The genetic and functional analysis of flavor in commercial tomato: the FLORAL4 gene underlies a QTL for floral aroma volatiles in tomato fruit

Abstract

SUMMARY Tomato ( Solanum lycopersicum L.) has become a popular model for genetic studies of fruit flavor in the last two decades. In this article we present a study of tomato fruit flavor, including an analysis of the genetic, metabolic and sensorial variation of a collection of contemporary commercial glasshouse tomato cultivars, followed by a validation of the associations found by quantitative trait locus (QTL) analysis of representative biparental segregating populations. This led to the identification of the major sensorial and chemical components determining fruit flavor variation and detection of the underlying QTLs. The high representation of QTL haplotypes in the breeders’ germplasm suggests that there is great potential for applying these QTLs in current breeding programs aimed at improving tomato flavor. A QTL on chromosome 4 was found to affect the levels of the phenylalanine‐derived volatiles (PHEVs) 2‐phenylethanol, phenylacetaldehyde and 1‐nitro‐2‐phenylethane. Fruits of near‐isogenic lines contrasting for this locus and in the composition of PHEVs significantly differed in the perception of fruity and rose‐hip‐like aroma. The PHEV locus was fine mapped, which allowed for the identification of FLORAL4 as a candidate gene for PHEV regulation. Using a gene‐editing‐based (CRISPR‐CAS9) reverse‐genetics approach, FLORAL4 was demonstrated to be the key factor in this QTL affecting PHEV accumulation in tomato fruit.

The Genetic Basis of Tomato Aroma

“…For this reason, we standardized the potential positional error across the reported studies by setting an empirically defined window of ±2.5 Mb around each identified QTL. This window was derived from the average inter-study standard deviation of QTL positions of the three most functionally explored tomato aroma loci-floral aroma on chromosome 4 [25,90,99,102], smoky aroma on chromosome 9 [25,90,102] and the malodorous locus on chromosome 8 [92,93,99]. The major genetic factors underlying these QTLs were identified and, therefore, the dispersion of QTL positions in these different studies could most likely be attributed to non-genetic sources of variation.…”

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

“…On the other hand, 3-methylbutanol precursor, the branched-chain amino acid leucine, was significantly increased, while no differences were observed in phenylalanine content. Even if gene editing validated the effect of FLORAL4 deleterious mutations in planta, the decarboxylase activity of the gene could not be verified in vivo (Tikunov et al 2020).…”

“…A recent study also mapped a QTL for phenylpropanoid-derived volatiles (2-phenylethanol, phenylacetaldehyde and 1-nitro-2-phenylethane) on chromosome 4, using a diversity panel of 94 cultivars and several F 2 and F 6 populations of a half diallel cross (Tikunov et al 2020). Near isogenic lines, harbouring the marker alleles associated to the genomic region on chromosome 4 for either low or high phenylpropanoid volatiles, allowed to confirm the correlation of this locus with fruity and rose-hip aroma (Tikunov et al 2020).…”

“…A recent study also mapped a QTL for phenylpropanoid-derived volatiles (2-phenylethanol, phenylacetaldehyde and 1-nitro-2-phenylethane) on chromosome 4, using a diversity panel of 94 cultivars and several F 2 and F 6 populations of a half diallel cross (Tikunov et al 2020). Near isogenic lines, harbouring the marker alleles associated to the genomic region on chromosome 4 for either low or high phenylpropanoid volatiles, allowed to confirm the correlation of this locus with fruity and rose-hip aroma (Tikunov et al 2020). Fine-mapping the locus on chromosome 4 narrowed down to 11 genes in the associated region, and one of them showed high similarity to a 3-methyl-2-oxobutanoate dehydrogenase, an enzyme with decarboxylase activity, and which may be involved in the decarboxylation of phenylalanine, to produce the common precursor of the three volatiles (Table 2).…”

“…Tieman et al (2017) detected a locus on chromosome 9 linked to the two metabolicallyrelated volatiles, and suggested that E8, a specific highlyexpressed ripening-related gene, could be the candidate based on the analysis of silenced tomato lines, even if the molecular mechanism remained unclear. On the other hand, using a combination of omics approaches, Tikunov et al (2013Tikunov et al ( , 2020 highlighted the role of a non-smoky glycosyltransferase (NSGT1), also located on chromosome 9, and responsible for the volatile release. Very recently, and taking advantage of the new long-read technology sequencing, a collection of 100 tomato accessions was sequenced, shedding light upon structural variants underlying important domestication traits, including the smoky locus (Alonge et al 2020).…”