Fruit quality and DNA methylation are affected by parental order in reciprocal crosses of tomato

Giménez, Magalí Diana; Vazquez, Dana Valeria; Trepat, Felipe; Cambiaso, Vladimir; Rodríguez, Gustavo

doi:10.1007/s00299-020-02624-x

Cited by 12 publications

(6 citation statements)

References 61 publications

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“…Although several crops such as rice exhibit strong correlation between heterosis occurrence and genetic distance between parental lines [ 45 , 46 ], we report poor correlation between them within the factorial design, as did [ 29 ] with the full diallel design they studied for 28 metabolite contents, or [ 47 ]. Indeed, the highest number of transgressions we observed for metabolite content (being over-recessive or over-dominant) was reported for the cross SLC3 × SP1 (12%) gathering parental lines with 41% marker difference while we found 7% of transgressions within the SL × SP2 cross gathering the most dissimilar parental lines (58% dissimilarity).…”

Section: Discussionmentioning

confidence: 62%

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

Bineau

Rambla

Duboscq

et al. 2022

IJMS

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Flavour and nutritional quality are important goals for tomato breeders. This study aimed to shed light upon transgressive behaviors for fruit metabolic content. We studied the metabolic contents of 44 volatile organic compounds (VOCs), 18 polyphenolics, together with transcriptome profiles in a factorial design comprising six parental lines and their 14 F1 hybrids (HF1) among which were five pairs of reciprocal HF1. After cluster analyses of the metabolome dataset and co-expression network construction of the transcriptome dataset, we characterized the mode of inheritance of each component. Both overall and per-cross mode of inheritance analyses revealed as many additive and non-additive modes of inheritance with few reciprocal effects. Up to 66% of metabolites displayed transgressions in a HF1 relative to parental values. Analysis of the modes of inheritance of metabolites revealed that: (i) transgressions were mostly of a single type whichever the cross and poorly correlated to the genetic distance between parental lines; (ii) modes of inheritance were scarcely consistent between the 14 crosses but metabolites belonging to the same cluster displayed similar modes of inheritance for a given cross. Integrating metabolome, transcriptome and modes of inheritance analyses suggested a few candidate genes that may drive important changes in fruit VOC contents.

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Section: Discussionmentioning

confidence: 62%

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

Bineau

Rambla

Duboscq

et al. 2022

IJMS

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Section: Dna Methylation Regulates the Quality Of Tomato Fruit Ripeningmentioning

confidence: 99%

“…The quality that affects tomato fruit ripening includes texture, color, flavor, nutrients, etc. A recent report found that the parental reciprocal order in tomato breeding impacts the interaction between DNA methylation and fruit quality, suggesting that DNA methylation might be one of the mechanisms involved in parent‐of‐origin effects (POEs; Gimenez et al, 2021). Therefore, clarifying the correlation between DNA methylation and fruit quality may provide clues to potential breeding goals, and it is also the long‐term goal of breeders of tomato.…”

Section: Dna Methylation Regulates the Quality Of Tomato Fruit Ripeningmentioning

confidence: 99%

DNA methylation in tomato fruit ripening

Liu

et al. 2022

Physiologia Plantarum

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Fleshy fruit, the most economical and nutritional value unique to flowering plants, is an important part of our daily diet. Previous studies have shown that fruit ripening is regulated by transcription factors and the plant hormone ethylene, but recent research has also shown that epigenetics also plays an essential role, especially DNA methylation. DNA methylation is the process of transferring –CH3 to the fifth carbon of cytosine residues under the action of methyltransferase to form 5‐methylcytosine (5‐mC). So far, most works have been focused on tomato. Tomato ripening is dynamically regulated by DNA methylation and demethylation, but the understanding of this mechanism is still in its infancy. The dysfunction of a DNA demethylase, DEMETER‐like DNA demethylases 2 (DML2), prevents the ripening of tomato fruits, but immature fruits ripen prematurely under the action of DNA methylation inhibitors. Additionally, studies have shown that the relationship between fruit quality and DNA methylation is not linear, but the specific molecular mechanism is still unclear. Here, we review the recent advances in the role of DNA methylation in tomato fruit ripening, the interaction of ripening transcription factors and DNA methylation, and its effects on quality. Then, a number of questions for future research of DNA methylation regulation in tomato fruit ripening is proposed.

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“…Unexpectedly, the maternal by paternal interaction effect DMRs showed two clusters: the pure strain (hatchery-hatchery and wild-wild) and hybrid offspring. While hybridization can often cause atypical methylation patterns compared to pure strains (Gimenez, Vazquez, Trepat, Cambiaso, & Rodríguez, 2021; Raza et al, 2017; Shen et al, 2012), it was surprising that pure wild and pure hatchery-origin offspring had similar methylation patterns at these loci. It is possible that hybridization between wild and hatchery salmon led to dysregulation of epigenetic marks, though we find this an unlikely explanation after a single generation of hatchery rearing.…”

Section: Discussionmentioning

confidence: 99%

Captive rearing effects on the methylome of Atlantic salmon after oceanic migration: sex-specificity and intergenerational stability

Venney

Bouchard

April

et al. 2022

Preprint

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In the absence of genetic evolution, captive rearing in salmon hatcheries can have considerable impacts on both fish phenotype and fitness in a single generation. Evidence for hatchery-induced changes in DNA methylation is becoming abundant, though questions remain on the sex-specificity of these effects, their persistence until spawning, and potential for transmission to future generations. Here we performed whole genome bisulfite sequencing for 16 hatchery and 16 wild Atlantic salmon (Salmo salar) returning to spawn in the Rimouski River, Québec. We identified two cohorts of hatchery-reared salmon through methylation analysis, one of which was epigenetically similar to wild fish, suggesting that supplementation efforts may be able to minimize the epigenetic effects of hatchery rearing. We found considerable sex-specific effects of hatchery rearing, with few genomic regions being affected in both males and females. We also analysed the methylome of 32 F1 offspring from four groups (pure wild, pure hatchery origin, and reciprocal hybrids). We found that few epigenetic changes due to parental hatchery rearing persisted in the F1 offspring though the patterns of inheritance appear to be complex, involving nonadditive effects. Our results suggest that the epigenetic effects of hatchery rearing could be minimizable in F0. There may also be minimal epigenetic inheritance and rapid loss of epigenetic changes associated with hatchery rearing. However, due to sex-specificity and nonadditive patterns of inheritance, methylation changes due to captive rearing are more complex than initially thought and may be difficult to account for in management decisions.

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Fruit quality and DNA methylation are affected by parental order in reciprocal crosses of tomato

Cited by 12 publications

References 61 publications

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

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

DNA methylation in tomato fruit ripening

Captive rearing effects on the methylome of Atlantic salmon after oceanic migration: sex-specificity and intergenerational stability

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