Rice Genetics IV - IRRI books - International Rice Research Institute

Predicted frequency100,00080,000Class IClass II60,00040,00020,0000BAC endsPAC and BACclonesESTsFig. 2. Predicted frequency of class I and class II microsatellites inthree sets of DNA sequence data: (1) BAC ends, (2) fully sequencedPAC and BAC clones, and (3) ESTs.Although several thousand new SSR-containing sequences were recently releasedby Monsanto/Pharmacia (www.riceresearch.org), this information is not directly comparableto results from this study because the information included only SSRs ≥ 24 bpin length. In summary, current estimates based on available genomic sequence informationof between 10,000 and 30,000 class I SSRs are slightly higher than previouspredictions based on hybridization experiments, with a total prediction of up to 100,000class I and class II SSRs in rice.Frequency of SSRs in different fractions of the rice genomeWe were interested in exploring why continuous genomic sequence appeared to bericher in SSRs than BAC end sequence. To address this question, we first comparedthe relative frequency of SSRs in coding and noncoding sequences, based on an analysisof the frequency of class I and class II SSRs in rice ESTs. The estimated frequency ofmicrosatellites in ESTs was even higher than that in continuous genomic sequence(Fig. 2). This suggested (1) that SSRs are abundant in genic regions, (2) that the fullysequenced BAC and PAC clones that were available were gene-rich, and (3) that theBAC end sequences were relatively gene-poor. These conclusions are consistent withthe fact that BAC end sequences, bounded by EcoRI (GAATTC) and HindIII(AAGCTT) restriction sites, are relatively AT-rich compared with the fully sequencedBAC and PAC clones or the ESTs. Although more precise estimates of class I andclass II SSR frequency in rice await the completion of the rice genomic sequence, thefact that regions of the rice genome that are richer in expressed genes also tend to bericher in SSR sequences has important implications for the usefulness of SSRs asgenetic markers.Microsatellite markers in rice: . . . 121