基于SLAF测序分析3个塔形马蹄螺群体的遗传结构和多样性*

doi:10.11978/2019136

Abstract

Abstract:

The marine mollusc Tectus pyramis inhabits the coral reef ecosystems surrounding Dapeng Bay in Shenzhen (SZ), Hainan Island, Xisha (XS) and Nansha Islands of China. In this study, the genetic diversity and genetic structure of three natural populations of T. pyramis from SZ, Sanya (SY) and XS were assessed using specific locus amplified fragment (SLAF) sequencing. A total of 115.74 Mb reads was obtained, with an average depth of 337.87-fold, and an average Q₃₀ value of 94.07 %. Based on 118679 polymorphic SLAF tags, we obtained 846502 highly consistent population single-nucleotide polymorphisms (SNPs), and found 155 SNPs displayed significant differences between populations. Average observed (H_o) and expected (H_e) heterozygosity values for the three populations ranged from 0.1441 to 0.1611 and from 0.2537 to 0.2695, respectively. Average polymorphism information content (PIC) values were between 0.2048 and 0.2176. The 45 individuals were roughly divided into three groups by phylogenetic tree analysis, principal component analysis (PCA) and clustering; and all the individuals from each population could be clustered into a single group. The genetic structures of SZ and SY populations were similar, yielding the lowest genetic distance (0.2510) and F_st value (0.0818). However, genetic differentiation between XS and the other two populations was significant, especially between SX and SZ (F_st= 0.1868). Genetic differentiation of the three populations may be correlated to ocean currents and geographical locations. The results of this study provide a theoretical basis for germplasm resource management and future aquaculture breeding programs.

Key words: specific locus amplified fragment sequencing, Tectus pyramis, genetic structure, germplasm resource

CLC Number:

P735.54

HUANG Jing, OU Zhekui, LIU Wenguang, HE Maoxian. Genetic Structure and Diversity Analysis of Three Natural Populations of Tectus pyramis Based on Specific Locus Amplified Fragment Sequencing*[J].Journal of Tropical Oceanography, 2020, 39(5): 1-18.

Figures/Tables 12

Marker	Pos	p-value (SY : XS)	p-value (SY : SZ)	p-value (XS : SZ)
Marker3275	8	5.97×10^-4	3.32×10^-5	2.09×10^-12
Marker5368	96	6.42×10^-5	5.24×10^-16	5.83×10^-6
Marker16106	153	2.51×10^-4	8.04×10^-5	8.21×10^-13
Marker29414	71	8.05×10^-5	8.05×10^-5	1.52×10^-14
Marker31028	126	1.30×10^-4	8.24×10^-4	7.82×10^-12
Marker32764	118	5.54×10^-13	1.10×10^-5	9.93×10^-4
Marker35459	119	1.72×10^-10	3.60×10^-4	5.97×10^-4
Marker39352	151	3.28×10^-5	6.11×10^-4	2.02×10^-13
Marker40948	162	5.83×10^-12	9.06×10^-4	3.33×10^-4
Marker43655	114	5.19×10^-5	9.18×10^-6	5.24×10^-16
Marker43655	195	2.46×10^-4	1.89×10^-6	5.24×10^-16
Marker48466	76	9.12×10^-4	4.49×10^-4	4.79×10^-11
Marker54309	156	7.97×10^-4	6.72×10^-4	6.70×10^-11
Marker56258	144	9.77×10^-4	2.29×10^-6	1.54×10^-14
Marker56258	153	9.77×10^-4	2.29×10^-6	1.54×10^-14
Marker56258	177	9.77×10^-4	2.29×10^-6	1.54×10^-14
Marker56258	187	9.77×10^-4	2.29×10^-6	1.54×10^-14
Marker56258	196	9.77×10^-4	2.29×10^-6	1.54×10^-14
Marker57704	38	1.83×10^-12	8.31×10^-5	4.12×10^-4
Marker57704	56	1.83×10^-12	8.31×10^-5	4.12×10^-4
Marker58004	63	7.97×10^-4	1.10×10^-5	9.23×10^-14
Marker58004	192	7.97×10^-4	1.10×10^-5	9.23×10^-14
Marker58561	4	1.78×10^-14	2.59×10^-6	4.78×10^-4
Marker58831	165	7.08×10^-4	9.92×10^-5	1.01×10^-11
Marker58831	179	7.08×10^-4	9.92×10^-5	1.01×10^-11
Marker59195	168	8.50×10^-14	3.92×10^-5	5.09×10^-4
Marker61327	50	4.25×10^-4	5.13×10^-4	1.01×10^-12
Marker62076	121	9.36×10^-5	3.65×10^-5	2.88×10^-14
Marker62305	23	4.53×10^-5	7.45×10^-5	8.23×10^-15
Marker64435	95	5.78×10^-5	3.54×10^-13	7.07×10^-4
Marker64938	164	1.26×10^-6	1.29×10^-4	5.24×10^-16
Marker64938	192	1.26×10^-6	1.29×10^-4	5.24×10^-16
Marker65298	19	1.26×10^-6	4.05×10^-4	4.66×10^-15
Marker72476	169	7.75×10^-5	9.41×10^-4	4.08×10^-11
Marker74137	39	9.84×10^-4	4.89×10^-6	1.78×10^-14
Marker74137	160	4.09×10^-5	1.66×10^-5	7.13×10^-16
Marker74137	197	4.09×10^-5	1.66×10^-5	7.13×10^-16
Marker77452	27	3.34×10^-4	1.62×10^-4	9.40×10^-12
Marker77571	174	7.37×10^-4	4.81×10^-7	2.00×10^-15
Marker78614	80	9.63×10^-4	9.43×10^-5	5.49×10^-12
Marker79010	46	5.56×10^-6	5.96×10^-4	1.13×10^-14
Marker79010	96	5.56×10^-6	5.96×10^-4	1.13×10^-14
Marker80829	28	4.18×10^-5	6.72×10^-4	9.86×10^-13
Marker85121	127	2.97×10^-4	1.04×10^-4	2.02×10^-13
Marker86368	91	3.80×10^-4	1.03×10^-9	9.11×10^-4
Marker89723	73	2.82×10^-5	4.83×10^-4	3.55×10^-13
Marker89828	32	7.08×10^-4	8.14×10^-4	2.12×10^-9
Marker91169	142	9.10×10^-4	1.61×10^-4	9.61×10^-12
Marker91169	143	9.10×10^-4	3.97×10^-4	2.55×10^-11
Marker91169	193	9.10×10^-4	1.61×10^-4	9.61×10^-12
Marker93033	35	5.09×10^-4	3.39×10^-4	5.69×10^-12
Marker94025	137	8.55×10^-4	4.15×10^-4	3.54×10^-13
Marker96746	95	3.15×10^-4	6.99×10^-4	5.37×10^-11
Marker97131	48	9.89×10^-5	9.28×10^-6	4.03×10^-15
Marker97131	64	9.89×10^-5	1.66×10^-5	8.23×10^-15
Marker97651	49	3.07×10^-4	2.13×10^-4	1.38×10^-11
Marker99962	152	6.07×10^-5	4.60×10^-4	2.87×10^-12
Marker101446	75	2.31×10^-4	4.98×10^-4	6.74×10^-11
Marker102130	123	2.82×10^-5	6.46×10^-4	2.32×10^-13
Marker103561	24	5.74×10^-4	7.97×10^-4	3.29×10^-11
Marker106244	7	3.73×10^-4	1.53×10^-4	1.18×10^-13
Marker114322	156	2.85×10^-5	8.53×10^-4	2.44×10^-12
Marker114487	160	9.77×10^-4	2.06×10^-4	6.96×10^-11
Marker115710	9	3.72×10^-4	7.06×10^-5	4.07×10^-13
Marker115710	37	3.72×10^-4	4.05×10^-4	9.61×10^-12
Marker116654	73	1.91×10^-4	8.85×10^-5	2.22×10^-13
Marker120806	120	3.64×10^-4	7.18×10^-10	4.58×10^-4
Marker128452	23	4.11×10^-13	2.60×10^-4	8.79×10^-6
Marker130399	64	2.87×10^-12	9.76×10^-4	2.59×10^-5
Marker131746	129	4.78×10^-4	6.66×10^-4	9.09×10^-11
Marker134085	78	1.05×10^-11	4.50×10^-4	2.22×10^-4
Marker135504	57	2.29×10^-7	7.97×10^-4	5.24×10^-16
Marker136107	156	8.50×10^-14	6.40×10^-4	6.95×10^-6
Marker142198	82	4.78×10^-4	3.68×10^-4	1.48×10^-11
Marker146079	23	7.48×10^-4	8.24×10^-5	1.44×10^-12
Marker146079	58	7.48×10^-4	8.24×10^-5	1.44×10^-12
Marker149477	131	8.47×10^-4	5.31×10^-4	1.62×10^-10
Marker153118	160	7.93×10^-4	8.65×10^-4	6.32×10^-10
Marker157365	21	9.10×10^-4	1.45×10^-4	1.62×10^-12
Marker164040	135	7.36×10^-4	5.21×10^-4	2.70×10^-10
Marker165818	206	2.35×10^-15	7.26×10^-5	1.67×10^-4
Marker169492	68	3.34×10^-4	1.39×10^-4	1.25×10^-12
Marker170499	42	2.35×10^-4	3.12×10^-4	9.23×10^-14
Marker170499	61	2.35×10^-4	3.12×10^-4	9.23×10^-14
Marker170499	70	2.35×10^-4	3.12×10^-4	9.23×10^-14
Marker170499	85	2.35×10^-4	3.12×10^-4	9.23×10^-14
Marker173073	161	5.88×10^-4	3.19×10^-8	3.44×10^-17
Marker174886	165	8.39×10^-15	3.44×10^-6	4.12×10^-4
Marker174886	174	8.39×10^-15	3.44×10^-6	4.12×10^-4
Marker176168	67	5.49×10^-12	2.51×10^-4	3.74×10^-4
Marker177413	57	6.14×10^-4	1.15×10^-4	3.74×10^-12
Marker181332	62	1.75×10^-4	6.40×10^-4	2.02×10^-11
Marker181637	22	1.98×10^-4	2.38×10^-5	2.83×10^-12
Marker181637	23	1.98×10^-4	2.38×10^-5	2.83×10^-12
Marker181637	33	4.98×10^-4	1.24×10^-5	2.83×10^-12
Marker181637	36	1.98×10^-4	2.38×10^-5	2.83×10^-12
Marker182931	24	4.13×10^-5	2.31×10^-4	5.69×10^-14
Marker182931	36	4.13×10^-5	2.31×10^-4	5.69×10^-14
Marker182931	38	4.99×10^-4	2.31×10^-4	1.44×10^-12
Marker182931	114	4.99×10^-4	4.90×10^-4	7.37×10^-12
Marker182931	171	4.99×10^-4	2.31×10^-4	1.44×10^-12
Marker184767	188	1.95×10^-12	3.64×10^-4	2.07×10^-5
Marker185952	36	3.34×10^-4	2.43×10^-4	1.89×10^-11
Marker186713	35	1.46×10^-6	3.41×10^-5	3.44×10^-17
Marker190981	52	4.12×10^-4	8.23×10^-5	7.84×10^-13
Marker192459	199	7.33×10^-4	3.39×10^-4	1.88×10^-11
Marker195736	85	1.72×10^-4	7.11×10^-4	1.59×10^-11
Marker195973	95	7.07×10^-4	5.24×10^-16	4.75×10^-7
Marker197784	195	8.47×10^-4	5.80×10^-4	3.01×10^-11
Marker202019	15	5.21×10^-4	1.19×10^-4	8.82×10^-12
Marker202019	84	5.21×10^-4	1.19×10^-4	8.82×10^-12
Marker203633	31	2.19×10^-11	7.35×10^-4	5.69×10^-4
Marker204262	11	4.11×10^-5	7.37×10^-4	1.89×10^-11
Marker204262	76	6.80×10^-4	7.37×10^-4	5.49×10^-10
Marker204262	145	4.11×10^-5	7.37×10^-4	1.89×10^-11
Marker204262	159	4.11×10^-5	7.37×10^-4	1.89×10^-11
Marker204262	162	4.11×10^-5	7.37×10^-4	1.89×10^-11
Marker204262	169	4.11×10^-5	7.37×10^-4	1.89×10^-11
Marker204894	204	4.99×10^-4	4.90×10^-4	7.37×10^-12
Marker215169	49	2.59×10^-5	9.10×10^-4	8.12×10^-13
Marker217857	37	7.82×10^-4	5.13×10^-4	6.01×10^-12
Marker217857	81	7.82×10^-4	5.13×10^-4	6.01×10^-12
Marker219928	157	1.15×10^-13	6.49×10^-4	5.18×10^-6
Marker220971	29	8.47×10^-4	2.38×10^-4	7.37×10^-12
Marker227957	59	3.55×10^-4	2.89×10^-6	1.13×10^-14
Marker240685	145	3.25×10^-4	1.52×10^-4	2.22×10^-13
Marker253092	204	9.93×10^-4	1.10×10^-5	5.54×10^-13
Marker253901	155	5.53×10^-4	3.77×10^-4	4.50×10^-11
Marker268253	137	1.07×10^-5	3.17×10^-12	5.97×10^-4
Marker273125	41	8.30×10^-4	6.05×10^-4	3.69×10^-10
Marker273125	51	8.30×10^-4	6.05×10^-4	3.69×10^-10
Marker273125	59	8.30×10^-4	6.05×10^-4	3.69×10^-10
Marker273125	67	8.30×10^-4	6.05×10^-4	3.69×10^-10
Marker273125	147	8.30×10^-4	6.05×10^-4	3.69×10^-10
Marker273125	187	8.30×10^-4	6.05×10^-4	3.69×10^-10
Marker280356	52	8.65×10^-4	8.85×10^-5	1.19×10^-11
Marker281848	160	2.56×10^-4	6.58×10^-4	1.38×10^-11
Marker289553	74	9.36×10^-5	2.07×10^-5	3.65×10^-14
Marker289553	128	9.36×10^-5	2.07×10^-5	3.65×10^-14
Marker296021	144	4.18×10^-5	2.99×10^-4	2.35×10^-15
Marker298184	70	3.93×10^-6	2.61×10^-5	3.44×10^-17
Marker308966	59	8.21×10^-13	2.49×10^-4	1.24×10^-4
Marker330769	199	1.58×10^-4	3.40×10^-4	2.02×10^-11
Marker350607	45	2.63×10^-10	1.48×10^-4	4.58×10^-4
Marker350607	49	2.63×10^-10	1.48×10^-4	4.58×10^-4
Marker350607	71	2.63×10^-10	1.48×10^-4	4.58×10^-4
Marker350607	73	2.63×10^-10	1.48×10^-4	4.58×10^-4
Marker350607	74	2.63×10^-10	1.48×10^-4	4.58×10^-4
Marker350607	82	2.63×10^-10	1.48×10^-4	4.58×10^-4
Marker350607	141	2.63×10^-10	1.48×10^-4	4.58×10^-4
Marker350607	163	2.63×10^-10	1.48×10^-4	4.58×10^-4
Marker350607	181	2.63×10^-10	1.48×10^-4	4.58×10^-4
Marker362138	51	1.48×10^-4	1.38×10^-4	8.82×10^-12
Marker389768	132	3.05×10^-4	7.36×10^-4	6.74×10^-11
Marker475043	205	1.26×10^-5	2.37×10^-4	8.23×10^-15

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Population Names	Location	Latitude	Longitude
SZ	Shenzhen	114°28′23.53″N	22°31′24.59″E
SY	Sanya	109°26′47.04″N	18°12′01.76″E
XS	Xisha	112°21′06.09″N	16°49′10.46″E

Sample ID	Total Reads Number	GC Percentage / %	Q₃₀ Percentage / %
SZ1	2646767	38.73	94.04
SZ2	2868617	38.82	93.27
SZ3	3060839	38.49	93.71
SZ4	2928250	38.94	94.69
SZ5	3236397	37.86	94.48
SZ6	3043836	38.27	94.40
SZ7	2817405	38.63	94.61
SZ8	2655334	38.56	94.77
SZ9	2725248	38.29	94.58
SZ10	3277567	37.43	94.59
SZ11	3492934	38.09	94.81
SZ12	3137716	38.41	94.67
SZ13	2039042	39.02	94.27
SZ14	1444547	39.31	94.19
SZ15	1654279	39.17	93.96
SY1	1618225	39.35	94.28
SY2	1683896	39.19	93.37
SY3	1495848	39.33	93.70
SY4	1645635	39.30	93.83
SY5	1832431	38.72	94.03
SY6	2114769	38.64	94.02
SY7	2547407	37.89	93.08
SY8	2000207	38.68	94.10
SY9	2194326	38.79	94.68
SY10	1967775	39.10	94.86
SY11	1841572	39.09	94.93
SY12	2123797	38.81	94.87
SY13	2151154	39.17	94.85
SY14	1954747	38.74	94.66
SY15	2514960	37.97	93.42
XS1	2060640	38.78	94.46
XS2	3164280	38.32	93.82
XS3	3272003	38.32	94.18
XS4	3171569	37.92	93.92
XS5	3202603	38.38	94.07
XS6	2744002	38.28	93.71
XS7	2303163	38.29	93.63
XS8	3218785	37.93	93.95
XS9	2972343	38.81	94.23
XS10	2844445	37.76	92.61
XS11	3272801	38.08	93.30
XS12	3035468	38.46	93.76
XS13	2943254	38.05	93.17
XS14	2583726	38.19	93.10
XS15	3196614	37.88	93.54
Control	1046368	43.03	92.64

Sample ID	SLAF number	Total depth	Average depth
SZ1	101537	1843808	18.16
SZ2	101886	2006414	19.69
SZ3	103244	2188358	21.20
SZ4	107505	2029284	18.88
SZ5	108067	2338011	21.63
SZ6	107524	2135565	19.86
SZ7	106819	1963328	18.38
SZ8	109780	1860332	16.95
SZ9	108621	1894662	17.44
SZ10	106877	2366741	22.14
SZ11	113736	2502851	22.01
SZ12	109751	2190045	19.95
SZ13	103761	1101996	10.62
SZ14	98465	781192	7.93
SZ15	100450	937431	9.33
SY1	97381	954691	9.80
SY2	98004	1017468	10.38
SY3	95481	909506	9.53
SY4	96922	996596	10.28
SY5	99774	1213282	12.16
SY6	101941	1350287	13.25
SY7	103004	1781398	17.29
SY8	101915	1228982	12.06
SY9	102675	1319548	12.85
SY10	101263	1145948	11.32
SY11	101126	1068060	10.56
SY12	103524	1246384	12.04
SY13	103145	1282700	12.44
SY14	103038	1148245	11.14
SY15	106571	1495169	14.03
XS1	103543	1212705	11.71
XS2	113977	2033850	17.84
XS3	113800	2082711	18.30
XS4	113523	2059873	18.14
XS5	114052	2075178	18.20
XS6	112858	1763198	15.62
XS7	109594	1472432	13.44
XS8	113536	2157654	19.00
XS9	112609	1938036	17.21
XS10	111522	1808792	16.22
XS11	113827	1923615	16.90
XS12	112561	1792407	15.92
XS13	112568	1747609	15.52
XS14	110288	1502944	13.63
XS15	113093	1927904	17.05
Total	218422	73797190	337.87

Sample ID	Total SNP number	SNP number	Hetloci ratio / %	Integrity ratio / %
SZ1	2010144	1101454	10.65	54.79
SZ2	2010144	1108987	10.99	55.16
SZ3	2010144	1124233	11.03	55.92
SZ4	2010144	1225287	11.18	60.95
SZ5	2010144	1199917	11.03	59.69
SZ6	2010144	1231716	11.21	61.27
SZ7	2010144	1205136	10.93	59.95
SZ8	2010144	1185877	11.65	58.99
SZ9	2010144	1206178	11.23	60.00
SZ10	2010144	1192230	10.94	59.31
SZ11	2010144	1283751	12.85	63.86
SZ12	2010144	1249074	11.64	62.13
SZ13	2010144	1222192	10.91	60.80
SZ14	2010144	1061836	9.44	52.82
SZ15	2010144	1102628	9.75	54.85
SY1	2010144	1038006	9.95	51.63
SY2	2010144	1039742	9.99	51.72
SY3	2010144	991652	9.56	49.33
SY4	2010144	1027875	9.87	51.13
SY5	2010144	1040267	10.05	51.75
SY6	2010144	1122866	10.85	55.85
SY7	2010144	1097668	11.22	54.60
SY8	2010144	1126900	10.79	56.06
SY9	2010144	1164083	11.26	57.91
SY10	2010144	1138116	10.73	56.61
SY11	2010144	1130375	10.70	56.23
SY12	2010144	1182425	11.26	58.82
SY13	2010144	1154786	11.52	57.44
SY14	2010144	1155444	11.03	57.48
SY15	2010144	1223114	12.02	60.84
XS1	2010144	1149640	11.35	57.19
XS2	2010144	1300295	13.19	64.68
XS3	2010144	1307590	13.18	65.04
XS4	2010144	1295832	13.14	64.46
XS5	2010144	1310729	13.41	65.20
XS6	2010144	1269962	12.86	63.17
XS7	2010144	1197594	11.65	59.57
XS8	2010144	1268115	12.84	63.08
XS9	2010144	1267870	12.57	63.07
XS10	2010144	1235461	12.47	61.46
XS11	2010144	1313024	13.94	65.31
XS12	2010144	1287328	13.38	64.04
XS13	2010144	1280442	13.48	63.69
XS14	2010144	1253266	12.95	62.34
XS15	2010144	1293659	13.75	64.35

Sample ID	PCA1	PCA2	PCA3
SZ1	0.28	-0.09	0.24
SZ2	0.29	-0.08	0.22
SZ3	0.27	-0.10	0.21
SZ4	0.10	-0.29	0.02
SZ5	0.05	-0.28	-0.07
SZ6	0.11	-0.30	0.03
SZ7	0.13	-0.27	0.06
SZ8	0.15	-0.27	0.07
SZ9	0.12	-0.28	0.04
SZ10	0.09	-0.29	-0.02
SZ11	0.06	-0.33	-0.06
SZ12	0.10	-0.30	-0.01
SZ13	0.11	-0.14	-0.06
SZ14	0.20	0.00	0.11
SZ15	0.19	-0.04	0.06
SY1	0.26	0.24	0.04
SY2	0.26	0.23	0.02
SY3	0.28	0.27	0.08
SY4	0.28	0.25	0.05
SY5	0.26	0.22	-0.03
SY6	0.21	0.15	-0.13
SY7	0.19	0.16	-0.16
SY8	0.20	0.14	-0.17
SY9	0.22	0.10	-0.10
SY10	0.22	0.13	-0.08
SY11	0.21	0.14	-0.13
SY12	0.19	0.08	-0.18
SY13	0.21	0.11	-0.11
SY14	0.18	0.12	-0.20
SY15	-0.17	-0.10	-0.50
XS1	-0.03	0.25	0.41
XS2	-0.36	0.03	0.07
XS3	-0.36	0.03	0.07
XS4	-0.36	0.04	0.05
XS5	-0.36	0.03	0.04
XS6	-0.35	0.05	0.07
XS7	-0.33	0.10	0.10
XS8	-0.34	0.05	0.08
XS9	-0.33	0.06	0.10
XS10	-0.36	0.07	0.03
XS11	-0.42	0.01	-0.05
XS12	-0.41	0.02	-0.04
XS13	-0.42	0.02	-0.05
XS14	-0.41	0.04	-0.05
XS15	-0.43	0.02	-0.07

Genetic Structure and Diversity Analysis of Three Natural Populations of Tectus pyramis Based on Specific Locus Amplified Fragment Sequencing*

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Parameter	SZ population	SY population	XS population
N_a	1.7719	1.8038	1.8095
N_e	1.4254	1.4463	1.4511
I	0.3847	0.4040	0.4081
H_o	0.1545	0.1441	0.1611
H_e	0.2537	0.2666	0.2695
PIC	0.2048	0.2152	0.2176
MAF	0.2414	0.2431	0.2437

Population	N_m and F_st			D and S
Population	SY	XS	SZ	SY	XS	SZ
SY	—	1.3914	2.8070	—	0.7240	0.7780
XS	0.1523	—	1.0882	0.3230	—	0.7189
SZ	0.0818	0.1868	—	0.2510	0.3300	—

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