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

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

[i] Motif – sequences inside parenthesis indicate the motif sequence of the microsatellite DNA and subscripted numbers indicate the number of repeats ; Temp. – annealing temperature for PCR

Table 2

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

[i] Ae – Effective allelic number; H_O – observed heterozygosity; H_E – expected heterozygosity; PIC – polymorphic information content; FIS – inbreeding coefficient

Table 3

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

Locus	Test in each population					Multi-population test
Locus	CH	GH	HZ	PY	TH	Multi-population test
AG12	0.000b	0.808	0.009b	0.015a	0.028a	0.015a
AG48	1.000	0.386	0.386	0.060	0.072	0.465
AG128	0.543	0.645	0.345	0.345	0.004b	0.345
CT30	0.000b	0.033a	0.018a	0.100	0.095	0.000b
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	0.044a	0.115
HLJYC17	0.015a	0.042a	0.003b	0.000b	0.032a	0.067
HLJYC31	0.118	0.003b	0.089	0.061	0.095	0.114
HLJYC45	0.089	0.028a	0.011a	1.000	0.005b	0.034a
HLJYC60	0.027a	0.065	0.083	0.299	0.156	0.318
HLJYC66	0.252	0.089	0.384	0.275	0.198	0.987
HSY105	0.001b	0.123	0.015a	0.015a	0.022a	0.009b
multi-locus test	0.387	0.957	0.215	1.000	1.000	1.000

b p < 0.01

a p < 0.05

b p < 0.01

a p < 0.05

b p < 0.01

a p < 0.05

b p < 0.01

a p < 0.05

b p < 0.01

a p < 0.05

b p < 0.01

a p < 0.05

b p < 0.01

a p < 0.05

b p < 0.01

Table 4

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

Population	CH	GH	HZ	PY	TH
CH	∗∗∗	0.0302b	0.0275b	0.0810b	0.0471b
GH	0.0806	∗∗∗	0.0170a	0.0642b	0.0258b
HZ	0.0722	0.0551	∗∗∗	0.0852b	0.0169a
PY	0.1377	0.1107	0.1409	∗∗∗	0.0746b
TH	0.1077	0.0712	0.0541	0.1253	∗∗∗

b p < 0.01

a p < 0.05

b p < 0.01

a p < 0.05

b p < 0.01

Table 5

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

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

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DOI: https://doi.org/10.1515/ohs-2018-0011 | Journal eISSN: 1897-3191 | Journal ISSN: 1730-413X

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Language: English

Page range: 99 - 106

Submitted on: Jun 5, 2017

Accepted on: Oct 20, 2017

Published on: Jun 18, 2018

Published by: University of Gdańsk

In partnership with: Paradigm Publishing Services

Publication frequency: 4 issues per year

Keywords:

Pelteobagrus fulvidraco,

genetic diversity,

population structure,

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© 2018 Liqiang Zhong, Minghua Wang, Jianlin Pan, Daming Li, Shengkai Tang, Wenji Bian, Xiaohui Chen, published by University of Gdańsk
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License.

Volume 47 (2018): Issue 2 (June 2018)

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

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