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Spatial genetic structure characteristics of natural populations of Glycine tomentella in two representative habitats in the southeast coast, China—a study of intrapopulation sampling strategy

WANG Hao-Chen1,2,WANG Ke-Jing1,HAN Juan2,*,LI Xiang-Hua1,*#br#

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  1. 1 Resource Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; 2 College of Agriculture, Northwest Agriculture & Forestry University, Yangling 712100, Shaanxi, China
  • Received:2025-03-21 Revised:2025-08-13 Accepted:2025-08-13 Published:2025-08-21
  • Supported by:
    This study was supported by the National Key Research and Development Program of China (2021YFD1200103).

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Abstract: Glycine tomentella is an important genetic resource in China, classified as a nationally protected plant (second-class), and holds significant potential for use in cultivated soybean breeding. Due to its self-pollinating nature and environmental heterogeneity, gene flow is limited, and individuals within G. tomentella populations often exhibit spatial genetic patchiness. To investigate the genetic structure of two primary habitat types in China—highly human-disturbed populations (cemetery natural populations) and minimally disturbed populations (flatland natural populations)—and to provide a theoretical basis for developing sampling strategies that preserve high levels of genetic diversity, this study employed 24 newly developed species-specific SSR markers to analyze genetic diversity and spatial genetic structure in two natural populations subject to different degrees of disturbance. The results showed that: (1) the average genetic diversity of the highly disturbed cemetery population (B) was not lower than that of the less disturbed natural population (A); (2) spatial autocorrelation analysis revealed that individuals in both populations exhibited genetic patch structures, with differing patch sizes: population A showed significant kinship within 17.44 m, while population B showed significant kinship within 14.59 m; (3) spatial autocorrelation and Mantel tests indicated that in highly disturbed populations, genetic relatedness between individuals declined with spatial distance, and the range of significant autocorrelation was reduced; (4) Python-based sampling simulations showed that to reach 95% of the total population values for Nei’s gene diversity index, Shannon’s information index and effective number of alleles at least 20, 30 and 30 individuals needed to be sampled in population A, and 20, 35, and 50 individuals in population B, respectively. Based on these findings, it is recommended that for routine germplasm collection of G. tomentella, a minimum of 30 individuals should be sampled, with an inter-plant spacing of 15–18 m.

Key words: sampling strategy, genetic structure, genetic diversity, SSR markers, Glycine tomentella

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