Is HRM analysis suitable for SSR genotyping of a mapping population? A comparison of HRM and capillary electrophoresis for SSR genotyping in a mapping population

The aim of the study was to compare two methods for detection of polymorphism in a microsatellite locus, i.e. Capillary Electrophoresis (CE) ABI and QIAxcel, and High Resolution Melting (HRM), in respect of correct and efficient genotyping of a narrow-leafed lupin mapping population. The difference in length of the generated products by three SSR primers, between the parental forms were: less than 10 bp, more than 10 bp, more than 20 bp. Both tested CE systems allowed to perform correct genotyping of the analyzed RILs and their parents. The HRM technique failed to correct genotype RILs and their parental forms with the markers generating polymorphic product difference in a length less than 10 bp. However, this technique enables correct and effective genotyping with the markers that generate polymorphic product difference in a length more than 10 pb. Of the two CE systems compared, QIAxcel was less time-and money-consuming.