Rice Genetics IV - IRRI books - International Rice Research Institute

Distribution of SSR motifsSignificant differences were observed when the frequencies of different class I SSRmotifs extracted from the three independent sources of sequence data were compared,that is, BAC end sequences, completely sequenced BAC and PAC clones, and riceESTs. As illustrated in Figure 3, the greatest differences were observed for GC-richpoly tri-nucleotides and poly(AT)n microsatellites. These observations suggested thatSSR motif categories were not randomly distributed. In agreement with a previousstudy in rice (Cho et al 2000) and in maize (Chin et al 1996), GC-rich tri-nucleotideSSRs appear to be concentrated in coding regions, whereas (AT) di-nucleotides arescarce in EST sequence but abundant in and around the AT-rich intergenic regionsrepresented by EcoRI- and HindIII-digested BAC end sequences. The relatively equalfrequency of GC-rich tri- and poly(AT)n di-nucleotides in the fully sequenced BACand PAC clones suggested that these clones have interspersed regions of coding andnoncoding sequence.When different motifs were compared, (AT)-rich tri-nucleotide and poly(GA)nmicrosatellites were unusual in that their frequencies were roughly equivalent in allthree types of sequence. This observation is consistent with the idea that these motifsare relatively uniformly distributed in the rice genome and make good targets for SSRmarker development. In contrast, poly(GC)n motifs were extremely rare in all sequencedata and poly(CA)n microsatellites occurred at low frequencies (Fig. 3).Frequency (%)605040BAC endsFully sequencedBAC and PAC clonesESTs3020100GACA CG AT GC-richTNRsDNRsAT-richTNRsTetrasFig. 3. Comparative frequencies of class I microsatellites from different sourcesof DNA sequence data classified by SSR motif category. Di-nucleotide repeats(DNR): poly(GA)n, poly(CA)n, poly(CG)n, poly(AT)n; tri-nucleotide repeats (TNR):GC-rich and AT-rich; and tetra-nucleotide repeats (tetramers).122 McCouch et al