Characterizing the genetic diversity of Atlas cedar and phylogeny of Mediterranean Cedrus species with a new multiplex of 16 SSR markers

Cedar is an emblematic Mediterranean forest tree. Genetic research activities on Mediterranean Cedrus species are progressively developed in relation to conservation, restoration, and exploitation plans of these forest tree species. However, currently available molecular biology tools supporting genetic research in these fields are still scarce and have a limited genetic resolution potential. We developed a new set of 12 nuclear microsatellite markers (nSSRs) on Cedrus atlantica that we combined with four previously developed ones in three multiplexes. We checked their monogenic inheritance in controlled crosses. We used a collection of 131 samples from six populations of C. atlantica to estimate null allele frequencies and probability of identity and to characterize the structure of genetic diversity in the fragmented distribution range of this species. We also tested the transferability of the markers to another set of 36 samples from the other Mediterranean Cedrus species and performed a phylogenetic analysis. The three multiplexes reached a high level of resolution potential that we used to evaluate sampling quality. Null allele frequency estimates showed no specific pattern across populations or across species and did not affect the results of biogeographic and phylogenic analyses. Our results reveal a very clear geographical genetic structure within C. atlantica, and the phylogenic tree matched previous analyses based on other markers. Our results confirm the potential interest of these nSSR multiplexes for genotyping in Cedrus.