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Evaluation of genetic diversity and population structure of five yellow catfish Pelteobagrus fulvidraco populations by microsatellite markers

Liqiang Zhong
Liqiang Zhong
, 
Minghua Wang
Minghua Wang
, 
Jianlin Pan
Jianlin Pan
, 
Daming Li
Daming Li
, 
Shengkai Tang
Shengkai Tang
, 
Wenji Bian
Wenji Bian
 and 
Xiaohui Chen
Xiaohui Chen
   | Jun 18, 2018
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Article Category: Original research paper
Published Online: Jun 18, 2018
Page range: 99 - 106
Received: Jun 05, 2017
Accepted: Oct 20, 2017
DOI: https://doi.org/10.1515/ohs-2018-0011
© 2018 Faculty of Oceanography and Geography, University of Gdańsk, Poland
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

Figure 1

Map of sampling locations (indicated by •) of yellow catfish from five lakes in the middle and lower reaches of the Yangtze River, China. The five sampling lakes were Taihu Lake (TH), Gehu Lake (GH), Hongzehu Lake (HZ), Chaohu Lake (CH), and Poyang Lake (PY)
Map of sampling locations (indicated by •) of yellow catfish from five lakes in the middle and lower reaches of the Yangtze River, China. The five sampling lakes were Taihu Lake (TH), Gehu Lake (GH), Hongzehu Lake (HZ), Chaohu Lake (CH), and Poyang Lake (PY)

Figure 2

UPGMA tree based on genetic distances between five yellow catfish populations
UPGMA tree based on genetic distances between five yellow catfish populations

Figure 3

Bayesian clustering analysis for five populations of yellow catfish. The bar plot represents admixture coefficients. Each vertical bar denotes one individual
Bayesian clustering analysis for five populations of yellow catfish. The bar plot represents admixture coefficients. Each vertical bar denotes one individual

Information of the thirteen microsatellite loci analyzed in five populations of yellow catfish

Locus Motif Primer sequence (5′–3′) Temp. (°C) Expected size (bp) Number of alleles Reference
AG12 (GA)6A(AG)26 F: TTCTGAGGGGATGGTG R: GCGGTGCTCTGTGGTTGTC 60 228–335 5 Wu et al. 2010
AG48 (AG)13GGT(GA)5GC(GA )9 F:GCTGATACATTCTTTATTAGGGCACC R: GTCGCACTTCCCCTCTGTCA 57 185–451 6
AG128 (AG)23 F: AAACCGACGGGACAAAAGAT R: CTCTGCCTCACTAACT 51 91–145 9
CT30 (CT)9T(TC)2TT(TC)21 F: ACACCAAAACATTGTGCTAC R: ATTCAGGAGATCCCGACACT 55 237–298 4
CT42 (TC)6 F: GCAGAGGGTTGCTTTTGCCTTTTA R: CAACAATCACATTCTATGAGGAGT 55 125–150 3
CT81 (CT)6G(TC)4TG( TC)8 F: GTCTCCATCACTGCCACAT R: TCAGCAATTATGTGAAAAGTGTCT 55 126–176 5
HLJYC13 (CA)23 F:GACCCAGTTCCCACATTG R:GGCTACCACATCCCTCAT 58 179–207 4 Li et al. 2009
HLJYC17 (TC)25 F:ATGGTATAAACATGGTGCTA R:ATGATGCTGATAGGGTGA 58 170–188 3
HLJYC31 (CA)26 F:CAGGATGGAGGTGTAAAG R:ATAAAGCTGTGATGTGCC 55 285–317 4
HLJYC45 (TG)29 F:TGGGTCTCTCTGGGTTCA R:GCGGCTTCACTCACTTCC 56 278–312 3
HLJYC60 (CA)28(TTTG)7 F:GATCAACGTCCAACAGAG R:GGAAAGAAAGATGGCTAG 56 250–282 4
HLJYC66 (TG)27 F:ACACTGACATACACTGGCATAA R:CTGGCAACGTGTTTCTGGCATAA 56 243–295 4
HSY105 (CTAT)14 F:ACTCACGTTGTCAGTTTATCAC R:ACACAAGAAATCCCCTCG 53 150–172 4 Liu et al. 2008

Polymorphic information at 13 microsatellite loci of five populations of yellow catfish

Locus CH GH HZ PY TH Overall
Ae HO HE PIC FIS Ae HO HE PIC FIS Ae HO HE PIC FIS Ae HO HE PIC FIS Ae HO HE PIC FIS Ae HO HE PIC FIS
AG 12 2.81 0.52 0.66 0.58 0.193 4.24 0.68 0.78 0.72 0.110 3.24 0.72 0.71 0.64 -0.041 4.50 0.68 0.79 0.74 0.126 3.98 0.68 0.76 0.71 0.092 4.07 0.66 0.76 0.68 0.096
AG48 4.39 0.60 0.79 0.74 0.223 4.05 0.68 0.77 0.71 0.097 4.18 0.92 0.78 0.72 -0.209 3.38 0.64 0.72 0.65 0.091 3.64 0.48 0.74 0.68 0.339 4.61 0.66 0.79 0.70 0.106
AG128 5.43 0.84 0.83 0.79 -0.029 7.10 0.84 0.88 0.84 0.022 6.10 0.56 0.85 0.82 0.330 5.00 0.84 0.82 0.77 -0.050 5.81 0.84 0.84 0.81 -0.015 6.48 0.78 0.85 0.81 0.053
CT30 3.69 0.44 0.74 0.67 0.396 2.51 0.32 0.61 0.52 0.468 3.56 0.64 0.73 0.67 0.110 2.80 0.34 0.66 0.59 0.503 2.89 0.60 0.67 0.60 0.082 3.59 0.46 0.72 0.61 0.307
CT42 1.22 0.20 0.19 0.18 -0.082 1.08 0.08 0.08 0.08 -0.031 1.04 0.04 0.04 0.04 -0.020 1.00 0.00 0.00 0.00 NA 1.08 0.08 0.08 0.08 -0.031 1.08 0..08 0.08 0.08 -0.055
CT81 1.47 0.28 0.32 0.31 0.123 1.51 0.36 0.34 0.31 -0.061 1.18 0.16 0.15 0.08 -0.070 1.33 0.28 0.26 0.24 -0.118 1.28 0.24 0.23 0.21 -0.087 1.35 0.26 0.26 0.23 -0.032
HLJYC13 3.62 0.72 0.74 0.67 0.006 3.23 0.56 0.70 0.63 0.189 3.37 0.60 0.72 0.65 0.147 1.79 0.44 0.45 0.37 0.004 3.62 0.56 0.74 0.67 0.227 3.57 0.58 0.72 0.60 0.123
HLJYC17 2.57 0.40 0.62 0.53 0.345 3.06 0.44 0.69 0.61 0.346 3.54 0.76 0.73 0.67 -0.059 2.68 0.48 0.64 0.55 0.235 3.10 0.56 0.70 0.63 0.185 3.59 0.53 0.72 0.60 0.204
HLJYC31 2.59 0.36 0.63 0.54 0.414 2.83 0.44 0.66 0.57 0.320 2.93 0.36 0.67 0.59 0.454 2.96 0.28 0.68 0.59 0.577 2.83 0.40 0.66 0.57 0.382 2.96 0.37 0.66 0.57 0.430
HLJYC45 2.94 0.76 0.67 0.56 -0.152 2.88 0.68 0.67 0.59 -0.042 3.34 0.52 0.72 0.64 0.258 3.16 0.64 0.70 0.63 0.064 3.73 0.60 0.75 0.68 0.180 3.39 0.64 0.71 0.62 0.067
HLJYC60 3.82 0.60 0.75 0.69 0.187 3.04 0.44 0.68 0.62 0.345 3.45 0.56 0.72 0.65 0.212 3.10 0.64 0.69 0.63 0.056 3.01 0.56 0.68 0.60 0.162 3.43 0.56 0.71 0.64 0.192
HLJYC66 2.75 0.44 0.65 0.58 0.308 3.71 0.24 0.75 0.68 0.671 2.92 0.28 0.67 0.61 0.575 1.22 0.16 0.19 0.18 0.138 3.05 0.44 0.69 0.61 0.345 3.03 0.31 0.67 0.53 0.459
HSY105 1.44 0.20 0.31 0.28 0.347 1.45 0.20 0.32 0.28 0.354 1.18 0.12 0.15 0.14 0.202 1.04 0.04 0.04 0.04 -0.020 1.28 0.12 0.22 0.21 0.449 1.27 0.14 0.21 0.19 0.335
Average 2.98 0.49 0.61 0.55 0.180 3.13 0.46 0.61 0.55 0.233 3.08 0.48 0.59 0.53 0.168 2.61 0.42 0.51 0.46 0.162 3.03 0.47 0.60 0.54 0.190 3.26 0.46 0.60 0.53 0.187

AMOVA analysis of five populations of yellow catfish

Source of variation d.f. Sum of squares Variance components Percentage of variation Fixation index p values
One group
Among populations 4 52.276 0.18565 Va 4.67 FST = 0.047 < 0.001
Within populations 245 927.680 3.78645 Vb 95.33
Two group (middle vs low)
Among groups 1 23.946 0.18128 Va 4.44 FCT = 0.044 < 0.001
Among populations within groups 3 28.330 0.11314 Vb 2.77 FSC = 0.029
Within populations 245 927.680 3.78645 Vc 92.79 FST = 0.072

Pairwise FST values (above diagonal) and genetic distances (below diagonal) between populations

Population CH GH HZ PY TH
CH ∗∗∗ 0.0302

p < 0.01

 0.0275

p < 0.01

 0.0810

p < 0.01

 0.0471

p < 0.01
GH 0.0806 ∗∗∗ 0.0170

p < 0.05

 0.0642

p < 0.01

 0.0258

p < 0.01
HZ 0.0722 0.0551 ∗∗∗ 0.0852

p < 0.01

 0.0169

p < 0.05
PY 0.1377 0.1107 0.1409 ∗∗∗ 0.0746

p < 0.01
TH 0.1077 0.0712 0.0541 0.1253 ∗∗∗

p-value of Hardy-Weinberg test on five populations of yellow catfish

Locus Test in each population Multi-population test
CH GH HZ PY TH
AG12 0.000

p < 0.01

 0.808 0.009

p < 0.01

 0.015

p < 0.05

 0.028

p < 0.05

 0.015

p < 0.05
AG48 1.000 0.386 0.386 0.060 0.072 0.465
AG128 0.543 0.645 0.345 0.345 0.004

p < 0.01

 0.345
CT30 0.000

p < 0.01

 0.033

p < 0.05

 0.018

p < 0.05

 0.100 0.095 0.000

p < 0.01
CT42 0.970 0.999 1.000 1.000 0.999 0.978
CT81 0.877 0.805 0.987 0.906 1.000 0.999
HLJYC13 0.840 0.114 0.213 0.989 0.044

p < 0.05

 0.115
HLJYC17 0.015

p < 0.05

 0.042

p < 0.05

 0.003

p < 0.01

 0.000

p < 0.01

 0.032

p < 0.05

 0.067
HLJYC31 0.118 0.003

p < 0.01

 0.089 0.061 0.095 0.114
HLJYC45 0.089 0.028

p < 0.05

 0.011

p < 0.05

 1.000 0.005

p < 0.01

 0.034

p < 0.05
HLJYC60 0.027

p < 0.05

 0.065 0.083 0.299 0.156 0.318
HLJYC66 0.252 0.089 0.384 0.275 0.198 0.987
HSY105 0.001

p < 0.01

 0.123 0.015

p < 0.05

 0.015

p < 0.05

 0.022

p < 0.05

 0.009

p < 0.01
multi-locus test 0.387 0.957 0.215 1.000 1.000 1.000
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