Genome‐Wide SNP Discovery and Population Genomic Characterisation in Indian Major Carp Labeo catla (Hamilton, 1822) Through Low‐Depth Whole‐Genome Resequencing

ABSTRACT Single nucleotide polymorphisms (SNPs) are key markers for population and conservation genetics in aquaculture species. Using low‐depth whole‐genome resequencing of 35 Labeo catla individuals from seven populations (three wild riverine, four hatchery), we generated the first genome‐wide SNP catalogue for this Indian major carp. Filtering against the L. catla reference genome (GCA_012976165.1) yielded 2.05 million high‐quality bi‐allelic SNPs (467 291–1 221 268 per population), with 27 000 shared across all populations. Heterozygosity (He = 0.4477–0.4532) and nucleotide diversity ( π = 0.4703–0.4816) were broadly comparable across populations. Pairwise F ST (0.079–0.106) and UPGMA clustering resolved Cauvery as most divergent population, grouping the remaining six into two clusters (PCA: PC1 = 21.4%, PC2 = 16.8%). A differentiation scan identified 270 candidate high‐differentiation SNPs (top 1%; score > 0.222) enriched for missense variants (~2.05‐fold; p = 0.021), implicating cell‐adhesion, extracellular‐matrix and muscle‐development genes in population differentiation. An independent chi‐square test of allele‐frequency heterogeneity, corrected for multiple testing ( q < 0.05), retained 114 of these 270 SNPs, mapping to 30 genes whose GO profile (endosome, granule and endolysosome lumen) differed from the broader 270‐SNP set indicating exploratory, hypothesis generating candidates rather than confirmed selection targets. Genome‐wide annotation of 2 521 013 SNPs classified 108 113 (1.14%) as moderate‐impact missense and 5266 (0.06%) as high‐impact variants. These findings align with prior genotyping‐by‐sequencing data but extend marker density ~200‐fold, providing the first genome‐wide diversity, differentiation and functional profile for L. catla . The dataset (BioProject PRJNA1441081; Figshare doi: https://doi.org/10.6084/m9.figshare.31829770 ) supports SNP array design, GWAS and conservation monitoring of Catla riverine stocks.