RAPD markers in maize genetic analysis

Genetic markers generated by amplification of random DNA segments using single primers of arbitrary nucleotide sequence were tested for their utility in genetic studies in maize. The amount of template DNA, the Mg2+ concentration and the primer concentration revealed to be the most critical variables to consider for the optimization of amplification reaction. Template DNAs from B73 and A7 inbred lines, their Fl and 45 F2 individuals were tested against 47 ten base oligonucleotide primers. Thirty-five primers produced clear and reproducible amplification patterns and 10 of these originated 17 products polymorphic between B73 and A7. The 17 RAPDs segregated as simple dominant mendelian factors and were placed on an RFLP map created in our laboratory for QTL mapping. Eleven primers were further utilized on second cycle inbred lines of known pedigree. Products obtained from the amplification of the DNA of the second cycle lines were also amplified from one or both original lines, revealing that RAPDs have been stably inherited.