基于全基因组SNP变异分析江苏克氏原螯虾7个天然群体的遗传多样性特征

doi:10.11924/j.issn.1000-6850.casb2024-0725

中国农学通报 ›› 2025, Vol. 41 ›› Issue (17): 144-151.doi: 10.11924/j.issn.1000-6850.casb2024-0725

基于全基因组SNP变异分析江苏克氏原螯虾7个天然群体的遗传多样性特征

徐宇¹(), 许志强¹(), 严维辉¹, 李佳佳¹, 黄鸿兵¹, 李旭光¹, 刘远柱², 潘建林¹

¹ 农业农村部淡水虾蟹遗传育种与养殖重点实验室（部省共建）/江苏省淡水水产研究所，南京 210017
² 南京螯龙现代农业科技研究院有限公司，南京 211800

收稿日期:2024-11-29 修回日期:2025-03-03 出版日期:2025-06-15 发布日期:2025-06-15
通讯作者:
许志强，男，1978年出生，江苏赣榆人，研究员，博士，主要从事水产动物种质资源保护与遗传育种研究。通信地址：210017 江苏南京建邺区南湖东路90号江苏省淡水水产研究所，E-mail：zhiqiangx@163.com。
作者简介:
徐宇，女，1986年出生，江苏高邮人，副研究员，硕士，研究方向：水产动物种质资源保护与遗传育种。通信地址：210017 江苏南京建邺区南湖东路90号江苏省淡水水产研究所，E-mail：jsgyxuyu@126.com。
基金资助:
江苏省种业振兴“揭榜挂帅”项目“克氏原螯虾优异种质创制与新品种选育”(JBGS〔2021〕119); 江苏现代农业（克氏原螯虾）产业技术体系种质创新与苗种繁育创新团队(JATS〔2023〕372); 国家重点研发计划“中华绒螯蟹、克氏原螯虾、螺蛳大规格抗逆新品种培育”(2022YFD2400700)

Genetic Diversity Analysis of Seven Natural Populations of Procambarus clarkii from Jiangsu Province Based on Whole-Genome SNP Variations

XU Yu¹(), XU Zhiqiang¹(), YAN Weihui¹, LI Jiajia¹, HUANG Hongbing¹, LI Xuguang¹, LIU Yuanzhu², PAN Jianlin¹

¹ Key Laboratory of Genetic Breeding and Cultivation for Freshwater Crustacean, Ministry of Agriculture and Rural Affairs, Nanjing 210017
² Nanjing Aolong Modern Agricultural Science and Technology Research Institute Co., LTD, Nanjing 211800

Received:2024-11-29 Revised:2025-03-03 Published:2025-06-15 Online:2025-06-15

摘要/Abstract

摘要：

为了解人工养殖活动对克氏原螯虾(Procambarus clarkii)天然群体遗传多样性的影响，本研究基于SLAF-Seq测序技术所开发的SNP分子标记，对江苏克氏原螯虾主产区（微山湖、高邮湖、洪泽湖和骆马湖）和非主产区（滆湖、固城湖和阳澄湖）7个天然群体进行遗传多样性和遗传结构特征分析。在7个群体210尾个体中共检测到176486个SNP和24828个Indel，平均Q30和GC含量分别为92.77%和44.31%。结果发现：7个克氏原螯虾天然群体的平均多态信息含量(PIC)为0.2070~0.2246；期望杂合度(H_e)为0.2388~0.2854，观测杂合度(H_o)为0.3204~0.3387，群体中存在杂合子过剩现象。群体间遗传分化系数(F_st)为0.033~0.124，表现为中度分化；7个群体可分为4个血统，洪泽湖、骆马湖、高邮湖、滆湖4个群体划为一群，微山湖、固城湖和阳澄湖3个群体均单独划为一群，不同群体间显示出明显的地理分布格局。连锁不平衡分析表明，克氏原螯虾群体的LD衰减距离较短，100 bp物理距离内r²衰减至0.1以下。进一步的选择清除分析显示，主产区与非主产区不同群体间共有153个受到强烈选择的基因组区域，受选基因显著富集在Cell cycle、AMPK signaling pathway以及Meiosis等与克氏原螯虾能量代谢、氧化应激以及生长发育等生物学功能密切相关的基因通路。本研究揭示了江苏克氏原螯虾主产区和非主产区天然群体的遗传多样性特征，以期为国内克氏原螯虾种质资源的开发、利用与保护工作提供理论依据。

关键词: 克氏原螯虾, SLAF-Seq测序, SNP, 群体遗传结构, 遗传多样性, 江苏省

Abstract:

To explore the influence of artificial breeding activities on the genetic diversity of natural Procambarus clarkii populations, SNP molecular markers developed via SLAF-Seq sequencing technology were employed to analyze the genetic diversity and genetic structure of seven natural P. clarkii populations in Jiangsu Province. These populations included the main production areas (Weishan Lake, Gaoyou Lake, Hongze Lake, and Luoma Lake) and non-main production areas (Ge Lake, Gucheng Lake, and Yangcheng Lake). In total, 176486 SNPs and 24828 Indels were detected in 210 individuals from these populations. The average Q30 and GC contents were 92.77% and 44.31%, respectively. The average polymorphic information content (PIC) of the seven populations ranged from 0.2070 to 0.2246. The expected heterozygosity (H_e) was between 0.2388 and 0.2854, while the observed heterozygosity (H_o) ranged from 0.3204 to 0.3387, suggesting a certain degree of heterozygote excess in these populations. The coefficient of genetic differentiation (F_st) among populations varied from 0.033 to 0.124, indicating moderate differentiation. The seven populations could be divided into four lineages. The populations from Hongze Lake, Luoma Lake, Gaoyou Lake, and Ge Lake were classified as one group, and the remaining three populations from Weishan Lake, Gucheng Lake, and Yangcheng Lake formed separate groups respectively. This demonstrated clear geographical distribution patterns among the populations. Linkage disequilibrium (LD) analysis showed that the LD decay distance in the P. clarkii populations was short, with the r² value decreasing to less than 0.1 within a 100-bp physical distance. Further selection sweep analysis revealed 153 strongly selected genomic regions between the main production area and non-main production area populations. These selected genes were significantly enriched in pathways such as the Cell cycle, AMPK signaling pathway, Meiosis, and other gene pathways closely related to the biological functions of P. clarkii. This study elucidated the genetic diversity characteristics of natural populations in both main and non-main production areas of P. clarkii in Jiangsu Province, thus providing a theoretical basis for the development, utilization and conservation of P. clarkii germplasm resources.

Key words: Procambarus clarkii, SLAF-seq, SNP, genetic structure, genetic diversity, Jiangsu Province

徐宇, 许志强, 严维辉, 李佳佳, 黄鸿兵, 李旭光, 刘远柱, 潘建林. 基于全基因组SNP变异分析江苏克氏原螯虾7个天然群体的遗传多样性特征[J]. 中国农学通报, 2025, 41(17): 144-151.

XU Yu, XU Zhiqiang, YAN Weihui, LI Jiajia, HUANG Hongbing, LI Xuguang, LIU Yuanzhu, PAN Jianlin. Genetic Diversity Analysis of Seven Natural Populations of Procambarus clarkii from Jiangsu Province Based on Whole-Genome SNP Variations[J]. Chinese Agricultural Science Bulletin, 2025, 41(17): 144-151.

图/表 8

参考文献 26

[7]	谭云飞, 蓬国辉, 熊礼静, 等. 长江中下游流域13个克氏原螯虾群体遗传多样性和遗传结构分析[J]. 华中农业大学学报, 2020, 39(2):33-39.
[8]	LI Y H, GUO X W, CAO X J, et al. Population genetic structure and post-establishment dispersal patterns of the red swamp crayfish Procambarus clarkii in China[J]. PLoS one, 2012, 7(7):e40652.
[9]	YI S K, LI Y H, SHI L L, et al. Characterization of Population Genetic Structure of red swamp crayfish, Procambarus clarkii, in China[J]. Scientific reports 8, 2018:5586.
[10]	XU Z Q, GAOT H, XU Y, et al. A chromosome-level reference genome of red swamp crayfish Procambarus clarkii provides insights into the gene families regarding growth or development in crustaceans[J]. Genomics, 2021, 113(5):3274-3284.
[11]	LI H, DURBIN R. Fast and accurate long-read alignment with Burrows-WHeeler transform[J]. Bioinformatics, 2010, 26(5):589-595. doi: 10.1093/bioinformatics/btp698 pmid: 20080505
[12]	DANECEK P, AUTON A, ABECASIS G, et al. The variant call formatand VCFtools[J]. Bioinformatics, 2011, 27(15):2156-2158.
[13]	ALEXANDER D H, NOVEMBRE J, LANGE K. Fast model-based estimation of ancestry in unrelated individuals[J]. Genome research, 2009, 19:1655-1664. doi: 10.1101/gr.094052.109 pmid: 19648217
[14]	STAMATAKIS A. RAxML version 8:A tool for phylogenetic analysis and post-analysis of large phylogenies[J]. Bioinformatics, 2014, 30:1312-1313.
[15]	PETR D, ADAM A, GONCALO A, et al. 1000 Genomes project analysis group, the variant call format and VCFtools[J]. Bioinformatics, 2011, 27(15):2156-2158. doi: 10.1093/bioinformatics/btr330 pmid: 21653522
[16]	MINORU K, MIHO F, YOKO S, et al. KEGG for taxonomy-based analysis of pathways and genomes[J]. Nucleic acids research, 2023, 51:587-592.
[17]	BOTSTEIN D, WHITE R L, SKOLNICK M, et al. Construction of a genetic linkage map in man using restriction fragment length polymorphisms[J]. American journal human genetics, 1980, 32(3):314-331.
[1]	HUNER J V. Procambarus in North America and elsewhere. In: HOLDICH D M, LOWERYR S. Freshwater crayfish: biology, management and exploitation[M]. Portland: timber press, 1988:239-261.
[2]	王祖峰. 浅谈我国小龙虾养殖产业发展面临的问题与建议[J]. 中国渔业经济, 2019, 5(37):107-111.
[3]	YUE G H, LI J, BAI Z, et al. Genetic diversity and population structure of the invasive alien red swamp crayfish[J]. Biological invasions, 2010, 12:2697-2706.
[4]	全国水产技术推广总站, 中国水产学会. 中国小龙虾产业发展报告(2024)[J]. 中国水产, 2024, 584(7):14-20.
[5]	徐宇, 许志强, 黄鸿兵, 等. 江苏小龙虾产业发展历程、现状和展望[J]. 水产养殖, 2021, 42(10):77-80.
[6]	刘国锋, 徐增洪, 徐跑, 等. 我国克氏原螯虾种苗产业发展现状[J]. 江苏农业科学, 2022, 50(9):1-6.
[18]	XIA Q, GUO Y, ZHANG Z, et al. Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx)[J]. Science, 2009, 326(5951):433-436. doi: 10.1126/science.1176620 pmid: 19713493
[19]	SIDNEY C H CHEUNG. The social life of American crayfish in Asia. In: JAMESF. Globalization, food and social identities in the Asia Pacific Region[M]. Tokyo, Sophia University institute of comparative culture, 2010.
[20]	LIU F, QU Y K, GENG C, et al. Analysis of the population structure and genetic diversity of the red swamp crayfish (Procambarus clarkii) in China using SSR markers[J]. Electronic journal of biotechnology, 2020, 47:59-71.
[21]	LIU J, SUN Y, CHEN Q, et al. Genetic diversity analysis of the red swamp crayfish Procambarus clarkii in three cultured populations based on microsatellite markers[J]. Animals, 2023, 13(11):1881.
[22]	刘炜. 克氏原螯虾肌肉肌苷酸含量及遗传多样性研究[D]. 扬州: 扬州大学, 2008:27-34.
[23]	曾怡锦. 温、热带玉米特异转座子的验证及功能初探[D]. 雅安: 四川农业大学, 2016:4-6.
[24]	罗依妮, 王露. 转座子的研究现状[J]. 中国细胞生物学学报, 2024, 46(7):1323-1334.
[25]	YASUDA K, ITO M, SUGITA T, et al. Utilization of transposable element mPing as a novel genetic tool for modification of the stress response in rice[J]. Molecular breeding, 2013, 32(3):505-516.
[26]	NATIO K, ZHANG F, TSUKIYAMA T, et al. Unexpected consequences of a sudden and massive transposon amplification on rice gene expression[J]. Nature, 2009, 461(7267):1130-1134.

群体	样品量	期望杂合度H_e	观测杂合度H_o	核苷酸多样性(π)	Nei’s多样性指数	Shannon多样性指数	PIC指数	TajimaʹD
微山湖	30	0.2488	0.3366	0.00022	0.3423	0.6178	0.2246	0.7773
骆马湖	30	0.2388	0.3204	0.00025	0.3258	0.5860	0.2119	0.6244
洪泽湖	30	0.2684	0.3293	0.00027	0.3349	0.5811	0.2099	0.7383
高邮湖	30	0.2854	0.3262	0.00029	0.3318	0.5738	0.2070	0.6940
固城湖	30	0.2660	0.3314	0.00024	0.3370	0.6029	0.2187	0.6976
滆湖	30	0.2649	0.3301	0.00025	0.3356	0.5842	0.2111	0.7492
阳澄湖	30	0.2405	0.3387	0.00023	0.3445	0.6170	0.2243	0.8157
总体	210	0.2281	0.3176	0.00025	0.3395	0.4690	0.1668	1.2166

群体	样品量	期望杂合度H_e	观测杂合度H_o	核苷酸多样性(π)	Nei’s多样性指数	Shannon多样性指数	PIC指数	TajimaʹD
微山湖	30	0.2488	0.3366	0.00022	0.3423	0.6178	0.2246	0.7773
骆马湖	30	0.2388	0.3204	0.00025	0.3258	0.5860	0.2119	0.6244
洪泽湖	30	0.2684	0.3293	0.00027	0.3349	0.5811	0.2099	0.7383
高邮湖	30	0.2854	0.3262	0.00029	0.3318	0.5738	0.2070	0.6940
固城湖	30	0.2660	0.3314	0.00024	0.3370	0.6029	0.2187	0.6976
滆湖	30	0.2649	0.3301	0.00025	0.3356	0.5842	0.2111	0.7492
阳澄湖	30	0.2405	0.3387	0.00023	0.3445	0.6170	0.2243	0.8157
总体	210	0.2281	0.3176	0.00025	0.3395	0.4690	0.1668	1.2166

群体	洪泽湖	骆马湖	滆湖	高邮湖	固城湖	阳澄湖
骆马湖	0.034
滆湖	0.043	0.042
高邮湖	0.038	0.033	0.041
固城湖	0.087	0.076	0.091	0.084
阳澄湖	0.093	0.088	0.084	0.087	0.124
微山湖	0.078	0.044	0.081	0.079	0.115	0.124

群体	洪泽湖	骆马湖	滆湖	高邮湖	固城湖	阳澄湖
骆马湖	0.034
滆湖	0.043	0.042
高邮湖	0.038	0.033	0.041
固城湖	0.087	0.076	0.091	0.084
阳澄湖	0.093	0.088	0.084	0.087	0.124
微山湖	0.078	0.044	0.081	0.079	0.115	0.124

通路名称	差异表达基因数量/个	P值
ko04111:Cell cycle - yeast	19	0.000241734
ko04152:AMPK signaling pathway	18	0.001390975
ko04113:Meiosis - yeast	13	0.004359486
ko04014:Ras signaling pathway	22	0.006334541
ko04931:Insulin resistance	15	0.007683583
ko04110:Cell cycle	18	0.013699122
ko04360:Axon guidance	17	0.014619571
ko00630:Glyoxylate and dicarboxylate metabolism	7	0.017398165
ko04261:Adrenergic signaling in cardiomyocytes	16	0.018982873
ko01521:EGFR tyrosine kinase inhibitor resistance	10	0.023830541
ko04068:FoxO signaling pathway	14	0.024708277
ko04070:Phosphatidylinositol signaling system	11	0.025133809
ko04071:Sphingolipid signaling pathway	16	0.025938795
ko04725:Cholinergic synapse	11	0.027207975
ko04910:Insulin signaling pathway	15	0.027948876
ko00562:Inositol phosphate metabolism	11	0.029402756
ko04370:VEGF signaling pathway	7	0.031595847
ko04012:ErbB signaling pathway	9	0.031703516
ko05214:Glioma	7	0.035155741
ko04022:cGMP-PKG signaling pathway	17	0.035532401

基于全基因组SNP变异分析江苏克氏原螯虾7个天然群体的遗传多样性特征

Genetic Diversity Analysis of Seven Natural Populations of Procambarus clarkii from Jiangsu Province Based on Whole-Genome SNP Variations

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