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 FST (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.