Association mapping reveals the genetic architecture of tomato response to water deficit: focus on major fruit quality traits

Albert, Elise; Segura, Vincent; Gricourt, Justine; Bonnefoi, Julien; Derivot, Laurent; Causse, Mathilde

doi:10.1093/jxb/erw411

Cited by 61 publications

(71 citation statements)

References 108 publications

(108 reference statements)

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“…() performed transcriptome‐based association mapping in a collection of 399 diverse tomato genotypes and identified 2566 cis eQTLs and 93 587 trans eQTLs involved in the expression level variations of 3465 genes. QTL‐by‐watering regime interactions were recently reported for tomato fruit quality traits, emphasizing their importance for its improvement (Gur et al ., ; Albert et al ., ,b). However, genetic variation in gene expression levels under water deficit has only been considered so far on a limited number of contrasted tomato accessions (Albert et al ., 2016a; Liu et al ., ) and the underlying genetic architecture remains to be explored.…”

Section: Introductionmentioning

confidence: 99%

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Allele‐specific expression and genetic determinants of transcriptomic variations in response to mild water deficit in tomato

et al. 2018

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Characterizing the natural diversity of gene expression across environments is an important step in understanding how genotype-by-environment interactions shape phenotypes. Here, we analyzed the impact of water deficit onto gene expression levels in tomato at the genome-wide scale. We sequenced the transcriptome of growing leaves and fruit pericarps at cell expansion stage in a cherry and a large fruited accession and their F hybrid grown under two watering regimes. Gene expression levels were steadily affected by the genotype and the watering regime. Whereas phenotypes showed mostly additive inheritance, ~80% of the genes displayed non-additive inheritance. By comparing allele-specific expression (ASE) in the F hybrid to the allelic expression in both parental lines, respectively, 3005 genes in leaf and 2857 genes in fruit deviated from 1:1 ratio independently of the watering regime. Among these genes, ~55% were controlled by cis factors, ~25% by trans factors and ~20% by a combination of both types of factors. A total of 328 genes in leaf and 113 in fruit exhibited significant ASE-by-watering regime interaction, among which ~80% presented trans-by-watering regime interaction, suggesting a response to water deficit mediated through a majority of trans-acting loci in tomato. We cross-validated the expression levels of 274 transcripts in fruit and leaves of 124 recombinant inbred lines (RILs) and identified 163 expression quantitative trait loci (eQTLs) mostly confirming the divergences identified by ASE. Combining phenotypic and expression data, we observed a complex network of variation between genes encoding enzymes involved in the sugar metabolism.

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Section: Introductionmentioning

confidence: 99%

“…Table S2. Pearson correlations between phenotypic traits measured in the RILs in 2013 (Albert et al ., ,b) and 2015. Table S3.…”

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Allele‐specific expression and genetic determinants of transcriptomic variations in response to mild water deficit in tomato

et al. 2018

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“…Tomato is a widely cultivated crop adapted to a variety of environmental conditions (Rothan et al 2019). However, important incidences of abiotic stress in the final productivity, fruit quality and reproductive performance have been noticed (Albert et al 2016; Estañ et al 2009; Mitchell et al 1991; Xu et al 2017). We quantified the level of GxE and the subjacent phenotypic plasticity in a multi-environment and multi-stress trial – involving induced water-deficit, salinity and heat stresses – in a highly recombinant tomato population.…”

Section: Discussionmentioning

confidence: 99%

Genetic basis of phenotypic plasticity and genotype x environment interaction in a multi-parental population

Diouf

Derivot²,

Koussevitzky³

et al. 2020

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Deciphering the genetic basis of phenotypic plasticity and genotype x environment interaction (GxE) is of primary importance for plant breeding in the context of global climate change. Tomato is a widely cultivated crop that can grow in different geographical habitats and which evinces a great capacity of expressing phenotypic plasticity. We used a multi-parental advanced generation intercross (MAGIC) tomato population to explore GxE and plasticity for multiple traits measured in a multi-environment trial (MET) design comprising optimal cultural conditions and water deficit, salinity and heat stress over 12 environments. Substantial GxE was observed for all the traits measured. Different plasticity parameters were estimated through the Finlay-Wilkinson and factorial regression models and used together with the genotypic means for quantitative trait loci (QTL) mapping analyses. Mixed linear models were further used to investigate the presence of interactive QTLs (QEI). The results highlighted a complex genetic architecture of tomato plasticity and GxE. Candidate genes that might be involved in the occurrence of GxE were proposed, paving the way for functional characterization of stress response genes in tomato and breeding for climate-adapted crop.HighlightThe genetic architecture of tomato response to several abiotic stresses is deciphered. QTL for plasticity and QTL x Environment were identified in a highly recombinant MAGIC population.

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“…(), who compared QTLs detected in three single environments, and showed that different QTLs were detected for a same trait, QTL and GWAS results have frequently presented variable effects according to the environment (Sauvage et al ., ; Zhang et al ., ). Recent studies on the impact of controlled abiotic stresses (water or salt stress) identified specific QTLs controlling the GxE interaction (QTLxE; Albert et al ., ; Diouf et al ., ). Therefore, to assess QTLxE effects and identify the genes controlling their variation, future studies should include a wide range of environmental conditions coupled with appropriate statistical methods (Malosetti et al ., ).…”

Section: Discovery Of Genetic Variations Underlying Major Traits In Tmentioning

confidence: 98%

“…To limit the impact of panel structure, Albert et al . () studied a new panel composed of cherry fruit accessions that showed a limited structure. Large panels of resequenced accessions also allowed the identification of several genes related to domestication traits (Lin et al ., ) or composition (Zhu et al ., ).…”

Section: Discovery Of Genetic Variations Underlying Major Traits In Tmentioning

confidence: 99%

Trait discovery and editing in tomato

2018

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Summary Tomato (Solanum lycopersicum), which is used for both processing and fresh markets, is a major crop species that is the top ranked vegetable produced over the world. Tomato is also a model species for research in genetics, fruit development and disease resistance. Genetic resources available in public repositories comprise the 12 wild related species and thousands of landraces, modern cultivars and mutants. In addition, high quality genome sequences are available for cultivated tomato and for several wild relatives, hundreds of accessions have been sequenced, and databases gathering sequence data together with genetic and phenotypic data are accessible to the tomato community. Major breeding goals are productivity, resistance to biotic and abiotic stresses, and fruit sensorial and nutritional quality. New traits, including resistance to various biotic and abiotic stresses and root architecture, are increasingly being studied. Several major mutations and quantitative trait loci (QTLs) underlying traits of interest in tomato have been uncovered to date and, thanks to new populations and advances in sequencing technologies, the pace of trait discovery has considerably accelerated. In recent years, clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 gene editing (GE) already proved its remarkable efficiency in tomato for engineering favorable alleles and for creating new genetic diversity by gene disruption, gene replacement, and precise base editing. Here, we provide insight into the major tomato traits and underlying causal genetic variations discovered so far and review the existing genetic resources and most recent strategies for trait discovery in tomato. Furthermore, we explore the opportunities offered by CRISPR/Cas9 and their exploitation for trait editing in tomato.

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Association mapping reveals the genetic architecture of tomato response to water deficit: focus on major fruit quality traits

Abstract: HighlightTomato quality could be improved under deficit irrigation while maintaining yield. The underlying genetic architecture is polygenic and varies with water availability. Candidate genes related to primary metabolism were identified.

Cited by 61 publications

References 108 publications

Allele‐specific expression and genetic determinants of transcriptomic variations in response to mild water deficit in tomato

Allele‐specific expression and genetic determinants of transcriptomic variations in response to mild water deficit in tomato

Genetic basis of phenotypic plasticity and genotype x environment interaction in a multi-parental population

Trait discovery and editing in tomato

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