基于基因组重测序的长江上游瓦氏黄颡鱼群体遗传结构

doi:10.17520/biods.2022391

生物多样性 ›› 2023, Vol. 31 ›› Issue (4): 22391. DOI: 10.17520/biods.2022391

• 研究报告: 遗传多样性 • 下一篇

基于基因组重测序的长江上游瓦氏黄颡鱼群体遗传结构

熊飞¹^,², 刘红艳¹^,²^,^*(), 翟东东¹^,², 段辛斌³^,^*(), 田辉伍³, 陈大庆³

1.江汉大学生命科学学院, 湖北省汉江流域特色生物资源保护开发与利用工程技术研究中心, 武汉 430056
2.江汉大学持久性有毒污染物环境与健康危害湖北省重点实验室, 武汉 430056
3.中国水产科学研究院长江水产研究所, 武汉 430223

收稿日期:2022-07-09 接受日期:2022-11-14 出版日期:2023-04-20 发布日期:2023-04-20
通讯作者: *E-mail: lhy9603@126.com; duan@yfi.ac.cn
基金资助:
国家自然科学基金(51979123);湖北省高等学校优秀中青年科技创新团队计划项目(T2020034);江汉大学科技创新专项项目(2021kjzx006)

Population genetic structure of Pelteobagrus vachelli in the upper Yangtze River based on genome re-sequencing

Fei Xiong¹^,², Hongyan Liu¹^,²^,^*(), Dongdong Zhai¹^,², Xinbin Duan³^,^*(), Huiwu Tian³, Daqing Chen³

1. School of Life Sciences, Jianghan University, Hubei Engineering Research Center for Protection and Utilization of Special Biological Resources in the Hanjiang River Basin, Wuhan 430056
2. Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Jianghan University, Wuhan 430056
3. Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223

Received:2022-07-09 Accepted:2022-11-14 Online:2023-04-20 Published:2023-04-20
Contact: *E-mail: lhy9603@126.com; duan@yfi.ac.cn

摘要/Abstract

摘要：

利用基因组重测序的方法获取高通量SNP标记, 分析了长江上游三峡大坝-白鹤滩大坝之间8个不同江段(太平溪、巴南、合川、岷江口、宜宾、邵女坪、桧溪、冯家坪)共136尾瓦氏黄颡鱼(Pelteobagrus vachelli)的遗传多样性和遗传分化水平, 阐明了长江上游瓦氏黄颡鱼群体遗传结构。结果显示: (1)三峡库区太平溪群体和巴南群体具有较高的SNP (single nucleotide polymorphism)数量和核苷酸多样性指数, 遗传来源丰富, 其遗传多样性高于其他群体; 上游的岷江口、宜宾、邵女坪和冯家坪群体遗传来源单一。(2)瓦氏黄颡鱼存在3个不同的遗传分支, 且不同遗传分支之间存在较大的遗传分化。(3)群体SNP数量和核苷酸多样性指数与河流坡降呈显著负相关, 群体遗传分化指数与地理距离和隔离时间无显著相关性。研究结果表明, 在三峡大坝-白鹤滩大坝江段, 瓦氏黄颡鱼上游群体具有更低的遗传多样性, 更易发生遗传漂变作用, 在鱼类遗传多样性保护中需要特别关注; 瓦氏黄颡鱼存在3种显著的遗传结构, 应视为3个不同遗传单元进行种质资源管理。

关键词: 瓦氏黄颡鱼, 长江上游, 遗传分化, 遗传多样性, 基因组重测序

Abstract

Aims: Pelteobagrus vachelli is an important economic fish in the Yangtze River. Nevertheless, it shows a trend of younger age and miniaturization, and the number of reproductive population above the third age was small, which is not benefit to the long-term maintenance of its resources. Therefore, more attention and conservation measure are needed for this species. The aim of this study is to clarify genetic diversity and genetic structure of P. vachelli.

Methods: We collected 136 samples of eight different river sections (Taipingxi, Banan, Hechuan, Minjiangkou, Yibin, Shaonüping, Huixi, Fengjiaping) from the Three Gorges Dam to Baihetan Dam in the upper Yangtze River. High-throughput SNP (single nucleotide polymorphism) markers through genome re-sequencing method was used to study genetic diversity and genetic differentiation of P. vachellipopulations.

Results: The number of SNP and nucleotide diversity of Taipingxi and Banan populations in the Three Gorges Reservoir region were significantly higher than those in the other populations, and there were three genetic branches and abundant genetic sources in the two populations. However, there was only one genetic branch and single genetic source in Minjiangkou, Yibin, Shaonüping and Fengjiaping populations. The populations could be divided into three distinct genetic groups with great genetic differentiation. All individuals in Fengjiaping and Minjiangkou belonged to group 1, all individuals in Shaonüping and Yibin belonged to group 2, Huixi and Hechuan populations had two genetic branches (group 1 and group 2), and Banan and Taipingxi populations had three genetic branches (group 1, group 2 and group 3). The SNP number and nucleotide diversity were significantly affected by channel slope. The genetic differentiation was not related to geographical distance and isolated time.

Conclusion: The upstream populations with lower genetic diversity are more prone to genetic drift and thus need more attention in the fish protection. There are three distinct genetic structures in the upper Yangtze River, which can be regarded as three different genetic units for management of germplasm resource.

Key words: Pelteobagrus vachelli, the upper Yangtze River, genetic differentiation, genetic diversity, genome re-sequencing

熊飞, 刘红艳, 翟东东, 段辛斌, 田辉伍, 陈大庆 (2023) 基于基因组重测序的长江上游瓦氏黄颡鱼群体遗传结构. 生物多样性, 31, 22391. DOI: 10.17520/biods.2022391.

Fei Xiong, Hongyan Liu, Dongdong Zhai, Xinbin Duan, Huiwu Tian, Daqing Chen (2023) Population genetic structure of Pelteobagrus vachelli in the upper Yangtze River based on genome re-sequencing. Biodiversity Science, 31, 22391. DOI: 10.17520/biods.2022391.

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链接本文: https://www.biodiversity-science.net/CN/10.17520/biods.2022391

https://www.biodiversity-science.net/CN/Y2023/V31/I4/22391

图/表 9

图1 长江上游瓦氏黄颡鱼的样点分布。S1: 太平溪(TP); S2: 巴南(BN); S3: 合川(HC); S4: 岷江口(MJ); S5: 宜宾(YB); S6: 邵女坪(SN); S7: 桧溪(HX); S8: 冯家坪(FJ)。

Fig. 1 Sampling sites of Pelteobagrus vachelli in the upper reaches of Yangtze River. S1, Taipingxi (TP); S2, Banan (BN); S3, Hechuan (HC); S4, Minjiangkou (MJ); S5, Yibin (YB); S6, Shaonüping (SN); S7, Huixi (HX); S8, Fengjiaping (FJ).

表1 瓦氏黄颡鱼8个群体的样点信息。样点缩写见图1。

Table 1 Sampling information in eight populations of Pelteobagrus vachelli. Site abbreviations are shown in Fig. 1.

群体 Population	采样时间 Sampling time	样本数 No. of sample	海拔 Elevation (m)	坡降 Channel slope (m/km)	生境类型 Habitat type
太平溪 TP	2019.8	14	110	0.12	水库 Reservoir
巴南 BN	2019.8	25	160	0.20	回水区 Backwater area
合川 HC	2019.9	4	187	1.85	水库 Reservoir
岷江口 MJ	2019.10	25	257	2.26	河流 River
宜宾 YB	2019.10	6	253	0.70	河流 River
邵女坪 SN	2019.10	12	296	0.90	水库 Reservoir
桧溪 HX	2019.10	25	356	1.40	河流 River
冯家坪 FJ	2019.10	25	578	1.50	河流 River

表2 瓦氏黄颡鱼8个群体重测序数据及群体遗传多样性参数

Table 2 The genome re-sequencing data and genetic diversity parameters in eight populations of Pelteobagrus vachelli

群体 Population	样本数 No. of sample	Clean data (Gb)	Q30 (%)	测序深度Sequencing depth	序列比对率 Sequence mapped (%)	基因组覆盖度Coverage of genomic reference (%)	SNP数目 Number of SNP	核苷酸多样性指数Nucleotide diversity
太平溪 TP	14	145.22	93.11	9.54	54.31	72.92	4,172,876	2.44 × 10^?3
巴南 BN	25	236.41	92.82	8.71	53.43	71.68	3,543,176	2.81 × 10^?3
合川 HC	4	35.77	92.81	8.38	49.94	66.28	534,504	8.59 × 10^?4
岷江口 MJ	25	217.32	92.73	8.25	50.68	66.39	419,733	5.60 × 10^?4
宜宾 YB	6	50.16	91.87	7.44	48.50	67.36	563,968	6.76 × 10^?4
邵女坪 SN	12	128.29	92.79	9.37	49.09	69.64	457,603	5.75 × 10^?4
桧溪 HX	25	258.76	92.79	9.20	49.22	68.87	597,465	6.60 × 10^?4
冯家坪 FJ	25	273.27	92.78	9.57	49.06	69.73	441,092	5.84 × 10^?4
总体 Total	136	1,345.21	92.78	8.95	50.73	69.43	7,341,959	1.19 × 10^?3

图2 基于SNP标记分析8个瓦氏黄颡鱼群体的遗传结构。(a)由交叉验证错误率确定的最优分组数; (b) K = 3时, 所有个体的分组情况; (c) PCA聚类情况; (d) ML聚类树。样点缩写见图1。

Fig. 2 Genetic structure based on SNP markers in eight populations of Pelteobagrus vaclerii. (a) The optimal number of clusters determined by cross-validated error rate valley. (b) Population structure (K = 3) of all individuals. (c) PCA plot of every individual. (d) ML phylogenetic tree. Site abbreviations are shown in Fig. 1.

表3 长江上游瓦氏黄颡鱼两两群体之间的遗传分化指数

Table 3 Genetic differentiation between the pairwise populations of Pelteobagrus vaclerii in the upper Yangtze River

群体 Population	太平溪 TP	巴南 BN	合川 HC	岷江口 MJ	宜宾 YB	邵女坪 SN	桧溪 HX
巴南 BN	0.050
合川 HC	?0.109	?0.039
岷江口 MJ	0.112	0.143	0.075
宜宾 YB	?0.020	0.043	0.152	0.233
邵女坪 SN	0.068	0.112	0.192	0.235	0.000
桧溪 HX	0.126	0.154	0.079	0.179	?0.008	0.002
冯家坪 FJ	0.125	0.152	0.092	0.016	0.261	0.257	0.193

图3 瓦氏黄颡鱼3个遗传分支内个体间的遗传相似度IBS值

Fig. 3 Genetic similarity within three genetic groups based on identity by state (IBS)

图4 瓦氏黄颡鱼SNP数量与河道海拔(a)和坡降(b)的相关性分析。P < 0.05表示显著相关。

Fig. 4 Correlation analysis of the SNP numbers with elevation (a) and channel slope (b). P < 0.05 indicates significant correlation.

图5 瓦氏黄颡鱼核苷酸多样性指数与海拔(a)和坡降(b)的相关性分析。P < 0.05表示显著相关。

Fig. 5 Correlation analysis of nucleotide diversity with elevation (a) and channel slope (b). P < 0.05 indicates significant correlation.

图6 遗传分化(a)与地理距离(b)和隔离时间的Mantel检验。Fst: 遗传分化指数。

Fig. 6 Mantel test of genetic differentiation with geographical distance and isolated time. Fst, Index of genetic differentiation.

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基于基因组重测序的长江上游瓦氏黄颡鱼群体遗传结构

Population genetic structure of Pelteobagrus vachelli in the upper Yangtze River based on genome re-sequencing

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