine (Pinus taeda, Pinaceae) metabolome.
abstract: The metabolome of a plant comprises all small molecule metabolites, which are produced during cellular processes. The genetic basis for metabolites in nonmodel plants is unknown, despite frequently observed correlations between metabolite concentrations and stress responses. A quantitative genetic analysis of metabolites in a nonmodel plant species is thus warranted. Here, we use standard association genetic methods to correlate 3563 single nucleotide polymorphisms (SNPs) to concentrations of 292 metabolites measured in a single loblolly pine (Pinus taeda) association population. A total of 28 single locus associations were detected, representing 24 and 20 unique SNPs and metabolites, respectively. Multilocus Bayesian mixed linear models identified 2998 additional associations for a total of 1617 unique SNPs associated to 255 metabolites. These SNPs explained sizeable fractions of metabolite heritabilities when considered jointly (56.6% on average) and had lower minor allele frequencies and magnitudes of population structure as compared with random SNPs. Modest sets of SNPs (n = 1-23) explained sizeable portions of genetic effects for many metabolites, thus highlighting the importance of multi-SNP models to association mapping, and exhibited patterns of polymorphism consistent with being linked to targets of natural selection. The implications for association mapping in forest trees are discussed.
authors: Department of Biology, Virginia Commonwealth University, Richmond, VA 23284, USA.
authors: Andrew J
authors: AJ
authors: Eckert
authors: Department of Plant Sciences, University of California at Davis, Davis, CA 95616, USA.
authors: Jill L
authors: JL
authors: Wegrzyn
authors: Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, USA.
authors: W Patrick
authors: WP
authors: Cumbie
authors: Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, USA.
authors: Barry
authors: B
authors: Goldfarb
authors: School of Forest Resources and Conservation, University of Florida, Gainesville, FL 32611, USA.
authors: Dudley A
authors: DA
authors: Huber
authors: Metabolomics Core Facility, Genome Center, University of California at Davis, Davis, CA 95616, USA.
authors: Vladimir
authors: V
authors: Tolstikov
authors: Department of Molecular and Cellular Biology, University of California at Davis, Davis, CA 95616, USA.
authors: Oliver
authors: O
authors: Fiehn
authors: Department of Plant Sciences, University of California at Davis, Davis, CA 95616, USA.
authors: David B
authors: DB
authors: Neale
mesh_terms: D001499:Bayes Theorem; D005787:Gene Frequency; D056726:Genetic Association Studies; D005828:Genetics, Population; D055442:Metabolome; D008957:Models, Genetic; D041603:Pinus taeda / Q000235:genetics* / Q000378:metabolism*; D020641:Polymorphism, Single Nucleotide; D015144:Southeastern United States