Genetic variation in farmed population of Rainbow trout (Onchorhynchus mykiss) based on microsatellite markers in Iran

A total of 64 specimens of rainbow trout (Onchorhynchus mykiss) from 3 different regions in
Iran were collected. About 2-3 g of caudal fin samples were removed from each specimen and
preserved in absolute ethyl alcohol and transferred to the genetic laboratory. Genomic DNA
was extracted using the phenol-chloroform method and then DNA content and quality was
determined using spectrophotometry and agarose gel electrophoresis, respectively.
Polymerase Chain Reaction (PCR) of genomic DNA fin samples was carried out using 8 pairs
of microsatellite primers. All PCR products were electrophoresed on 6% polyacrylamide gel
and stained with silver nitrate. Following the scoring of alleles, all parameters including
effective number of alleles, observed and expected heterozygosity, shanon index, Hardy-
Weinberg equilibrium test and FST were calculated using AMOVA analysis in the GenAlex
and Popgene programs. The results showed that 8 pairs of microsatellite primers were
polymorphic. In total, alleles were determined with the range size of 64-280 bp. The locus
OtsG 249 had maximum number of allele (9) and loci OtsG 432 and OtsG 474 had minimum
number of allele (2). The observed heterozygosity was between 0.869 and 0.916. Hardy-
Weinberg departure was observed for most loci from all farms and were disequilibrium. The
Fst results showed that maximum FST (0.079) were between farms in Tehran and Yasuj and
minimum (0.041) were between farms in Hamadan and Yasuj. Based on the results of
AMOVA analysis, significant differences were detected between all farms. The results
suggest that the unique genetic variation of rainbow trout in hatchery farms of Iran represents
a highly valuable genetic resource and provide useful information for creating a based
population in the future breeding programs.