New multiplex PCR assays for estimating genetic diversity in rainbow trout (Oncorhynchus mykiss) by polymorphism of microsatellite DNA

Multiplex PCR is a useful technique for estimating genetic diversity. This paper presents 3 new sets of primer pairs for effectively amplifying 10 microsatellite DNA loci from rainbow trout (Oncorhynchus mykiss). Unlike other sets of primer pairs that have been developed for amplifying rainbow trout microsatellite loci, ours do not require the hot-start PCR technique. In the paper, we describe the steps taken to choose the loci for each multiplex assay and to verify the genotyping results. We provide the compositions of the PCR mixture and the characteristics of the PCR thermal profile recommended for amplification.