Abstract

The migratory shad, Hilsa (Tenualosa ilisha) is an iconic species of profound economic and cultural value across the Indian sub-continent due to its delicious taste and significant contributions to gross domestic product (GDP). Lack of fundamental genomic data regarding sex determination, impedes development of optimized breeding techniques and target conservation goals. In this study, a next-generation sequencing (NGS)-based genotyping technique was applied to identify sex-linked markers, modes of sex determination, putative sex-determining genes and the population genomic structure of Hilsa. Genotyping of 94 Hilsa individuals (46 males and 48 females) collected from four distinct locations of Bangladesh (three different river systems and Bay of Bengal as a marine site) revealed 31,696 single-nucleotide polymorphisms (SNPs) and 12,754 presence/absence (PA) loci. Among these SNPs and PA, we identified 20 SNPs that were heterozygous in females but homozygous in males and 4 PA loci which were only present in females. Therefore, this study conclusively identifies a female heterogametic (ZZ/ZW) sex determination system in Hilsa. Comparative BLAST analysis using sex-linked loci against Hilsa genomes resulted in the identification of five candidate genes potentially involved in sex-determination pathways. Moreover, population genetic analysis revealed low spatial genetic differentiation among the four sampling sites but notable divergence between males and females (minimum 1.8–2.8% variation in principal coordinate analysis). For most of the sampling sites, higher observed heterozygosity (Ho) compared to expected heterozygosity (He) is the indicative of a robust population status with minimal evidence of inbreeding. Our study provides a baseline for further improving the management and conservation of the wild populations of the species.

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