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 F 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 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.

DNA sequence and shape are predictive for meiotic crossovers throughout the plant kingdom

“…As input for training a machine‐learning model, both a positive set (regions containing COs) and a negative set (regions not containing COs) are needed. We prepared a positive set consisting of 4‐kb‐long CO regions from tomato ( n = 664) obtained in our previous study (Demirci et al ., ). Because the absence of a CO in a given region does not automatically imply that a CO could not occur, generating a negative set is not straightforward.…”

“…Genome annotation features described repeat elements, gene elements and (eu)chromatin state. The latter was defined as described previously (Demirci et al ., ), based on results from cytogenetic analyses of pachytene chromosomes, which display long continuous stretches of less condensed euchromatin in chromosome arms flanked by highly condensed heterochromatin at the telomere ends and centromeres. Finally, features based on parental genome information included SNPs and INDELs between the parental genomes.…”

“…in gene promoters in tomato and Arabidopsis (Choi et al ., ; Wijnker et al ., ; Demirci et al ., ; de Haas et al ., ). In addition to their preferential occurrence in promoters, CO regions are also rich in particular sequence motifs, including poly‐A sequence motifs in Arabidopsis and tomato, for example (Choi et al ., ; Wijnker et al ., ; Demirci et al ., ). In maize, GC sequences are over‐represented in recombination regions (Rodgers‐Melnick et al ., ).…”

Genetic and epigenetic variation of transposable elements in Arabidopsis

“…Indeed recombination between repeated sequences poses a risk for non-allelic recombination and the potential for structural change. Consistent with this crossover hotspots are enriched at gene promoters in Arabidopsis and Tomato [50–52], and artificial introduction of DNA methylation to a known hotspot is sufficient to silence crossover [53]. In Arabidopsis DNA methylation in CG contexts, which is enriched in pericentromeric and centromeric regions, is almost completely lost in met1 and ddm1 [9].…”

Pairing analysis and in situ Hybridisation reveal autopolyploid-like behaviour in Solanum commersonii × S. tuberosum (potato) interspecific hybrids

“…Variable homoeologous recombination rates have been found through molecular markers and sequence data in introgression lines of S. lycopersicoides (Canady et al 2006) or S. pimpinellifolium (Demirci et al 2017) with tomato. Significant structural rearrangements have been described among species belonging to the tomato clade (Anderson et al 2010;Verlaan et al 2011;Szinay et al 2012).…”