Genetic analysis of fruit quality in tomato

This thesis focused on two important fruit quality aspects, fruit shelf life and fruit flavour by utilisation of two sources of genetic variation: (1) segregating populations based on cultivated tomato germplasm and (2) a diverse tomato core collection that consist of wild relatives, land races and old cultivars. In chapter 2 and 3 of this thesis we have evaluated a tomato core collection consisting of 122 landraces, heirloom varieties and wild accessions for variation in several plant growth and fruit quality-related traits. This collection provided a good resource of superior alleles to incorporate in future breeding programs. 66 of the 88 cultivated accessions of this collection have been sequenced and explored for the presence of known mutations or sequence variations in key genes underlying important domestication and agronomic traits. In chapter 3, the 88 cultivated accessions of this collection plus two additional modern genotypes have been characterised in more detail for post-harvest shelf-life and thus we have now uncovered in that material novel sources for fruit shelf-life improvement. in chapter 4 and 5 of this thesis, we have investigated two metabolite QTLs involved in flavour of tomato by using a segregating population based on cultivated tomato genotypes. In chapter 4 we have fine mapped a major QTL for a volatile organic compound (2-phenyethanol) which is highly associated with consumer liking and flavour intensity (Knudsen et al., 1993; Tieman et al., 2007; Tieman et al., 2017). In chapter 5 we have identified and fine mapped the genomic region controlling the amino acid glutamate, which is a flavour enhancer and key factor conferring umami taste in tomato (Yilmaz, 2000). These results facilitate the molecular breeding of cultivars with improved flavour and also lead to a better understanding of the biosynthesis pathway underlying these two metabolites.</p

Exploration of a Resequenced Tomato Core Collection for Phenotypic and Genotypic Variation in Plant Growth and Fruit Quality Traits

A tomato core collection consisting of 122 gene bank accessions, including landraces, old cultivars, and wild relatives, was explored for variation in several plant growth, yield and fruit quality traits. The resequenced accessions were also genotyped with respect to a number of mutations or variations in key genes known to underlie these traits. The yield-related traits fruit number and fruit weight were much higher in cultivated varieties when compared to wild accessions, while, in wild tomato accessions, Brix was higher than in cultivated varieties. Known mutations in fruit size and shape genes could well explain the fruit size variation, and fruit colour variation could be well explained by known mutations in key genes of the carotenoid and flavonoid pathway. The presence and phenotype of several plant architecture affecting mutations, such as self-pruning (sp), compound inflorescence (s), jointless-2 (j-2), and potato leaf (c) were also confirmed. This study provides valuable phenotypic information on important plant growth- and quality-related traits in this collection. The allelic distribution of known genes that underlie these traits provides insight into the role and importance of these genes in tomato domestication and breeding. This resource can be used to support (precision) breeding strategies for tomato crop improvement

Exploration of a Resequenced Tomato Core Collection for Phenotypic and Genotypic Variation in Plant Growth and Fruit Quality Traits

A tomato core collection consisting of 122 gene bank accessions, including landraces, old cultivars, and wild relatives, was explored for variation in several plant growth, yield and fruit quality traits. The resequenced accessions were also genotyped with respect to a number of mutations or variations in key genes known to underlie these traits. The yield-related traits fruit number and fruit weight were much higher in cultivated varieties when compared to wild accessions, while, in wild tomato accessions, Brix was higher than in cultivated varieties. Known mutations in fruit size and shape genes could well explain the fruit size variation, and fruit colour variation could be well explained by known mutations in key genes of the carotenoid and flavonoid pathway. The presence and phenotype of several plant architecture affecting mutations, such as self-pruning (sp), compound inflorescence (s), jointless-2 (j-2), and potato leaf (c) were also confirmed. This study provides valuable phenotypic information on important plant growth- and quality-related traits in this collection. The allelic distribution of known genes that underlie these traits provides insight into the role and importance of these genes in tomato domestication and breeding. This resource can be used to support (precision) breeding strategies for tomato crop improvement

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

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.</p