The blast algorithms: Practical application in molecular cloning, marker-assisted selection (MAS) and introgression of wheat

BLAST (Basic Local Alignment Search) analyses of Hordeum chilense RAPD mark ers have shown DNA sequence similarities with several plant genes. Biologic ally significant hits were scored for: plastocianin (Hordeum vulgare), alph a -gliadin (Triticum aestivum), Grandel-6 retrotransposon (Zen diploperenni s), retrofit (gag/pol) copia-like, transposon-like element (Oryza longistam inata), copia-like retrotransposon Hopscotch polyprotein (gag/pol) (Zea may s) and several retrotransposons/retroelements from other species (Arabidops is thaliana, Oryza sativa, Pisum sativum and Zea mays). Statistically signi ficant hits also included endochitinase (Brassica napus), ribulose-1,5-bisp hosphate carboxylase (Euglena gracilis), piruvate, orthophosphate dikinase (Flaveria trinervia), and an ORF flanked by ARS sequences (Triticum aestivu m). Interestingly, it was also found that the currently recommended BLAST a lgorithm (version 2.0.11; gapped) at < http:/ / www.ncbi.nlm.nih.gov > did not produce any biologically significant hits, whereas the previous version (1.4.11; ungapped) did generate biologically significant results. Thus, we suggest using the new BLAST 2.0.x when strong homologies are expected in s hort sequence stretches between closely related species. In other instances land particularly when searching for lower similarities, yet spanning sign ificantly larger stretches between more distant species), the BLAST 1.4.x c ould yield additional results. BLAST searches are valuable tools to identif y and clone DNA sequences of interest, with applications in Marker-Assisted Selection (MAS) and wheat introgression.