Discovery and Characterization of Polymorphic Sites in the Jatropha curcas Genome

In this study we’ve aimed at discovering and characterizing polymorphic sites in the Jatropha curcas genome. To sample the genetic diversity of the species, we collected 704 leaf samples from 174 unique accessions. DNA was extracted and sent for DArT-Pty for DArTSeq development. More than 2 million reads per genotype was obtained and used to search for polymorphic sites including PAVs and SNPs. The characterization of the polymorphic sites was performed based on physical mapping of the sequences to the public available reference genome (RG). We discovered a total of 1144 PAVs and 1087 SNPs with unique hits to the RG. Out of 39.277 scaffolds comprising the whole-genome sequence of Jatropha 25379 (64.46%) contained predicted gene models. The polymorphic sites we´ve discovered in the genome however has a much more concentrated pattern of distribution. The PAVs mapped against 897 scaffolds (2.2%) while the SNPs were distributed among 1311 scaffolds (3.3%). This indicates that polymorphic sites uncovered through DArTSeq are sampling only a limited part of the genome. Nevertheless, both PAVs and SNPs are sampling gene-enriched regions of the genome. Out of the 897 and 1311 scalffolds carrying PAVs and SNPs, respectively, 98.1% and 95.9% also carried gene models. To increase genome sampling, focusing on gene-enriched regions other combinations of restriction enzymes need therefore to be tested on a panel of individuals with broader genetic diversity. This is expected to allow the selection of molecular markers sets to be used for downstream applications such as genomic selection and association mapping.

Financial support: Brazilian Ministry of Science, Innovation and Technology (MCTI) through FINEP’s grant BRJATROPHA.