Salmonids

Abstract

In the last decade, advances in molecular methods have permitted the detection of major genes or chromosomal regions (quantitative trait loci, QTLs) that account for an important fraction of the phenotypic variance of productive traits in many domestic animals, principally mammals. These discoveries have only been possible due to the development of statistical methods, molecular markers, and dense linkage maps. In salmonids, the development of genetic maps and QTL identification has been slower. These fish have a long interval between generations, a tetraploid genomic background, and few informative markers—all factors that impede mapping efforts. In spite of these factors, first generation linkage maps for the principal commercial salmon species have been developed, and many interesting QTLs have been located. In this chapter, as introductory topics, we revisit the taxonomic status, distribution, and biological and life history characteristics of salmonids (Salmo, Oncorhynchus, Coregonus, and Hucho), as well as the history of salmon culture since the fourteenth century and the principal genetic improvement programs for selected traits in commercial species. We describe the principal linkage maps published from 1990 to 2006, including four maps for rainbow trout, two maps for Atlantic salmon, and single maps for pink salmon, brown trout, Arctic charr and lake whitefish. In general, two mapping strategies have been used for salmon species, either using anonymous dominant markers (AFLP) and a cross design using doubled haploid fish, or using anonymous co-dominant markers (principally SSR) in a backcross mating design. These mapping studies have revealed the effect of ancestral tetraploidy, remarkable differences in the recombination rate between sexes, and syntenic regions across different species and genera. Second generation maps are under construction, including efforts to produce additional genomic resources (BAC libraries, sequencing and development of type I markers). QTL detection has been centered principally in rainbow trout and Atlantic salmon, with different approaches, mating designs, and results. Traits that have been studied include upper temperature tolerance, spawning date, body mass or weight, fork length, condition factor, resistance to diseases (IPN, IHN, ISA, or parasites), as well as other meristic and embryonic traits. Association studies using selective genotyping or bulked segregant analysis have produced specific markers for the Y chromosome, reproductive traits, flesh color, and albinism. Many of these markers, coding genes, telomeric regions, and ribosomal genes have been physically mapped using FISH. Finally, all the QTL mapping, markers, and other information on specific chromosome regions are being used to integrate the genetic and cytogenetic maps.