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Genetic Diversity Analysis of Seven Natural Populations of Procambarus clarkii from Jiangsu Province Based on Whole-Genome SNP Variations
XU Yu, XU Zhiqiang, YAN Weihui, LI Jiajia, HUANG Hongbing, LI Xuguang, LIU Yuanzhu, PAN Jianlin
Chin Agric Sci Bull ›› 2025, Vol. 41 ›› Issue (17) : 144-151.
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Abbreviation (ISO4): Chin Agric Sci Bull
Editor in chief: Yulong YIN
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Genetic Diversity Analysis of Seven Natural Populations of Procambarus clarkii from Jiangsu Province Based on Whole-Genome SNP Variations
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 (He) was between 0.2388 and 0.2854, while the observed heterozygosity (Ho) ranged from 0.3204 to 0.3387, suggesting a certain degree of heterozygote excess in these populations. The coefficient of genetic differentiation (Fst) 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.
Procambarus clarkii / SLAF-seq / SNP / genetic structure / genetic diversity / Jiangsu Province
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