title: Network-Guided GWAS Improves Identification of Genes Affecting Free Amino Acids.
abstract: Amino acids are essential for proper growth and development in plants. Amino acids serve as building blocks for proteins but also are important for responses to stress and the biosynthesis of numerous essential compounds. In seed, the pool of free amino acids (FAAs) also contributes to alternative energy, desiccation, and seed vigor; thus, manipulating FAA levels can significantly impact a seed's nutritional qualities. While genome-wide association studies (GWAS) on branched-chain amino acids have identified some regulatory genes controlling seed FAAs, the genetic regulation of FAA levels, composition, and homeostasis in seeds remains mostly unresolved. Hence, we performed GWAS on 18 FAAs from a 313-ecotype Arabidopsis (Arabidopsis thaliana) association panel. Specifically, GWAS was performed on 98 traits derived from known amino acid metabolic pathways (approach 1) and then on 92 traits generated from an unbiased correlation-based metabolic network analysis (approach 2), and the results were compared. The latter approach facilitated the discovery of additional novel metabolic interactions and single-nucleotide polymorphism-trait associations not identified by the former approach. The most prominent network-guided GWAS signal was for a histidine (His)-related trait in a region containing two genes: a cationic amino acid transporter (CAT4) and a polynucleotide phosphorylase resistant to inhibition with fosmidomycin. A reverse genetics approach confirmed CAT4 to be responsible for the natural variation of His-related traits across the association panel. Given that His is a semiessential amino acid and a potent metal chelator, CAT4 orthologs could be considered as candidate genes for seed quality biofortification in crop plants.
authors.affiliation: Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211 (R.A., A.B.); angelovicir@missouri.edu.|Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (N.D., S.G.-J., D.D.); angelovicir@missouri.edu.|Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom (S.G.-J.); angelovicir@missouri.edu.|Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14854 (M.A.G.); and angelovicir@missouri.edu.|French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel 84990 (A.F.) angelovicir@missouri.edu.
authors.forename: Ruthie
authors.identifier: 0000-0001-5150-0695
authors.initials: R
authors.lastname: Angelovici
authors.affiliation: Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211 (R.A., A.B.).|Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (N.D., S.G.-J., D.D.).|Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom (S.G.-J.).|Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14854 (M.A.G.); and.|French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel 84990 (A.F.).
authors.forename: Albert
authors.identifier: 0000-0001-5562-0731
authors.initials: A
authors.lastname: Batushansky
authors.affiliation: Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211 (R.A., A.B.).|Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (N.D., S.G.-J., D.D.).|Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom (S.G.-J.).|Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14854 (M.A.G.); and.|French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel 84990 (A.F.).
authors.forename: Nicholas
authors.initials: N
authors.lastname: Deason
authors.affiliation: Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211 (R.A., A.B.).|Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (N.D., S.G.-J., D.D.).|Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom (S.G.-J.).|Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14854 (M.A.G.); and.|French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel 84990 (A.F.).
authors.forename: Sabrina
authors.identifier: 0000-0002-0783-1929
authors.initials: S
authors.lastname: Gonzalez-Jorge
authors.affiliation: Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211 (R.A., A.B.).|Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (N.D., S.G.-J., D.D.).|Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom (S.G.-J.).|Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14854 (M.A.G.); and.|French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel 84990 (A.F.).
authors.forename: Michael A
authors.identifier: 0000-0001-6896-8024
authors.initials: MA
authors.lastname: Gore
authors.affiliation: Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211 (R.A., A.B.).|Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (N.D., S.G.-J., D.D.).|Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom (S.G.-J.).|Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14854 (M.A.G.); and.|French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel 84990 (A.F.).
authors.forename: Aaron
authors.identifier: 0000-0002-9073-8441
authors.initials: A
authors.lastname: Fait
authors.affiliation: Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211 (R.A., A.B.).|Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (N.D., S.G.-J., D.D.).|Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom (S.G.-J.).|Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14854 (M.A.G.); and.|French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel 84990 (A.F.).
authors.forename: Dean
authors.initials: D
authors.lastname: DellaPenna
mesh_terms: D000596:Amino Acids / Q000235:genetics / Q000378:metabolism*; D000597:Amino Acids, Branched-Chain / Q000235:genetics / Q000378:metabolism; D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism*; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism; D018506:Gene Expression Regulation, Plant; D014644:Genetic Variation; D055106:Genome-Wide Association Study; D006239:Haplotypes; D053858:Metabolic Networks and Pathways / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D012639:Seeds / Q000235:genetics / Q000378:metabolism
chemical_list: D000596:Amino Acids; D000597:Amino Acids, Branched-Chain; D029681:Arabidopsis Proteins