Performance comparison of gel and capillary electrophoresis-based microsatellite genotyping strategies in a population research and kinship testing framework

Abstract

Objective The advancement of molecular techniques in an era in which high-throughput sequencing has revolutionized biology renders old-fashioned alternatives to high-throughput methods obsolete. Such advanced molecular techniques, however, are not yet accessible to economically disadvantaged region-based laboratories that still obtain DNA profiles using gel-based techniques. To explore whether cost-efficient techniques can produce results that are as robust as those obtained using high-throughput methods, we compared the performance of polyacrylamide gel electrophoresis (PAGE)- and capillary electrophoresis (CE)-derived genomic data in estimating genetic diversity and inferring relatedness using 70 individuals of fine flounder (Paralichthys adspersus) selected from a hatchery population and genotyped for five microsatellite loci. Results Here, we show that PAGE- and CE-derived genomic datasets yield comparable genetic diversity levels regarding allelic diversity measures and heterozygosity. However, relatedness inferred from each dataset showed that the categorization of dyads in the different relationship categories strongly differed. This suggests that while scientists can reliably use PAGE-derived genomic data to estimate genetic diversity, they cannot use the same for parentage testing. The findings could help laboratories committed to population research not be discouraged from using the PAGE system if high-throughput technologies are unavailable and the method is adequate to address the biological question.

Molecular Parentage Analysis in Aquaculture: Principles, Applications, and Challenges: A Review

“…Therefore, electrophoresis using 8-12% polyacrylamide gels, in combination with silver staining, was used to achieve better resolution of fragment separation [43]. Capillary electrophoresis technology enhances the precision and speed of measuring and genotyping microsatellite alleles [44]. The scoring of genotypes is more efficient with the software that each semi-automated DNA sequencer has.…”

Assessment of Microsatellite Markers for Parentage Testing in Jersey Crossbred Cattle in Tamil Nadu

“…The markers were also recommended by the International Society for Animal Genetics (ISAG) -Food and agriculture organization (FAO) Advisory Group on Animal Genetic Diversity in 2011) 13 to be used for paternity exclusion tests due to their extensive utility in parentage control in several species, high abundance, informativeness, and relatively low costs 14 . Accurate allele sizes of the microsatellite loci can be determined by using cutting-edge techniques like capillary electrophoresis 15 , which has numerous benefits over conventional separation techniques like PAGE, such as separation efficiency, short analysis time, low sample and solvent consumption, low operating costs, and lower matrix effects 16 . Using fluorescent dye-labelled primers with automatic capillary electrophoresis is one of the most popular high-sizing precision method termed "Fragment analysis" to assess the polymorphisms of the loci [17][18][19] .…”