title: Distribution, position and genomic characteristics of crossovers in tomato recombinant inbred lines derived from an interspecific cross between Solanum lycopersicum and Solanum pimpinellifolium.
abstract: We determined the crossover (CO) distribution, frequency and genomic sequences involved in interspecies meiotic recombination by using parent-assigned variants of 52 F6recombinant inbred lines obtained from a cross between tomato, Solanum lycopersicum, and its wild relative, Solanum pimpinellifolium. The interspecific CO frequency was 80% lower than reported for intraspecific tomato crosses. We detected regions showing a relatively high and low CO frequency, so-called hot and cold regions. Cold regions coincide to a large extent with the heterochromatin, although we found a limited number of smaller cold regions in the euchromatin. The CO frequency was higher at the distal ends of chromosomes than in pericentromeric regions and higher in short arm euchromatin. Hot regions of CO were detected in euchromatin, and COs were more often located in non-coding regions near the 5' untranslated region of genes than expected by chance. Besides overrepresented CCN repeats, we detected poly-A/T and AT-rich motifs enriched in 1-kb promoter regions flanking the CO sites. The most abundant sequence motifs at CO sites share weak similarity to transcription factor-binding sites, such as for the C2H2 zinc finger factors class and MADS box factors, while InterPro scans detected enrichment for genes possibly involved in the repair of DNA breaks.
authors: Bioinformatics Group, Wageningen University and Research, Wageningen, The Netherlands.|Business Unit of Bioscience, Cluster Applied Bioinformatics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
authors: Sevgin
authors: S
authors: Demirci
authors: Business Unit of Bioscience, Cluster Applied Bioinformatics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.|Biometris, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
authors: Aalt D J
authors: AD
authors: van Dijk
authors: Bioinformatics Group, Wageningen University and Research, Wageningen, The Netherlands.|Business Unit of Bioscience, Cluster Applied Bioinformatics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
authors: Gabino
authors: G
authors: Sanchez Perez
authors: Business Unit of Bioscience, Cluster Applied Bioinformatics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
authors: Saulo A
authors: SA
authors: Aflitos
authors: Bioinformatics Group, Wageningen University and Research, Wageningen, The Netherlands.
authors: Dick
authors: D
authors: de Ridder
authors: Business Unit of Bioscience, Cluster Applied Bioinformatics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
authors: Sander A
authors: SA
authors: Peters
mesh_terms: D020121:5' Untranslated Regions / Q000235:genetics; D032461:Chromosomes, Plant / Q000235:genetics*; D003433:Crosses, Genetic; D003434:Crossing Over, Genetic; D018744:DNA, Plant / Q000235:genetics; D022041:Euchromatin / Q000235:genetics; D017343:Genes, Plant / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics*; D006239:Haplotypes; D006570:Heterochromatin / Q000235:genetics; D007178:Inbreeding; D018551:Solanum lycopersicum / Q000235:genetics*; D000069600:Plant Breeding / Q000379:methods; D032322:Solanum / Q000235:genetics*
chemical_list: D020121:5' Untranslated Regions; D018744:DNA, Plant; D022041:Euchromatin; D006570:Heterochromatin
keywords: 
  Solanum pimpinellifolium
  ; cold regions; crossover; homeologous; hot regions; meiotic recombination; recombinant inbred lines; tomato