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

Zhong, Liqiang; Wang, Minghua; Pan, Jianlin; Li, Daming; Tang, Shengkai; Bian, Wenji; Chen, Xiaohui

doi:10.1515/ohs-2018-0011

Figures & Tables

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)

UPGMA tree based on genetic distances between five yellow catfish populations

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	H_O	H_E	PIC	F_IS	Ae	H_O	H_E	PIC	F_IS	Ae	H_O	H_E	PIC	F_IS	Ae	H_O	H_E	PIC	F_IS	Ae	H_O	H_E	PIC	F_IS	Ae	H_O	H_E	PIC	F_IS
	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	F_ST = 0.047	< 0.001
Within populations	245	927.680	3.78645 Vb	95.33		< 0.001
Two group (middle vs low)
Among groups	1	23.946	0.18128 Va	4.44	F_CT = 0.044	< 0.001
Among populations within groups	3	28.330	0.11314 Vb	2.77	F_SC = 0.029
Within populations	245	927.680	3.78645 Vc	92.79	F_ST = 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

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

Figures & Tables

Figure 1

Figure 2

Figure 3

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

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

AMOVA analysis of five populations of yellow catfish

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

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

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