Microsatellite markers in maize: challenges and guidelines for implementing multiplex SSR analyses
Alessandra Koltun, Priscila Alves da Silva, Isabela Yamauchi Torres, Fernando Bonifácio-Anacleto and Juliana Erika de Carvalho Teixeira Yassitepe
Abstract: Microsatellites have been widely used to genotype individuals and to address a myriad of biological questions in many research fields for decades. However, when implementing a microsatellite marker analysis routine from scratch, various problems can arise throughout the process from DNA extraction to allele scoring, including inputting errors in the database, decreasing the reliability of results and having profound negative impacts on the derived decisions. Therefore, correctly assigning a genotype to a sample is crucial and dependent on acquiring knowledge of the technique steps, such as the chemistry of reactions, software, and data curation. This study tested two previously constructed simple sequence repeat (SSR) sets containing ten primer pairs each (tenplex) in 1142 maize genotypes. Here, we describe the challenges faced when implementing this microsatellite-based genotyping protocol in our laboratory and possible ways to overcome them, hopefully aiding other novice research teams in this field.