Assessing the Genetic Diversity of a Core Set of Jatropha curcas Accessions By High-Density Sequence-Based DArT-Seq Genotyping

Genetic diversity of the Jatropha Brazilian Germplasm Collection (JBGC) composed of 192 accessions was found limited based on a previous assessment carried out with a limited number of RAPD and SSR markers. Since that first study however, new accessions from other countries (e.g. Guatemala and Mexico) were introduced without prior information of their relationships to the existing collection. We now report on an extended assessment of the genetic diversity of a core set of 42 accessions from the JBGC together with eight new introductions and three elite genotypes using high-density genome-wide DArT-Seq genotyping. The genotype-by-sequencing approach of DArT-Seq, firstly used in the crop, yielded 747 polymorphic SNPs and 2.724 informative presence-absence variants. This is likely the highest genotyping density achieved to date in Jatropha, providing relatively good genome-wide coverage, and potentially more informative diversity and relationship estimates. Pair-wise genetic dissimilarities (GD) were estimated based on Jaccard´s coefficient, and clustering analysis performed by the UPGMA algorithm. The mean GD among accessions was low (0.165), confirming that the diversity in the JBGC is indeed limited. The introduced genotypes were the most divergent, forming a separate cluster from the Brazilian accessions, indicating that such new additions will be important to foster future breeding efforts.