Genetic diversity variation during the natural regeneration of Vatica guangxiensis, an endangered tree species with extremely small populations

Vatica guangxiensis X. L. Mo (Dipterocaceae) is a valuable timber tree species endemic to China and a typical plant species with extremely small populations (PSESP). To understand the pattern variations in the genetic diversity of V. guangxiensis during natural regeneration, large-scale genome-wide SNPs were developed using genotyping by sequencing (GBS) to assess genetic diversity and population structure and to infer demographic history. The observed heterozygosity (HO), expected heterozygosity (HE), and nucleotide diversity (π) of V. guangxiensis were 0.1810, 0.2128, and 0.2178, respectively, demonstrating a low genetic diversity characteristic similar to most PSESP. However, further analysis of trees at different periods of natural regeneration revealed that both small trees and medium trees had lower genetic diversity than big trees. One important cause of the low and declining genetic diversity of V. guangxiensis may be the inbreeding that is forced due to the very small population size. Notably, a rare genetic component was detected in the genomes of several individuals in the medium tree and small tree groups, which may have been derived from other big trees that have died. In addition, the Tajima’D value (0.0689) and Stairway plot revealed a population bottleneck along with a continuous decline in the effective population size of V. guangxiensis since the last glacial period. These findings expand the understanding of the evolutionary history of the diversity of PSESP and the variation patterns in their genetic diversity, thus providing a basis to develop an effective conservation strategy. •Large-scale genomic SNPs were developed in Vatica guangxiensis.•The genetic diversity is low and shows further decline in natural regeneration.•The pattern variations of genetic diversity may be related to inbreeding and demographic history.