Experimental Estimation of Mutation Rates in a Wheat Population With a Gene Genealogy Approach

Abstract

Microsatellite markers are extensively used to evaluate genetic diversity in natural or experimental evolving populations. Their high degree of polymorphism reflects their high mutation rates. Estimates of the mutation rates are therefore necessary when characterizing diversity in populations. As a complement to the classical experimental designs, we propose to use experimental populations, where the initial state is entirely known and some intermediate states have been thoroughly surveyed, thus providing a short timescale estimation together with a large number of cumulated meioses. In this article, we derived four original gene genealogy-based methods to assess mutation rates with limited bias due to relevant model assumptions incorporating the initial state, the number of new alleles, and the genetic effective population size. We studied the evolution of genetic diversity at 21 microsatellite markers, after 15 generations in an experimental wheat population. Compared to the parents, 23 new alleles were found in generation 15 at 9 of the 21 loci studied. We provide evidence that they arose by mutation. Corresponding estimates of the mutation rates ranged from 0 to 4.97 3 10 À3 per generation (i.e., year). Sequences of several alleles revealed that length polymorphism was only due to variation in the core of the microsatellite. Among different microsatellite characteristics, both the motif repeat number and an independent estimation of the Nei diversity were correlated with the novel diversity. Despite a reduced genetic effective size, global diversity at microsatellite markers increased in this population, suggesting that microsatellite diversity should be used with caution as an indicator in biodiversity conservation issues. B ECAUSE microsatellite markers (tandemly repeated DNA motifs of 1-6 bp in length) are highly polymorphic and since they are distributed across the whole genome (Wu and Tanksley 1993;Plaschke et al. 1995;Pejic et al. 1998), they constitute a powerful tool to assess the level of genetic differentiation within and among experimental or natural populations at different generations. The high degree of polymorphism at microsatellite markers is directly related to their underlying mutation rates, which can be explained by two mutational mechanisms: polymerase slippage during DNA replication and unequal crossing over during recombinationbut not excluding SNP mutations at a lower rate. These two mechanisms involve changes in the number of motif repeats. Understanding the evolutionary properties of microsatellites is hence necessary for correctly interpreting diversity data when studying populations across generations and/or populations that have spatially diverged (Ellegren 2004).An increasing number of studies have been devoted to the estimation of mutation rates at microsatellite loci (e.g., Schug et al. 1998;Symonds and Lloyd 2003;Denver et al. 2004;Thuillet et al. 2004), which reveal a far more complex scheme for microsatellite evolution than previously stated (Schlö tterer 2000;Elleg...

Effectiveness of in situ and ex situ conservation of crop diversity. What a Phaseolus vulgaris L. landrace case study can tell us

“…The Ne value for the in situ population was similar to those observed in experimental populations of another autogamous species (i.e. wheat) that were multiplied ex situ for 10-15 generations sowing a similar number of plants as sown by farmers for this landrace (Goldringer et al 2001;Raquin et al 2008). In contrast, Ne values after one or two generations of ex situ multiplication were ten times lower than the Ne value Fig.…”

“…As commonly found (Frankham 1995;Goldringer et al 2001;Raquin et al 2008), the estimated effective size was much smaller than the demographic effective size based on the true number of plants cultivated in each generation.…”

Efficiently Tracking Selection in a Multiparental Population: The Case of Earliness in Wheat

“…Conversely, 31 markers were polymorphic in the evolved population but not among the parents. This could be explained by (i) alleles specific of the four lines missing from our parental panel, (ii) alleles lost for some parental lines during the management procedure in genebanks (regeneration through selfing cycles; Esquinas-Alcazar 2005), as they could have presented initial residual heterozygosity, (iii) contamination (migration) despite the isolation of plots (Hucl and Matus-Cadiz 2001), and (iv) mutation, as found for SSR markers in another wheat experimental population (Raquin et al 2008). The observed heterozygosity in the evolved population was 3.2%.…”

Vitamin C, flower color and ploidy variation of hybrids from a ploidy-unbalanced Actinidia interspecific cross and SSR characterization

“…But since it's an interspecific and interploidy cross, with a high level of progeny heterozygosity, and the molecular markers were the hypervariable microsatellites, it's not such a surprise when novel alleles present. It's considered that the instability of the simple repeats are mainly caused by the unequal crossing over during recombination and polymerase slippage during DNA replication (Sia et al 1997;Raquin et al 2008), and the allele mutations or variations of the SSR loci is correlated both with the high heterozygosity and the presence of multiple alleles (Vigouroux et al 2002;Ellegren 2004). It's suggested that six of the seven SSR loci in present study had null alleles as have been reported in Actinidia by Fraser et al (2005).…”