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

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

Abstract

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

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.

Figures/Tables 8

References 26

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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