Comparative Genomics

Breeding context

Breeders rely on introgression hybridization to introduce valuable traits from related wild species into cultivated tomato crops via hom(e)ologous recombination. However, many cases of such breeding programs have met with severe problems at different phases of the interspecific hybridisations and backcrosses including introgressed target genes and unwanted genes for which the linkage cannot be broken by repeated back-crossing (linkage drag). A difference in chromosome colinearity has a direct effect on chromosome pairing at meiosis and determines the rate and amount of chromatin transfer into a recipient crop, and hence determines the success of recovering an elite genotype by backcrossing. Genome structure of the parental species is a crucial factor influencing crossing success. However, genome structure and colinearity of most tomato accessions and related wild species are largely unknown, complicating the identification of compatible donor species and recipient crops for precise introgression breeding. To fully benefit from the genetic potential of wild tomato species and to allow advances towards a sequence based ‘precision breeding’ approach, disclosure of genome organization and topological context of target genes underlying agronomical important traits in cultivated tomato and its wild relatives is therefore needed. This requires a good understanding of the genetic resources on a genomics, genetics and biosystematics/biodiversity level, and assessment of the effect of colinearity and sequence differences in relation to linkage drag, location and frequency of crossovers.