# Development and Application of SSR Markers for Aquilaria sinensis on the Basis of Whole-Genome Resequencing Data

## TL;DR

This study develops and validates SSR markers for Aquilaria sinensis using whole-genome resequencing data to better understand its genetic diversity and support conservation efforts.

## Contribution

The study introduces a novel SSR marker framework for A. sinensis using resequencing data to enhance genetic resource management.

## Key findings

- 56,657 SSR sequences were identified, with dinucleotide repeats being the most common.
- 20 high-quality SSR primer pairs successfully classified 149 accessions into three subpopulations with 95.97% accuracy.
- Genetic variation within individuals accounted for 84% of the total variation in A. sinensis.

## Abstract

Aquilaria sinensis (Lour.) Spreng. is an economically important tree specie that produces agarwood, a valuable medicinal and aromatic resin, when injured. However, its large-scale cultivation has led to confusion regarding its resources and genetic backgrounds, hindering the conservation and management of A. sinensis accessions. This study systematically developed and validated simple sequence repeat (SSR) molecular markers by using whole-genome resequencing (WGR) data from 60 A. sinensis accessions to elucidate their genetic diversity and population structure. A total of 56,657 SSR sequences (24,430 loci) were identified, which were dominated with dinucleotide repeat motifs (73.59%). After stringent quality control, 46 high-quality SSR loci were obtained, and 93 primer pairs were designed for amplification validation. Ultimately, 20 primer pairs with stable amplification and high polymorphism were selected, of which 11 exhibited high polymorphism (polymorphic information content: 0.554–0.688). These 20 primer pairs identified a total of 121 alleles, with an average of 6 alleles per locus. These primers successfully classified 149 A. sinensis accessions into three subpopulations, achieving a discrimination rate of 95.97%. The analysis of molecular variance revealed that genetic variation within the individuals accounted for 84% of the total variation. This study establishes a rapid and efficient SSR-based method by leveraging resequencing data for large-scale marker discovery in A. sinensis. It further provides a robust technical framework for the conservation and sustainable utilization of this valuable species.