Chin J Plan Ecolo ›› 2015, Vol. 39 ›› Issue (10): 1003-1011.doi: 10.17521/cjpe.2015.0097

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Population genetic diversity of wild Lycium ruthenicum in Qaidam inferred from AFLP markers

WANG Jin-Nan1,*, CHEN Jin-Fu2,*, Chen Wu-Sheng1, Zhou Xin-Yang3, XU Dong1, LI Ji-Hong1,**(), QI Xiao1   

  1. 1Key Laboratory of Agricultural Ecology and Environment, College of Forestry, Shandong Agricultural University, Tai’an, Shandong 271018, China
    2Forestry Research Institute of Qinghai Province, Xining 810016, China
    3School of Pharmaceutical Sciences, Shandong University , Jinan 250012, China
  • Online:2015-10-24 Published:2015-10-01
  • Contact: Jin-Nan WANG,Jin-Fu CHEN,Ji-Hong LI E-mail:jhli@sdau.edu.cn
  • About author:

    # Co-first authors

Abstract: <i>Aims</i>

Lycium ruthenicum is a perennial shrub plant. It grows among rocks in deserts, and its populations are spatially scattered in the distribution range. The objectives of this study were investigating the population genetic diversity and genetic structure of L. ruthenicum in Qaidam and determining relationships between genetic diversity and environmental factors.

<i>Methods</i>

We analyzed the genetic diversity of 120 individuals from 5 natural populations using amplified fragment length polymorphism (AFLP) markers.

<i>Important findings</i>

We obtained 1691 unambiguous bands from the nine pairs of selected primers, 1678 bands (99.23%) of which were polymorphic across all individuals. At the species level, the Nei’s gene diversity was 0.3649, and the Shannon’s information index was 0.5422. Analysis of molecular variance (AMOVA) analysis indicated that most variations (92.0%) existed within populations, with only a small proportion of total variations residing among populations (8.0%, genetic differentiation coefficient is 0.08). The genetic similarity among the populations ranged from 0.9709 to 0.9922 with an average of 0.9835. Results of the Mantel test (γ = 0.3368, p = 0.8064) and unweighted pair group method with arithmetic mean (UPGMA) cluster of the Qaidam populations indicated that the correlation between geographical distance and genetic distance was not significant. Principal coordinate analysis of all sampled individuals showed that individuals from each population did not cluster together. The genetic diversity of the same population indicated that the L. ruthenicum of Nomhon had high level of genetic variations, which indicated Nomhon is the center of the Qaidam wild L. ruthenicum populations.

Key words: Lycium ruthenicum, Qaidam, genetic diversity, AFLP

Table 1

Habitats and localities of the sampled Lycium ruthenicum populations"

种群
Population
海拔
Altitude (m)
纬度
Latitude (N)
经度
Longitude (E)
样品数
Sampling size
德令哈怀头他拉 Huaitoutala, Delingha (DLH1) 2 810 37.25° 96.83° 24
诺木洪贝壳梁 Beikeliang, Nomhon (NMH1) 2 703 36.50° 96.22° 24
诺木洪奥斯勒草场 Osler grassland, Nomhon (NMH2) 2 770 36.45° 96.45° 24
格尔木乌图美仁 Urt Moron, Glomud (GEM1) 2 890 36.88° 93.12° 24
格尔木鱼水河 River water, Glomud (GEM2) 2 750 36.48° 94.95° 24

Table 2

Polymorphism of AFLP bands obtained by selective amplification based on the primer combinations"

引物组合
Primer combination
总带数
Total No. of
bands
多态带数
No. of polymorphic
bands
多态带比例
Percentage of polymorphic bands (%)
E-AAG/M-CAC 182 182 100.00
E-AAG/M-CAG 192 189 98.43
E-ACA/M-CAA 190 189 99.47
E-ACA/M-CAC 180 180 100.00
E-ACT/M-CTT 205 201 98.05
E-AGG/M-CAA 193 193 100.00
E-AGG/M-CAC 177 177 100.00
E-AGG/M-CAG 184 182 98.91
E-AGG/M-CTG 188 185 98.40
合计 Summation 1 691 1 678
平均 Mean 211.40 209.75 99.23

Table 3

Genetic diversity level of Lycium ruthenicum based on different primer combinations"

引物组合
Primer combination
有效等位
基因数
Ne
Nei’s基因
多样性指数
H
Shannon多态性
信息指数
I
E-AAG/M-CAC 1.500 1 0.337 9 0.453 5
E-AAG/M-CAG 1.456 4 0.318 6 0.430 2
E-ACA/M-CAA 1.473 2 0.322 5 0.431 3
E-ACA/M-CAC 1.494 9 0.335 0 0.450 0
E-ACT/M-CTT 1.432 9 0.302 2 0.406 1
E-AGG/M-CAA 1.491 9 0.336 7 0.453 6
E-AGG/M-CAC 1.501 4 0.342 4 0.461 9
E-AGG/M-CAG 1.445 2 0.311 2 0.419 9
E-AGG/M-CTG 1.444 5 0.314 2 0.424 2
平均 Mean 1.471 2 0.324 5 0.436 7

Table 4

Genetic diversity of the five Lycium ruthenicum populations"

种群
Population
有效等位
基因数
Ne
Nei’s基因
多样性指数
H
Shannon多态性
信息指数
I
DLH1 1.343 4b 0.216 9b 0.349 6b
NMH1 1.366 2ab 0.225 9ab 0.359 5a
NMH2 1.373 4a 0.231 1a 0.366 1a
GEM1 1.347 5b 0.222 8b 0.357 5b
GEM2 1.351 0b 0.224 8b 0.349 2b

Table 5

Genetic divergence of Lycium ruthenicum populations in Qaidam area"

变异来源
Source of variation
自由度
dt
基因多样性指数
Gene diversity index
占总变异百分率(%)
Percentage of total variation
p
种群间 Among populations 9 0.075 6 8 <0.001
种群内 Within populations 70 0.164 3 92 <0.001

Table 6

genetic identity and genetic distance between five Lycium ruthenicum populations based on AFLP"

种群
Population
DLH1 NMH1 NMH2 GEM1 GEM2
DLH1 0.986 3 0.977 2 0.970 9 0.971 0
NMH1 0.013 9 0.992 2 0.986 4 0.986 1
NMH2 0.023 1 0.007 8 0.989 8 0.984 7
GEM1 0.029 5 0.014 4 0.009 7 0.990 2
GEM2 0.029 7 0.014 5 0.015 5 0.009 5

Fig. 1

Correlation between geographical distance and genetic distance revealed by Mantel test. DLH1, NMH1, NMH2, GEM1, GEM2, see Table 1."

Fig. 2

Dendrogram of UPGMA analysis of the five populations of Lycium ruthenicum based on AFLP makers."

Fig. 3

Coordinate analysis of the 120 samples of Lycium ruthenicum based on AFLP markers."

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