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

Pott, Delphine M.; Durán-Soria, Sara; Osorio, Sonia; Vallarino, José G.

doi:10.1186/s43170-020-00021-8

CABI Agriculture and Bioscience

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)

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