基于SNP分子标记的极小种群植物荔波杜鹃保护遗传学

doi:10.17521/cjpe.2025.0008

摘要/Abstract

摘要： 荔波杜鹃(Rhododendron liboense)是分布于喀斯特石灰岩山顶的极小种群植物, 具有较高的观赏和科学研究价值, 其生境脆弱且野生种群稀少, 亟待开展保护遗传学研究。该研究以荔波杜鹃3个种群的43株个体为对象, 采用简化基因组测序技术(ddRAD-seq)获得单核苷酸多态性(SNP)数据, 分析荔波杜鹃种群的遗传多样性和遗传结构, 并推断种群历史动态。结果表明: 荔波杜鹃的遗传多样性相对较低(期望杂合度(H_e) = 0.139 62 ± 0.003 32, 核苷酸多样性(π) = 0.157 64 ± 0.003 83), 种群间遗传分化水平中等(遗传分化系数(F_ST) = 0.075 8), 种群内变异(88.22%)大于种群间变异(11.78%)。Structure分析、主成分分析和聚类分析将荔波杜鹃的3个种群划分为2个遗传分组。种群历史动态分析表明, 荔波杜鹃的有效种群大小从末次冰消期后开始持续上升, 可能与气候逐步变得温暖适宜其生存有关。基于上述研究结果和种群现状, 建议将荔波杜鹃划分两个管理单元进行就地保护, 同时加强人工繁育技术研究, 辅助荔波杜鹃迁地保护和野外回归。

关键词: 荔波杜鹃, 极小种群植物, 遗传多样性, 遗传结构, 种群历史动态

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

黄承玲, 黎荣瀚, 覃红玲, 杨胜雄, 田晓玲, 夏国威, 陈正仁, 周玮. 基于SNP分子标记的极小种群植物荔波杜鹃保护遗传学. 植物生态学报, 2025, 49(10): 1677-1684. DOI: 10.17521/cjpe.2025.0008

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. Chinese Journal of Plant Ecology, 2025, 49(10): 1677-1684. DOI: 10.17521/cjpe.2025.0008

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链接本文: https://www.plant-ecology.com/CN/10.17521/cjpe.2025.0008

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

图/表 9

表1 荔波杜鹃采样信息

Table 1 Information on the sampling of Rhododendron liboense

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

表2 荔波杜鹃种群遗传多样性参数(平均值±标准差)

Table 2 Genetic diversity parameters of Rhododendron liboense populations (mean ± SD)

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

表3 荔波杜鹃种群的分子方差分析(AMOVA)

Table 3 Analysis of molecular variance (AMOVA ) of Rhododendron liboense populations

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

表4 荔波杜鹃群体遗传分化系数(FST)与地理距离

Table 4 Genetic differentiation coefficient (FST) values and geographic distances among Rhododendron liboense populations

种群 Population	DB	DT	XZ
DB		0.0894	0.0524
DT	16.38		0.0857
XZ	5.24	12.73

图1 荔波杜鹃种群遗传差异程度(ΔK)随分组数(K)变化的趋势。

Fig. 1 Trend of genetic differentiation (ΔK) with number of groups (K) of Rhododendron liboense populations.

图2 当分组数(K)为2时荔波杜鹃的Structure图。种群同表1。

Fig. 2 Structure plot of Rhododendron liboense with number of groups (K) is 2. Population see Table 1.

图3 荔波杜鹃参试个体的主成分(PC)分析。种群同表1。

Fig. 3 Principal component (PC) analysis of Rhododendron liboense individuals. Population see Table 1.

图4 荔波杜鹃参试个体聚类图。种群同表1。

Fig. 4 Cluster diagram of individual participants about Rhododendron liboense. Population see Table 1.

图5 荔波杜鹃种群动态历史分析。浅色和深色阴影分别表示95%和75%置信区间。

Fig. 5 Demographic history of Rhododendron liboense lineages. The light and dark shaded areas represent the 95% and 75% confidence intervals, respectively.

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