First high-density linkage map based on GBS derived genome wide SNP markers in Labeo catla (Hamilton, 1822)

Labeo catla is a commercially important Indian Major Carp, yet its genetic improvement has been hindered by a lack of high-resolution genomic resources. We report the construction of the first high-density SNP-based genetic linkage map for this species and present the associated genomic datasets deposited in public repositories. Mapping populations derived from five full-sib families (CF1, CF5, CF7, CF8, and CF11) comprising 196 individuals (10 parents and 190 offspring) were genotyped via Genotyping-by-Sequencing (GBS), generating 133.94 GB of raw sequence data. Using 782 informative SNP markers and Kosambi's mapping function, we resolved 25 complete linkage groups (LGs), consistent with the haploid karyotype of L. catla (n = 25). The resulting map spans a total genetic distance of 1279.8 cM, achieving a high-resolution average marker interval of 1.63 cM. Beyond linkage mapping, these markers were utilized to anchor 668 previously unplaced scaffolds, effectively organizing 502.33 Mb (49.29%) of the L. catla draft genome into pseudo-chromosomes. LG2 was identified as the largest pseudo-chromosome (213.83 Mb), while LG4 was the smallest (1.8 Mb). The average chromosome size was approximately 36.39 Mb. Comparative genomic analysis confirmed extensive chromosomal colinearity and conserved synteny between L. catla and Labeo rohita, with significantly higher structural divergence observed against the Danio rerio model. This high-density map and the subsequent chromosome-level scaffold anchoring provide a critical genomic framework for positional cloning, Marker-Assisted Selection (MAS), and the identification of Quantitative Trait Loci (QTLs) for traits such as rapid growth and disease resistance, accelerating the genetic enhancement of this species in Asian aquaculture.