DNA amplification fingerprinting (DAF) as a new source of molecular markers in bread wheat

Abstract

Polymorphism in seven bread wheat genotypes (differing for four quality traits) was studied using DAF. Ten arbitrary, 8- mer, GC rich, linear primers and ten 1 1-mer minihairpin primers, each having a 3-mer core sequence at 3' end, were utilized for DNA amplification. Nine linear primers and four mini-hairpin primers produced characteristic fingerprinting patterns involving polymorphism. The remaining primers gave poor DAF profiles with high background smear, which was associated with relatively higher GC content of these primers. It could partly also be due to large genome size of bread wheat. Both linear as well as mini-hairpin primers producing good DAF profiles, also revealed polymorphic DAF products, some of which were unique to a genotype. Contrary to earlier claims, neither the average number, nor the proportion of polymorphic products obtained with mini-hairpin primers suggested their superiority over the linear primers. In view of our earlier unpublished results with RAPDs and MP-PCR on the same set of genotypes, giving no reproducible polymorphism, we conclude that DAF technology may be a useful tool for detecting polymorphism in a difficult crop such as bread wheat.