BAC-FISH in wheat identifies chromosome landmarks consisting of different types of transposable elements

Abstract

Fluorescence in situ hybridization (FISH) has been widely used in the physical mapping of genes and chromosome landmarks in plants and animals. Bacterial artificial chromosomes (BACs) contain large inserts making them amenable for FISH mapping. We used BAC-FISH to study genome organization and evolution in hexaploid wheat and its relatives. We selected 56 restriction fragment length polymorphism (RFLP) locus-specific BAC clones from libraries of Aegilops tauschii (the D-genome donor of hexaploid wheat) and A-genome diploid Triticum monococcum. Different types of repetitive sequences were identified using BAC-FISH. Two BAC clones gave FISH patterns similar to the repetitive DNA family pSc119; one BAC clone gave a FISH pattern similar to the repetitive DNA family pAs1. In addition, we identified several novel classes of repetitive sequences: one BAC clone hybridized to the centromeric regions of wheat and other cereal species, except rice; one BAC clone hybridized to all subtelomeric chromosome regions in wheat, rye, barley and oat; one BAC clone contained a localized tandem repeat and hybridized to five D-genome chromosome pairs in wheat; and four BAC clones hybridized only to a proximal region in the long arm of chromosome 4A of hexaploid wheat. These repeats are valuable markers for defined chromosome regions and can also be used for chromosome identification. Sequencing results revealed that all these repeats are transposable elements (TEs), indicating the important role of TEs, especially retrotransposons, in genome evolution of wheat.

The bacterial artificial chromosome (BAC) library of the narrow-leafed lupin (Lupinus angustifolius L.)

“…Molecular cytogenetics can contribute to genome mapping through the assignment of genetic linkage groups to chromosomes [47,48]. Localization of BAC clones using fluorescence in situ hybridization (BAC-FISH) was shown to be an effective approach to physically map specific DNA sequences and develop chromosome-specific cytogenetic markers [49,50]. Our preliminary results indicate that FISH with BAC clones selected from the lupin BAC library will facilitate physical mapping of important genes.…”

A Molecular-Cytogenetic Method for Locating Genes to Pericentromeric Regions Facilitates a Genomewide Comparison of Synteny Between the Centromeric Regions of Wheat and Rice

“…Positive BAC clones for specific genes digested with HindIII were first screened with three centromere-specific clones pAet6-09, Hi10, and pRCS1 to reveal their potential centromeric locations (Abbo et al 1995;Dong et al 1998;P. Zhang et al 2004).…”

An integrated molecular cytogenetic map of Cucumis sativus L. chromosome 2

“…Large insert DNA clones, such as bacterial artificial chromosome (BAC) or yeast artificial chromosomes (YAC) clones, are likely to contain dispersed repetitive sequences that will cause high background signal in FISH [6]. BACs from species such as wheat, with very large genomes do not generate unique locus-specific FISH signals [7]. Small fosmid clones (30-40 kb) likely to contain less dispersed repetitive sequences compared to large insert DNA clones, will be more suitable as DNA probes.…”