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Distribution, position and genomic characteristics of crossovers in tomato recombinant inbred lines derived from an interspecific cross between Solanum lycopersicum and Solanum pimpinellifolium
Author(s) -
Demirci Sevgin,
Dijk Aalt D.J.,
Sanchez Perez Gabino,
Aflitos Saulo A.,
Ridder Dick,
Peters Sander A.
Publication year - 2017
Publication title -
the plant journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.058
H-Index - 269
eISSN - 1365-313X
pISSN - 0960-7412
DOI - 10.1111/tpj.13406
Subject(s) - euchromatin , biology , solanum , genetics , heterochromatin , orfs , gene , interspecific competition , botany , chromosome , peptide sequence , open reading frame
Summary We determined the crossover ( CO ) distribution, frequency and genomic sequences involved in interspecies meiotic recombination by using parent‐assigned variants of 52 F 6 recombinant 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 CO s 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.