Genome-wide and chromosomal microsatellite marker landscape analysis within the genus Crassostrea

Abstract

Microsatellite is a classical codominant marker frequently used to study genetics and evolution of living entities as well as molecular breeding in commercially important species. Although it has a tremendous application in oyster aquaculture, the lack of knowledge about its type, distribution pattern, and comparative analysis is limited. Thus, in this study, we conducted a genome-wide as well as chromosomal microsatellite landscape analysis within the genus Crassostrea. The genome-wide microsatellites number varied from 169432-212368, with relative abundance (RA) and relative density (RD) ranging from 310.18-336.5 loci/Mb and 7553.4-8793.42 bp/Mb, respectively. About 14.99-16.75% of total microsatellites were considered compound microsatellites having cRA and cRD, 21.78-25.5 loci/Mb, and 1332.81-1694.54 bp/Mb, respectively. The mononucleotide microsatellites were predominant followed by di and tetranucleotide. The RA and RD of the SSRs revealed no correlation with genome size but a significant correlation with GC content. However, the number of SSRs showed a significant relationship with the genome size but no relation with GC content. In contrast, the incidence of cSSR was positively associated with genome size and GC content. Finally, 29 cSSR loci were developed and validated in C. hongkonensis using one wild population followed by its cross-species amplification. The allele number (Ne), observed heterozygosity (Ho), expected heterozygosity (He), inbreeding co-efficient (Fis), the polymorphic information content (PIC), ranged from 2-10, 0.092-0.897, 0.0001-1, 0.088-0.828, respectively. The present study elucidated microsatellite evolution within the Crassostrea genome and the loci developed can be utilized for brood stock analysis, parentage assignment, and construction of linkage map of the respective species.