Aquaculture Reports (Aug 2023)
Population structure and genetic diversity of rainbow trout (Oncorhynchus mykiss) broodstocks from Brazil using SNP markers
Abstract
Rainbow trout (Oncorhynchus mykiss) are native to the Pacific Ocean coast of North America and the Kamchatka Peninsula of Russia. Brazilian populations of rainbow trout derive from various imports from European countries, the United States of America (U.S.A.) and Canada, from the 1950 s onwards. A total of 347 samples from nine commercial broodstock groups sampled from five farms in Brazil were genotyped with a panel of 96 SNPs to analyze the genetic diversity and structure of commercial rainbow trout farmed in Brazil. Pairwise coefficients of relatedness of individual animals and coefficients of genetic differentiation and inbreeding of broodstock groups were obtained, in addition to tests of genetic allocation of animals to their respective group. The mean observed and expected heterozygosities were 0.405 and 0.398, respectively. The total Fst was 0.172 and the pairwise Fst estimates considering all strains ranged from 0.036 to 0.338. The UPGMA genetic distance tree shows that broodstocks declared to be originally from Canada (Kamloops region) and from Northern California (Mount Shasta) are the most genetically distant from each other and from the remaining studied groups. Genetic structure analyses suggest a best value of K= 2, separating broodstock groups originally from the U.S.A. and Canada. Structure and Principal Component Analyses (PCA) indicate that the management practices of one of the farms was efficient in properly maintaining different broodstocks separated, while in another farm unwanted admixture has been occurring. Reclassification of these animals using Structure analysis results were corroborated with PCA and GeneClass2 analyses, providing evidence that advanced analyzes with low-density SNP data can be used to improve farm management practices and even correct past errors. The present study represents the first analysis of diversity and genetic structure of commercial rainbow trout farmed in Brazil using SNP markers.
