First microsatellite markers for the Amazonian species Copaifera multijuga Hayne developed using next-generation sequencing.

Abstract

Background: Native to the Amazon region, Copaifera multijuga Hayne is a large tree (≈ 36 m in height) that is heavily exploited for extraction of its oleoresin. Many studies have addressed the phytochemical properties and applications of this raw material; however, there are few initiatives that have focused on the genetic characterization of native populations of this species. To this end, our objective was to develop microsatellite markers for C. multijuga, which were previously unavailable, and apply them to the characterization of a native population located in the Adolpho Ducke Forest Reserve (Manaus, Amazonas, Brazil).

Methods and results: Using next-generation sequencing technology on the Ion Torrent PGM™ platform, 19 pairs of microsatellite primers were designed and developed. For the characterization and validation, we used a group of 47 C. multijuga trees. After preliminary tests, amplification conditions were standardized for 14 loci. The CmH05 locus was excluded from the analyses for being monomorphic, and the remaining loci were used to estimate key genetic parameters for the species, such as observed (Ho) and expected heterozygosity (He), total number of alleles (A), fixation index (f), and polymorphic information content (PIC), among others. The population showed levels of genetic diversity that were higher than 0.63 (Ho: 0.67; He: 0.64) and an average number of 5.4 alleles. According to the PIC estimates, all loci were considered highly (9) or moderately informative (3), except for CmH11, which had a value that was below 0.2.

Conclusions: The 13 developed microsatellites were efficient in characterizing the genetic diversity of C. multijuga and may be advantageous in future investigations aimed at defining effective conservation strategies for the species.