Development of genome-wide novel microsatellite markers and genetic variability analysis of Asian seabass, Lates calcarifer (Bloch, 1790)

The Asian seabass, Lates calcarifer, is an important species in the Asia-Pacific region and is cultured widely. The growing demand for its seed has led to an increase in commercial introductions from other nations to India. In the current study, we developed novel microsatellite markers and analysed the natural genetic diversity of L. calcarifer. The whole genome was sequenced on PacBio RSII to generate low-depth data. A total of 519 microsatellites were mined from the assembled genome. Genetic diversity and population structure were analysed in L. calcarifer using the newly developed set of microsatellite loci. Most of the loci exhibited high polymorphic information content (PIC) with an average of 0.637. A total of 213 alleles were detected. The mean observed and expected heterozygosity were 0.548 and 0.679, respectively. The probability of identity (PID/PIDsib) demonstrated the utility of loci for individual identification. Moderate to high levels of genetic diversity was evident, with an overall F of 0.031. The pairwise F and AMOVA results showed significant divergence among the populations and suggested that the samples were not drawn from a single gene pool. The clustering (PCoA and DAPC) suggested the possibility of the presence of distinct genetic populations on Indian coasts. The study developed a validated marker set for deciphering genetic diversity and will be useful for various purposes of conservation and aquaculture, such as identifying selection signatures, parentage assignment, and genetic improvement.