Dataset Information

Tunisian Table Olive Oil Traceability and Quality Using SNP Genotyping and Bioinformatics Tools.

ABSTRACT: To enhance and highlight the authentication and traceability of table olive oil, we considered the analysis of 11 Tunisian table olive cultivars based on seven SNP molecular markers (SOD, CALC, FAD2.1, FAD2.3, PAL70, ANTHO3, and SAD.1) localized in six different genes. Accordingly, we assessed the potential genotype-phenotypes links between the seven SNPs, on the one hand, and the quantitative and qualitative parameters, on the other. The obtained genotypes were analyzed with computational biology tools based on bivariate analysis, multinomial logistic regression, and the Bayesian networks modeling. Obtained results showed that PAL70 SNP marker was negatively influenced by the phenol rate (r = -0.886; p <0.001), the oxidative stability (r = -0.884; p <0.001), traducing a direct effect of the PAL70 genotype deviations on the proportion of total phenol for each variety. Additionally, we revealed a significant association of SAD.1 marker with the content of the linolenic unsaturated fatty acids (C18:3; p=0.046). Moreover, SAD.1 was positively correlated with the saturated stearic acid C18:0 (r = 0.644; p = 0.032) based on multinomial logistic regression and Bayesian networks modeling, respectively. This research work provides better understanding and characterization of the quality of Tunisian table olive and supplies a significant knowledge and data information for table olive traceability and breeding.

SUBMITTER: Ben Ayed R

PROVIDER: S-EPMC6381586 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Tunisian Table Olive Oil Traceability and Quality Using SNP Genotyping and Bioinformatics Tools.

Ben Ayed Rayda R Rebai Ahmed A

BioMed research international 20190206

To enhance and highlight the authentication and traceability of table olive oil, we considered the analysis of 11 Tunisian table olive cultivars based on seven SNP molecular markers (SOD, CALC, FAD2.1, FAD2.3, PAL70, ANTHO3, and SAD.1) localized in six different genes. Accordingly, we assessed the potential genotype-phenotypes links between the seven SNPs, on the one hand, and the quantitative and qualitative parameters, on the other. The obtained genotypes were analyzed with computational biolo ...[more]

PMID: 30881998

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Project description:BACKGROUND:Breast cancer is the most common cancer in women worldwide. Around 50% of breast cancer familial risk has been so far explained by known susceptibility alleles with variable levels of risk and prevalence. The vast majority of these breast cancer associated variations reported to date are from populations of European ancestry. In spite of its heterogeneity and genetic wealth, North-African populations have not been studied by the HapMap and the 1000Genomes projects. Thus, very little is known about the genetic architecture of these populations. METHODS:This study aimed to investigate a subset of common breast cancer loci in the general Tunisian population and to compare their genetic composition to those of other ethnic groups. We undertook a genome-wide haplotype study by genotyping 135 Tunisian subjects using the Affymetrix 6.0-Array. We compared Tunisian allele frequencies and linkage disequilibrium patterns to those of HapMap populations and we performed a comprehensive assessment of the functional effects of several selected variants. RESULTS:Haplotype analyses showed that at risk haplotypes on 2p24, 4q21, 6q25, 9q31, 10q26, 11p15, 11q13 and 14q32 loci are considerably frequent in the Tunisian population (>?20%). Allele frequency comparison showed that the frequency of rs13329835 is significantly different between Tunisian and all other HapMap populations. LD-blocks and Principle Component Analysis revealed that the genetic characteristics of breast cancer variants in the Tunisian, and so probably the North-African populations, are more similar to those of Europeans than Africans. Using eQTl analysis, we characterized rs9911630 as the most strongly expression-associated SNP that seems to affect the expression levels of BRCA1 and two long non coding RNAs (NBR2 and LINC008854). Additional in-silico analysis also suggested a potential functional significance of this variant. CONCLUSIONS:We illustrated the utility of combining haplotype analysis in diverse ethnic groups with functional analysis to explore breast cancer genetic architecture in Tunisia. Results presented in this study provide the first report on a large number of common breast cancer genetic polymorphisms in the Tunisian population which may establish a baseline database to guide future association studies in North Africa.

Dataset Information

Tunisian Table Olive Oil Traceability and Quality Using SNP Genotyping and Bioinformatics Tools.

Publications

Tunisian Table Olive Oil Traceability and Quality Using SNP Genotyping and Bioinformatics Tools.

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