Chin Bull Bot ›› 2018, Vol. 53 ›› Issue (3): 313-321.doi: 10.11983/CBB17193

Special Issue: Medicinal Plant

• EXPERIMENTAL COMMUNICATIONS • Previous Articles     Next Articles

Analysis on Genetic Diversity of Cynomorium songaricum by ITS Sequence

Ren Mengyun1,2, Du Leshan1, Chen Yanjun1,2, Zhang Dun2, Shen Qi2, Guan Xiao1,*(), Zhang Yindong2,*()   

  1. 1Chinese Research Academy of Environmental Sciences, Beijing 100012, China
    2College of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
  • Received:2017-10-18 Accepted:2018-04-30 Online:2018-09-11 Published:2018-05-01
  • Contact: Guan Xiao,Zhang Yindong E-mail:cynthia815@126.com;23300558@163.com

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 (Hd=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

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

Table 2

Variable sites of ITS sequence haplotypes of Cynomorium songaricum"

Haplotype Variable sites Abundance
63 86 197 274 421 605 623
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

Table 3

Haplotype diversity and composition of Cynomorium songaricum from18 populations"

Population code Samples Haptotypes Hd
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

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."

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."

Table 4

Genetic structural parameters of Cynomorium songaricum"

Sequence HS (SE) HT (SE) GST (SE) NST (SE)
ITS 0.179 (0.0390) 0.277 (0.0820) 0.353 (0.1914) 0.408 (0.2038)

Table 5

Analysis of molecular variance for ribosome haplotypes of Cynomorium songaricum"

Source of variation df Sum of squares Variance components Percentage FST 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
Total 375 63.072 0.17253

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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