Proceedings of the XLV Italian Society of Agricultural Genetics - SIGA Annual Congress

Salsomaggiore Terme, Italy - 26/29 September, 2001

ISBN 88-900622-1-5

Oral Communication Abstract

ESTIMATE OF MUTATION RATE OF MICROSATELLITES IN NORWAY SPRUCE: A SIMULATION APPROACH

MAGNI F.*, SCOTTI I.*, MORGANTE M.*^,**

* Dipartimento di Produzione Vegetale e Tecnologie Agrarie, Università degli Studi di Udine, Udine, Italy

federica.magni@dpvta.uniud.it; ivan.scotti@dpvta.uniud.it

** DuPont Agricultural Biotechnology, Delaware Technology Park-USA

Morgante@USA.dupont.com

Picea abies K., microsatellites, population genetics, mutation rates

The analyses presented here provide an approach for estimating mutation rates at microsatellite loci.

Numerous population genetic studies addressed the question of estimating effective population size (N) and mutation rate (n) at genetic loci, two basic parameters for understanding the genetic structure and the evolutionary dynamics of a population. For species with large generation time and overlapping generations, as Norway spruce (Picea abies L. (K.), measuring these indexes directly is problematic.

Recent theoretical works suggest that under the generalised stepwise mutation model (SMM), the within-population variance of repeat unit sizes at microsatellite loci is proportional to the product of N and n, allowing the indirect estimate of mutation rates in relative terms at loci grouped by their motif types and with alleles distinguished by their number of repeat.

Following the method proposed by Chakraborty (Chakraborty et al., PNAS, 1997), the relative mutation rates of microsatellites, grouped by repeat motif type, have been computed through the analysis of variance of population survey data. A two-way ANOVA has been applied to the distributions of the allele sizes at 8 SSRs, clustered in two classes (5 dinucleotides vs 3 trinucleotides), from a set of 15 populations (overall sample size: 2158 individuals). The motif type specific mutation rates and the effect of population size differences have been estimated. As the locus motif type resulted to be the dominating main effect in the analysis, while the dependence on population size was not significant, the estimated motif type specific levels are equal, up a moltiplicative constant C, to logarithms of motif type specific average mutation rates.

To obtain an estimate of absolute mutation rates, a coalescent backward approach has been simulated based on species history information. Five hundred replicates of the coalescent simulation were produced for a range of population parameters. We will show the dependence of the results of the simulations on the different parameters that were tested and show that size variance is not strongly influenced by effective population size under the selected demographic model. Observed allele size variances obtained from the previous analyses have been used to calculate the putative mutation rate of microsatellite loci.

The dinucleotides appear to have mutation rates 18 times higher than the trinucleotides, and hypervariable dinucleotides seem to be evolving at a rate 6 times greater than hypovariable dinucleotides. The range of absolute mutation rates derived from the simulations for the different classes of loci will be presented and discussed in light of mutation rates estimated for other species.