(2004) demonstrated that the correlation network properties of metabolites better capture the systemic responses to genetic alterations than do changes to metabolic levels ( Weckwerth et al., 2004). Interestingly, studies also suggest that the latent dynamics of the metabolic network are strongly connected to the underlying reaction pathway structure ( Steuer et al., 2003 Weckwerth, 2003). Similarly, two correlation-based network analyses of more than 50 primary metabolite profiles spanning late seed maturation and desiccation demonstrated that FAAs form a highly interconnected metabolic cluster with only positive correlations ( Angelovici et al., 2009 Toubiana et al., 2012). For example, a correlation-based network metabolic reconstruction of FAA levels revealed that individual FAAs are strongly correlated during seed development compared with leaf or fruit development ( Toubiana et al., 2012), which suggests a much tighter interaction of this metabolic network in seeds. Reconstructions of seed metabolic networks in several model species and tissues have offered important insights into these underlying metabolic interactions and regulation ( Lu et al., 2008 Toubiana et al., 2013, 2015). In addition, several amino acid catabolic products, such as those emanating from branched-chain amino acids ( BCAAs) or Lys degradation pathways, can be channeled toward cellular energy production under both standard and stress growth conditions ( Angelovici et al., 2009, 2011 Araújo et al., 2010 Peng et al., 2015).
At high concentrations, this inhibition can lead to starvation of a downstream metabolic product, Met, which inhibits plant growth ( Bright et al., 1982 Rognes et al., 1983 Heremans and Jacobs, 1995). For example, increasing Lys and Thr inhibits the activity of Asp kinase via a feedback inhibition loop ( Clark and Lu, 2015). One reason is that FAA metabolism is tightly intertwined with essential cellular processes in plants, and manipulating FAA levels can have strong deleterious, pleiotropic effects on the entire system ( Guyer et al., 1995 Galili, 2011 Ingle, 2011 Pratelli and Pilot, 2014). Still, the genetic control of FAA metabolism in seed remains poorly understood. Studies of both developing and germinating seeds also have implicated FAAs in proper seed development and germination ( Angelovici et al., 2010 Galili and Amir, 2013).
FAAs serve as building blocks for protein synthesis and also are precursors for osmolytes, alternative energy, hormones, and key secondary metabolites ( Rai, 2002 Araújo et al., 2010 Tzin and Galili, 2010 Angelovici et al., 2011). 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.įree amino acids ( FAAs) play a pivotal role in the central metabolism of plants. A reverse genetics approach confirmed CAT4 to be responsible for the natural variation of His-related traits across the association panel. 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. The latter approach facilitated the discovery of additional novel metabolic interactions and single-nucleotide polymorphism-trait associations not identified by the former approach. 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. Hence, we performed GWAS on 18 FAAs from a 313-ecotype Arabidopsis ( Arabidopsis thaliana) association panel. 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.
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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. Amino acids serve as building blocks for proteins but also are important for responses to stress and the biosynthesis of numerous essential compounds. Amino acids are essential for proper growth and development in plants.
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