High-resolution chromosome mapping of BACs using multi-colour FISH and pooled-BAC FISH as a backbone for sequencing tomato chromosome 6

D. Szinay, S.B. Chang, L.I. Khrustaleva, S.A. Peters, E.G.W.M. Schijlen, Y. Bai, W. Stiekema, R.C.H.J. van Ham, H. de Jong, R.M. Klein Lankhorst

Research output: Contribution to journalArticleAcademicpeer-review

63 Citations (Scopus)

Abstract

Within the framework of the International Solanaceae Genome Project, the genome of tomato (Solanum lycopersicum) is currently being sequenced. We follow a 'BAC-by-BAC' approach that aims to deliver high-quality sequences of the euchromatin part of the tomato genome. BACs are selected from various libraries of the tomato genome on the basis of markers from the F2.2000 linkage map. Prior to sequencing, we validated the precise physical location of the selected BACs on the chromosomes by five-colour high-resolution fluorescent in situ hybridization (FISH) mapping. This paper describes the strategies and results of cytogenetic mapping for chromosome 6 using 75 seed BACs for FISH on pachytene complements. The cytogenetic map obtained showed discrepancies between the actual chromosomal positions of these BACs and their markers on the linkage group. These discrepancies were most notable in the pericentromere heterochromatin, thus confirming previously described suppression of cross-over recombination in that region. In a so called pooled-BAC FISH, we hybridized all seed BACs simultaneously and found a few large gaps in the euchromatin parts of the long arm that are still devoid of seed BACs and are too large for coverage by expanding BAC contigs. Combining FISH with pooled BACs and newly recruited seed BACs will thus aid in efficient targeting of novel seed BACs into these areas. Finally, we established the occurrence of repetitive DNA in heterochromatin/euchromatin borders by combining BAC FISH with hybridization of a labelled repetitive DNA fraction (Cot-100). This strategy provides an excellent means to establish the borders between euchromatin and heterochromatin in this chromosome.
Original languageEnglish
Pages (from-to)627-637
JournalThe Plant Journal
Volume56
Issue number4
DOIs
Publication statusPublished - 2008

Fingerprint

Chromosomes, Human, Pair 6
Chromosome Mapping
Euchromatin
Lycopersicon esculentum
fluorescence in situ hybridization
Fluorescence In Situ Hybridization
chromosome mapping
Seeds
Color
tomatoes
Heterochromatin
chromosomes
heterochromatin
color
seeds
genome
Genome
cytogenetics
Cytogenetics
Solanaceae

Keywords

  • molecular linkage maps
  • lycopersicon-esculentum
  • root-knot
  • genome sequence
  • pachytene chromosomes
  • metaphase chromosomes
  • arabidopsis-thaliana
  • meiotic pachytene
  • dna-sequences
  • rice genome

Cite this

@article{26b9150d00a54850a25fa4b4685693c9,
title = "High-resolution chromosome mapping of BACs using multi-colour FISH and pooled-BAC FISH as a backbone for sequencing tomato chromosome 6",
abstract = "Within the framework of the International Solanaceae Genome Project, the genome of tomato (Solanum lycopersicum) is currently being sequenced. We follow a 'BAC-by-BAC' approach that aims to deliver high-quality sequences of the euchromatin part of the tomato genome. BACs are selected from various libraries of the tomato genome on the basis of markers from the F2.2000 linkage map. Prior to sequencing, we validated the precise physical location of the selected BACs on the chromosomes by five-colour high-resolution fluorescent in situ hybridization (FISH) mapping. This paper describes the strategies and results of cytogenetic mapping for chromosome 6 using 75 seed BACs for FISH on pachytene complements. The cytogenetic map obtained showed discrepancies between the actual chromosomal positions of these BACs and their markers on the linkage group. These discrepancies were most notable in the pericentromere heterochromatin, thus confirming previously described suppression of cross-over recombination in that region. In a so called pooled-BAC FISH, we hybridized all seed BACs simultaneously and found a few large gaps in the euchromatin parts of the long arm that are still devoid of seed BACs and are too large for coverage by expanding BAC contigs. Combining FISH with pooled BACs and newly recruited seed BACs will thus aid in efficient targeting of novel seed BACs into these areas. Finally, we established the occurrence of repetitive DNA in heterochromatin/euchromatin borders by combining BAC FISH with hybridization of a labelled repetitive DNA fraction (Cot-100). This strategy provides an excellent means to establish the borders between euchromatin and heterochromatin in this chromosome.",
keywords = "molecular linkage maps, lycopersicon-esculentum, root-knot, genome sequence, pachytene chromosomes, metaphase chromosomes, arabidopsis-thaliana, meiotic pachytene, dna-sequences, rice genome",
author = "D. Szinay and S.B. Chang and L.I. Khrustaleva and S.A. Peters and E.G.W.M. Schijlen and Y. Bai and W. Stiekema and {van Ham}, R.C.H.J. and {de Jong}, H. and {Klein Lankhorst}, R.M.",
year = "2008",
doi = "10.1111/j.1365-313X.2008.03626.x",
language = "English",
volume = "56",
pages = "627--637",
journal = "The Plant Journal",
issn = "0960-7412",
publisher = "Wiley",
number = "4",

}

High-resolution chromosome mapping of BACs using multi-colour FISH and pooled-BAC FISH as a backbone for sequencing tomato chromosome 6. / Szinay, D.; Chang, S.B.; Khrustaleva, L.I.; Peters, S.A.; Schijlen, E.G.W.M.; Bai, Y.; Stiekema, W.; van Ham, R.C.H.J.; de Jong, H.; Klein Lankhorst, R.M.

In: The Plant Journal, Vol. 56, No. 4, 2008, p. 627-637.

Research output: Contribution to journalArticleAcademicpeer-review

TY - JOUR

T1 - High-resolution chromosome mapping of BACs using multi-colour FISH and pooled-BAC FISH as a backbone for sequencing tomato chromosome 6

AU - Szinay, D.

AU - Chang, S.B.

AU - Khrustaleva, L.I.

AU - Peters, S.A.

AU - Schijlen, E.G.W.M.

AU - Bai, Y.

AU - Stiekema, W.

AU - van Ham, R.C.H.J.

AU - de Jong, H.

AU - Klein Lankhorst, R.M.

PY - 2008

Y1 - 2008

N2 - Within the framework of the International Solanaceae Genome Project, the genome of tomato (Solanum lycopersicum) is currently being sequenced. We follow a 'BAC-by-BAC' approach that aims to deliver high-quality sequences of the euchromatin part of the tomato genome. BACs are selected from various libraries of the tomato genome on the basis of markers from the F2.2000 linkage map. Prior to sequencing, we validated the precise physical location of the selected BACs on the chromosomes by five-colour high-resolution fluorescent in situ hybridization (FISH) mapping. This paper describes the strategies and results of cytogenetic mapping for chromosome 6 using 75 seed BACs for FISH on pachytene complements. The cytogenetic map obtained showed discrepancies between the actual chromosomal positions of these BACs and their markers on the linkage group. These discrepancies were most notable in the pericentromere heterochromatin, thus confirming previously described suppression of cross-over recombination in that region. In a so called pooled-BAC FISH, we hybridized all seed BACs simultaneously and found a few large gaps in the euchromatin parts of the long arm that are still devoid of seed BACs and are too large for coverage by expanding BAC contigs. Combining FISH with pooled BACs and newly recruited seed BACs will thus aid in efficient targeting of novel seed BACs into these areas. Finally, we established the occurrence of repetitive DNA in heterochromatin/euchromatin borders by combining BAC FISH with hybridization of a labelled repetitive DNA fraction (Cot-100). This strategy provides an excellent means to establish the borders between euchromatin and heterochromatin in this chromosome.

AB - Within the framework of the International Solanaceae Genome Project, the genome of tomato (Solanum lycopersicum) is currently being sequenced. We follow a 'BAC-by-BAC' approach that aims to deliver high-quality sequences of the euchromatin part of the tomato genome. BACs are selected from various libraries of the tomato genome on the basis of markers from the F2.2000 linkage map. Prior to sequencing, we validated the precise physical location of the selected BACs on the chromosomes by five-colour high-resolution fluorescent in situ hybridization (FISH) mapping. This paper describes the strategies and results of cytogenetic mapping for chromosome 6 using 75 seed BACs for FISH on pachytene complements. The cytogenetic map obtained showed discrepancies between the actual chromosomal positions of these BACs and their markers on the linkage group. These discrepancies were most notable in the pericentromere heterochromatin, thus confirming previously described suppression of cross-over recombination in that region. In a so called pooled-BAC FISH, we hybridized all seed BACs simultaneously and found a few large gaps in the euchromatin parts of the long arm that are still devoid of seed BACs and are too large for coverage by expanding BAC contigs. Combining FISH with pooled BACs and newly recruited seed BACs will thus aid in efficient targeting of novel seed BACs into these areas. Finally, we established the occurrence of repetitive DNA in heterochromatin/euchromatin borders by combining BAC FISH with hybridization of a labelled repetitive DNA fraction (Cot-100). This strategy provides an excellent means to establish the borders between euchromatin and heterochromatin in this chromosome.

KW - molecular linkage maps

KW - lycopersicon-esculentum

KW - root-knot

KW - genome sequence

KW - pachytene chromosomes

KW - metaphase chromosomes

KW - arabidopsis-thaliana

KW - meiotic pachytene

KW - dna-sequences

KW - rice genome

U2 - 10.1111/j.1365-313X.2008.03626.x

DO - 10.1111/j.1365-313X.2008.03626.x

M3 - Article

VL - 56

SP - 627

EP - 637

JO - The Plant Journal

JF - The Plant Journal

SN - 0960-7412

IS - 4

ER -