Anne-Marie A. Wolters, Myluska Caro, Shufang Dong, Richard Finkers, Jianchang Gao, Richard G. F. Visser, Xiaoxuan Wang, Yongchen Du, Yuling Bai

Theoretical and Applied Genetics; October 2015, Volume 128, Issue 10, pp 1987-1997

http://link.springer.com/article/10.1007/s00122-015-2561-6

Abstract

Key message

A chromosomal inversion associated with the tomato Ty - 2 gene for TYLCV resistance is the cause of severe suppression of recombination in a tomato Ty - 2 introgression line.

Abstract

Among 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.

Fig. 4

Analysis of inversion breakpoint (a) Location of breakpoint primers bpTyF1 and bpTyR1 (red arrows) flanking the inversion breakpoint in the BAC sequence obtained from the Ty-2 introgression line (middle sequence). Location of these primers is also shown in the S. lycopersicum ‘Heinz’ region (upper sequence) and S. habrochaites LYC4 superscaffold (lower sequence). Green arrows indicate sequences homologous to NB-LRR genes. Blue dotted lines indicate co-linear regions. b PCR with primers bpTyF1 and bpTyR1 flanking the inversion breakpoint. Only in the Ty-2 introgression line a PCR product is obtained