Development of the new microsatellite multiplex PCR panel and genetic variation of farmed snakeskin gourami, Trichopodus pectoralis

Abstract

Genetically distinct populations have been used to found genetically diverse base populations, which are a prerequisite for successful selective breeding programs. Genetic markers are very useful in this regard as a tool for characterization of genetic diversity. In the present study, a panel of eight multiplex microsatellite primers was developed and seven of them were used to assess genetic diversity of farmed snakeskin gourami, which have been domesticated for more than 30 years. The microsatellites developed showed number of alleles per locus (A) of 3 to 22 alleles, expected heterozygosity (He) range of 0.328–0.923, and Polymorphic Information Content (PIC) range of 0.227–0.915. Four farmed populations of snakeskin gourami (n = 50 fish/population) possessed moderate genetic diversity (FST = 0.056; pairwise FST = − 0.047–0.041; genetic distance = 0.034–0.087), with all but one population pair significantly different as revealed by pairwise FST. Population structuring assigned the studied populations to two clusters. Genetic variation within populations was characterized, with average number of alleles/locus of 6.7–8.0 and expected heterozygosity of 0.65–0.68. Effective population size ranged from 13.2 to 37.7. Our study was the first to report a multiplex microsatellite panel for snakeskin gourami, and it showed genetic distinction among farmed stocks of this species.