Development of novel microsatellite markers for aquaculture important species, milkfish (Chanos chanos Forsskål, 1775) with implications of conservation and management

A total of 20 polymorphic microsatellites were developed and characterized for a potential aquaculture species, Chanos chanos, utilizing the comprehensive whole genome data of C. chanos obtained from the GenBank database (accession number: LR697106). Using the MIcroSAtellite (MISA) tool, potential microsatellite motifs were identified in the assembled contigs and unigenes and with the PRIMER 3 input software (Version 4.1.0), new primers were developed. The number of alleles per locus in C. chanos varied from 9 to 16, with observed heterozygosities ranging from 0.710 to 0.926, while the expected heterozygosities were within the range of 0.720 to 0.902. Among the 20 microsatellite loci, the majority exhibited PIC values > 0.75. Validation of these microsatellite markers proved that these markers can be used as a significant tool for analysing genetic differentiation as well genetic relationships among C. chanos.