Pollen sequencing reveals barriers and aberrant patterns of recombination in interspecific tomato hybrids

Tomato is the most consumed vegetable in the world. Increasing its natural resistance and resilience is key for ensuring food security within a changing climate. Plant breeders improve those traits by generating crosses of cultivated tomatoes with their wild relatives. Specific allele introgression relying on meiotic recombination, is hampered by structural divergence between parental genomes. However, previous studies of interspecific tomato hybridization focused in single cross or lacked resolution due to prohibitive sequencing costs of large segregating populations. Here, we used pooled-pollen sequencing to reveal unprecedented details of recombination patterns in five interspecific tomato hybrids. We detected hybrid-specific recombination coldspots that underscore the influence of structural divergence in shaping recombination landscape. Crossover regions and coldspots show strong association with specific TE superfamilies exhibiting differentially accessible chromatin between somatic and meiotic cells. We also found gene complexes associated with metabolic processes, stress resistance and domestication syndrome traits, revealing undesired consequences of recombination suppression to phenotypes. Finally, we demonstrate that by using resequencing data of wild and domesticated tomato populations, we can screen for alternative parental genomes to overcome recombination barriers. Overall, our results will allow breeders better informed decisions on generating disease-resistant and climate-resilient tomato.