Genetic diversity, genetic structure, and demographic history of Cinnamomum chago, a plant species with extremely small populations in China

As a species with restricted and fragmented distribution in Yunnan Province, Cinnamomum chago possesses high economic and phylogenetic values. Although this species has been categorized as an endangered plant in the IUCN Red List and has extremely small populations in China, the genetic information of C. chago has been rarely studied. In the present study, we used 4 pairs of DNA markers and 11 pairs of expressed sequence tag–simple sequence repeat markers to conduct a systematic and comprehensive assessment about the genetic diversity, genetic structure, and demographic history of 5 C. chago populations. A low genetic diversity but a significant genetic differentiation were detected (Na=2.509, Np=3.8, Ra=2.423, AE=1.635, HO=0.177, He=0.340). The five populations presented obvious inbreeding phenomenon given the high value of inbreeding coefficient (Fis=0.462) and low value of outcrossing rate (t = 0.365). Although the genetic distance and geographic distance were not correlated, geographical structures were detected in C. chago. Extremely low historical and contemporary gene flow was detected between pairwise populations of C. chago. Additionally, the remnant populations of C. chago experienced a recent historical bottleneck, but the neutrality tests and mismatch distribution analysis revealed that this species did not underwent a recent population expansion. In consideration of the above consequence, we advocate in situ conservation of natural habitats and remaining individuals of C. chago, as well as artificial breeding. This study not only provides important insights into the genetic characteristic but also emphasizes the relevance of the conservation of C. chago and other extremely endangered plants.