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

A.M.A. Wolters, C.M. Caro Rios, S. Dong, H.J. Finkers, J. Gao, R.G.F. Visser, X. Wang, Y. Du, Y. Bai

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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.
Original languageEnglish
Pages (from-to)1987-1997
JournalTheoretical and Applied Genetics
Volume128
Issue number10
DOIs
Publication statusPublished - 2015

Fingerprint

genome assembly
Solanum lycopersicum
Lycopersicon esculentum
introgression
Organism Cloning
molecular cloning
wild relatives
tomatoes
Genome
Genetic Recombination
Solanum habrochaites
Tomato yellow leaf curl virus
breeding
Breeding
clones
chromosomes
Chromosomes, Human, Pair 11
genome
crops
genes

Cite this

@article{1823034dc5e34f0f952856c91f88ea95,
title = "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 = "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.",
author = "A.M.A. Wolters and {Caro Rios}, C.M. and S. Dong and H.J. Finkers and J. Gao and R.G.F. Visser and X. Wang and Y. Du and Y. Bai",
year = "2015",
doi = "10.1007/s00122-015-2561-6",
language = "English",
volume = "128",
pages = "1987--1997",
journal = "Theoretical and Applied Genetics",
issn = "0040-5752",
publisher = "Springer Verlag",
number = "10",

}

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. / Wolters, A.M.A.; Caro Rios, C.M.; Dong, S.; Finkers, H.J.; Gao, J.; Visser, R.G.F.; Wang, X.; Du, Y.; Bai, Y.

In: Theoretical and Applied Genetics, Vol. 128, No. 10, 2015, p. 1987-1997.

Research output: Contribution to journalArticleAcademicpeer-review

TY - JOUR

T1 - 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

AU - Wolters, A.M.A.

AU - Caro Rios, C.M.

AU - Dong, S.

AU - Finkers, H.J.

AU - Gao, J.

AU - Visser, R.G.F.

AU - Wang, X.

AU - Du, Y.

AU - Bai, Y.

PY - 2015

Y1 - 2015

N2 - 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.

AB - 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.

U2 - 10.1007/s00122-015-2561-6

DO - 10.1007/s00122-015-2561-6

M3 - Article

VL - 128

SP - 1987

EP - 1997

JO - Theoretical and Applied Genetics

JF - Theoretical and Applied Genetics

SN - 0040-5752

IS - 10

ER -