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Table 2 Candidate genes involved in nutritional and organoleptic crop quality traits

From: Combining metabolomic and transcriptomic approaches to assess and improve crop quality traits

Candidate gen Gen function Specie Technique Associated metabolite(s) Candidate validation Reference
Arogenate dehydratase Aromatic amino acid synthesis Maize GWAS Phenylalanine InDel in 5′UTR correlated with lower gene expression and Phe content Wen et al. (2015, 2018)
Opaque2 bZIP TF Maize GWAS / QTL mapping Lysine/total amino acid ratio Cis-eQTL identification Deng et al. (2017); Liu et al. (2017)
Acetolactate synthase 1 Branched-chain amino acid metabolism Maize GWAS / QTL mapping Leucine/total amino acid ratio Cis- and trans-eQTL identification Deng et al. (2017)
Tryptophan descarboxylase Tryptamine synthesis from tryptophan Bread wheat GWAS Tryptamine In vitro assay Peng et al. (2018)
Lin5 Cell wall invertase Tomato GWAS / QTL mapping Sugar content (glucose, fructose, SSC) Amino acid change in the protein sequence / Stable silencing and overexpression of the two different alleles Bauchet et al. (2017); Sauvage et al. (2014); Tieman et al. (2017)
Unknown gene Unkown Tomato GWAS Malate Polymorphism in gene sequence Sauvage et al. (2014); Bauchet et al. (2017)
Aluminium-activated malate transporter-like Malate accumulation/fruit acidity Tomato GWAS Malate Nonsynonymous mutation in protein transmembrane domain Sauvage et al. (2014); Bauchet et al. (2017)
Aluminium-activated malate transporter9 Malate accumulation Tomato GWAS Malate 3pb deletion in promotor sequence resulting in higher gene expression /gene editing by CRISPR  
SIbHLH59 Regulation of D-man/L-Gal ascorbate biosynthetic pathway Tomato GWAS / QTL mapping Ascorbate 8-pb-insertion in the promotor resulting in higher downstream gene expression / Stable RNAi silencing Sauvage et al. (2014); Ye et al. (2019)
TomLoxC Lipid-derived C5 and C6 volatiles Tomato QTL mapping Lipid-derived and apocarotenoid volatiles 4-kb substitution in promotor region / Stable silencing D’Angelo et al. (2018, 2019); Gao et al. 2019)
FLORAL4 Phenylalanine decarboxylation Tomato QTL mapping Phenylpropanoid-derived volatiles Gene editing by CRISPR Tikunov et al. (2020)
E8 and NSGT1 Non-smoky glycosyltransferase Tomato GWAS / omic approaches Phenylpropanoid-derived volatiles Haplotype analysis confirmed multiple mutant alleles for nsgt1 / F2 population segregating for the 23-kb deletion removing E8 and NSGT1 Alonge et al. (2020); Tieman et al. (2017); Tikunov et al. (2013, 2020)
APPR2 Ripening-related TF Melon, watermelon, cucumber, tomato, pepper Linkage analysis Chlorophyll and carotenoid pigments Haplotype analysis confirmed multiple independent polymorphisms. Stable overexpression in tomato Liu et al. (2016); Oren et al. (2019); Pan et al. (2013)
Orange Chromoplast biogenesis Sweet potato, melon, carrot QTL mapping / GWAS Carotenoid pigments Haplotyte analysis with polymorphisms leading to amino acid changes / Site-directed mutagenensis of CmOr in Arabidopsis calli Ellison et al. (2018); Gemenet et al. (2020); Tzuri et al. (2015)