Microsatellites as genetic tools for monitoring escapes and introgression

Transcription

1 Microsatellites as genetic tools for monitoring escapes and introgression Alexander TRIANTAFYLLIDIS & Paulo A. PRODÖHL

2 What are microsatellites? Microsatellites (SSR Simple Sequence Repeats) The repeat units are generally di-, tri-, tetra-, or pentanucleotides Using a panel of several microsatellite loci, a unique combined SSR genotype profile can be produced for each individual

3

4 Why use Microsatellites 1) Highly Polymorphic 2) Highly abundant 3) PCR based 4) Neutral 5) Codominant 6) availability of high-throughput capillary sequencers or mass spectrometry 7) Can be used at a range of genetic scales a random individual would have a low probability of matching a given genotype

5 Where to use Microsatellites In the field of fisheries and aquaculture Population genetics Estimation of genetic differentiation Characterization of genetic stocks Conservation/management of biological resources (ESUs, MUs etc)

6 Where to use Microsatellites Constructing dense linkage maps S. aurata Linkage Map, Franch R, et al Genetics in press Mapping economically important quantitative traits, identifying genes responsible for these traits and aiding in marker-assisted breeding programmes.

7 In recent years, the development of powerful analytical methods/statistical programmes, has shifted the focus from populations to individuals

8 It is now possible to assign or exclude individuals originating from a claimed population, parental group etc The individual-centred programs aim to detect the strange individuals, since individuals will present different multilocus genotypes than expected for native individuals

9 Paternity and relatedness analysis of natural populations and hatchery broodstock In species such as: Atlantic salmon, raibow trout, turbot, sea bass, sea bream

10 Trade control of fish products Frecuencia 0,25 0,2 0,15 0,1 0, * * * ** * * * ** * * 230 ** * * * * * * * M. bilinearis M. hubbsi M. merluccius M. capensis ** * * Number of private alleles: - North American: 10 - South American : 3 - European: 10 - African: 2 Total number of alleles: 52 Mmer UEA W01 Tamaño alelos Castillo AGF, et al

11 Identification of the genetic origin of specific individuals The one that did not get away: Individual assignment using microsatellites detects a case of fishing competition fraud (Primmer et al. 1999)

12 Identification of hatchery individuals / Assessment of introgression into wild populations Baseline populations- historical samples existant in these two cases

13 Impact on fitness of introgressed/stocked populations

14 Individuals are allocated to predefined populations (classification: frequency, bayesian, distance: GeneClass2 Piry et al 2004) or to virtual populations (clustering: bayesian: STRUCTURE Pritchard et al 2000) Success depends on 1) Number of loci 2) Number of alleles 3) Levels of genetic differentiation 4) Sample sizes

15 Conclusion SSRs are the current favorites for genetic monitoring of farmed stocks, artificially reared individuals and analysis of impact of their release into wild populations

16 The Future More comparisons needed on the different theoretical models used (often giving contradictory results) More research on difficult situations (low differentiation, no H-W, unequal samples,genotyping problems, co-ancestry Guinand et al 2006) what are the alternatives? More research with real data sets (Excoffier & Heckel 2006) Hitch-hiking mapping (Rise et al. 2004), QTL mapping as regards identification of hatchery adaptation genes Combination with other markers, especially SNPs (Morin et al 2004)

17 References 1. Schlötterer C Nature Reviews Genetics 5: Chistiakov DA, Hellemans B & Volckaert FAM Aquaculture 255: Hansen MM, Kenchington E & Nielsen EE Fish and Fisheries 2: Primmer CR., Koskinen MT & Piironen J Proceedings of the Royal Society of London, B Biological Sciences 267: Hauser L, Seamons TR, Dauer M, Naish KA & Quinn TP Molecular Ecology 15: Renshaw MA, Saillant E, Broughton RE & Gold JR Forensic Science International 156: Bravington MV & Ward RD Molecular Ecology 13: Excoffier L. & Heckel G Nature Reviews Genetics 7: Piry S, Alapetite A, Cornuet J-M, Paetkau D, Baudouin L & Estoup A Journal of Heredity 95: Pritchard JK, Stephens M & Donnelly P Genetics 155: Manel S, Gaggiotti OE & Waples RS Trends in Ecology & Evolution 20: Guinand et al Genetica 127: Castillo AGF, Martinez JL, Garcia-Vazquez E J. Food Protection 66: Morin PA, Luikart G, Wayne RK SNP workshop group 2004 TREE 19: Franch R, et al Genetics in press /genetics Rise et al Genome Research 14: