Rice Genetics IV - IRRI books - International Rice Research Institute

parent but not in the other can be scored in the progeny and used to determine thechromosomal location of the MITE. In this way, more than 250 Hbr markers werescored in a B73 × Mo17 recombinant inbred mapping population and found to bedistributed relatively uniformly over the ten chromosomes of maize (Casa et al 2000).Given the genic preference of Hbr and other MITEs, MITE markers may be an extremelyvaluable addition to the mapmaker’s toolbox.A key feature in the success of MITE-TD is the identification of a suitable consensussequence adjacent to the TIR. This sequence is employed to synthesize aprimer(s) that is used in conjunction with the restriction site adapter primer in thePCR amplification steps. For the maize MITE Hbr, and for other maize MITEs, thissequence was derived by aligning the sequences of several related elements recoveredfrom small insert genomic libraries (Casa et al 2000, Zhang et al 2000). In contrast,MITE primer selection is far simpler in rice, which has a large genomic sequencedatabase. Related elements are simply identified through database searchesand Boxshade alignments, like that shown for the MITE Olo (Fig. 2A). In this way,suitable primers can be easily designed and employed in TD (Fig. 2B). Databaseassistedprimer design led to successful TDs for several other MITEs in the rice genomes(Fig. 2B).Oryza as a model genus to study TEs and evolutionThe availability of the entire sequence of Oryza sativa cv. Nipponbare will permitidentification of virtually all TEs and their relative positions with respect to knowngenes and open reading frames. This information can be used to understand howdifferent TE families become established, amplified, and spread throughout the genome.The genome sequence can also be used to derive primers for transposon displayof the high copy number MITEs and retrotransposons. Transposon display, inturn, when used in conjunction with the 20 or more species of Oryza, will providedata on the contribution of each TE family to intrageneric diversity. It is hoped that,eventually, these data will furnish the raw material for determining whether TEs are asignificant factor in generating the diversity that fuels both natural and artificial selection.112 Wessler et al