# Breeding Tomato Hybrids for Flavour: Comparison of GWAS Results Obtained on Lines and F1 Hybrids
## 4 Discussion
### Strategy for F1 Hybrids Quality Improvement  
As stated in [8], flavour is a highly polygenic trait that requires a robust strategy for quality improvement to be achieved. We know the metabolic pathways involved in VOC synthesis, some of the underlying gene functions, and even more importantly we know a subset of approximately 30 VOCs that impact tomato aroma. Based on this information that constitutes the first step of a strategy to improve tomato aroma, we herein tackled the next central issue for tomato breeders: how does heterozygosity encountered in commercialized F1 hybrids affect VOC abundancy, and which allelic combinations would be preferable to achieve sensible flavour improvement with so many target traits. Given the common regulation of volatiles belonging to the same metabolic pathway as found in the cluster analysis, an overall regulation of key metabolic pathways could be achieved by selecting overlapping associations for VOCs clustering with one another. Since we cannot estimate yet how many favourable alleles are necessary to make significant flavour differences in the breeding material, we proposed the most important breeding regions encompassing these overlaps to achieve multi-VOC regulation. We also indicated regions where promising CGs could be found based on the same criteria. The next and final criteria was selecting among these regions those that displayed a consistent effect of FTMW homozygous genotype across VOCs belonging to the same metabolic pathway and on VOCs with similar impact on consumer liking in order to (i) control and understand the taste differences that could be accomplished and (ii) increase VOCs with positive impact on consumer liking while simultaneously decreasing those leading to off-flavours. For this strategy to work on F1 hybrids, we highlighted regions with F1 specific associations, or overlapping between F1 hybrid (TCI TCT) and line (CCI) panels. With only nine and five associations commonly found between CCI and CCI and TCT, respectively, and six associations shared between the three panels, we underlined the utmost importance of considering associations fit to design F1 hybrid varieties instead of considering QTLs identified only on homozygous plant material. We revealed novel regions where phenotypic means for a given volatile are more contrasted when we compare the homozygous and heterozygous locus versions versus the two homozygous genotypes at the locus. Although the environmental effect causing lack of overlaps between line and hybrid panels cannot be ruled out, the high correlations calculated between CCI and TCI are evidence that novel associations in F1 hybrids did not result solely from an environmental effect. Additionally, we defined stringent CIs around associated markers by accounting for both population structure and kinship when calculating local LD between neighbouring markers, and we called \"overlap\" CI boundaries separated by less than 0.1 Mbp. Those parameters led to few overlaps. With less stringent parameters, more overlaps would be detected. Apart from the four cloned genes that we found back in hybrid panel associations and 6% of hybrid specific associations for VOCs carrying CGs previously suggested in [20], we identified novel associations for VOCs. Nonetheless, the \(\chi^{2}\) test we performed on each metabolic pathway and each panel separately mostly showed significant enrichment of CG presence in the CI of our associations. This underlined that the MLMM method paired with the definition of narrow CIs allowed us to retrieve CGs accurately. As part of our strategy, we also gave insight into the best allelic combinations for breeding by giving the relative position of the heterozygous class compared to FTMV homozygous genotype for a given trait-marker association. For each breeding region we selected, and even more in the elite plant material, we found associated markers with balanced MAF, which highlighted that many regions in small fruited accessions showed the allelic version of the common parent FTMV entirely lacking flavour.