Detection of an inversion in the Ty-2 region between S. lycopersicum and S. habrochaites by a combination of de novo genome assembly and BAC cloning

Abstract

Key messageA chromosomal inversion associated with the tomatoTy-2gene for TYLCV resistance is the cause of severe suppression of recombination in a tomatoTy-2introgression line.AbstractAmong tomato and its wild relatives inversions are often observed, which result in suppression of recombination. Such inversions hamper the transfer of important traits from a related species to the crop by introgression breeding. Suppression of recombination was reported for the TYLCV resistance gene, Ty-2, which has been introgressed in cultivated tomato (Solanum lycopersicum) from the wild relative S. habrochaites accession B6013. Ty-2 was mapped to a 300-kb region on the long arm of chromosome 11. The suppression of recombination in the Ty-2 region could be caused by chromosomal rearrangements in S. habrochaites compared with S. lycopersicum. With the aim of visualizing the genome structure of the Ty-2 region, we compared the draft de novo assembly of S. habrochaites accession LYC4 with the sequence of cultivated tomato (‘Heinz’). Furthermore, using populations derived from intraspecific crosses of S. habrochaites accessions, the order of markers in the Ty-2 region was studied. Results showed the presence of an inversion of approximately 200 kb in the Ty-2 region when comparing S. lycopersicum and S. habrochaites. By sequencing a BAC clone from the Ty-2 introgression line, one inversion breakpoint was identified. Finally, the obtained results are discussed with respect to introgression breeding and the importance of a priori de novo sequencing of the species involved.Electronic supplementary materialThe online version of this article (doi:10.1007/s00122-015-2561-6) contains supplementary material, which is available to authorized users.

Evaluation of tomato entries with different combinations of resistance genes to tomato yellow leaf curl disease in Tunisia

“…Ty-2 was derived from S. habrochaites f. sp. glabratum accession B6013 (Kalloo and Banerjee 1990) and was mapped to the long arm of chromosome 11 (Hanson et al 2000, Ji et al 2009a, Wolters et al 2015. Ty-4 minor gene, derived from S. chilense, was mapped to the long arm of chromosome 3 (Ji et al 2008(Ji et al , 2009b.…”

“…, Wolters et al. ). Ty‐4 minor gene, derived from S. chilense , was mapped to the long arm of chromosome 3 (Ji et al.…”

“…TYLCD incidence and severity of the final evaluation, averaged over two years, of tomato entries with or without TYLCD resistance genes tested inTunisia, 2013 and2015 …”

Molecular Markers for Selecting Diverse Disease Resistances in Tomato Breeding Programs

“…Since Ty1 and Ty3 were independently identified from different tomato accessions, different DNA markers that were closely linked to Ty1 or Ty3 were used in tomato breeding programs. However, it was recently confirmed that these two are in allelic relationship at a single locus (Verlaan et al 2013;Caro et al 2015). Resistance spectra and levels conferred by Ty1 and Ty3 are currently under investigation.…”

“…In the case of Ty2 resistance, a sequence characterized amplified regions (SCAR) marker, T0302, was used reliably for the selection. However, it was recently mapped to a 300-kb interval on chromosome 11, gene identification that would allow development of gene-based marker is in progress (Wolters et al 2015). A gene-based derived-cleaved amplified polymorphic Lapidot et al (2015).…”