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Traditionally, plant geneticists and plant breeders relied on easily recognizable phenotypic differences, such as flower color, in their studies. More recently, isozyme marker systems, which distinguish among different forms of enzymes, have increased the number of readily scoreable phenotypes. With the advent of restriction fragment length polymorphism (RFLP) markers, it is now possible to detect differences in DNA sequences that do not necessarily result in phenotypic differences. This is because RFLP markers are different among homologous DNA fragment lengths that result from base pair changes in the restriction enzyme recognition sites between genotypes. RFLP markers can be observed after the restriction fragments have been separated by agarose gel electrophoresis, Southern blotted, and hybridized with a radioactively labeled DNA probe which is homologous to these fragments (locus). Therefore, RFLPs serve as genetic markers.


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