title: BAC 'landing' on chromosomes of Brachypodium distachyon for comparative genome alignment.
abstract: Fluorescence in situ hybridization (FISH) using bacterial artificial chromosomes (BACs) with large genomic DNA inserts as probes (BAC 'landing') is a powerful means by which eukaryotic genomes can be physically mapped and compared. Here we report a BAC landing protocol that has been developed specifically for the weedy grass species Brachypodium distachyon, which has been adopted recently by the scientific community as an alternative model for the temperate cereals and grasses. The protocol describes the preparation of somatic and meiotic chromosome substrates for FISH, the labeling of BACs, a chromosome mapping strategy, empirical conditions for optimal in situ hybridization and stringency washing, the detection of probes and the capturing and processing of images. The expected outcome of the protocol is the specific assignment of BACs containing single-copy inserts to one of the five linkage groups of the genome of this species. Once somatic or meiotic material is available, the entire protocol can be completed in about 3 d. The protocol has been customized empirically for B. distachyon and its near relatives, but it can be adapted with minor modifications to diverse plant species.
authors.affiliation: Institute of Biological Sciences, University of Wales Aberystwyth, Penglais, Aberystwyth, Ceredigion SY23 3DA, UK. gmj@aber.ac.uk
authors.forename: Glyn
authors.initials: G
authors.lastname: Jenkins
authors.forename: Robert
authors.initials: R
authors.lastname: Hasterok
mesh_terms: D002874:Chromosome Mapping / Q000379:methods*; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics*; D005819:Genetic Markers; D005821:Genetic Techniques; D018745:Genome, Plant / Q000235:genetics*; D017404:In Situ Hybridization, Fluorescence / Q000379:methods; D006109:Poaceae / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods
chemical_list: D005819:Genetic Markers