Genome-wide diversity in native populations of Croton grewioides Baill., a future crop with fungicidal and antioxidant activity, using SNP markers

Croton grewioides Baill. is a medicinal and aromatic species with proven biological activity. Considering the economic potential of the species, the use of molecular markers for genetic diversity studies is of utmost importance to develop viable strategies for its management, conservation, and use. Thus, the aim of this study was to evaluate the genetic diversity and structure of natural populations of C. grewioides using SNP markers, and select genotypes to compose the species collection in an Active Germplasm Bank. Genotypes were sampled from two populations, the first in the state of Sergipe (SE) and the second in the state of Bahia (BA). A total of 6,942 high quality SNPs were identified through genotyping-by-sequencing (GBS). Genetic diversity was estimated by observed and expected heterozygosities (H o : 0.211 < H e : 0.225), the Shannon Index ( I : 0.357), inbreeding coefficient ( f : 0.056), and number of exclusive alleles (BA: 1296 and SE: 799). Analysis of molecular variance (AMOVA) showed greater genetic variation within the populations. The multivariate analyses performed (Discriminant analysis of principal components—DAPC; bayesiana—Structure; Principal Components Analysis—PCA; and the dendrogram based on Rogers’ genetic distance) allowed separation of the genotypes according to the population of origin. Thirteen (13) genotypes from the SE population and 17 from the BA population were selected to compose the species collection. The selection of genotypes coming from the two populations studied is fundamental for effective conservation of the genetic variability detected.