Restriction fragment length polymorphisms in genetic improvement: methodologies, mapping and costs

Abstract

Recently a new class of genetic polymorphism, restriction fragment length polymorphisms (RFLPs), has been uncovered by the use of restriction endonucleases which cleave DNA molecules at specific sites and cloned DNA probes which detect specific homologous DNA fragments. RFLPs promise to be exceedingly numerous and are expected to have genetic characteristics - lack of dominance, multiple allelic forms and absence of pleiotropic effects on economic traits - of particular usefulness in breeding programs. The nature of RFLPs and the methodologies involved in their detection are described and estimated costs per polymorphism determination are derived. The anticipated costs of applying RFLPs to genome mapping are considered in terms of the number of RFLPs required for a given degree of genome coverage, the number of probe × enzyme combinations tested per polymorphism uncovered, and the total number of individuals and polymorphisms scored for mapping purposes. The anticipated costs of applying RFLPs to genetic improvement are considered in terms of the number of individuals and the number of polymorphisms per individual that are scored for the various applications. Applications considered include: varietal identification, identification and mapping of quantitative trait loci, screening genetic resource strains for useful quantitative trait alleles and their marker-assisted introgression from resource strain to commercial variety, and marker-assited early selection of recombinant inbred lines in plant pedigree breeding programs and of young sires in dairy cattle improvement programs. In most cases anticipated costs appear to be commensurate with the scientific or economic value of the application.