Genetic Diversity and Structure of Largemouth Black Bass in Aquaculture Using Whole-genome SSR and SNP Markers

Simple Sequence Repeats (SSRs) and Single Nucleotide Polymorphisms (SNPs) offer distinct yet complementary insights into genetic diversity and population structure. This study compared whole-genome SSRs and SNPs to characterize Largemouth Black Bass (Micropterus salmoides) populations, a critical Chinese aquaculture species. We analyzed the selectively bred 'Zhejiang Black Bass No.1' F4 strain (ZL1f4) against two introduced cultured populations (Anhui: AL, Panzhihua: PL). High-throughput whole-genome resequencing yielded over one million high-quality SNP loci, and 28,250 (LobSTR) and 2,142 (SSRgenotyper) polymorphic SSRs, enabling robust comparative marker assessment. Results consistently demonstrated significantly reduced genetic diversity in selectively bred ZL1f4 (e.g., ZL1f4 average expected heterozygosity via LobSTR: 0.445 vs. AL: 0.536), reflecting artificial selection's genetic consequences. Both marker types revealed population differentiation, but SNPs consistently exhibited superior resolution (e.g., ZL1f4 vs. AL Fst: 0.1049 for SNPs vs. 0.0644 for LobSTR-SSR). Despite diversity differentiation, genetic structure analysis indicated retained shared ancestral components, suggesting selection influenced allele frequencies and heterozygosity, not fundamental genetic architecture. This research underscores SSR and SNP complementary strengths, advocating their integrated application for robust genetic characterization and informing sustainable aquaculture. Findings provide crucial data for effective genetic enhancement and long-term population management of Largemouth black bass, contributing to germplasm and aquatic biodiversity preservation.

• Publication year

  2025

• Venue

  Turkish Journal of Fisheries and Aquatic Sciences

• Publication date

  2025-07-23

• Fields of study

  Not labeled

• Identifiers
  DOI 10.4194/trjfas27297
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar

• No claims are published for this paper.

• No concepts are published for this paper.

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  2020influential reference
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• A framework for variation discovery and genotyping using next-generation DNA sequencing data

  2011influential reference
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• adegenet 1.3-1: new tools for the analysis of genome-wide SNP data

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  2010influential reference
• pegas: an R package for population genetics with an integrated-modular approach

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• Fast model-based estimation of ancestry in unrelated individuals.

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• Inferring weak population structure with the assistance of sample group information

  2009influential reference
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• A large genome center's improvements to the Illumina sequencing system

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• Taxonomic status and genetic diversity of cultured largemouth bass Micropterus salmoides in China

  2008influential reference
• PLINK: a tool set for whole-genome association and population-based linkage analyses.

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• CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure

  2007influential reference
• Detecting the number of clusters of individuals using the software structure: a simulation study

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  1999cited by this paper
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  1982cited by this paper
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• The detection of disease clustering and a generalized regression approach.

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