Breeding Tomato Hybrids for Flavour: Comparison of GWAS Results Obtained on Lines and F1 Hybrids

Abstract

Tomato flavour is an important goal for breeders. Volatile organic compounds (VOCs) are major determinants of tomato flavour. Although most tomato varieties for fresh market are F1 hybrids, most studies on the genetic control of flavour-related traits are performed on lines. We quantified 46 VOCs in a panel of 121 small fruited lines and in a test cross panel of 165 hybrids (the previous panel plus 44 elite cherry tomato lines crossed with a common line). High and consistent heritabilities were assessed for most VOCs in the two panels, and 65% of VOC contents were strongly correlated between lines and hybrids. Additivity was observed for most VOCs. We performed genome wide association studies (GWAS) on the two panels separately, along with a third GWAS on the test cross subset carrying only F1 hybrids corresponding to the line panel. We identified 205, 183 and 138 associations, respectively. We identified numerous overlapping associations for VOCs belonging to the same metabolic pathway within each panel; we focused on seven chromosome regions with clusters of associations simultaneously involved in several key VOCs for tomato aroma. The study highlighted the benefit of testcross panels to create tasty F1 hybrid varieties.

Inheritance of Secondary Metabolites and Gene Expression Related to Tomato Fruit Quality

“…We also assessed high heritabilities when considering the three biological replicates with 17 out of 18 phenolics exhibiting h 2 > 0.4 and 20/33 VOCs with h 2 > 0.4. These results are consistent with those reported in [ 25 ]. From the metabolic diversity observed within the trial, we found back metabolic pathways previously identified and support still pending biological hypotheses as to the origin of several VOCs impacting tomato aroma such as the carotenoid-derived BDAM or lipid-derived 2EFUR [ 34 ].…”

“…For the other traits, heritability values ranged from 0.24 for the carotenoid-derived NERAL to 0.99 for the alkaloid LYPR, and 50 traits had heritability values higher than 0.4. The cluster analysis on secondary metabolites and SSC of these 20 genotypes was consistent with [ 25 , 34 ] studies.…”

“…We identified two major clusters of fatty-acid-derived VOCs that matched those previously described [ 25 , 34 ]: in the first cluster the C 5 PENAL and C 7 to C 10 lipid-derived VOCs, while in the second the four C 6 lipid-derived volatiles associated with ‘green’/‘grassy’ aroma in addition with 2EFUR, and further though still in the same cluster two C 5 and two C 7 fatty acid derived VOCs ( Figure S3 ).…”

“…The genetic architecture of fruit flavour and nutritional quality has been thoroughly studied in homozygous plant material such as Introgression Lines (‘ILs’) and Recombinant Inbred Lines (‘RILs’) derived from biparental populations, or Genome Wide Association Study (‘GWAS’) panels covering the genetic diversity of a species. Hundreds of QTLs [ 15 , 16 , 17 , 18 , 19 , 20 ] and association signals [ 11 , 21 , 22 , 23 , 24 , 25 ] have been suggested to control flavour and nutritional quality-related traits. However, while most tomato varieties are commercialized as HF1, the impact of the heterozygous state on flavour-related traits has long been overlooked.…”

“…However, while most tomato varieties are commercialized as HF1, the impact of the heterozygous state on flavour-related traits has long been overlooked. [ 25 ] performed the first GWAS on a testcross panel to identify associations specific to HF1, or shared between HF1 and line panels for flavour-related traits. The authors suggested seven chromosome regions with clusters of associations simultaneously involved in several key VOCs for tomato aroma, where improvement for flavour-related traits may be more efficient than QTLs only identified in line panels.…”