Meiotic recombination profiling of interspecific hybrid F1 tomato pollen by linked read sequencing

Summary Genome wide screening of pooled pollen samples from a single interspecific F1 hybrid obtained from a cross between tomato, Solanum lycopersicum and its wild relative, Solanum pimpinellifolium using linked read sequencing of the haploid nuclei, allowed profiling of the crossover (CO) and gene conversion (GC) landscape. We observed a striking overlap between cold regions of CO in the male gametes and our previously established F6 recombinant inbred lines (RILs) population. COs were overrepresented in non‐coding regions in the gene promoter and 5′UTR regions of genes. Poly‐A/T and AT rich motifs were found enriched in 1 kb promoter regions flanking the CO sites. Non‐crossover associated allelic and ectopic GCs were detected in most chromosomes, confirming that besides CO, GC represents also a source for genetic diversity and genome plasticity in tomato. Furthermore, we identified processed break junctions pointing at the involvement of both homology directed and non‐homology directed repair pathways, suggesting a recombination machinery in tomato that is more complex than currently anticipated. Significance Statement This paper reports a technical advance of using linked‐read sequencing to identify meiotic recombination events, both crossovers and non‐crossovers, from the pollen of an F1 tomato hybrid. Meiotic recombination is of basic importance, and also has strategic relevance to crop improvement, particularly in crop species such as tomato where large regions of the chromosomes are non‐recombining.