Abstract
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
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.