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GrainGenes Reference Report: GNM-45-431

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Reference	GNM-45-431
Title	Isolation of A/D and C genome specific dispersed and clustered repetitive DNA sequences from Avena sativa
Journal	Genome
Year	2000
Pages	431-441
Author	Ananiev EV Vales MI Phillips RL Rines HW
Abstract	Summary: DNA gel-blot and in situ hybridization with genome-specific repeated sequences have proven to be valuable tools in analyzing genome structure and relationships in species with complex allopolyploid genomes such as hexaploid oat (Avena sativa L., 2n = 6x = 42; AACCDD genome). In this report, we describe a systematic approach for isolating genome-, chromosome-, and region-specific repeated and low-copy DNA sequences from oat that can presumably be applied to any complex genome species. Genome-specific DNA sequences were first identified in a random set of A. sativa genomic DNA cosmid clones by gel-blot hybridization using labeled genomic DNA from different Avena species. Because no repetitive sequences were identified that could distinguish between the A and D genomes, sequences specific to these two genomes are refereed to as A/D genome specific. A/D or C genome specific DNA subfragments were used as screening probes to identify additional genome-specific cosmid clones in the A. sativa genomic library. We identified clustered and dispersed repetitive DNA elements for the A/D and C genomes that could be used as cytogenetic markers for discrimination of the various oat chromosomes. Some analyzed cosmids appeared to be composed entirely of genome-specific elements, whereas others represented regions with genome- and non-specific repeated sequences with interspersed low-copy DNA sequences. Thus, genome-specific hybridization analysis of restriction digests of random and selected A. sativa cosmids also provides insight into the sequence organization of the oat genome
Keyword	[ Hide all but 1 of 44 ] allopolyploid avena avena sativa complexes cosmid clones cosmids discrimination distinguish dna dna elements dna hybridization element genome genome analysis genome specific genome structure genomic dna genomic library hexaploid hexaploid oat hybridization in situ in situ hybridization isolation low-copy dna nucleotide sequence oat organization probe region relationships repeated sequences repetitive dna repetitive dna element repetitive dna sequence restriction restriction digests restriction endonuclease analysis screening sequence sequence organization situ hybridization structure tool

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