PAR Tomato Collection

The PAR collection, consisting of commercial and experimental tomato (Solanum lycopersicum L.) varieties and populations, was characterized at the molecular level using DNA sequencing approaches based on SPET (Single Primer Enrichment Technology). The sequenced samples were subsequently genotyped and phenotypically evaluated.

The phenotypic characterization included morphological, agronomic, and fruit quality traits related to plant architecture, flowering time, fruit morphology, and parameters relevant to industrial processing. Specifically, the following traits were measured: presence or absence of chloroplasts in leaf veins (obscuravenosa), presence or absence of the fruit shoulder, presence or absence of the fruit peduncle (jointed/jointless), peak flowering time, plant growth habit and height, overall plant structure, fruit firmness, whole fruit weight and volume, fruit density, soluble solids content (°Brix), pericarp weight, pericarp water content, pericarp-to-fruit weight ratios, fruit perimeter and cross-sectional area, and additional pericarp-related morphometric parameters obtained through image analysis.

In the dataset, the evaluated phenotypic traits are coded as follows:

OBV = obscuravenosa, indicating the presence/absence of chloroplasts in leaf veins, controlled by the obv gene on chromosome 05. This trait has no direct agronomic relevance and is used as a positive control, given the extensive and well-documented literature supporting its genetic basis. Validation of the analytical pipeline on this trait supports its reliability for traits with unknown genetic determinants.

GUG = presence/absence of the fruit shoulder, controlled by the SlGLK2 (GOLDEN2-LIKE 2) gene, also known as “u”, on chromosome 10. This trait is also used as a positive control.

JNT = presence/absence of the fruit peduncle. At harvest, the peduncle may remain attached to the fruit (jointed) or to the plant (jointless).

FLO = peak flowering time, expressed either as a calendar date or as the number of days from transplanting.

HAB = plant growth habit/height: plants are classified as erect if they predominantly grow upward, or prostrate otherwise.

STR = overall plant structure score, based on leaf morphology and canopy distribution.

FIR = fruit firmness measured using a durometer.

WHT_g = whole fruit weight (g).

VOL_ml = whole fruit volume (mL).

WHT_VOL_ratio = ratio between fruit weight and volume, used as an estimate of fruit density.

BRIX = soluble solids (sugar) content.

PERICARP_WHT_g = pericarp weight (g), measured after removal of the locular cavities containing the seeds. This parameter estimates the proportion of fruit biomass suitable for industrial processing (e.g., purées and sauces), where seeds are typically discarded.

PERICARP_WATER_g = water content of the pericarp (g), measured after centrifugation. This parameter provides an indirect estimate of dry matter content and industrial yield potential. A high pericarp weight with high water content may still result in low processing yield, whereas industry aims to obtain the same amount of processed product starting from less fresh material.

PER_WAT_PER_WHT_ratio = ratio between pericarp water content and pericarp weight.

PER_WHT_WHT_ratio = ratio between pericarp weight and total fruit weight, representing the percentage of pericarp relative to total fruit mass.

Perimeter_Mean_cm = mean perimeter (cm) of the fruit cut latitudinally at the equator.

Tomato_Pericarp_Area_Mean_cm² = mean cross-sectional area (cm²) of the fruit cut latitudinally at the equator.

The following additional parameters were extracted using the Tomato Analyzer software and are related to industrial yield, particularly to pericarp thickness and morphology:

Lobedness_Degree_Mean
Tomato_Pericarp_Area_Ratio_Mean
Tomato_Pericarp_Thickness_Mean_cm
Tomato_Pericarp_Thickness_Ratio_Mean