Comparison of SSR polymorphisms using automated capillary sequencers, and polyacrylamide and agarose gel electrophoresis: Implications for the assessment of genetic diversity and relatedness in almond

Abstract

In this work we have performed a comparative study of the utilization of three electrophoresis separation methods for the analysis of peach SSR polymorphism in almond and its implications in the assessment of genetic diversity and relatedness. Automated SSR detection and polyacrylamide gel electrophoresis were the most efficient methods and would be able to resolve allelic variation at a finer scale than the electrophoresis in MetaPhor® agarose. Moreover, automated electrophoresis detection is much more expensive in terms of cost of equipment and cost of the analysis. In addition, SSR detection using polyacrylamide gel electrophoresis showed similar results than automated sequencing, although it is more time-consuming and toxic than electrophoresis in agarose gels. Discrepancies among polyacrylamide and automated capillary, and MetaPhor® were observed when differences in SSR polymorphisms were between 1 and 5 bp. While the use of MetaPhor® agarose appears less indicated for genotype characterization, this technique may be the most convenient in other applications, i.e. mapping of population, due to its lower cost and easier routine application. The utilization MetaPhor® agarose produced a slightly different clustering of genotypes in spite of the big differences observed in the DNA fingerprinting. However, bootstrap values using MetaPhor® agarose were lower indicating a lower accuracy of this SSR polymorphism analysis method.