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¹ Hangzhou Academy of Agricultural Sciences, Hangzhou, China (310024)
² Zhejiang Fisheries Technical Extension Center, Hangzhou, China (310023) DOI : 10.4194/TRJFAS27297 Viewed : 97 - Downloaded : 62 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. Keywords : Genetic diversity Ssr markers Snp markers Largemouth black bass