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Combining Association and Haplotype Studies Towards the Improvement of Fruit Quality in Tomato

Abstract : Consumers have been complaining about tomato flavor for decades. Tomato taste is mainly influenced by sugars, acids and a diverse set of volatiles. Improving tomato flavor remains one of the main challenges for improving tomato sensory quality and consumer acceptability in modern tomato breeding. The main purpose of this thesis was to decipher the genetic and evolutionary control of tomato flavor by using high density SNPs and a diverse set of flavor-related metabolites, including sugars, acids, amino acids and volatiles. In the first part, I performed multiple haplotype-based analyses on a tomato core collection. Several approaches were used and compared to identify the genomic regions under selection. Haplotype and SNP-based Bayesian models identified 108 significant associations for 26 traits. Among these associations, some promising candidate genes were identified. I also compared marker local haplotype sharing (mLHS) with LD in determining the candidate regions. In addition, some general benefits of using haplotypes were also provided as general discussions. In the second part, I pioneered in introducing meta-analysis of genome-wide association studies using three tomato association panels. I demonstrated the efficiency of genotype imputation in increasing the genome-wide SNP coverage. Both fixed-effect and random-effect models (for those SNPs with heterogeneity I2 > 25) of meta-analysis were performed in order to control cross-study heterogeneity. A total of 305 significant loci were identified and 211 of which were new. Among them, 24 loci exhibited cis-eQTLs in a previous transcriptome-wide association study in fruit tissue. Enrichment analysis for all associations showed that up to 10 biological processes were significantly enriched and all of which were closely involved in flavor-related metabolites. A list of promising candidate genes was provided, which could be of great interest for functional validation. I also demonstrated the possibility to significantly increase the content of volatiles that positively contribute to consumer preferences while reducing unpleasant volatiles, by selection of the relevant allele combinations. Taken together, this thesis provides a comprehensive knowledge of the genetic control of tomato flavor, which will promote its improvement.
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Submitted on : Saturday, December 12, 2020 - 1:01:37 AM
Last modification on : Wednesday, February 24, 2021 - 3:24:34 AM
Long-term archiving on: : Saturday, March 13, 2021 - 6:14:53 PM


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  • HAL Id : tel-02790163, version 1
  • PRODINRA : 496146



Jiantao Zhao. Combining Association and Haplotype Studies Towards the Improvement of Fruit Quality in Tomato. Agricultural sciences. Université d'Avignon, 2019. English. ⟨NNT : 2019AVIG0712⟩. ⟨tel-02790163⟩



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