Genetic variability is extremely important, not only for the species’ adaptation to environmental challenges, but also for the creation of novel varieties through plant breeding. Tomato is an important vegetable crop, as well as a model species in numerous genomic studies. Its genome was fully sequenced in 2012 for the ‘Heinz 1706’ variety, and since then, resequencing efforts have revealed genetic variability data that can be used for multiple purposes, including triggering mechanisms of biotic and abiotic stress resistance. The present study focused on the analysis of the genome variation for eight Romanian local tomato varieties using next-generation sequencing technique, and as a case study, the sequence analysis of the Ve1 and Ve2 loci, to determine which genotypes might be good candidates for future breeding of tomato varieties resistant to Verticillium species. The analysis of the Ve locus identified several genotypes that could be donors of the Ve1 gene conferring resistance to Verticillium race 1. Sequencing for the first time Romanian genotypes enriched the existing data on various world tomato genetic resources, but also opened the way for the molecular breeding in Romania. Plant breeders can use these data to create novel tomato varieties adapted to the ever-changing environment.

Goji berries, long valued in Traditional Chinese Medicine and Asian cuisine for their wide range of medicinal benefits, are now considered a ‘superfruit’ and functional food worldwide. Because of growing demand, Europe and North America are increasing their goji berry production, using goji berry varieties that are not originally from these regions. European breeding programs are focusing on producing Lycium varieties adapted to local conditions and market demands. By 2023, seven varieties of goji berries were successfully registered in Romania, developed using germplasm that originated from sources outside the country. A broader project focused on goji berry breeding was initiated in 2014 at USAMV Bucharest. In the present research, five cultivated and three wild L. barbarum genotypes were compared to analyse genetic variation at the whole genome level. In addition, a case study presents the differences in the genomic coding sequences of BODYGUARD (BDG) 3 and 4 genes from chromosomes 4, 8, and 9, which are involved in cuticle-related resistance. All three BDG genes show distinctive differences between the cultivated and wild-type genotypes at the SNP level. In the BDG 4 gene located on chromosome 8, 69% of SNPs differentiate the wild from the cultivated genotypes, while in BDG 3 on chromosome 4, 64% of SNPs could tell the difference between the wild and cultivated goji berry. The research also uncovered significant SNP and InDel differences between cultivated and wild genotypes, in the entire genome, providing crucial insights for goji berry breeders to support the development of goji berry cultivation in Romania.

Since its domestication about a century ago in North America, highbush blueberry (Vaccinium corymbosum L.) has gained appreciation by consumers worldwide, and the demand for new blueberry varieties is increasing. Whole-genome resequencing can help plant breeders to decrease the time needed to create novel varieties by identifying novel genes linked to fruit-quality traits. The present study analyzed the genetic variability of eight V. corymbosum genotypes, seven Romanian varieties (‘Prod’, ‘Vital’, ‘Azur’, ‘Simultan’, ‘Delicia’, ‘Compact’, and ‘Safir’), and the American variety, ‘Bluecrop’. The analysis of the first ~10 Mb from scaffold 22, a hotspot of genomic variation, in the above-mentioned varieties revealed multiple differences in 11 upregulated and 50 downregulated genes involved in fruit growth and development. Of these differentially regulated genes, two upregulated and five downregulated genes were fully covered by at least 1× coverage depth by sequencing. The genes’ sequence analysis confirmed the high genetic variability of the region, with most of the genes presenting numerous SNPs and some InDels, and indicated that an attempted 10× medium-coverage depth of sequencing for V. corymbosum varieties yields useful preliminary data for use in breeding programs.

The blueberry (Vaccinium corymbosum L.) is known for its high content of bioactive compounds, which are widely recognized for their health-promoting properties. This study aimed to characterize the fruit quality, total phenolic content (TPC), total monomeric anthocyanin content (TMA), anthocyanin profile and antioxidant activity of the nine Romanian V. corymbosum genotypes (‘Augusta’, ‘Azur’, ‘Delicia’, ‘Lax’, ‘Pastel’, ‘Prod’, ‘Safir’, ‘Simultan’, and ‘Vital’) over three consecutive harvest seasons (2023–2025). Significant genotype- and year-dependent variation was observed for all parameters. ‘Lax’ consistently accumulated the highest total anthocyanin content across all three seasons, while ‘Simultan’ exhibited the highest antioxidant activity and total monomeric anthocyanin content. ‘Prod’ consistently recorded the lowest phytochemical values despite achieving the highest firmness in 2025. UPLC analysis identified 10 anthocyanins, covering all five major anthocyanidin classes. Strong positive correlations were found between TPC, TMA, and antioxidant activity. These results confirm that genotype is the primary determinant of blueberry phytochemical composition, as indicated by the largest effect sizes in the two-way ANOVA, with harvest year and genotype × year interaction as statistically significant but secondary modulating factors, and identify ‘Lax’, ‘Simultan’, and ‘Safir’ as promising cultivars for nutraceutical and breeding applications.

Numerous varieties of Capsicum annuum L. with multiple valuable traits, such as adaptation to biotic and abiotic stress factors, can be found in south-east Romania, well known for vegetable cultivation and an important area of biodiversity conservation. To obtain useful information about sustainable agriculture, management, and conservation of local pepper varieties, we analyzed the genetic diversity and conducted deep molecular characterization using whole genome resequencing (WGS) for variant/mutation detection. The pepper varieties used in the present study were registered by VRDS in the ISTIS catalog between 1974 and 2019 and maintained in conservative selection; however, no studies have been published yet using WGS analysis in order to characterize this specific germplasm. The genome sequences, annotation, and alignments provided in this study offer essential resources for genomic research as well as for future breeding efforts using the C. annuum local varieties.

Goji berries, long valued in Chinese medicine and cuisine for their wide range of medicinal benefits, are considered a 'superfruit' and functional food. Out of the nearly 100 Lycium species known for their genetic diversity, L. barbarum and L. chinense currently dominate the market. Due to increasing market demand and concerns about food safety and sustainability, Europe and the Americas are expanding the local goji berry production, using as starting material plants originated from China. European breeding programs are focusing on Lycium to develop varieties adapted to local conditions, especially in response to climate change. By 2023, Romania registered seven goji berry varieties, both from L. barbarum and L. chinense species, without incorporating local germplasm. Advanced genomic studies, including NGS sequencing of five cultivated and three wild goji berry plant genomes, have been conducted to analyse their genetic variation, with a particular focus on the BODYGUARD 3 and 4 genes. This research uncovered significant differences between cultivated and wild genotypes, both in the entire genome and specifically in the BODYGUARD genes, providing crucial insights for goji berry breeders to support the development of goji berry cultivation in Romania.