Morphoagronomic characterization and whole-genome resequencing of eight highly diverse wild and weedy S. pimpinellifolium and S. lycopersicum var. cerasiforme accessions used for the first interspecific tomato MAGIC population

Abstract

The wild Solanum pimpinellifolium (SP) and the weedy S. lycopersicum var. cerasiforme (SLC) are largely unexploited genetic reservoirs easily accessible to breeders, as they are fully cross-compatible with cultivated tomato (S. lycopersicum var. lycopersicum). We performed a comprehensive morphological and genomic characterization of four wild SP and four weedy SLC accessions, selected to maximize the range of variation of both taxa. These eight accessions are the founders of the first tomato interspecific multi-parent advanced generation inter-cross (MAGIC) population. The morphoagronomic characterization was carried out with 39 descriptors to assess plant, inflorescence, fruit and agronomic traits, revealing the broad range of diversity captured. Part of the morphological variation observed in SP was likely associated to the adaptation of the accessions to different environments, while in the case of SLC to both human activity and adaptation to the environment. Whole-genome resequencing of the eight accessions revealed over 12 million variants, ranging from 1.2 to 1.9 million variants in SLC and from 3.1 to 4.8 million in SP, being 46.3% of them (4,897,803) private variants. The genetic principal component analysis also confirmed the high diversity of SP and the complex evolutionary history of SLC. This was also reflected in the analysis of the potential footprint of common ancestors or old introgressions identified within and between the two taxa. The functional characterization of the variants revealed a significative enrichment of GO terms related to changes in cell walls that would have been negatively selected during domestication and breeding. The comprehensive morphoagronomic and genetic characterization of these accessions will be of great relevance for the genetic analysis of the first interspecific MAGIC population of tomato and provides valuable knowledge and tools to the tomato community for genetic and genomic studies and for breeding purposes.

Newly Developed MAGIC Population Allows Identification of Strong Associations and Candidate Genes for Anthocyanin Pigmentation in Eggplant

“…The introduction of multiple founders with an increased genetic and phenotypic diversity, together with the multiple rounds of inter-crossing and selfing, increases the number of accumulated recombinant events and, thus, improves the mapping accuracy ( Scott et al, 2020 ). By introducing a wild relative as a founder parent, the genetic variability in the population increases, which is a key point for QTL identification ( Gramazio et al, 2020a ). Here, we present the first eggplant S3MEGGIC population of which one of the founders was one accession of the close wild relative S. incanum .…”

“…The incorporation of crop wild relatives (CWRs) as founders could be a way of including multiple wild genomic fragments or introgressions into cultivated background genomes ( Arrones et al, 2020 ). Apart from being of great interest for genetic analysis, interspecific MAGIC populations can be useful for broadening the genetic base of crops and provide new variation for breeding multiple traits, including those related to adaption to climate change ( Gramazio et al, 2020a ). However, so far, the potential of interspecific MAGIC populations for plant breeding has largely remained unexploited ( Arrones et al, 2020 ).…”

DNA Variation in a Diversity Panel of Tomato Genetic Resources

“…The finding of extensive novel genomic and morphological variation in cherry tomato accessions from Ecuador and Peru suggested their untapped potential as breeding material (Mata-Nicol as et al, 2020). In comparison with the Heinz 1706 reference genome, 1.2 to 1.9 million mutations were identified in four cherry tomato accessions (Gramazio et al, 2020). The complex genetic relationships among large-fruited cultivated tomatoes, S. pimpinellifolium, and cherry tomato also supported the assertion that unmined alleles for crop improvement are available from the latter two taxa, which will easily cross-fertilize with modern cultivars (Razifard et al, 2020).…”

Breeding for Nutritional and Organoleptic Quality in Vegetable Crops: The Case of Tomato and Cauliflower

“…In the framework of those projects, traditional tomato germoplasm resources characterized by high resilience (e.g., Spanish and Italian 'da serbo' Landraces) as well as accessions of underexploited genetic reservoirs and derived populations (the wild species Solanum pimpinellifolium and Solanum cheesmaniae and the weedy S. lycopersicum var. cerasiforme) have been deeply genotyped for further use in organic breeding programs [22][23][24][25][26].…”