# Genetic Diversity and Population Structure of Shanlan Upland Rice Germplasm Based on SSR Markers

## TL;DR

This study explores the genetic diversity and population structure of Shanlan upland rice using SSR markers to guide conservation and utilization.

## Contribution

The study identifies genetic diversity patterns and population structure in Shanlan upland rice from southern China using SSR markers.

## Key findings

- Shanlan upland rice shows moderate genetic diversity with PIC values of 0.74.
- Genetic variation primarily occurs within individual plants rather than between regions.
- Five subgroups were identified, with Qiongzhong rice in Hainan showing central genetic diversity.

## Abstract

Shanlan upland rice is a unique rice resource of the Li and Miao ethnic group in China and serves as a valuable gene pool adapted to tropical mountainous environments. To explore the genetic relationships of Shanlan upland rice from different geographical origins, 21 SSR markers were used to conduct genetic diversity and population structure analyses on 288 Shanlan upland rice accessions from 10 provinces (regions) in southern China. Results: The study revealed that the mean values of effective allele number (Ne), Shannon’s information index (I), polymorphic information content (PIC), observed heterozygosity (Ho), and expected heterozygosity (He) for Shanlan upland rice were 1.616, 0.491, 0.74, 0.129, and 0.306, respectively. Genetic diversity analysis and molecular variance analysis (AMOVA) showed that the main source of variation between materials was the individual Shanlan upland rice plants. Genetic distance and differentiation results revealed the phylogenetic relationships among Shanlan upland rice populations. Both clustering and population structure analyses divided the materials into five subgroups, suggesting that the Shanlan upland rice from Qiongzhong, Hainan, might be the center of genetic diversity for the Hainan Shanlan upland rice, while rice from Dongfang, Hainan, and the inland populations exhibit genetic isolation. This study provides foundational data for the prioritized conservation and innovative utilization of Shanlan upland rice germplasm resources.