Combined Use of Genome-Wide Association Data and Correlation Networks Unravels Key Regulators of Primary Metabolism in Arabidopsis thaliana

Abstract

Plant primary metabolism is a highly coordinated, central, and complex network of biochemical processes regulated at both the genetic and post-translational levels. The genetic basis of this network can be explored by analyzing the metabolic composition of genetically diverse genotypes in a given plant species. Here, we report an integrative strategy combining quantitative genetic mapping and metabolite‒transcript correlation networks to identify functional associations between genes and primary metabolites in Arabidopsis thaliana. Genome-wide association study (GWAS) was used to identify metabolic quantitative trait loci (mQTL). Correlation networks built using metabolite and transcript data derived from a previously published time-course stress study yielded metabolite‒transcript correlations identified by covariation. Finally, results obtained in this study were compared with mQTL previously described. We applied a statistical framework to test and compare the performance of different single methods (network approach and quantitative genetics methods, representing the two orthogonal approaches combined in our strategy) with that of the combined strategy. We show that the combined strategy has improved performance manifested by increased sensitivity and accuracy. This combined strategy allowed the identification of 92 candidate associations between structural genes and primary metabolites, which not only included previously well-characterized gene‒metabolite associations, but also revealed novel associations. Using loss-of-function mutants, we validated two of the novel associations with genes involved in tyrosine degradation and in β-alanine metabolism. In conclusion, we demonstrate that applying our integrative strategy to the largely untapped resource of metabolite–transcript associations can facilitate the discovery of novel metabolite-related genes. This integrative strategy is not limited to A. thaliana, but generally applicable to other plant species.

Genome-Wide Association Mapping Reveals That Specific and Pleiotropic Regulatory Mechanisms Fine-Tune Central Metabolism and Growth in Arabidopsis

“…GWAS have already been employed to detect QTL for primary and secondary metabolites (Chan et al, 2010a(Chan et al, , 2011Riedelsheimer et al, 2012;Verslues et al, 2014;Wu et al, 2016). These studies have confirmed the involvement of genes previously identified by reverse genetics and QTL mapping with biparental populations and have also revealed novel genes.…”

“…In two independent experiments, 12 (37%) and 24 (67%) of the 36 scored traits showed statistically significant associations (LOD $ 5.5, FDR control of 5%), while in earlier GWAS on primary metabolism, associations were detected for 38% of all annotated metabolites (Wu et al, 2016).…”

“…GWAS has become a standard procedure for dissecting complex genetic traits, with proven success in plants (Meijón et al, 2014;Dubin et al, 2015), but it has only occasionally been applied to plant primary metabolism (Zhang et al, 2015;Wu et al, 2016). Here, we produced a comprehensive, highly defined QTL data set for plant central metabolism.…”

The Arabidopsis thaliana gene annotated by the locus tag At3g08860 encodes alanine aminotransferase

“…Other work based on gene expression networks in A. thaliana suggested that alanine:glyoxylate aminotransferase/β‐alanine:pyruvate aminotransferase could be putative functions for the locus tag At3g08860 (Obayashi, Hayashi, Saeki, Ohta, & Kinoshita, ; Obayashi & Kinoshita, ). The locus tag At4g39660 was linked to β‐alanine metabolism since knockout lines in A. thaliana accumulate more β‐alanine compared with wild‐type (Wu et al, ). At4g39660 is therefore considered a candidate for a β‐alanine:pyruvate aminotransferase and is homologous to At2g38400, At3g08860, and Zm01g05170, a maize gene linked to β‐alanine metabolism (Wu et al, ).…”

“…The locus tag At4g39660 was linked to β‐alanine metabolism since knockout lines in A. thaliana accumulate more β‐alanine compared with wild‐type (Wu et al, ). At4g39660 is therefore considered a candidate for a β‐alanine:pyruvate aminotransferase and is homologous to At2g38400, At3g08860, and Zm01g05170, a maize gene linked to β‐alanine metabolism (Wu et al, ). Although genome‐wide analysis and knockout studies link all four genes into a large gene family of β‐alanine aminotransferases conserved both in monocot and in dicot plants, At3g08860 clusters in a separate branch from other dicots (Wu et al, ).…”