Stylosanthes species are important forage legumes in tropical and subtropical areas. S. macrocephala and S. capitata germplasm collections that consist of 134 and 192 accessions, respectively, are maintained at the Brazilian Agricultural Research Corporation Cerrados (Embrapa-Cerrados). Polymorphic microsatellite markers were used to assess genetic diversity and population structure with the aim to assemble a core collection. The mean values of HO and HE for S. macrocephala were 0.08 and 0.36, respectively, whereas the means for S. capitata were 0.48 and 0.50, respectively. Roger’s genetic distance varied from 0 to 0.83 for S. macrocephala and from 0 to 0.85 for S. capitata. Analysis with STRUCTURE software distinguished five groups among the S. macrocephala accessions and four groups among those of S. capitata. Nei’s genetic diversity was 27% in S. macrocephala and 11% in S. capitata. Core collections were assembled for both species. For S. macrocephala, all of the allelic diversity was represented by 23 accessions, whereas only 13 accessions were necessary to represent all allelic diversity for S. capitata. The data presented herein evidence the population structure present in the Embrapa-Cerrados germplasm collections of S. macrocephala and S. capitata, which may be useful for breeding programs and germplasm conservation.

Microsatellites were developed for Stylosanthes macrocephala, aiming at developing tools for studying the genetic diversity of this species. A total of 13 polymorphic microsatellite markers were isolated from a S. macrocephala enriched genomic library. The isolated microsatellites were characterized in 20 accessions of the S. macrocephala germplasm collection belonging to the Empresa Brasileira de Pesquisa Agropecuária (Embrapa) Cerrados. The number of alleles per locus varied from 2 to 11, with an average of 4 alleles per locus. The observed and expected heterozygosities ranged from 0 to 0.25 and 0.05 to 0.90, respectively. Cross-amplification of the S. macrocephala polymorphic microsatellites was evaluated in three other Stylosanthes species. The microsatellites reported herein are the first set of microsatellite markers developed for S. macrocephala and are potentially useful for further studies on genetic diversity, conservation and breeding of this species.

Stylosanthes capitata is an important tropical pasture legume. Knowledge of genetic diversity and structure of S. capitata populations is of great importance for the conservation and germplasm management of this species. Thus, eight microsatellite markers were developed from an S. capitata-enriched library. They were characterized in 20 accessions from the germplasm collection of the Empresa Brasileira de Pesquisa Agropecuária (Embrapa). The observed and expected heterozygosities ranged from 0.16 to 0.85 and from 0.40 to 0.85, respectively. These microsatellites are the first set of molecular markers from this species and will contribute towards studies of genetic diversity, conservation and breeding of S. capitata.