A second generation genetic map for rainbow trout (Oncorhynchus mykiss)

Abstract

Background: Genetic maps characterizing the inheritance patterns of traits and markers have been developed for a wide range of species and used to study questions in biomedicine, agriculture, ecology and evolutionary biology. The status of rainbow trout genetic maps has progressed significantly over the last decade due to interest in this species in aquaculture and sport fisheries, and as a model research organism for studies related to carcinogenesis, toxicology, comparative immunology, disease ecology, physiology and nutrition. We constructed a second generation genetic map for rainbow trout using microsatellite markers to facilitate the identification of quantitative trait loci for traits affecting aquaculture production efficiency and the extraction of comparative information from the genome sequences of model fish species.

Rapid parallel evolution of standing variation in a single, complex, genomic region is associated with life history in steelhead/rainbow trout

“…The locus with the highest pairwise F ST value was in complete linkage disequilibrium (LD) with a second outlier locus, and both loci map to the same position on O. mykiss chromosome Omy5 [43,44]. A third outlier locus on Omy5 was also in LD with the first two [42].…”

The Birds and the Bees and the Flowers and the Trees: Lessons from Genetic Mapping of Sex Determination in Plants and Animals

“…Male heterogametic species are denoted by XY, even when there is no known chromosome heteromorphism, and female heterogametic species are similarly denoted by ZW. Sex determination in silversides has been shown to have a genetic component, although it is not known whether males or females are the heterozygous sex (Conover and Kynard 1981). microsatellite loci is starting to indicate some chromosomal homologies, even between distantly related fish (Rexroad et al 2008). However, these homologies have not yet been shown to extend to entire chromosomes having the same gene content in distant relatives, and fish chromosomes appear to have been extensively rearranged (Naruse et al 2004) and it is unlikely that entire arms will be recognizable as they are in Drosophila and Hymenoptera.…”

A major effect quantitative trait locus for whirling disease resistance identified in rainbow trout (Oncorhynchus mykiss)

“…JoinMap 4 assigned markers to map positions using a minimum logarithm of the odds (LOD) threshold of three and a recombination threshold of 0.49, combined with previous knowledge of marker positions from published maps (Guyomard et al, 2006;Rexroad et al, 2008). The Haldane mapping function was used to convert recombination frequencies to map distances (cM).…”

“…Microsatellite markers were chosen based on previously published O. mykiss linkage maps (Danzmann et al, 2005;Guyomard et al, 2006;Rexroad et al, 2008) to provide adequate coverage across all chromosomes. For the F 2 mapping families, 3-12 microsatellite loci were multiplexed in each reaction using M13, SP6, T7P or T7T universal primer tails (Schuelke, 2000) labeled with 6-FAM, VIC, NED or PET fluorescent dyes (Applied Biosystems).…”