Analysis on Genetic Diversity of Cynomorium songaricum by ITS Sequence

doi:10.11983/CBB17193

Abstract

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

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

Figures/Tables 8

References 35

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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

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

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

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

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