Development of nuclear microsatellite markers in Yerba mate (Ilex paraguariensis St. Hil., Aquifoliaceae Bartl.) from whole-genome sequence data

Ilex paragariensis St. Hil. (yerba mate) (Aquifoliaceae Bartl.) is a plant species with great economic and cultural importance because its leaves are processed and ground to make infusions like mate or terere. The species is distributed in a continuous area that includes southern Brazil, and part of Paraguay and Argentina. Uruguay represents the southern distribution limit of the species, where small populations can be found as part of riparian forests. Although there are previous reports of molecular markers for this and other species in the genus, the available markers were not informative enough to represent the intra and interpopulation genetic diversity in these marginal populations. In this study, we developed highly informative nuclear polymorphic microsatellite markers to optimize genetic studies in I. paraguariensis. Markers were identified in contigs from the genome sequence of two individuals and then tested for amplification and polymorphism in a diverse panel and at population level. Markers which passed these tests detected levels of heterozygosity similar to those reported for Brazilian populations and great diversity within populations from Uruguay. This set of markers were successfully multiplexed, substantially reducing the costs of the analysis. In combination with previously reported nuclear and plastid markers, they can be used to evaluate the genetic diversity of rear edge populations, identify genotypes for paternity studies and provide relevant information for the conservation and management of germplasm.