title: Mapping translocation breakpoints using a wheat microarray.
abstract: We report mapping of translocation breakpoints using a microarray. We used complex RNA to compare normal hexaploid wheat (17,000 Mb genome) to a ditelosomic stock missing the short arm of chromosome 1B (1BS) and wheat-rye translocations that replace portions of 1BS with rye 1RS. Transcripts detected by a probe set can come from all three Triticeae genomes in ABD hexaploid wheat, and sequences of homoeologous genes on 1AS, 1BS and 1DS often differ from each other. Absence or replacement of 1BS therefore must sometimes result in patterns within a probe set that deviate from hexaploid wheat. We termed these 'high variance probe sets' (HVPs) and examined the extent to which HVPs associated with 1BS aneuploidy are related to rice genes on syntenic rice chromosome 5 short arm (5S). We observed an enrichment of such probe sets to 15-20% of all HVPs, while 1BS represents approximately 2% of the total genome. In total 257 HVPs constitute wheat 1BS markers. Two wheat-rye translocations subdivided 1BS HVPs into three groups, allocating translocation breakpoints to narrow intervals defined by rice 5S coordinates. This approach could be extended to the entire wheat genome or any organism with suitable aneuploid or translocation stocks.
authors: Department of Botany and Plant Sciences, University of California, Riverside, California 92521-0124, USA.
authors: Prasanna R
authors: PR
authors: Bhat
authors: Adam
authors: A
authors: Lukaszewski
authors: Xinping
authors: X
authors: Cui
authors: Jin
authors: J
authors: Xu
authors: Jan T
authors: JT
authors: Svensson
authors: Steve
authors: S
authors: Wanamaker
authors: J Giles
authors: JG
authors: Waines
authors: Timothy J
authors: TJ
authors: Close
mesh_terms: D019457:Chromosome Breakage; D002874:Chromosome Mapping / Q000379:methods*; D003627:Data Interpretation, Statistical; D005819:Genetic Markers; D018745:Genome, Plant; D023281:Genomics / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015345:Oligonucleotide Probes; D012275:Oryza / Q000235:genetics; D014178:Translocation, Genetic; D014908:Triticum / Q000235:genetics*
chemical_list: D005819:Genetic Markers; D015345:Oligonucleotide Probes