Skip to main content

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)