锁阳ITS序列遗传多样性分析

doi:10.11983/CBB17193

摘要/Abstract

摘要：

为阐明锁阳(Cynomorium songaricum)的遗传结构与遗传多样性, 以甘肃省河西走廊地区及青海省共18个居群的188个锁阳个体为研究对象, 利用现代分子生物学技术, 采用序列分析方法从核-质基因方面对遗传结构进行了分析。结果显示, 锁阳ITS序列总长度为687 bp, 含有7个变异位点, 定义9个单倍型, 整体单倍型多态性H_d=0.294 20, 核苷酸多样性π=0.000 49。在整个单倍型网络中介图中, 单倍型H1位于中心位置, 并在所有的居群中均有分布, 为核心的古老单倍型。分子方差分析结果显示, 锁阳种群变异主要来源于种群内。根据ITS序列得到的群体间遗传分化系数以及Mantel检验结果, 锁阳种群间的遗传距离与地理距离之间不存在相关性, 表明现存的锁阳居群是相对近期发生生境片段化的产物。中性检验结果表明, 锁阳拒绝中性进化, 群体历经扩张或者基因座位受到负选择作用, 其中性零假说不能被排除。该研究为锁阳的系统分类、资源鉴定以及保护措施的制定提供了分子证据。

关键词: 锁阳, ITS, 遗传多样性, 中性假说

Abstract:

To elucidate the genetic structure and genetic diversity of Cynomorium songaricum, modern molecular biology techniques at the DNA level were used to study the genetic structure of 188 C. songaricum individuals from 18 wild populations in the Hexi Corridor Region of Gansu and Qinghai. After alignment, all amplified sequence lengths were 687 bp. The 687 bp ITS sequence detected 7 mutation sites in 188 individuals, defining 9 haplotypes. Processing these 9 haplotype sequences led to a data matrix for calculating the haplotype diversity (H_d=0.294 20) and nucleotide diversity (π=0.000 49). In the haplotype network map, H1 is located in the center and distributed in all populations, and is the ancient and core haplotype. AMOVA revealed that the variation in C. songaricum mainly occurs in populations. According to the genetic differentiation coefficient and Mantel test of ITS sequences, we found no significant relation between genetic and geographic distances, so the current distribution of C. songaricum represents the fragmentation product in recent time. Detection of historical expansion of populations showed that the Tajima’s D test rejected a neutral mutation evolution, and the population expansion history or gene locus is under negative selection pressure, so the null hypothesis cannot be ruled out. Our study provides molecular evidence for the classification system, identification and protection measures of C. songaricum.

Key words: Cynomorium songaricum, ITS, genetic diversity, neutral hypothesis

任梦云, 杜乐山, 陈彦君, 张盾, 沈奇, 关潇, 张银东. 锁阳ITS序列遗传多样性分析. 植物学报, 2018, 53(3): 313-321.

Ren Mengyun, Du Leshan, Chen Yanjun, Zhang Dun, Shen Qi, Guan Xiao, Zhang Yindong. Analysis on Genetic Diversity of Cynomorium songaricum by ITS Sequence. Chinese Bulletin of Botany, 2018, 53(3): 313-321.

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链接本文: https://www.chinbullbotany.com/CN/10.11983/CBB17193

https://www.chinbullbotany.com/CN/Y2018/V53/I3/313

图/表 8

表1 18个锁阳居群样地分布信息

Table 1 Location of 18 populations of Cynomorium songaricum

Sample No.	Location	Longitude E (°)	Latitude N (°)	Height (m)	Number
R1	Zhangye, Gansu	102.522	36.822	1803	11
R2	Minqin, Gansu	100.772	39.223	1370	17
R3	Jinchang, Gansu	102.54	38.44	1466	7
R4	Sandan, Gansu	101.118	38.897	2020	10
R5	Gaotai, Gansu	99.086	39.787	1339	11
R6	Sunan, Gansu	99.176	39.604	1395	10
R7	Sunan, Gansu	99.474	39.445	1391	12
R8	Jiuquan, Gansu	98.55	40.3	1232	4
R9	Yumen, Gansu	97.196	40.516	1395	10
R10	Guazhou, Gansu	95.585	40.212	1343	11
R11	Dunhuang, Gansu	94.583	40.368	1033	11
R12	Subei, Gansu	96.619	39.397	2355	10
R13	Delingha, Qinghai	97.334	37.206	2780	11
R14	Geermu, Qinghai	92.839	36.701	2790	7
R15	Dulan, Qinghai	98.164	36.476	2972	12
R16	Wulan, Qinghai	98.622	36.458	2917	12
R17	Gonghe, Qinghai	100.183	36.446	2904	11
R18	Guide, Qinghai	101.639	36.219	2389	11

表2 锁阳核糖体ITS序列的单倍型多态性位点

Table 2 Variable sites of ITS sequence haplotypes of Cynomorium songaricum

Haplotype	Variable sites							Abundance
Haplotype	63	86	197	274	421	605	623	Abundance
H1	G	G	G	T	G	C	G	143
H2	A	G	G	T	G	C	T	3
H3	G	A	G	T	G	C	G	1
H4	G	A	G	T	G	G	G	2
H5	A	G	G	T	G	C	G	26
H6	G	G	A	T	G	C	G	5
H7	G	G	A	G	G	C	G	1
H8	G	G	G	T	G	G	G	4
H9	G	G	G	T	A	C	G	3

表3 锁阳18个居群的单倍型遗传多样性组成

Table 3 Haplotype diversity and composition of Cynomorium songaricum from18 populations

Population code	Samples	Haptotypes	H_d
R1	11	H1, H2, H3, H4	0.25974
R2	17	H1, H5, H6	0.11586
R3	7	H1, H5	0.43956
R4	10	H1, H2, H5	0.42632
R5	11	H1, H6	0.24675
R6	10	H1, H7, H8	0.19474
R7	12	H1, H5	0.08333
R8	4	H1, H5, H9	0.60714
R9	10	H1, H8	0.10000
R10	11	H1, H5, H8	0.17749
R11	11	H1, H4, H6	0.17749
R12	10	H1	0
R13	11	H1	0
R14	7	H1, H6	0.14286
R15	12	H1, H9	0.08333
R16	12	H1, H9	0.08333
R17	11	H1, H8	0.09091
R18	11	H1	0
Total	188		0.29420

图1 基于锁阳ITS序列的严格一致性树步长=784, CI=0.949 0, RI=0.911 7, RCI=0.865 2。分支上的数字分别代表MP/ML/BI的支持率。

Figure 1 Strict consensus tree based on the ITS sequence of Cynomorium songaricumLength=784, CI=0.949 0, RI=0.911 7, RCI=0.865 2. The num- bers on the branch represent the support rate of MP/ML/BI, respectively.

图2 锁阳18个居群基于ITS序列的单倍型网络图圆圈的大小与单倍型的相对频率成正比; 不同颜色代表锁阳属不同种群。

Figure 2 Haplotype network based on ITS sequence of Cynomorium songaricum from 18 populationsThe size of circles are proportional to the relative frequency of the haplotype; Different colors represent different populations of Cynomorium songaricum.

表4 锁阳种群遗传结构参数

Table 4 Genetic structural parameters of Cynomorium songaricum

Sequence	H_S(SE)	H_T(SE)	G_ST(SE)	N_ST(SE)
ITS	0.179 (0.0390)	0.277 (0.0820)	0.353 (0.1914)	0.408 (0.2038)

表5 锁阳核糖体基因单倍型分子方差分析

Table 5 Analysis of molecular variance for ribosome haplotypes of Cynomorium songaricum

Source of variation	df	Sum of squares	Variance components	Percentage	F_ST	P
Among populations	17	28.833	0.07689 Va	44.57	0.44566	<0.001*
Within populations	358	34.239	0.09564 Vb	55.43	0.44566	<0.001*
Total	375	63.072	0.17253

图3 基于ITS序列的锁阳种群失配分析柱形代表变异位点在群体扩张模型下的预期分布; 虚线代表变异位点的实际分布。

Figure 3 Mismatch distribution analysis for the populations of Cynomorium songaricum based on ITS sequenceCylindricality represents the expected distribution of variation sites under the population expansion model; dotted line represents the actual distribution of variation sites.

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