基于微卫星标记9个缢蛏群体的遗传多样性分析

doi:10.11978/2024117

热带海洋学报 ›› 2025, Vol. 44 ›› Issue (2): 124-136.doi: 10.11978/2024117CSTR: 32234.14.2024117

基于微卫星标记9个缢蛏群体的遗传多样性分析

吴贵清¹(), 李瑞华¹, 肖意豪¹, 陈彦林¹, 罗璇², 刘相全³, 朱佳杰¹, 吴雪萍¹()

1.广西民族大学海洋与生物技术学院, 广西南宁 530007
2.广西壮族自治区水产技术推广站, 广西南宁 530016
3.山东省海洋生态修复重点实验室(山东省海洋资源与环境研究院), 山东烟台 264006

收稿日期:2024-06-01 修回日期:2024-08-19 出版日期:2025-03-10 发布日期:2025-04-11
通讯作者: 吴雪萍
作者简介:
吴贵清(2000—), 男, 广西壮族自治区柳州市人, 硕士研究生, 从事贝类遗传与育种研究。email: 18077267931@163.com
基金资助:
广西民族大学引进人才启动基金(2017KJQD007); 广西自然科学基金资助项目(2020GXNSFBA159010); 2022年广西壮族自治区大学生创新创业训练计划项目(S202210608162); 2022年广西壮族自治区大学生创新创业训练计划项目(S202210608163); 2023年广西壮族自治区大学生创新创业训练计划项目(S202310608040)

Analysis of genetic diversity in 9 populations of Sinonovacula constricta using microsatellite markers

WU Guiqing¹(), LI Ruihua¹, XIAO Yihao¹, CHEN Yanlin¹, LUO Xuan², LIU Xiangquan³, ZHU Jiajie¹, WU Xueping¹()

1. School of Marine Science and Biotechnology, Guangxi Minzu University, Nanning 530007, China
2. Guangxi Fisheries Technical Extension Station, Nanning 530016, China
3. Shandong Provincial Key Laboratory of Restoration for Marine Ecology (Shandong Marine Resource and Environment Research Institute), Yantai 264006, China

Received:2024-06-01 Revised:2024-08-19 Online:2025-03-10 Published:2025-04-11
Contact: WU Xueping
Supported by:
High Level Introduction of Talent Research Start-up Projects of Guangxi Minzu University(2017KJQD007); Guangxi Natural Science Foundation Grant(2020GXNSFBA159010); Innovation and Entrepreneurship Training Program for College Students of Guangxi in 2022(S202210608162); Innovation and Entrepreneurship Training Program for College Students of Guangxi in 2022(S202210608163); Innovation and Entrepreneurship Training Program for College Students of Guangxi in 2023(S202310608040)

摘要/Abstract

摘要：

利用基于简化基因组测序(restriction site associated DNA sequencing, RAD-seq)技术开发了10对新的多态性微卫星引物, 对辽宁丹东(DD)、河北秦皇岛(QHD)、辽宁庄河(ZH)、山东青岛(QD)、江苏连云港(LYG)、浙江宁波(NB)、福建厦门(XM)、广东惠州(HZ)和广西北海(BH)共9个缢蛏群体进行了遗传多样性分析, 在270个缢蛏个体中共检测到了352个等位基因。平均等位基因数(N_a, number of alleles)在3.2000~4.3000之间、平均有效等位基因数(N_e, effective number of alleles)在1.8789~2.5433之间; 观测杂合度(H_o, observed heterozygosity)范围为0.0000~0.9667、平均观测杂合度在0.3088~0.5533之间; 期望杂合度(H_e, expected heterozygosity)范围为0.0000~0.7945、平均期望杂合度在0.3456~0.5715之间; 平均多态信息含量(PIC, polymorphic information content)在0.3373~0.5989之间。遗传多样性评估显示, 9个缢蛏群体的遗传多样性水平属于中等。群体间的遗传分化系数(F_st, genetic differentiation coefficient)在0.0547~0.3511之间, 其中QHD和ZH群体之间的F_st值最低为0.0547, 而LYG和BH群体之间的F_st值最高为0.3511。基因流(N_m, gene flow)在0.4620至4.3204之间, 其中QHD和ZH群体之间的N_m值最高为4.3204, 而LYG和BH群体之间的N_m值最低为0.4620。分子方差分析(analysis of molecular variance, AMOVA)分析结果显示, 群体间的遗传变异占总变异的33.04% (p < 0.01), 而群体内的遗传变异占总变异的66.96% (p < 0.01), 表明遗传变异不仅存在于个体间, 也存在于群体间, 但个体间的遗传变异大于群体间的遗传变异。非加权组平均法(unweighted pair-group method with arithmetic means, UPGMA)、Structure软件的聚类结果以及主坐标分析(principal coordinate analysis, PCoA)结果一致。研究结果显示, 9个缢蛏群体可分为3大支: 第一支由QHD、ZH、QD、DD 4个群体组成; 第二支由LYG、NB、XM、HZ 4个群体组成; 第三支由BH群体独立成支。

关键词: 缢蛏, 微卫星, 遗传多样性, 遗传分化

Abstract:

RAD-seq technology was utilized to develop 10 pairs of novel polymorphic microsatellite primers for assessing genetic 有时候diversity in nine populations of Sinonovacula constricta of Dandong in Liaoning (DD), Qinhuangdao in Hebei (QHD), Zhuanghe in Liaoning (ZH), Qindao in Shandong (QD), Lianyungang in Jiangsu (LYG), Ningbo in Zhejiang (NB), Xiamen in Fujian (XM), Huizhou in Guangdong (HZ), and Beihai in Guangxi (BH). In 270 individuals of S. constricta, a total of 352 alleles were detected. The average number of alleles (N_a) ranged from 3.2000 to 4.3000, with the average effective number of alleles (N_e) falling between 1.8789 and 2.5433. Observed heterozygosity (H_o) varied from 0.0000 to 0.9667, with an average ranging from 0.3088 to 0.5533. Expected heterozygosity (H_e) spanned from 0.0000 to 0.7945, with an average of 0.3456 to 0.5715. The average polymorphic information content (PIC) ranged from 0.3373 to 0.5989. Genetic diversity analysis indicated a moderate level of genetic diversity across the nine populations of S. constricta. The genetic differentiation coefficient (F_st) among populations ranged from 0.0547 to 0.3511, with the lowest F_st value observed between QHD and ZH (0.0547) and the highest between LYG and BH (0.3511). Gene flow (N_m) values ranged from 0.4620 to 4.3204, with the highest N_m value recorded between QHD and QD (4.3204) and the lowest between LYG and BH (0.4620). AMOVA analysis revealed that 33.04% of the total genetic variation existed among populations (p < 0.01), while 66.96% was within populations (p < 0.01), indicating that the genetic variation was observed not only among individuals but also among populations. However, the variation among individuals was greater than that among populations. Consistent results were obtained from UPGMA clustering, Structure clustering, and principal coordinate analysis (PCoA). The study delineated three main groups among the nine populations: the first group comprised QHD, ZH, QD and DD populations; the second group included LYG, NB, XM, and HZ populations; and the third group was independently represented by BH population.

Key words: Sinonovacula constricta, microsatellites, genetic diversity, genetic differentiation

中图分类号:

P735.542

吴贵清, 李瑞华, 肖意豪, 陈彦林, 罗璇, 刘相全, 朱佳杰, 吴雪萍. 基于微卫星标记9个缢蛏群体的遗传多样性分析[J]. 热带海洋学报, 2025, 44(2): 124-136.

WU Guiqing, LI Ruihua, XIAO Yihao, CHEN Yanlin, LUO Xuan, LIU Xiangquan, ZHU Jiajie, WU Xueping. Analysis of genetic diversity in 9 populations of Sinonovacula constricta using microsatellite markers[J]. Journal of Tropical Oceanography, 2025, 44(2): 124-136.

图/表 11

表1

表2

表3

9个缢蛏群体的平均遗传多样参数"

群体	参数	SC03	SC04	SC05	SC06	SC07	SC08	SC11	SC13	SC17	SC19	均值
DD	N_a	3.0000	3.0000	4.0000	5.0000	6.0000	5.0000	4.0000	4.0000	4.0000	4.0000	4.2000
	N_e	1.7527	1.9674	2.3810	4.3239	2.9268	3.4118	3.2200	1.8127	1.4207	2.2161	2.5433
	H_o	0.6000	0.0357	0.1000	0.4138	0.3333	0.6207	0.7667	0.2667	0.2333	0.0690	0.3439
	H_e	0.4367	0.5006	0.5898	0.7822	0.6695	0.7193	0.7011	0.4559	0.3011	0.5584	0.5715
	PIC	0.4510	0.4130	0.7330	0.7730	0.6070	0.9080	0.6650	0.4390	0.2870	0.4580	0.5734
	P-value	1.0000	0.0000^*	0.0000^*	0.0000^*	0.0033	0.0042	0.8245	0.0002^*	0.0561	0.0000^*	0.1888
QHD	N_a	5.0000	3.0000	5.0000	5.0000	4.0000	5.0000	3.0000	5.0000	4.0000	2.0000	4.1000
	N_e	2.2416	1.4551	3.5644	4.4888	2.9851	3.3835	2.0619	1.6949	1.2721	1.9627	2.5110
	H_o	0.7333	0.0333	0.5333	0.3667	0.4667	0.6000	0.9667	0.4000	0.2333	0.0345	0.4368
	H_e	0.5633	0.3181	0.7316	0.7904	0.6763	0.7164	0.5237	0.4169	0.2175	0.4991	0.5453
	PIC	0.5690	0.2860	0.7040	0.7550	0.6230	0.8260	0.3980	0.4050	0.2050	0.3700	0.5141
	P-value	0.9964	0.0000^*	0.0000^*	0.0641	0.0025	1.0000	0.0459	1.0000	0.0000^*	0.0205	0.3129
ZH	N_a	4.0000	3.0000	6.0000	5.0000	4.0000	6.0000	3.0000	5.0000	3.0000	3.0000	4.2000
	N_e	2.5388	1.1450	2.9561	4.1570	2.5678	4.5113	2.3866	1.9759	1.2685	1.4019	2.4909
	H_o	0.2667	0.0000	0.4138	0.3667	0.2000	0.6000	0.6071	0.4000	0.2333	0.0000	0.3088
	H_e	0.6164	0.1288	0.6733	0.7723	0.6209	0.7915	0.5916	0.5023	0.2153	0.2915	0.5204
	PIC	0.5360	0.1230	0.6750	0.7330	0.5300	0.8940	0.5080	0.4630	0.1990	0.2600	0.4921
	P-value	0.0205	0.0003^*	0.0022	0.0000^*	0.0001^*	0.0000^*	0.0386	0.2979	1.0000	0.0000^*	0.1359
QD	N_a	5.0000	2.0000	4.0000	5.0000	3.0000	4.0000	3.0000	5.0000	2.0000	4.0000	3.7000
	N_e	1.6559	1.0689	3.4682	4.5421	1.3072	3.4221	2.0202	1.3206	1.0339	1.6408	2.1480
	H_o	0.4000	0.0000	0.5333	0.2963	0.2000	0.7000	0.8667	0.2000	0.0333	0.1333	0.3363
	H_e	0.4028	0.0655	0.7237	0.7945	0.239	0.7198	0.5136	0.2469	0.0333	0.3972	0.4136
	PIC	0.3770	0.0620	0.0730	0.7560	0.2220	0.8590	0.3930	0.2340	0.0320	0.3650	0.3373
	P-value	0.0316	0.0169	0.0036	0.0000^*	0.2409	0.0000^*	1.0000	0.0146	0.0000^*	0.0002^*	0.1308
LYG	N_a	1.0000	1.0000	5.0000	2.0000	2.0000	6.0000	4.0000	5.0000	3.0000	3.0000	3.2000
	N_e	1.0000	1.0000	1.9956	1.2596	1.9978	4.2254	3.1634	1.7787	1.2237	1.1443	1.8789
	H_o	0.0000	0.0000	0.3667	0.2333	0.9667	0.7333	0.6333	0.3667	0.1333	0.0667	0.3500
	H_e	0.0000	0.0000	0.5073	0.2096	0.5079	0.7763	0.6955	0.4452	0.1859	0.1282	0.3456
	PIC	0.0000	0.0320	0.6650	0.1850	0.3750	0.8710	0.6190	0.4160	0.1800	0.1240	0.3467
	P-value	0.0000^*	1.0000	0.0000^*	1.0000	1.0000	0.1941	0.2597	0.0006^*	0.0669	0.0169	0.3538
NB	N_a	5.0000	2.0000	5.0000	5.0000	2.0000	5.0000	3.0000	5.0000	2.0000	4.0000	3.8000
	N_e	3.1746	1.0689	3.3835	3.1142	1.4274	4.0909	2.2727	2.2814	1.0339	1.4718	2.3319
	H_o	0.4667	0.0000	0.4667	0.4333	0.3667	0.5333	0.9333	0.4000	0.0333	0.1000	0.3733
	H_e	0.6966	0.0655	0.7164	0.6904	0.3045	0.7684	0.5695	0.5712	0.0333	0.3260	0.4742
	PIC	0.6560	0.0620	0.8160	0.6430	0.2550	0.9030	0.4610	0.5500	0.0640	0.3050	0.4715
	P-value	0.1371	0.0169	0.0000^*	0.0058	1.0000	0.0217	0.9827	0.0000^*	1.0000	0.0000^*	0.3164
XM	N_a	2.0000	1.0000	4.0000	5.0000	5.0000	5.0000	3.0000	4.0000	4.0000	5.0000	3.8000
	N_e	1.6000	1.0000	2.2876	3.5573	1.9063	3.8793	2.2032	2.1102	1.4634	1.8653	2.1873
	H_o	0.4333	0.0000	0.3462	0.3667	0.4333	0.8000	0.9333	0.4333	0.2000	0.1000	0.4046
	H_e	0.3814	0.0000	0.5739	0.7311	0.4836	0.7548	0.5554	0.5350	0.3220	0.4718	0.4809
	PIC	0.6720	0.4410	0.8840	0.4420	0.4410	0.8840	0.4420	0.5260	0.2950	0.4440	0.5471
	P-value	0.0000^*	0.0044	0.6226	0.8616	0.0044	0.6226	0.8616	0.0068	0.0048	0.0000^*	0.2989
HZ	N_a	5.0000	3.0000	5.0000	5.0000	2.0000	5.0000	4.0000	4.0000	2.0000	4.0000	3.9000
	N_e	2.2939	1.2649	2.4931	3.4417	1.5139	3.8710	2.8257	1.3657	1.0339	1.5139	2.1618
	H_o	0.5333	0.0333	0.2333	0.5667	0.4333	0.6333	0.7667	0.3000	0.0333	0.1333	0.3667
	H_e	0.5734	0.2130	0.6090	0.7215	0.3452	0.7542	0.6571	0.2723	0.0333	0.3452	0.4524
	PIC	0.5880	0.2130	0.7830	0.7260	0.3520	0.9010	0.6570	0.2450	0.0330	0.3460	0.4844
	P-value	0.0937	0.0001^*	0.0000^*	0.0683	1.0000	0.0000^*	0.6531	1.0000	0.0000^*	0.0263	0.2841
BH	N_a	5.0000	3.0000	5.0000	3.0000	5.0000	5.0000	5.0000	5.0000	3.0000	4.0000	4.3000
	N_e	2.2032	1.2270	2.4658	1.3943	4.5226	1.8927	2.8939	2.8571	1.9231	1.7561	2.3136
	H_o	0.6333	0.2000	0.4333	0.3333	0.7667	0.5333	0.6667	0.7667	0.6667	0.5333	0.5533
	H_e	0.5554	0.1881	0.6045	0.2876	0.7921	0.4797	0.6655	0.6610	0.4881	0.4379	0.5160
	PIC	0.5030	0.1770	0.7760	0.2510	0.8590	0.6010	0.7320	0.7160	0.6220	0.7520	0.5989
	P-value	0.9440	1.0000	0.0181	1.0000	0.4223	0.7689	0.9183	1.0000	0.9940	0.9761	0.8042

表3

表4

表5

表6

图1

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图5

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采样地点	经度	纬度	样本量/个	采样时间
DD	124°16′54′′E	39°56′15′′N	30	2022年11月22日
QHD	119°26′11′′E	39°47′47′′N	30	2022年11月05日
ZH	122°38′59′′E	39°31′36′′N	30	2022年10月23日
QD	120°67′16′′E	36°16′06′′N	30	2022年10月15日
LYG	119°17′08′′E	34°46′50′′N	30	2022年9月27日
NB	121°43′55′′E	29°32′01′′N	30	2022年9月18日
XM	118°11′50′′E	24°29′18′′N	30	2022年8月25日
HZ	114°38′26′′E	22°45′40′′N	30	2022年8月12日
BH	109°06′33′′E	21°25′25′′N	30	2022年7月10日

位点	序列号	引物序列(5′-3′)	退火温度/℃	片段大小/bp
SC03	PP409554	F: CTTATCTTTATCCTCCTCGCCAT R: TGATGATAATGTTGAGGCTGTTG	54	120~160
SC04	PP409555	F: AGATAAAGCCAGGAAAACACAGA R: GTTTACAATGAAAAGACAGATGGC	52	110~150
SC05	PP409556	F: TCTTGGTTAGAGTGGGTTGTTGT R: TGCTTTCTAATGTGCCTTTCATT	52	130~170
SC06	PP409557	F: TTTCATGTTGTTGGTTGTTTGTT R: AATGTTGCCAAATCAAAACATTC	54	110~150
SC07	PP409558	F: CATCATCATTAACCGTCCTCCTA R:AGAAATTGGCATTGATAGCAAAA	52	120~160
SC08	PP409559	F: CCATGCATGAGAGTTAAGTAACAAA R: CCAAGAATGCACAATAAAATTGA	52	120~160
SC11	PP409560	F: GACAATTATGATTGCGATTGGTT R: TTGATACCCTTCATTCCAGCTTA	53	120~150
SC13	PP409560	F: ACAACGCCAGCAGTAACCTATAA R: CGGTTGTGGAAGCAGTAGTAGTAG	54	100~140
SC17	PP409562	F: CACCTCTGTCTGAAAAACAAAAA R: AGGGACACCCAGTACACATCTAT	50	130~170
SC19	PP409563	F: CAAAACCGGTTGGTAATGAATAA R: TTTTGTTGTTGTTTTGTTGTTGC	55	120~160

群体	DD	QHD	ZH	QD	LYG	NB	XM	HZ	BH
DD	—	2.7297	1.6497	1.0460	0.5298	0.8741	0.8756	0.8188	0.8586
QHD	0.0839	—	4.3204	1.5281	0.6187	1.1282	1.4507	0.9450	0.7350
ZH	0.1316	0.0547	—	2.6981	0.7194	1.5093	1.2707	0.8271	0.8508
QD	0.1929	0.1406	0.0848	—	0.7186	1.2951	0.9248	1.0665	0.5406
LYG	0.3206	0.2878	0.2579	0.2581	—	1.7892	1.0146	1.0294	0.4620
NB	0.2224	0.1814	0.1421	0.1618	0.1226	—	2.1219	1.1939	0.6296
XM	0.2221	0.1470	0.1644	0.2128	0.1977	0.1054	—	3.4211	0.6309
HZ	0.2339	0.2092	0.2321	0.1899	0.1954	0.1142	0.0681	—	0.6009
BH	0.2255	0.2538	0.2721	0.3162	0.3511	0.2842	0.2838	0.2938	—

变异来源	自由度	平方和	方差分量	变异百分比/%
群体间	8	630.102	1.26981^Va	33.04^**
群体内	531	1366.717	2.57385^Vb	66.96^**
总计	539	1996.819	3.84367	100

群体	DD	QHD	ZH	QD	LYG	NB	XM	HZ	BH
DD	—	0.7501	0.6262	0.5149	0.1806	0.3759	0.3309	0.3403	0.1000
QHD	0.2875	—	0.8632	0.6573	0.2957	0.5220	0.5833	0.4370	0.0712
ZH	0.4681	0.1471	—	0.8187	0.4218	0.6405	0.5575	0.4148	0.0680
QD	0.6637	0.4196	0.2000	—	0.4845	0.6434	0.4846	0.5954	0.0613
LYG	1.7115	1.2185	0.8631	0.7247	—	0.7722	0.5684	0.5911	0.0559
NB	0.9785	0.6501	0.4455	0.4411	0.2586	—	0.7310	0.7133	0.0792
XM	1.1059	0.5391	0.5843	0.7244	0.5649	0.3134	—	0.8574	0.0659
HZ	1.0780	0.8278	0.8798	0.5185	0.5257	0.3378	0.1538	—	0.0566
BH	2.3022	2.6421	2.6885	2.7917	2.8838	2.5353	2.7198	2.8723	—

基于微卫星标记9个缢蛏群体的遗传多样性分析

Analysis of genetic diversity in 9 populations of Sinonovacula constricta using microsatellite markers

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