The dataset contains raw data associated to the publication "Inheritance of Secondary Metabolites and Gene Expression Related to Tomato Quality ", Bineau et al (2022) Int J Molecular Sciences
It contains 6 files :
DV1: phenotypic data of the 3 biological replicates of the 20 genotypes studied within the factorial design. Genotypes are named based on the species they belong to with 'SP': S. pimpinellifolium; 'SLC': Solanum lycopersicum var. cerasiforme; 'SL': Solanum lycopersicum lycopersicum. HF1 are named after the "female"x"male" they originate from. The biological replicates are indicated at the end of the genotype names as '_1', '_2' and '_3'.
DV2: mode of inheritance of the 66 secondary metabolites, SSC and weight assessed within the 14 crosses. For each cross individually, we estimated additive (A) and dominance (D) components of the genetic variation when the one way ANOVA test resulted in a significant genotype effect in overall trait variation among the parents and hybrid. Traits were classified as over-recessive (OR), recessive (R), additive (A), dominant (D) or overdominant (OD) in a given cross depending on the D/A ratio. We classified the trait heredity as 'ns' when no significant genotype effect could be found within a cross as presented in (Pascual et al. 2013).
DV3: normalized read counts of the 13,127 genes found expressed in the factorial design for all 3 biological replicates of each of the 20 genotypes studied withi the factorial design.
DV4: the 12,896 DEGs identified in at least one of the 190 possible contrasts among the 13,127 genes found expressed in the factorial design. Genes found differentially expressed in a contrast are specified with a '1'.
dv5: mode of inheritance of the 12,896 DEGs assessed within the 14 crosses. For each cross individually, we estimated additive (A) and dominance (D) components of the genetic variation when the one way ANOVA test resulted in a significant genotype effect in overall trait variation among the parents and hybrid. Traits were classified as over-recessive (OR), recessive (R), additive (A), dominant (D) or overdominant (OD) in a given cross depending on the D/A ratio. We classified the trait heredity as 'ns' when no significant genotype effect could be found within a cross as presented in (Pascual et al. 2013).
DV6: genes comprised within each of the 12 co-expression modules built using the WGCNA package on the 12,896 genes found differentially expressed. We indicate significant correlation and associated p-value of each gene with the 66 metabolites and SSC. We did not include the 13th module gathering genes displaying no co-expression with other patterns identified in the 12 modules.
