柴达木野生黑果枸杞的空间遗传结构

doi:10.17521/cjpe.2019.0298

摘要/Abstract

摘要：

基于cpDNA序列, 研究柴达木野生黑果枸杞(Lycium ruthenicum)的遗传多样性、遗传结构和单倍型进化关系, 可为其种群的遗传保护提供理论依据。该研究基于3个筛选的叶绿体多态引物: psbA-trnH、psbK-psbI和trnV, 利用群体遗传分析方法研究柴达木盆地野生黑果枸杞的遗传变异格局: 利用软件DnaSP 6.0和Permut 2.0计算分子多样性指标, 利用分子方差分析研究组间和种群间的遗传变异来源, 利用单倍型网络分析和主坐标分析研究单倍型的聚类关系; 利用最大似然树和贝叶斯系统树分析单倍型的谱系进化关系。结果显示: 叶绿体序列psbA-trnH、psbK-psbI和trnV拼接后的总长度为1 454 bp, 鉴别出14个核苷酸变异位点, 共定义了7个单倍型。种群间总的遗传多样(h_T)和种群内遗传多样性(h_S)分别为0.916和0.512。AMOVA分析结果表明, 80%以上的遗传变异来源于组间和种群间。叶绿体单倍型的贝叶斯系统树和最大似然树均表明柴达木盆地黑果枸杞种群聚为2支: 德令哈和格尔木为一支, 诺木洪为另一支。单倍型网络和主坐标分析结果揭示的拓扑结构和聚类关系与系统树一致。Mantel检验结果表明柴达木黑果枸杞种群间的遗传距离与地理距离存在显著的弱相关关系(r = 0.591 1, p = 0.000 9)。柴达木盆地黑果枸杞种群具有较高的遗传多样性, 种群间遗传分化显著。从遗传多样性保护的角度而言, 具有较高遗传多样性的诺木洪林业站和格尔木新乐村种群可划分为保护管理单元。

关键词: 黑果枸杞, 柴达木盆地, 叶绿体片段, 遗传变异, 遗传结构

Abstract:

Aims Based on the cpDNA sequences, we studied the genetic diversity, genetic structure and haplotype evolution of wild Lycium ruthenicum in the Qaidam Basin and provided the scientific basis for the genetic conservation of this species.
Methods We used three filtered high polymorphic cpDNA fragments (psbA-trnH, psbK-psbI and trnV) to study the genetic variation pattern of L. ruthenicum in the Qaidam Basin by employing the population genetic analysis methods. The molecular diversity indices were calculated by using the software of DnaSP 6.0 and Permut 2.0. Genetic differentiation among populations and the defined groups was estimated by the AMOVA analysis. The median-joining network and principal coordinate analysis (PCoA) were used to identify the clustering relationship of haplotype. The maximum likelihood method and Bayesian method were used to reconstruct the phylogenetic tree based on cpDNA haplotypes.
Important findings The combined length of psbA-trnH, psbK-psbI and trnV was 1 454 bp. 14 polymorphic sites were detected, and a total of seven haplotypes were identified. The total genetic diversity (h_T) and within-population genetic diversity (h_S) were 0.916 and 0.512, respectively. Results from AMOVA suggested that more than 80% of the observed variation was due to differences among groups and populations. The maximum likelihood analysis and Beast analysis revealed that seven haplotypes clustered into two clusters, corresponding to Golmud and Delingha regions and Nuomuhong region, respectively. The revealed topological structure and clusters of haplotype network and PCoA analyses were consistent with the phylogenetic trees. Results of the Mantel test (r = 0.591 1, p = 0.000 9) indicated a non-significant correlation between geographical distance and genetic distance. The L. ruthenicum populations in the Qaidam Basin have high levels of genetic diversity and significant genetic differentiation among populations. In relation to conservation management, we identified the Nuomuhong forestry station and Xinle Village of Golmud City as having a high degree of genetic diversity and these should be the areas of the greatest focus for conservation.

Key words: Lycium ruthenicum, Qaidam Basin, chloroplast fragments, genetic variation, genetic structure

王春成, 马松梅, 张丹, 王绍明. 柴达木野生黑果枸杞的空间遗传结构. 植物生态学报, 2020, 44(6): 661-668. DOI: 10.17521/cjpe.2019.0298

WANG Chun-Cheng, MA Song-Mei, ZHANG Dan, WANG Shao-Ming. Spatial genetic structure of Lycium ruthenicum in the Qaidam Basin. Chinese Journal of Plant Ecology, 2020, 44(6): 661-668. DOI: 10.17521/cjpe.2019.0298

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链接本文: https://www.plant-ecology.com/CN/10.17521/cjpe.2019.0298

https://www.plant-ecology.com/CN/Y2020/V44/I6/661

图/表 6

表1 柴达木盆地黑果枸杞自然种群的采样信息及遗传信息

Table 1 Sampling information and genetic information of natural populations of Lycium ruthenicum in the Qaidam Basin

种群名称及编码 Population name and code	海拔 Altitude (m)	经纬度 Latitude and Longitude	采样数 Sample size	单倍型及个体数 Haplotype and the individual numbers	单倍型多样性 Haplotype diversity (H_d ± SD)	核苷酸多样性 Nucleotide diversity (π ± SD)
德令哈市红光村 Hongguang Village of Delingha City (DLH)	2 970	37.38° N, 97.34° E	10	H1 (2), H4 (8)	0.356 ± 0.025	0.000 73 ± 0.33
都兰县诺木洪林业站 Nuomuhong Forestry Station of Dulan County (NMH1)	2 820	36.41° N, 96.45° E	15	H5 (7), H6 (6), H7 (2)	0.604 ± 0.069	0.000 46 ± 0.09
都兰县诺木洪乡田格力村 Tiangeli Village of Nuomuhong Township of Dulan County (NMH2)	2 762	36.39° N, 96.19° E	12	H5 (5), H7 (7)	0.530 ± 0.053	0.000 37 ± 0.05
格尔木市新乐村 Xinle Village of Golmud City (GEM1)	2 787	36.39° N, 94.86° E	12	H1 (7), H2 (4), H3 (1)	0.591 ± 0.011	0.001 26 ± 0.03
格尔木市大格勒乡 Dagele Township of Golmud City (GEM2)	2 837	36.44° N, 95.75° E	11	H1 (3), H2 (8)	0.436 ± 0.018	0.000 09 ± 0.03

表2 柴达木盆地黑果枸杞7个叶绿体单倍型及其变异位点

Table 2 Variable nucleotide sites of seven chloroplast haplotypes of Lycium ruthenicum in the Qaidam Basin

单倍型 Haplotype	变异位点 Variable nucleotide sites
	psbA-trnH										psbK-psbI		trnV
	1	10	217	318	319	333	365	371	421	426	528	595	1039	1208
H1	A	C	C	G	G	T	-	G	G	G	-	T	T	G
H2	●	●	●	●	●	●	-	●	●	C	A	●	C	●
H3	●	-	A	●	●	●	-	●	●	●	-	●	C	●
H4	●	●	●	●	●	A	C	●	A	●	-	●	●	●
H5	-	●	●	C	C	●	-	C	A	●	A	C	●	●
H6	-	●	●	C	C	●	-	C	A	●	A	C	●	T
H7	-	●	●	C	C	●	-	C	A	●	A	C	C	●

图1 柴达木盆地黑果枸杞7个叶绿体单倍型(H1-H7)的地理分布及其单倍型网络。图中居群编码与表1一致, 饼图表示各居群的单倍型频率。 A, 单倍型网络, 图中圆圈大小与单倍型频率成正比, 节点间的分支长度大致与单倍型的突变数成正比, 相应分支附近附有步长; 龙葵作为外类群。

Fig. 1 Geographical distribution and the haplotype network of seven chloroplast haplotypes (H1-H7) of Lycium ruthenicum in the Qaidam Basin. The population codes in this figure are consistent with Table 1. Pie graphs indicate the frequency of each haplotype at these locations. A, In the median-joining haplotypes network, the sizes of the circles in the network are proportional to the haplotype frequencies. Branch lengths are roughly proportional to the number of mutation steps between haplotypes and nodes. The true number of steps is shown near the corresponding branch sections. Solanum nigrum was used as outgroup.

表3 柴达木盆地黑果枸杞种群的分子方差分析(AMOVA)

Table 3 Analysis of molecular variance (AMOVA) of Lycium ruthenicum in the Qaidam Basin

变异来源 Source of variation	自由度 df	平方和 Sum of squares	变异组成 Variance components	变异所占比例 Percentage of variation (%)	固定指数 Fixation index
种群间 Among populations	4	105.305	2.159 37	80.01	F_ST = 0.800 07
种群内 Within populations	55	29.679	0.539 61	19.99
总变异 Total	59	135.953	2.698 99
组间 Among groups	1	100.383	3.254 96	82.04	F_CT = 0.820 43
组内种群间 Among populations within groups	3	6.917	0.145 46	3.67	F_SC = 0.204 18
种群内 Within populations	56	28.408	0.566 95	14.29	F_ST = 0.857 10
总变异 Total	60	135.003	3.967 37

图2 柴达木盆地黑果枸杞基于种群水平的前三个坐标的主坐标分析(PCoA)。

Fig. 2 Plots of the first three coordinates of the principal coordinates analysis (PCoA) at the population level for Lycium ruthenicum in the Qaidam Basin.

图3 柴达木盆地黑果枸杞叶绿体单倍型的系统发育树。 A, 最大似然(ML)树, 分支点上方的数字为大于等于80的自展支持率。B, 贝叶斯树, 分支节点右侧的数字表示所有大于0.80的后验概率值。两系统发育树右侧的黑条表示相应的分支。

Fig. 3 Phylogenetic trees of chloroplast haplotypes of Lycium ruthenicum in the Qaidam Basin. A, Maximum likelihood (ML) tree. Bootstrap values equal to or greater than 80 are shown above the corresponding branching points. B, Bayesian tree. The values on the right of the branching points represent the posterior probability greater than 0.80. The black bars on the right of the two phylogenetic trees indicate the corresponding clades.

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