This study aimed to develop a novel tomato (Solanum lycopersicum L.) cultivar enriched in phytoene and phytofluene, colorless carotenoids known for their health-promoting properties. Parental lines with diverse fruit colors and morphological traits were selected and crossbred to generate three F₁ hybrids: ‘Rubybell’, ‘INDIGO-G’, and ‘BLACK-B’. The phytoene and phytofluene contents of the hybrids were quantified using high-performance liquid chromatography. Among them, ‘Rubybell’ exhibited the highest concentrations of phytoene (0.105 mg/g) and total phytofluene (0.118 mg/g), representing increases of 51% and 29% compared to the maternal line APR-52-MU, and 14% and 1% compared to the paternal line CAPP1745, respectively. Compared to commercial tomato cultivars, ‘Rubybell’ exhibited 76- and 23-fold higher levels of phytoene and phytofluene, respectively. Furthermore, ‘Rubybell’ accumulated higher levels of these functional compounds when cultivated in March and October, underscoring the influence of the planting season on carotenoid biosynthesis. These findings offer valuable insights into the breeding of high-value functional tomatoes and support their potential use in health-promoting food applications (Registration number: 10514).

Marker-assisted backcrossing is a powerful method for developing new cultivars. To develop genomic-wide markers, genotyping-by-sequencing (GBS) can be an efficient method. However, unrefined low-quality markers and missing data between markers can contribute to hampering the marker selection process, particularly in multi-way crosses. In this study, we aimed to calculate the recovery rate of offspring individuals and minimize errors that occur among a large number of markers. Initially, missing data were imputed by comparing samples using the k-nearest neighbor (k-NN) algorithm. Thereafter, low-quality single-nucleotide polymorphisms (SNPs) were corrected by applying the graphical representation method based on the k-NN algorithm in order of the SNPs in a chromosome designed for a multi-parental population. Four-way cross and double-backcrossed tomato BC₁F₁ (230 lines) and BC₂F₁ (96 lines) populations were genotyped by GBS. The genotype of samples of the BC₁F₁ and BC₂F₁ populations was determined based on the parental haplotype. Thus, the method of visualizing the genotype of offspring individuals, generated via crosses of multiple parents, not only improves estimation of the recovery rate but also facilitates easier selection in breeding programs.

Cherry tomato ‘TY Candy’ F₁ Hybrid was bred in Tomato Life Science and Research Institute from 2008 to 2014, which has indeterminate plant type, oblong fruit shape, average fruit weight 17 ~ 22 g and sugar content brix 8 ~ 9. Female line was selected and fixed with vigorous plant, firm fruit texture, Fusarium and Cladosporium resistance. Male line was selected and fixed with medium internode, deep leaf color, high brix, Yellow leaf curl virus and Nematode resistance. F₁ combination was made and pollinated in 2011 year, hybrid selection and sample seed production were progressed in 2012 year, farmers’ field trial was conducted at major tomato cultivation area and resulted good performance in 2013 ~ 2014. The distinctive characteristics of ‘TY Candy’ are higher yield, fruit quality and TYLCV, Nematode, Cladosporium etc. multi-disease resistance compared to existed varieties.