QTL mapping in domesticated and natural fish populations

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1 QTL mapping in domesticated and natural fish populations A. TRIANTAFYLLIDIS & A. VASEMÄGI

2 Quantitative trait locus QTL Trait with measurable phenotypic variation influenced by multiple polymorphic genes and environmental factors. 2 classes: Indirect markers for QTL Causal mutations in target genes agricultural yield, disease resistance, temperature tolerance, growth rate, reproductive output, even fitness

3 Identification of relative chromosomal positions constructing a genetic linkage map combination of the map with pedigrees p or Divergent populations/strains assessment of quantitative traits to identify molecular markers closely associated (linked) to QTL = Livestock subject to relatively recent and strong directional selection >selective allele sweeps > allele fixation>hitch-hiking closely linked loci >Linkage disequilibrium (LD) Positioning of QTL on the linkage map

4 Identification of relative chromosomal positions Most commercial species <5 generations of selection (except salmon, trout, tilapia and carps) No large differences between strains Long generation intervals (2-4 yrs) Progeny testing difficult due to vulnerability of breeders Hybridisation between closely related species possible Large numbers of Full-sib progeny possible

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6 Fine mapping of QTL QTLs are mapped to a relatively wide chromosomal region typically consisting hundreds of genes More polymorphic markers near the chromosomal regions containing the QTL are needed. Often more time-consuming and difficult The mapping of QTL accelerated through comparative genomics (though additional problems due to tetraploidy)

7 QTN,, quantitative trait nucleotide The identification of the causative polymorphisms, however, is based on a set of criteria Polymorphisms can fall to two extreme categories 1) Small number of genes each with large additive phenotypic effect. 2) Large number of genes contribute with very small effect on phenotype, also exhibiting varying degrees of nonadditive interactions

8 QTLs in Aquaculture Genetic linkage and QTL mapping not as advanced as other production species Though at least 27 linkage maps underway in aquaculture species, including various salmonid species, oysters, see bass, sea bream, catfish and tilapia

9 Montpellier IAGA9

10 QTLs in Aquaculture QTL for upper thermal tolerance, spawning time, stress tolerance, body weight, condition factor, meristic traits and embryonic development rate in rainbow trout QTL linked to feed conversion efficiency in catfish. Several groups are working on QTL mapping of disease and parasite resistance as well as various immunological and physiological traits (Gibson 2002, Cnaani et al 2004, Moen et al 2004, Zimmerman et al 2004, AQUAFIRST)

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13 Marker Assisted Selection-MAS To date, most of the genetic improvements of aquaculture broodstocks have been through the use of traditional selective breeding techniques: selection, crossbreeding, and hybridization (Hulata( 2001). MAS=Use of information on QTLs in efficiently crossing different strains of cultured species to maximize desirable traits (Poompuang( & Hallerman 1997). Future breeders are chosen based on genotypes. Selection of one trait may be made at the expense of another A well-planned MAS program should take all economically important traits into consideration.

14 Functional genetic variation in the wild Gradual increase but most experiments done in semi-wild conditions. Why? Individuals of measured phenotype, A pedigreed population, A genetic map of variable markers are in most cases unavailable for most free-living natural populations. Slate 2005

15 Functional genetic variation Slate 2005

16 What do we know about domestication processes? Zebrafish (Danio rerio) ) is a good model species Recent QTL analysis of behavioural and morphologic differentiation between wild and laboratory zebrafish identified several QTLs affecting boldness, anti-predator behaviour, weight and fat content (Wright et al 2006). Do domesticated phenotypes of different fish species reflect selection of similar physiological pathways (i.e. parallel evolution) or is it a case of convergent evolution?

17 Other alternatives? multiple-marker-based neutrality tests (hitchhiking mapping and genome scans), environmental association studies, admixture mapping and association analysis Combining QTL analysis with the above strategies provide new insights to the evolutionary processes behind adaptation and speciation (Vasemägi & Primmer 2005)

18 Vasemägi & Primmer 2005

19 The Future QTL studies are now exploring issues such as genetic correlations, gene-by by- environment interactions, epistasis and the adaptive importance of particular genes. These advances should permit the analysis of QTLs directly related to fitness of aquaculture individuals in the wild, and/ or the changes in the genetic architecture of wild individuals being domesticated.