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Genetic structure and identification of divergent genomic regions of Solen grandis from three geographic populations based on whole genome resequencing

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This study investigates the genetic structure and variation of the economically significant grand jackknife clam, Solen grandis, across three geographical populations in China: Huludao, Rizhao, and Dongtai. Through whole-genome resequencing of 81 individuals, we uncovered low genetic diversity in all populations, with observed heterozygosity ranging from 0.097 to 0.101. Notably, population structure analysis revealed clustering of the Rizhao and Dongtai populations. This research enhances our understanding of S. grandis genetics and provides insights into conservation efforts.
Genetic structure and identification of divergent genomic regions of Solen grandis from three geographic populations based on whole genome resequencing

The recent study on the genetic structure of *Solen grandis*, commonly known as the grand jackknife clam, sheds light on the genetic variation across three geographical populations in China: Huludao (HLD), Rizhao (RZ), and Dongtai (DT). Utilizing whole-genome resequencing, researchers found that these populations exhibit low genetic diversity, as evidenced by specific metrics such as observed heterozygosity ranging from 0.097 to 0.101. While these figures may seem alarming, they also underscore the importance of understanding genetic diversity in marine species, a topic that resonates with ongoing discussions in marine biology, such as those explored in Estimating genetic diversity of abundant oceanic dolphins through repeated environmental DNA sampling and Genomic insights into population structure and somatic condition in the European sardine.

The low genetic diversity found in *Solen grandis* is particularly significant given its high economic value in mariculture. This finding raises critical questions about the resilience of these clam populations in the face of environmental changes and anthropogenic pressures. With an inbreeding coefficient (FIS) ranging from 0.042 to 0.053, there are implications for the long-term viability of these populations. Such conditions could hinder their ability to adapt to changing environments, making them more susceptible to diseases and fluctuations in habitat conditions. The genetic insights derived from this study could serve as a reference point for conservation strategies, emphasizing the need for proactive measures in managing genetic resources effectively.

The study's identification of 32 candidate selected regions and 10 significant genes also opens doors for future research. These genes, including ACE and RPS13, may play crucial roles in the clam's physiological processes and resilience to stressors. Understanding these genetic mechanisms can inform selective breeding programs aimed at enhancing the adaptability and productivity of *Solen grandis*. As we continue to confront challenges such as climate change and habitat degradation, the implications of this research extend beyond academic interest; they are vital for sustainable fisheries management and the economic stability of coastal communities reliant on this bivalve.

Moving forward, the role of genetic research in marine species conservation cannot be overstated. This study serves as a reminder that genetic diversity is not merely a statistic; it is a key component of ecological resilience. As we observe developments in marine genomics and conservation strategies, it is crucial to ask how we can leverage these insights for broader ecological benefits. Will the findings on *Solen grandis* prompt a reevaluation of mariculture practices in light of genetic health? The intersection of genetics and environmental stewardship is an area worth monitoring closely, as it holds the potential to guide future efforts in preserving not just *Solen grandis*, but a myriad of marine species facing similar challenges.

The grand jackknife clam, Solen grandis, is a crucial mariculture bivalve with high economic value. To investigate the genetic variation of S. grandis in China, the whole-genome resequencing was carried out on 81 individuals from three S. grandis geographical populations (Huludao [HLD], Rizhao [RZ], and Dongtai [DT]) to develop the genome-wide SNPs. Generally, all three populations indicated low genetic diversity. For each population, the observed heterozygosity (HO) ranged from 0.097 to 0.101, the expected heterozygosity (HE) from 0.105 to 0.109, the number of effective alleles (Ne) from 1.329 to 1.343, nucleotide diversity (π) between 0.0107 and 0.0111, the polymorphism information content (PIC) from 0.156 to 0.160, and the inbreeding coefficient (FIS) values of 0.042 to 0.053. Meanwhile, the fixation index pairwise (FST) values among the three S. grandis populations ranged from 0.008 to 0.023, which were low differentiation. Additionally, population structure analysis revealed that the RZ and DT populations first clustered together and were further grouped with the HLD population. Moreover, the genome-wide outlier analysis identified 32 candidate selected regions with a total size of 5.50Mb, as well as 10 candidate genes including ACE (Angiotensin-converting enzyme), KIAA1161 (Myogenesis regulating glycosidase), CES1 (Carboxylesterase 1), RPS13 (Ribosomal protein S13), APOD (Apolipoprotein D), PPP1R13B (Protein phosphatase 1 regulatory subunit 13B), and CHDH (Choline dehydrogenase), etc. Overall, this study enriches the genetic resources of S. grandis and improves our understanding of its population genetic structure and selection signatures, providing a useful reference for future genetic resource conservation and management.

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#Solen grandis#whole genome resequencing#genetic variation#geographical populations#genetic diversity#SNPs#candidate genes#genetic resources#observed heterozygosity#expected heterozygosity#population structure analysis#candidate regions#effective alleles#nucleotide diversity#polymorphism information content#selection signatures#inbreeding coefficient#fixation index#mariculture bivalve#genomic regions