Abstract
Tomato flavor has changed over the course of long-term domestication and intensive breeding. To understand the genetic control of flavor, we report the meta-analysis of genome-wide association studies (GWAS) using 775 tomato accessions and 2,316,117 SNPs from three GWAS panels. We discover 305 significant associations for the contents of sugars, acids, amino acids, and flavor-related volatiles. We demonstrate that fruit citrate and malate contents have been impacted by selection during domestication and improvement, while sugar content has undergone less stringent selection. We suggest that it may be possible to significantly increase volatiles that positively contribute to consumer preferences while reducing unpleasant volatiles, by selection of the relevant allele combinations. Our results provide genetic insights into the influence of human selection on tomato flavor and demonstrate the benefits obtained from meta-analysis.
Highlights
Tomato flavor has changed over the course of long-term domestication and intensive breeding
We report the first meta-analysis of genome-wide association studies (GWAS) in tomato using results of three publicly available GWAS panels: 163 tomato accessions from panel S8, 291 accessions from panel B11, and 402 accessions from panel T6 (Fig. 1)
We analyzed a large set of tomato flavor-related quality chemicals, including sugars, organic acids, amino acids, and volatiles measured in each of these panels
Summary
Tomato flavor has changed over the course of long-term domestication and intensive breeding. To understand the genetic control of flavor, we report the meta-analysis of genome-wide association studies (GWAS) using 775 tomato accessions and 2,316,117 SNPs from three GWAS panels. Our results provide genetic insights into the influence of human selection on tomato flavor and demonstrate the benefits obtained from meta-analysis. Flavor is centrally influenced by sugars, acids, amino acids and a diverse set of volatiles[4,5,6] Most of these compounds are quantitatively inherited as shown by many QTL studies but only a few QTLs have been positionally cloned[7]. We perform a meta-GWAS on 775 tomato accessions and 2,316,117 SNPs and discover 305 significant associations for diverse flavor-related traits.
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