Anchor probes for comparative mapping of grass genera

Abstract

 Comparative mapping of cDNA clones provides an important foundation for examining structural conservation among the chromosomes of diverse genera and for establishing hypotheses about the relationship between gene structure and function in a wide range of organisms. In this study, “anchor probes” were selected from cDNA libraries developed from rice, oat, and barley that were informative for comparative mapping in the grass family. One thousand eight hundred probes were screened on garden blots containing DNA of rice, maize, sorghum, sugarcane, wheat, barley, and oat, and 152 of them were selected as “anchors” because (1) they hybridized to the majority of target grass species based on Southern analysis, (2) they appeared to be low or single copy in rice, and (3) they helped provide reasonably good genome coverage in all species. Probes were screened for polymorphism on mapping parents, and polymorphic markers were mapped onto existing species-specific linkage maps of rice, oat, maize, and wheat. In wheat, both polymorphic and monomorphic markers could be assigned to chromosomes or chromosome arms based on hybridization to nullitetrasomic and ditelosomic stocks. Linkage among anchored loci allowed the identification of homoeologous regions of these distantly related genomes. Anchor probes were sequenced from both ends, providing an average of 260 bp in each direction, and sequences were deposited in GenBank. BLAST was used to compare the sequences with each other and with a non-redundant protein sequence database maintained at the European Molecular Biology Laboratory (EMBL). Of the anchor probes identified in this study 78% showed significant similarity to protein sequences for known genes with BLASTX scores exceeding 100.