ArticlePlant physiology2017
Network-Guided GWAS Improves Identification of Genes Affecting Free Amino Acids.
Article in Plant physiology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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33 citing papers in PubMed, 74 citations in OpenAlex.
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- Network analysis combined with genome-wide association study helps identification of genes related to amino acid contents in soybean.BMC genomics · 2025Article
- Genome-wide association study of metabolic traits in the giant duckweed Spirodela polyrhiza.Plant biology (Stuttgart, Germany) · 2025Article
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- QT-GWAS: A novel method for unveiling biosynthetic loci affecting qualitative metabolic traits.Molecular plant · 2023Article
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- Mapping Genetic Variation in Arabidopsis in Response to Plant Growth-Promoting BacteriumMicroorganisms · 2023Article
- Genome-wide association study of soybean (Frontiers in plant science · 2023Article
- Genetic dissection reveals the complex architecture of amino acid composition in soybean seeds.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2023Article
- Co-expression pan-network reveals genes involved in complex traits within maize pan-genome.BMC plant biology · 2022Article
- 4D genetic networks reveal the genetic basis of metabolites and seed oil-related traits in 398 soybean RILs.Biotechnology for biofuels and bioproducts · 2022Article
- Multiomics approach reveals a role of translational machinery in shaping maize kernel amino acid composition.Plant physiology · 2022Article
- Guidelines for correlation coefficient threshold settings in metabolite correlation networks exemplified on a potato association panel.BMC bioinformatics · 2021Article
- Tissue-Dependent Variation Profiles of Tea Quality-Related Metabolites in New Shoots of Tea Accessions.Frontiers in nutrition · 2021Article
- Understanding Omics Driven Plant Improvement andFrontiers in genetics · 2021Review
- Genomic Prediction Informed by Biological Processes Expands Our Understanding of the Genetic Architecture Underlying Free Amino Acid Traits in DryG3 (Bethesda, Md.) · 2020Article
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
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