Rice Genetics IV - IRRI books - International Rice Research Institute

MITEs as a source of allelic diversity in maize and riceThrough numerous studies, a great deal has been learned about the comparative structureof the genomes of members of the grass clade including rice, sorghum, maize,and wheat (reviewed in Bennetzen 2000). The take-home message from these studiesis that grass genomes are highly conserved for coding exon sequences and gene orderbut completely different for the presence or absence of TEs at particular loci (definedherein as TE-insertion site polymorphism). This situation has led to speculation thatTEs play a major role in creating the variation that fuels speciation in the grass clade(Zhang et al 2000).This hypothesis cannot be tested through intergeneric comparisons or by decipheringthe complete genome sequence of one strain. Although such studies are criticalto understanding gene function, they do not reveal how genes or genomes evolve.To address evolutionary questions, it is necessary to first quantify the extent of TEinsertionsite polymorphism between members of the same species and then to determinewhether this polymorphism is functionally significant and/or generated in responseto external cues. To understand the contribution of MITEs to the creation ofallelic diversity, we are focusing on MITEs that have recently spread through thegenome in maize and rice. Two features distinguish such MITEs: they have highwithin-family sequence identity (usually >90%) and their insertion sites are highlypolymorphic within the species.Several recently amplified MITEs in maizeThe first member of the MITE family, Hbr, was isolated from a mutant allele of themaize HM1 disease resistance gene (Johal and Briggs 1992). Subsequent studies revealedthat there are about 3,000–4,000 Hbr elements in maize with more than 90%sequence identity (Zhang et al 2000). Although the majority of the maize genomecontains moderate to highly repetitive DNA, randomly chosen Hbr elements are predominantlyin single or low-copy genic regions. Preliminary studies have identifiedthree additional maize MITE families each with more than 5,000 copies per haploidgenome, with more than 90% sequence identity, and with target site preference: B2-Tourist (Bureau and Wessler 1992, N. Jiang and S. Wessler, unpublished data), mPIF(Walker et al 1997, X. Zhang, Q. Zhang, and S.Wessler, unpublished data), and Hb2(Spell et al 1988, Z. Magbanua and S. Wessler, unpublished data).Transposon display: assaying TE polymorphismMITE-transposon display (MITE-TD) is a modification of the amplified fragmentlength polymorphism (AFLP) technique and the transposon display technique (Vos etal 1995, Van den Broeck et al 1998) that permits the simultaneous detection of manyMITEs from high copy number lines. Unlike conventional AFLP products that aredelimited by two restriction sites, one restriction site (usually Mse1 or Bfa1) and aMITE delimit MITE-TD polymerase chain reaction (PCR) products. MITE-TD hasbeen applied to several MITEs from maize including Hbr (Casa et al 2000). As withAFLP, the segregation of a MITE product that is present in the parent of one mappingMiniature inverted repeat transposable elements . . . 111