Plant Genome III Conference Plant Genome III Conference
AFLP (Amplified Fragment Length Polymorphism)and IRA (Inter-Repeat Amplification) analysis allow many polymorphic DNA bands to be visualized in a single lane and therefore provide potengagy rapid and efficient methods for scanning an entire plant genome. In contrast RFLP analysis is time consuming as a fingerprinting tool because of the low frequency of polymorphism detected per Southern blot. Furthermore, RFLPs often detect only modest amounts of genetic variability within a single subspecies of rice (Oryza saliva) or within an Isolated breeding pool such as the rice cultivars of the United States. The AFLP technique (M. Zabeau and P.Vos, Keygene, Wageningen, Netherlands) is based on the selective PCR amplification of specific restriction fragments resulting from single or double digests of genomic DNA. The IRA technique involves the PCR amplification of regions between two adjacent, inversely- oriented minisatellite sequences. Although conceptually similar to the use of RAPDs for fingerprinting, IRAs are potentially superior because they detect many more loci per reaction, especially in genomes with abundant microsatellites, and these loci tend to be hypervariable. Non-radioactive protocols were developed for the AFLP and IRA techniques and were used to evaluate a set of 54 rice varieties representative of the diversity of cultivated germplasm. The AFLP and IRA data were compared and used to group the genotypes by principle component analysis. The restults of these PCR-based approaches were also compared to previous RFLP and isozyme surveys of the same varieties, to determine their utility in the phylogenotic and taxonomic analysis of rice. The segregation pattern and map locations of AFLP and IRA markers were studied using an interspecific backcross population to determine if these techniques will be reliable for future mapping and gene tagging objectives. Results indicate that both methods are promising for high resolution screening of genetic variability among rice varieties and for the development of new markers for saturated mapping of specific genomic regions.