Genetic Diversity of Huaihe Strain of Pelodiscus sinensis Based on Microsatellite Markers

doi:10.11924/j.issn.1000-6850.casb20190500185

Abstract

Abstract:

To investigate the genetic background of Huaihe strain of Pelodiscus sinensis, 25 microsatellite DNA markers were used to analyze the genetic structure and genetic diversity of Huaihe (H), Yellow River (Y) and Japanese (R) strain of Pelodiscus sinensis, respectively. The results showed that the average allele number (N_A) of the H, Y and R Pelodiscus sinensis strain was 5.08, 5.44 and 6.20, respectively. The average effective allele number (N_E) was 2.696, 2.733 and 3.221, respectively. The expected heterozygosity (H_E) of the H strain was 0.572, which was higher than that of the Y strain (0.556) and lower than that of the R strain (0.603). The genetic diversity of the R strain was the most abundant, followed by that of the H strain, and the genetic diversity of Y strain was the lowest. All the 25 microsatellite loci showed high polymorphism, and the average PIC of the H, Y and R strain was 0.513, 0.498 and 0.558, respectively. Both the H and R strain were highly polymorphic (PIC>0.5), and the Y strain was moderately polymorphic (0.25 <PIC<0.5). The genetic differentiation index (F_ST) indicated that the H and Y strain were moderately differentiated (0.05<F_ST<0.15), the H and R, Y and R strain were highly differentiated (0.15<F_ST<0.25). The genetic relationship between the H and the Y strain was closer than that between the H and the R strain. The study indicates that the Huaihe strain of Pelodiscus sinensis has higher genetic diversity and better genetic potential.

Key words: Huaihe strain, Yellow River strain, Japanese strain, Pelodiscus sinensis, microsatellite, genetic diversity

CLC Number:

S932.4

Wang Lihua, Zhang Yingping, Zou Guiwei, Xu Degao, Ling Chen, Liang Hongwei. Genetic Diversity of Huaihe Strain of Pelodiscus sinensis Based on Microsatellite Markers[J]. Chinese Agricultural Science Bulletin, 2020, 36(23): 134-141.

Figures/Tables 7

References 29

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位点	引物序列(5'-3')	退火温度/℃	片段大小/bp	位点	引物序列(5'-3')	退火温度/℃	片段大小/bp
ZHB2	F：TTGAGAGGATACTCCTCCATGAC	60	222~231	ZHB135	F：GACCAGCTCTCTGACCAAGG	60	146~159
ZHB2	R：CAAGTCAAGAATGGCACCAA	60	222~231	ZHB135	R：TGTTGGCCATGTATCTTCCA	60	146~159
ZHB7	F：ACTGCACTGTGAGGAATATCAA	57	249~297	ZHB150	F：TTGCCTATACTTAGCTCTGTTGGTT	60	227~233
ZHB7	R：CAGTTGTGAGTTGAAGCATGG	57	249~297	ZHB150	R：CACGTTCACAGAGTGCAACA	60	227~233
ZHB15	F：CCGTGTTGCATCTGGTATTG	60	272~285	ZHB155	F：GACAGGATGCATGACAATGG	60	179~184
ZHB15	R：CTACATGTTCCATGCCACCA	60	272~285	ZHB155	R：GGCCAGAGCAGATCCAAGTA	60	179~184
ZHB27	F：AGAGGAGGCCAGAGGATTGT	60	152~164	ZHB164	F：GGCTGAACATACACAGGCAGA	61	148~164
ZHB27	R：GTTCAGCCAGTGTTGGAGGT	60	152~164	ZHB164	R：TGTAAGGAGAGCTAATCAATGGTC	61	148~164
ZHB41	F：TGGACAAGTTAGAGCAAGGATG	59	266~273	ZHB176	F：TCTCGCTCTCTGGCGCTAA	62	94~135
ZHB41	R：GAGCAGCGTGTACTGGTGAA	59	266~273	ZHB176	R：GCTCGTTCCTCTGCTACCTC	62	94~135
ZHB44	F：AGCAGTAGTGAGGCCAGAGC	60	267~288	ZHB197	F：CTCTGCCGGTCTCTCTGAAC	60	235~252
ZHB44	R：GAAGCGAAGCCACACACAG	60	267~288	ZHB197	R：TCAGATAGCTACTGCATTGAGACA	60	235~252
ZHB52	F：CACCAACTAACGCCAAGGTT	60	154~180	ZHB203	F：CTGCCAATGGACCTAGCAGT	60	255~262
ZHB52	R：CATGCTCAGTGAAGCAGGAG	60	154~180	ZHB203	R：CAGCTGAAGACGCAGACAAG	60	255~262
ZHB53	F：CACCAACTAACGCCAAGGTT	60	247~279	ZHB204	F：CAGACATCAGTTCCATGGTGTT	60	223~240
ZHB53	R：CAGTGTCCGAAGCAAGCAG	60	247~279	ZHB204	R：TTGCAACTTAGCAGCAGACC	60	223~240
ZHB65	F：AGCTGGCACCTGTCTCTGAT	60	258~272	ZHB213	F：TGCAACTTCGGACAAGACAG	60	232~244
ZHB65	R：AGAGGCTCTTGTGCTGGAAG	60	258~272	ZHB213	R：GCAGCACATGCTACCACTACC	60	232~244
ZHB88	F：AAGGACTGATGTTCTCTGTGTCC	60	276~284	ZHB222	F：CTTCAGGCGATGAGAAGGAA	60	224~248
ZHB88	R：TTGAGATTCCTTGGTGTACGG	60	276~284	ZHB222	R：TCTGTATCCTCGTCGCTGTG	60	224~248
ZHB91	F：GCAGACCACTGTGCTGGTAA	60	295~303	ZHB276	F：TCAGATAGCTACTGCATTGAGACA	59	232~251
ZHB91	R：ACCGACACATGCAGAGCATA	60	295~303	ZHB276	R：CTCTGCCGGTCTCTCTGAAC	59	232~251
ZHB101	F：ATGCGCATGCGTACTTGAG	61	279~305	ZHB278	F：GTGTAGCTGCCAGTGCGTAA	60	279~289
ZHB101	R：TGAGCAGCTTGAAGAGGTGA	61	279~305	ZHB278	R：CAGTCTCGATCAGCCAACAA	60	279~289
ZHB120	F：CAGAGGCGATTGTCTGGAAT	60	127~139
ZHB120	R：GAAGCTTGCAGCAGTCTTAGG	60	127~139

位点	引物序列(5'-3')	退火温度/℃	片段大小/bp	位点	引物序列(5'-3')	退火温度/℃	片段大小/bp
ZHB2	F：TTGAGAGGATACTCCTCCATGAC	60	222~231	ZHB135	F：GACCAGCTCTCTGACCAAGG	60	146~159
ZHB2	R：CAAGTCAAGAATGGCACCAA	60	222~231	ZHB135	R：TGTTGGCCATGTATCTTCCA	60	146~159
ZHB7	F：ACTGCACTGTGAGGAATATCAA	57	249~297	ZHB150	F：TTGCCTATACTTAGCTCTGTTGGTT	60	227~233
ZHB7	R：CAGTTGTGAGTTGAAGCATGG	57	249~297	ZHB150	R：CACGTTCACAGAGTGCAACA	60	227~233
ZHB15	F：CCGTGTTGCATCTGGTATTG	60	272~285	ZHB155	F：GACAGGATGCATGACAATGG	60	179~184
ZHB15	R：CTACATGTTCCATGCCACCA	60	272~285	ZHB155	R：GGCCAGAGCAGATCCAAGTA	60	179~184
ZHB27	F：AGAGGAGGCCAGAGGATTGT	60	152~164	ZHB164	F：GGCTGAACATACACAGGCAGA	61	148~164
ZHB27	R：GTTCAGCCAGTGTTGGAGGT	60	152~164	ZHB164	R：TGTAAGGAGAGCTAATCAATGGTC	61	148~164
ZHB41	F：TGGACAAGTTAGAGCAAGGATG	59	266~273	ZHB176	F：TCTCGCTCTCTGGCGCTAA	62	94~135
ZHB41	R：GAGCAGCGTGTACTGGTGAA	59	266~273	ZHB176	R：GCTCGTTCCTCTGCTACCTC	62	94~135
ZHB44	F：AGCAGTAGTGAGGCCAGAGC	60	267~288	ZHB197	F：CTCTGCCGGTCTCTCTGAAC	60	235~252
ZHB44	R：GAAGCGAAGCCACACACAG	60	267~288	ZHB197	R：TCAGATAGCTACTGCATTGAGACA	60	235~252
ZHB52	F：CACCAACTAACGCCAAGGTT	60	154~180	ZHB203	F：CTGCCAATGGACCTAGCAGT	60	255~262
ZHB52	R：CATGCTCAGTGAAGCAGGAG	60	154~180	ZHB203	R：CAGCTGAAGACGCAGACAAG	60	255~262
ZHB53	F：CACCAACTAACGCCAAGGTT	60	247~279	ZHB204	F：CAGACATCAGTTCCATGGTGTT	60	223~240
ZHB53	R：CAGTGTCCGAAGCAAGCAG	60	247~279	ZHB204	R：TTGCAACTTAGCAGCAGACC	60	223~240
ZHB65	F：AGCTGGCACCTGTCTCTGAT	60	258~272	ZHB213	F：TGCAACTTCGGACAAGACAG	60	232~244
ZHB65	R：AGAGGCTCTTGTGCTGGAAG	60	258~272	ZHB213	R：GCAGCACATGCTACCACTACC	60	232~244
ZHB88	F：AAGGACTGATGTTCTCTGTGTCC	60	276~284	ZHB222	F：CTTCAGGCGATGAGAAGGAA	60	224~248
ZHB88	R：TTGAGATTCCTTGGTGTACGG	60	276~284	ZHB222	R：TCTGTATCCTCGTCGCTGTG	60	224~248
ZHB91	F：GCAGACCACTGTGCTGGTAA	60	295~303	ZHB276	F：TCAGATAGCTACTGCATTGAGACA	59	232~251
ZHB91	R：ACCGACACATGCAGAGCATA	60	295~303	ZHB276	R：CTCTGCCGGTCTCTCTGAAC	59	232~251
ZHB101	F：ATGCGCATGCGTACTTGAG	61	279~305	ZHB278	F：GTGTAGCTGCCAGTGCGTAA	60	279~289
ZHB101	R：TGAGCAGCTTGAAGAGGTGA	61	279~305	ZHB278	R：CAGTCTCGATCAGCCAACAA	60	279~289
ZHB120	F：CAGAGGCGATTGTCTGGAAT	60	127~139
ZHB120	R：GAAGCTTGCAGCAGTCTTAGG	60	127~139

位点	等位基因数(N_A)	有效等位基因数(N_E)	观察杂合度(H_O)	期望杂合度(H_E)	多态信息含量(PIC)
ZHB2	5	2.550	0.500	0.611	0.554
ZHB7	7	1.475	0.256	0.324	0.296
ZHB15	6	1.133	0.089	0.118	0.115
ZHB27	4	2.057	0.389	0.517	0.398
ZHB41	6	2.112	0.222	0.529	0.477
ZHB44	14	4.535	0.578	0.784	0.751
ZHB52	9	3.100	0.278	0.681	0.621
ZHB53	17	5.126	0.119	0.810	0.785
ZHB65	13	7.663	0.167	0.874	0.855
ZHB88	7	5.074	0.622	0.807	0.776
ZHB91	9	3.619	0.533	0.728	0.677
ZHB101	12	5.134	0.348	0.810	0.781
ZHB120	11	4.201	0.578	0.766	0.730
ZHB135	9	3.537	0.767	0.721	0.673
ZHB150	7	2.979	0.056	0.668	0.628
ZHB155	6	1.856	0.124	0.464	0.423
ZHB164	7	2.931	0.489	0.663	0.599
ZHB176	12	5.042	0.400	0.806	0.776
ZHB197	8	1.713	0.213	0.418	0.397
ZHB203	6	2.593	0.411	0.618	0.538
ZHB204	7	2.765	0.356	0.642	0.570
ZHB213	9	2.587	0.600	0.617	0.567
ZHB222	11	4.180	0.656	0.765	0.735
ZHB276	9	2.399	0.279	0.587	0.529
ZHB278	9	4.833	0.644	0.798	0.765
均值	8.80	3.408	0.387	0.645	0.601

位点	等位基因数(N_A)	有效等位基因数(N_E)	观察杂合度(H_O)	期望杂合度(H_E)	多态信息含量(PIC)
ZHB2	5	2.550	0.500	0.611	0.554
ZHB7	7	1.475	0.256	0.324	0.296
ZHB15	6	1.133	0.089	0.118	0.115
ZHB27	4	2.057	0.389	0.517	0.398
ZHB41	6	2.112	0.222	0.529	0.477
ZHB44	14	4.535	0.578	0.784	0.751
ZHB52	9	3.100	0.278	0.681	0.621
ZHB53	17	5.126	0.119	0.810	0.785
ZHB65	13	7.663	0.167	0.874	0.855
ZHB88	7	5.074	0.622	0.807	0.776
ZHB91	9	3.619	0.533	0.728	0.677
ZHB101	12	5.134	0.348	0.810	0.781
ZHB120	11	4.201	0.578	0.766	0.730
ZHB135	9	3.537	0.767	0.721	0.673
ZHB150	7	2.979	0.056	0.668	0.628
ZHB155	6	1.856	0.124	0.464	0.423
ZHB164	7	2.931	0.489	0.663	0.599
ZHB176	12	5.042	0.400	0.806	0.776
ZHB197	8	1.713	0.213	0.418	0.397
ZHB203	6	2.593	0.411	0.618	0.538
ZHB204	7	2.765	0.356	0.642	0.570
ZHB213	9	2.587	0.600	0.617	0.567
ZHB222	11	4.180	0.656	0.765	0.735
ZHB276	9	2.399	0.279	0.587	0.529
ZHB278	9	4.833	0.644	0.798	0.765
均值	8.80	3.408	0.387	0.645	0.601

标记	H					Y					R
标记	N_A	N_E	H_O	H_E	PIC	N_A	N_E	H_O	H_E	PIC	N_A	N_E	H_O	H_E	PIC
ZHB2	4	2.632	0.633	0.631	0.551	4	2.029	0.567	0.516	0.421	5	2.476	0.3	0.606	0.533
ZHB7	4	1.854	0.367	0.468	0.393	4	1.514	0.3	0.345	0.313	4	1.107	0.1	0.098	0.095
ZHB15	2	1.069	0	0.066	0.062	4	1.227	0.167	0.188	0.177	3	1.106	0.1	0.098	0.094
ZHB27	3	1.873	0.5	0.474	0.372	4	1.639	0.5	0.397	0.337	2	1.684	0.167	0.413	0.324
ZHB41	3	1.402	0.267	0.292	0.26	4	1.227	0.067	0.188	0.177	5	1.952	0.333	0.496	0.445
ZHB44	7	3.742	0.633	0.745	0.692	6	2.123	0.367	0.538	0.505	2	6.294	0.733	0.855	0.822
ZHB52	7	2.639	0.433	0.632	0.594	5	3.13	0.167	0.692	0.619	6	1.633	0.233	0.394	0.359
ZHB53	10	4.369	0.035	0.785	0.742	12	6.039	0.2	0.851	0.816	7	1.95	0.133	0.496	0.465
ZHB65	8	4.905	0.167	0.81	0.766	9	7.258	0.133	0.877	0.847	9	5.696	0.2	0.838	0.804
ZHB88	6	3.79	0.5	0.749	0.692	5	2.74	0.667	0.646	0.567	6	4.072	0.7	0.767	0.716
ZHB91	6	3.384	0.467	0.716	0.647	4	3.072	0.5	0.686	0.605	6	3.448	0.633	0.722	0.663
ZHB101	6	2.022	0.276	0.514	0.466	7	3.719	0.367	0.744	0.697	10	5.172	0.4	0.82	0.781
ZHB120	6	3.01	0.567	0.679	0.617	5	2.302	0.5	0.575	0.479	9	4.878	0.667	0.809	0.767
ZHB135	3	2.486	0.933	0.608	0.517	5	2.719	0.933	0.643	0.564	7	3.442	0.433	0.722	0.67
ZHB150	5	2.242	0.033	0.563	0.503	4	1.756	0.033	0.438	0.373	5	4.091	0.1	0.768	0.711
ZHB155	3	2.632	0	0.631	0.548	6	1.287	0.172	0.227	0.217	4	1.693	0.2	0.416	0.378
ZHB164	2	1.835	0.433	0.463	0.351	4	2.259	0.367	0.567	0.463	6	4.216	0.667	0.776	0.726
ZHB176	8	4.186	0.6	0.774	0.727	7	3.18	0.4	0.697	0.645	9	5.438	0.2	0.83	0.792
ZHB197	4	1.529	0.267	0.352	0.328	4	1.366	0.2	0.272	0.254	6	2.382	0.172	0.59	0.539
ZHB203	6	2.817	0.6	0.656	0.611	5	2.201	0.533	0.555	0.467	2	1.514	0.1	0.345	0.282
ZHB204	4	2.239	0.5	0.563	0.46	6	2.103	0.333	0.533	0.464	5	2.936	0.233	0.671	0.604
ZHB213	6	2.504	0.6	0.611	0.541	6	3.564	0.867	0.732	0.669	5	1.62	0.333	0.389	0.348
ZHB222	3	1.106	0.1	0.098	0.094	8	4.945	1	0.811	0.767	8	4.8	0.867	0.805	0.763
ZHB276	5	2.687	0.333	0.638	0.556	4	1.967	0.138	0.5	0.423	7	2.209	0.37	0.558	0.519
ZHB278	6	4.45	0.69	0.789	0.741	4	2.951	0.724	0.673	0.591	7	4.712	0.517	0.802	0.758
均值	5.08	2.696	0.397	0.572	0.513	5.44	2.733	0.408	0.556	0.498	6.2	3.221	0.356	0.603	0.558