基于SNP标记的青海湖裸鲤遗传多样性及种群结构研究

罗慧; 方弟安; 何苗; 毛成诚; 匡箴; 祁洪芳; 徐东坡

doi:10.12131/20220091

基于SNP标记的青海湖裸鲤遗传多样性及种群结构研究

doi: 10.12131/20220091

罗慧^{1, 2,},
方弟安^{1, 2, ,},
何苗¹,
毛成诚²,
匡箴²,
祁洪芳³,
徐东坡²

1.
上海海洋大学水产与生命学院，上海 201306
2.
中国水产科学研究院淡水渔业研究中心/农业农村部淡水渔业和种质资源利用重点实验室，江苏无锡 214081
3.
青海湖裸鲤救护中心，青海西宁 810000

基金项目: 国家重点研发计划项目 (2019YFD0900604)；西北地区重点水域渔业资源与环境调查专项青海湖渔业资源与环境调查(XB2019-2021)；中国水产科学研究院基本科研业务费专项资金 (2020TD61)

详细信息

作者简介:
罗慧：罗　慧 (1998—)，女，硕士研究生，研究方向为渔业资源。E-mail: 673131080@qq.com

通讯作者:
方弟安 (1978—)，男，研究员，博士，研究方向为渔业资源。E-mail: fangda@ffrc.cn

中图分类号: S 932
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- 文章访问数: 129
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- 被引次数: 0
出版历程
- 收稿日期: 2022-04-02
- 修回日期: 2022-05-23
- 录用日期: 2022-07-17
- 网络出版日期: 2022-11-22
- 刊出日期: 2023-02-03

Genetic diversity and population structure of Gymnocypris przewalskii based on SNP markers

LUO Hui^{1, 2
,},
FANG Di'an^{1, 2
, ,},
HE Miao¹,
MAO Chengcheng²,
KUANG Zhen²,
QI Hongfang³,
XU Dongpo²

1.
College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China
2.
Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences/Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Wuxi 214081, China
3.
Rescues Center of Qinghai Lake Naked Carp, Xining 810000, China

摘要

摘要: 为探究青海湖裸鲤 (Gymnocypris przewalskii) 的种质资源现状，为该物种保护措施的制定提供参考依据。首次利用基因分型技术 (Genotyping-by-sequencing, GBS)，对青海湖水域的6个地理群体共72尾青海湖裸鲤进行单核苷酸多态性 (Single nucleotide polymorphism, SNP) 标记开发和遗传特征分析。共检测出1 600 061个SNP位点，质控后筛选出45 266个高质量的SNP位点用于遗传分析，发现核苷酸多样性 (P_i) 为0.317 0~0.327 4，观测杂合度 (H_o) 和期望杂合度 (H_e) 分别为0.459 4~0.482 3和0.336 7~0.344 4。6个地理群体的遗传距离 (D) 为0.018 4~0.023 3，两两群体的遗传分化系数 (F_st) 均不显著 (P>0.05)。分子方差分析 (Analysis of molecular variances, AMOVA) 显示102.37%的遗传变异来自群体内；群体遗传结构和系统发育进化树分析均显示6个群体属于一个集群，具有遗传同质性；而主成分判别分析 (Discriminant analysis of principal components, DAPC) 表明哈尔盖河、黑马河和沙柳河群体相互交叉聚类，其余3个地理群体分别聚类。综上，6个青海湖裸鲤群体的H_o均大于H_e，种群结构单一。
- 青海湖裸鲤 /
- 单核苷酸多态性 /
- 基因分型技术 /
- 遗传分化 /
- 渔业资源
Abstract: To investigate the genetic diversity and genetic differentiation of natural resources of Gymnocypris przewalskii, and provide references for its conservation measures, we collected 72 individuals of G. przewalskii from six natural populations in Qinghai Lake to analyze the genomic SNP and genetic characteristics by using simplified genome sequencing. Altogether 1 600 061SNP markers were obtained, and 45 266 high-quality SNP loci were screened for genetic analysis after filtering. The average P_i diversity index was 0.317 0–0.327 4. The average observed heterozygosity (H_o) and expected heterozygosity (H_e) were 0.459 4–0.482 3 and 0.336 7–0.344 4, respectively. The genetic distance (D) was 0.018 4–0.023 3 and the genetic differentiation index (Fst) were not significant (P>0.05). AMOVA analysis shows that the genetic variation was 102.37% within populations. Further-more, both population structure and phylogenetic tree analysis show that the six G. przewalskii populations clustered into one glade with similar genetic structure. In contrast, the genetic structure obtained from DAPC analysis was relatively clearer, showing that the Haergai, Heima and Shaliu River populations cross-clustered with each other, while the remaining three populations clustered into three other branches. In conclusion, the observed heterozygosity of the six geographic populations was higher than the expected value, with a homogeneous population structure.
- Gymnocypris przewalskii /
- Single nucleotide polymorphism /
- Genotyping by sequencing /
- Genetic differentiation /
- Fishery resources

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图 1 青海湖裸鲤采样地点图

Figure 1. Sampling site of G. przewalskii

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图 2 青海湖裸鲤样品聚类结果

Figure 2. Clustering results of G. przewalskii samples

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图 3 ADMIXTURE 交叉验证K值曲线图

Figure 3. ADMIXTURE cross-validation K value plot

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图 4 6个青海湖裸鲤群体的系统进化树

Figure 4. Phylogenetic tree of six G. przewalskii populations

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图 5 DAPC最优主成分数目的a-score优化

Figure 5. DAPC a-score optimization of number of retained PCs

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图 6 DAPC聚类图

Figure 6. Plots of DAPC clusters

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表 1 青海湖裸鲤的样品采集信息

Table 1. Sample information of G. przewalskii

采集地点 Sampling site	经纬度 Latitude and longitude	数量 Sample size/尾	取样部位 Sampling part
布哈河 BHH	99°44'24''E, 37°02'24''N	12	尾鳍
哈尔盖河 HEG	100°28'48''E, 37°13'12''N	12	尾鳍
黑马河 HMH	99°46'12''E, 36°43'48''N	12	尾鳍
泉吉河 QJH	99°53'24''E, 37°14'24''N	12	尾鳍
沙柳河 SLH	100°10'48''E, 37°14'24''N	12	尾鳍
一郎剑 YLJ	100°24'00''E, 36°42'00''N	12	尾鳍

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表 2 GBS测序数据统计

Table 2. Data statistics after genotyping by sequencing

样品 Sample	原始数据量 Raw base/bp	有效测序数量 Clean base/bp	Q20/%	Q30/%	比对率 Ratio/%	覆盖度 Cover/%	GC/%
BHH01	1 389 577 920	1 360 512 534	97.20	92.24	72.38	41.86	39.43
BHH02	1 927 663 064	1 910 163 826	97.00	91.73	71.71	44.45	39.28
BHH03	1 355 388 864	1 330 014 564	97.23	92.29	72.40	41.63	39.38
BHH04	1 854 567 996	1 840 004 206	97.14	92.08	68.34	44.96	39.35
BHH05	2 265 476 520	2 228 411 786	97.24	92.33	74.30	44.36	39.34
BHH06	1 602 581 328	1 578 477 056	97.16	92.14	72.72	43.72	39.33
BHH07	1 493 156 128	1 486 185 014	96.56	90.65	68.29	41.88	39.62
BHH08	3 625 787 104	3 582 205 358	96.78	91.19	69.32	47.85	39.82
BHH09	4 188 671 696	4 152 405 788	96.70	91.03	66.88	49.40	39.92
BHH10	3 783 676 336	3 743 104 234	96.83	91.29	69.96	48.18	39.83
BHH11	2 886 390 548	2 857 277 330	96.82	91.26	69.67	48.13	39.83
BHH12	2 436 548 180	2 404 222 590	96.86	91.36	71.23	45.73	39.80
HEG01	4 452 147 016	4 387 873 466	96.49	90.46	71.07	50.54	39.53
HEG02	3 773 555 144	3 725 723 130	96.44	90.34	70.17	48.07	39.55
HEG03	4 206 118 100	4 143 796 870	96.45	90.39	71.59	48.20	39.51
HEG04	5 078 768 024	5 001 034 014	96.47	90.42	71.66	49.81	39.56
HEG05	1 153 394 716	1 139 883 590	96.54	90.61	73.61	39.84	39.45
HEG06	4 843 459 540	4 792 194 098	96.43	90.37	73.01	48.96	39.54
HEG07	1 501 577 864	1 481 599 170	97.26	92.36	74.21	40.65	39.47
HEG08	2 693 727 504	2 657 441 746	97.31	92.46	76.19	44.39	39.39
HEG09	1 194 213 752	1 168 489 596	97.31	92.39	76.99	38.43	39.40
HEG10	1 372 619 144	1 339 243 546	96.89	91.50	72.82	40.60	39.33
HEG11	3 088 083 656	3 050 778 984	97.11	92.02	74.10	45.97	39.42
HEG12	1 619 334 204	1 585 556 642	97.16	92.14	75.77	41.52	39.28
HMH01	1 232 127 752	1 200 318 504	97.02	91.83	71.56	40.28	39.22
HMH02	3 026 290 652	2 985 218 180	97.23	92.31	73.98	44.96	39.25
HMH03	1 399 119 468	1 372 569 888	97.27	92.41	73.46	41.05	39.17
HMH04	1 970 927 056	1 921 307 060	97.28	92.39	73.24	43.12	39.30
HMH05	2 647 884 508	2 596 362 030	97.23	92.30	74.44	44.43	39.30
HMH06	1 708 154 352	1 660 462 320	97.29	92.44	73.06	41.96	39.26
HMH07	4 025 817 860	3 985 350 084	97.69	93.28	70.09	48.71	38.17
HMH08	5 205 970 488	5 117 137 470	96.65	90.89	73.81	48.98	39.20
HMH09	4 940 601 456	4 863 779 832	96.65	90.91	75.28	48.08	39.24
HMH10	1 963 437 692	1 945 709 624	96.60	90.76	73.03	43.03	39.22
HMH11	1 666 515 692	1 642 075 532	96.55	90.67	72.54	41.39	39.09
HMH12	4 347 827 000	4 286 730 938	96.56	90.69	71.40	48.89	39.35
QJH01	5 147 123 416	5 090 638 928	96.32	90.09	70.17	55.23	39.50
QJH02	3 584 795 680	3 565 628 068	95.95	89.37	66.88	49.55	39.44
QJH03	6 454 315 492	6 410 786 704	95.95	89.35	71.12	51.56	39.43
QJH04	3 914 473 956	3 894 271 390	95.87	89.22	67.09	48.68	39.41
QJH05	5 765 227 264	5 711 763 208	96.41	90.36	73.91	60.43	39.40
QJH06	1 578 283 708	1 552 126 286	96.41	90.24	74.89	50.12	39.39
QJH07	1 396 840 084	1 358 462 200	96.85	91.53	72.06	47.11	39.26
QJH08	2 275 133 940	2 251 308 686	97.01	91.90	70.44	52.56	39.29
QJH09	1 340 744 972	1 315 726 238	97.13	92.17	74.67	41.01	39.25
QJH10	2 048 956 056	2 009 990 568	97.09	92.05	71.84	44.26	39.38
QJH11	2 092 240 212	2 061 253 446	97.04	91.95	71.65	45.25	39.40
QJH12	2 039 776 892	1 992 244 374	97.13	92.16	72.73	44.70	39.35
SLH01	7 040 469 056	6 945 862 130	96.65	90.81	70.87	52.34	39.45
SLH02	4 498 263 220	4 427 530 468	96.69	90.89	71.71	49.57	39.50
SLH03	5 164 724 600	5 075 426 948	96.66	90.86	71.14	50.79	39.57
SLH04	1 272 379 640	1 259 999 052	96.63	90.74	73.42	39.66	39.41
SLH05	1 050 489 020	1 032 232 476	96.59	90.67	73.08	37.98	39.22
SLH06	2 360 256 124	2 322 023 500	96.63	90.75	72.68	44.17	39.56
SLH07	2 787 269 152	2 752 924 192	97.26	92.34	71.90	45.18	39.52
SLH08	1 659 152 708	1 635 202 024	97.22	92.24	70.67	42.13	39.55
SLH09	1 974 618 488	1 936 922 806	97.16	92.16	68.63	43.39	39.57
SLH10	1 434 149 732	1 414 000 878	97.20	92.20	67.84	42.37	39.50
SLH11	1 465 104 312	1 452 041 076	97.13	92.12	67.80	42.89	39.64
SLH12	1 593 403 584	1 565 068 850	96.44	90.59	73.79	41.90	39.02
YLJ01	1 458 951 168	1 441 355 132	97.14	92.12	71.91	41.68	39.51
YLJ02	1 933 206 744	1 917 865 930	97.14	92.17	67.47	44.98	39.14
YLJ03	3 128 604 208	3 093 206 580	97.14	92.21	72.61	47.09	39.06
YLJ04	1 343 484 720	1 316 565 174	97.24	92.32	76.23	40.09	38.99
YLJ05	1 588 695 432	1 551 573 180	97.07	91.93	72.37	42.47	38.97
YLJ06	3 330 149 352	3 289 825 750	97.25	92.34	70.46	47.58	39.00
YLJ07	1 873 001 868	1 844 675 484	97.30	92.47	72.27	43.94	39.03
YLJ08	2 175 175 880	2 142 504 822	96.39	90.46	71.81	44.84	39.17
YLJ09	3 172 296 188	3 134 366 418	96.33	90.34	72.60	47.36	39.14
YLJ10	2 801 743 496	2 774 569 032	96.34	90.37	69.66	47.28	39.06
YLJ11	2 270 060 848	2 236 343 778	96.47	90.63	72.99	44.74	39.09
YLJ12	2 007 127 400	1 987 101 014	96.34	90.38	71.46	44.26	39.08

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表 3 青海湖裸鲤遗传多样性分析

Table 3. Genetic diversity of G. przewalskii

群体　　　 Population	观测杂合度 H_o	观测纯合度 OH	期望杂合度 H_e	期望纯合度 EH	核苷酸多样性 P_i
布哈河 BHH	0.459 8	0.540 2	0.337 3	0.662 7	0.317 2
哈尔盖河 HEG	0.468 6	0.531 4	0.342 1	0.657 9	0.321 7
黑马河 HMH	0.466 1	0.533 9	0.340 0	0.660 0	0.320 5
泉吉河 QJH	0.482 3	0.517 7	0.344 4	0.655 6	0.327 4
沙柳河 SLH	0.465 8	0.534 2	0.343 3	0.656 8	0.318 1
一郎剑 YLJ	0.459 4	0.540 6	0.336 7	0.663 3	0.317 0

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表 4 青海湖裸鲤的遗传距离和遗传分化系数表

Table 4. Genetic differentiation and distance of G. przewalskii

群体 Population	BHH	HEG	HMH	QJH	SLH	YLJ
布哈河 BHH		0.022 8	0.022 7	0.019 1	0.023 2	0.023 3
哈尔盖河 HEG	−0.021 7		0.021 9	0.018 6	0.022 6	0.022 7
黑马河 HMH	−0.022 3	−0.022 4		0.018 4	0.022 5	0.022 4
泉吉河 QJH	−0.021 5	−0.023 0	−0.023 0		0.019 2	0.019 3
沙柳河 SLH	−0.027 2	−0.025 7	−0.026 6	−0.029 8		0.023 2
一郎剑 YLJ	−0.021 4	−0.021 7	−0.022 4	−0.021 2	−0.027 0
注：下三角为群体间遗传分化系数，上三角为群体间遗传距离。
Note: The lower triangle is the genetic differentiation coefficient (F_st) among populations, and the upper triangle is the genetic distance (D) among　　 populations.

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表 5 6个青海湖裸鲤群体的分子变异分析 (AMOVA)

Table 5. Analysis of molecular variation (AMOVA) of six populations of G. przewalskii

变异来源 Source of variation	自由度 Degree of freedom	平方和 Sum of squares	变异组分 Variance components	变异百分率 Percentage of variation/%
群体间 Among population	5	13 287.29	−138.528 8Va	−2.37
群体内 Within population	138	825 536.29	5 982.147 0Vb	102.37
总计 Total	143	838 823.58	5 843.618 3

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