Conservation genetics of Rhododendron liboense based on SNP molecular markers, a plant species with extremely small populations

doi:10.17521/cjpe.2025.0008

Abstract

Abstract:

Aims Rhododendron liboense, a rare plant species endemic to limestone mountains, currently persists in extremely small populations. Despite possessing significant ornamental and scientific value, this species faces critical conservation challenges from its fragile habitat and severely limited wild populations, creating an urgent imperative for comprehensive genetic studies to inform conservation strategies.
Methods This study employed double-digest restriction-site associated DNA sequencing (ddRAD-seq) to obtain single-nucleotide polymorphisms (SNP) in 43 individuals from three distinct populations. Genetic diversity, population structure, and historical population dynamics were subsequently analyzed.
Important findings The study revealed relatively low genetic diversity in R. liboense (expected heterozygosity (H_e) = 0.139 62 ± 0.003 32, nucleotide diversity (π) = 0.157 64 ± 0.003 83) with moderate genetic differentiation between populations (genetic differentiation coefficient (F_ST) = 0.075 8). Analysis indicated that within-population variation (88.22%) exceeded between-population variation (11.78%). Structure analysis, principal component analysis, and cluster analysis classified the three populations into two distinct genetic groups. Historical population dynamics analysis demonstrated a continuous increase in effective population size since the last glacial period, likely influenced by gradual climate warming conducive to species survival. Based on these findings and the population status, we recommend establishing two management units for in situ conservation and enhancing research on artificial breeding techniques to support ex situ conservation and reintroduction efforts for R. liboense.

Key words: Rhododendron liboense, plant species with extremely small populations, genetic diversity, genetic structure, historical population dynamics

HUANG Cheng-Ling, LI Rong-Han, QIN Hong-Ling, YANG Sheng-Xiong, TIAN Xiao-Ling, XIA Guo-Wei, CHEN Zheng-Ren, ZHOU Wei. Conservation genetics of Rhododendron liboense based on SNP molecular markers, a plant species with extremely small populations[J]. Chin J Plant Ecol, 2025, 49(10): 1677-1684.

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https://www.plant-ecology.com/EN/Y2025/V49/I10/1677

Figures/Tables 9

References 40

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采样地点 Sampling location	种群 Population	采样数 Number of samples	经度 Longitude	纬度 Latitude	海拔 Altitude (m)	是否在保护区内 Located within the Maolan Natural Reserv (Y/N)
洞泊 Dongbo	DB	19	107.98° E	25.37° N	890	N
洞塘 Dongtang	DT	19	107.88° E	25.25° N	650	Y
西竹 Xizhu	XZ	5	107.95° E	25.33° N	900	N

采样地点 Sampling location	种群 Population	采样数 Number of samples	经度 Longitude	纬度 Latitude	海拔 Altitude (m)	是否在保护区内 Located within the Maolan Natural Reserv (Y/N)
洞泊 Dongbo	DB	19	107.98° E	25.37° N	890	N
洞塘 Dongtang	DT	19	107.88° E	25.25° N	650	Y
西竹 Xizhu	XZ	5	107.95° E	25.33° N	900	N

种群 Population	特有等位基因 Private allele	期望杂合度 H_e	核苷酸多样性 π	近交系数 F_IS
DB	1 076	0.149 24 ± 0.002 96	0.162 41 ± 0.005 17	0.138 26 ± 0.012 71
DT	1 010	0.143 97 ± 0.003 01	0.158 15 ± 0.003 14	0.307 79 ± 0.038 75
XZ	357	0.125 67 ± 0.003 98	0.152 35 ± 0.003 19	0.341 78 ± 0.034 49
平均值 Average value	814	0.139 62 ± 0.003 32	0.157 64 ± 0.003 83	0.262 61 ± 0.028 65

种群 Population	特有等位基因 Private allele	期望杂合度 H_e	核苷酸多样性 π	近交系数 F_IS
DB	1 076	0.149 24 ± 0.002 96	0.162 41 ± 0.005 17	0.138 26 ± 0.012 71
DT	1 010	0.143 97 ± 0.003 01	0.158 15 ± 0.003 14	0.307 79 ± 0.038 75
XZ	357	0.125 67 ± 0.003 98	0.152 35 ± 0.003 19	0.341 78 ± 0.034 49
平均值 Average value	814	0.139 62 ± 0.003 32	0.157 64 ± 0.003 83	0.262 61 ± 0.028 65

变异来源 Source of variation	自由度 df	总方差 Sum of squares	变异组分 Variance components	变异比 Percentage variation (%)
种群间 Among populations	2	463.938	6.910 1	11.78
种群内 Within populations	81	4 169.336	51.726 3	88.22
共计 Total	83	4 633.274	58.636 4