Low genetic diversity and weak population structure of Albizia odoratissima on Hainan Island.

Abstract

Background: The increasing demand for wood owing to societal development has highlighted the potential of Albizia odoratissima, a valuable timber species, to address significant timber shortages in China. However, the lack of effective genetic and genomic resources has limited the development and utilization of this species.

Results: In this study, we utilised 95.3 Gb of HiFi reads to assemble a draft genome of A. odoratissima, resulting in a genome size of 788 Mb, comprising 511 contigs. We conducted whole-genome resequencing on 106 individuals from 7 populations on Hainan Island to explore these resources. Our analysis identified 498,308 high-quality single nucleotide polymorphisms, which were used to assess the genetic diversity, structure, and demographic history of A. odoratissima on Hainan Island. The results indicated that the genetic diversity of A. odoratissima on Hainan Island is relatively low (observed heterozygosity = 0.189, expected heterozygosity = 0.189, genetic diversity = 1.319 × 10^-4) with minimal genetic differentiation (Fst = 0.0151) among the seven populations. Furthermore, molecular variance, principal coordinate analysis, neighbour-joining tree analysis, and genetic structure analysis revealed a shallow population structure. The linkage disequilibrium (LD) decay ranged from 11.4 kb for Jianfengling (JFL) to 39.2 kb for Wuzhishan (WZS). LD decay, demographic history, and Tajima's D analyses indicated that the WZS population has experienced a bottleneck effect.

Conclusions: This study offers new insights into the genetic diversity and population structure of A. odoratissima on Hainan Island, providing a foundation for future resource utilization and genetic improvement strategies for this species.