Linking genetic resources, genomes and phenotypes of solanaceus crops

Resumen

The impact of climate change on horticultural crops is increasingly evident, leading to drastic loss and erosion of genetic diversity. This poses significant challenges for crop improvement, which requires the exploration of plant genetic resources conserved in germplasm banks and the development of technologies. However, the current situation of germplasm collections is characterized by the existence of unidentified duplicates among collections, taxonomic mislabelling, insufficient and unavailable documentation for researchers and breeders, and a lack of funding for proper conservation and management. This greatly hampers the utilization of these resources. This thesis addresses this problem by starting with the unification of passport, phenotyping, and image data from the main collections of tomato, pepper, and eggplant. Genotyping these collections enables the creation of core collections, enhancing knowledge of genotypic and phenotypic variability for researchers and breeders. In the first chapter, an inventory of available passport and phenotypic data of tomato, pepper, and eggplant accessions conserved in major European and non-European germplasm banks were conducted to improve the efficiency of plant genetic resource management. The second chapter focuses on the development and optimization of a high-quality, fast, and cost-effective genomic DNA extraction method that combines the advantages of the CTAB-based extraction method with nucleic acid purification on a silica matrix. The efficiency of the resulting genomic DNA was evaluated on different sequencing platforms, such as Single Primer Enrichment Technology (SPET) and Oxford Nanopore, yielding promising results. This facilitates the prerequisite step of DNA extraction before genotyping the collections. Chapter three addresses the genotyping of the collections. The high number of accessions for each crop, particularly tomato, poses an often insurmountable economic problem. Therefore, chapter three is focused on evaluating the potential of SPET sequencing technology, which is more cost-effective than other known methods, for high-throughput genotyping of tomato and eggplant germplasm collections. The results reveal that SPET genotyping is a robust and high-performance technology for genetic studies, including the identification of duplicates and taxonomic misclassifications in the accessions stored in the germplasm banks. Based on the information generated in the first three chapters, core collections were established for each crop, encompassing maximum genetic and phenotypic diversity in a set of 450 individuals. Finally, in the fourth chapter, the genetic and phenotypic analysis of the tomato core collection is examined and described using an approach based on establishing genetic groups based on their genetic proximity. Genetic and phenotypic diversity analysis revealed distinct patterns of variation among different genetic groups, contradicting previous claims of a decrease in genetic diversity due to genetic improvement and uncovering unique correlations between morphological traits within different groups. The study highlights the importance of considering both genetic and phenotypic diversity in tomato breeding initiatives, with a particular emphasis on aspects such as fruit size, shape, color, and quality. In conclusion, this thesis enhances knowledge and accessibility to major Solanaceae collections in germplasm banks, while providing molecular tools for genotypic evaluation. It underscores germplasm banks' role as genetic diversity reservoirs, despite challenges such as data limitations and inaccuracies, emphasizing the importance of data standardization and maintenance. These advancements lay a foundation for conservation and breeding programs in the future.