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Genome-wide QTL analysis of tomato fruit cuticle deposition and composition.

ABSTRACT: Genetics of traits related to fruit cuticle deposition and composition was studied in two red-fruited tomato species. Two mapping populations derived from the cross between the cultivated tomato (Solanum lycopersicum L.) and its closest relative wild species Solanum pimpinellifolium L. were employed to conduct a QTL analysis. A combination of fruit cuticle deposition, components and anatomical traits were investigated and the individual effect of each QTL evaluated. A total of 70 QTLs were identified, indicating that all the cuticle traits analyzed have a complex polygenic nature. A combination of additive and epistatic interactions was observed for all the traits, with positive contribution of both parental lines to most of them. Colocalization of QTLs for various traits uncovered novel genomic regions producing extensive changes in the cuticle. Cuticle density emerges as an important trait since it can modulate cuticle thickness and invagination thus providing a strategy for sustaining mechanical strength without compromising palatability. Two genomic regions, located in chromosomes 1 and 12, are responsible for the negative interaction between cuticle waxes and phenolics identified in tomato fruit. Several candidate genes, including transcription factors and structural genes, are postulated and their expression analyzed throughout development.

SUBMITTER: Barraj Barraj R

PROVIDER: S-EPMC8087829 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundFruit ripening is a complex developmental process that depends on a coordinated regulation of numerous genes, including ripening-related transcription factors (TFs), fruit-related microRNAs, DNA methylation and chromatin remodeling. It is known that various TFs, such as MADS-domain, MYB, AP2/ERF and SBP/SPL family proteins play key roles in modulating ripening. However, little attention has been given to members of the large NF-Y TF family in this regard, although genes in this family are known to have important functions in regulating plant growth, development, and abiotic or biotic stress responses.ResultsIn this study, the evolutionary relationship between Arabidopsis thaliana and tomato (Solanum lycopersicum) NF-Y genes was examined to predict similarities in function. Furthermore, through gene expression analysis, 13 tomato NF-Y genes were identified as candidate regulators of fruit ripening. Functional studies involving suppression of NF-Y gene expression using virus induced gene silencing (VIGS) indicated that five NF-Y genes, including two members of the NF-YB subgroup (Solyc06g069310, Solyc07g065500) and three members of the NF-YA subgroup (Solyc01g087240, Solyc08g062210, Solyc11g065700), influence ripening. In addition, subcellular localization analyses using NF-Y proteins fused to a green fluorescent protein (GFP) reporter showed that the three NF-YA proteins accumulated in the nucleus, while the two NF-YB proteins were observed in both the nucleus and cytoplasm.ConclusionsIn this study, we identified tomato NF-Y genes by analyzing the tomato genome sequence using bioinformatics approaches, and characterized their chromosomal distribution, gene structures, phylogenetic relationship and expression patterns. We also examined their biological functions in regulating tomato fruit via VIGS and subcellular localization analyses. The results indicated that five NF-Y transcription factors play roles in tomato fruit ripening. This information provides a platform for further investigation of their biological functions.

Project description:Two important biophysical properties, the thermal and UV-Vis screening capacity, of isolated tomato fruit cuticle membranes (CM) have been studied by differential scanning calorimetry (DSC) and UV-Vis spectrometry, respectively. A first order melting, corresponding to waxes, and a second order glass transition (T g ) thermal events have been observed. The glass transition was less defined and displaced toward higher temperatures along the fruit ripening. In immature and mature green fruits, the CM was always in the viscous and more fluid state but, in ripe fruits, daily and seasonal temperature fluctuations may cause the transition between the glassy and viscous states altering the mass transfer between the epidermal plant cells and the environment. CM dewaxing reduced the T g value, as derived from the role of waxes as fillers. T g reduction was more intense after polysaccharide removal due to their highly interwoven distribution within the cutin matrix that restricts the chain mobility. Such effect was amplified by the presence of phenolic compounds in ripe cuticle membranes. The structural rigidity induced by phenolics in tomato CMs was directly reflected in their mechanical elastic modulus. The heat capacity (Cp rev ) of cuticle membranes was found to depend on the developmental stage of the fruits and was higher in immature and green stages. The average Cp rev value was above the one of air, which confers heat regulation capacity to CM. Cuticle membranes screened the UV-B light by 99% irrespectively the developmental stage of the fruit. As intra and epicuticular waxes contributed very little to the UV screening, this protection capacity is attributed to the absorption by cinnamic acid derivatives. However, the blocking capacity toward UV-A is mainly due to the CM thickness increment during growth and to the absorption by flavone chalconaringenin accumulated during ripening. The build-up of phenolic compounds was found to be an efficient mechanism to regulate both the thermal and UV screening properties of cuticle membranes.

Project description:BACKGROUND: The traditional strategy to map QTL is to use linkage analysis employing a limited number of markers. These analyses report wide QTL confidence intervals, making very difficult to identify the gene and polymorphisms underlying the QTL effects. The arrival of genome-wide panels of SNPs makes available thousands of markers increasing the information content and therefore the likelihood of detecting and fine mapping QTL regions. The aims of the current study are to confirm previous QTL regions for growth and body composition traits in different generations of an Iberian x Landrace intercross (IBMAP) and especially identify new ones with narrow confidence intervals by employing the PorcineSNP60 BeadChip in linkage analyses. RESULTS: Three generations (F3, Backcross 1 and Backcross 2) of the IBMAP and their related animals were genotyped with PorcineSNP60 BeadChip. A total of 8,417 SNPs equidistantly distributed across autosomes were selected after filtering by quality, position and frequency to perform the QTL scan. The joint and separate analyses of the different IBMAP generations allowed confirming QTL regions previously identified in chromosomes 4 and 6 as well as new ones mainly for backfat thickness in chromosomes 4, 5, 11, 14 and 17 and shoulder weight in chromosomes 1, 2, 9 and 13; and many other to the chromosome-wide signification level. In addition, most of the detected QTLs displayed narrow confidence intervals, making easier the selection of positional candidate genes. CONCLUSIONS: The use of higher density of markers has allowed to confirm results obtained in previous QTL scans carried out with microsatellites. Moreover several new QTL regions have been now identified in regions probably not covered by markers in previous scans, most of these QTLs displayed narrow confidence intervals. Finally, prominent putative biological and positional candidate genes underlying those QTL effects are listed based on recent porcine genome annotation.

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Genome-wide QTL analysis of tomato fruit cuticle deposition and composition.

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