Comparisons of mutation rate variation at genome-wide microsatellites: evolutionary insights from two cultivated rice and their wild relatives

Li-Zhi Gao,Hongyan Xu

doi:10.1186/1471-2148-8-11

Abstract

BackgroundMutation rate (μ) per generation per locus is an important parameter in the models of population genetics. Studies on mutation rate and its variation are of significance to elucidate the extent and distribution of genetic variation, further infer evolutionary relationships among closely related species, and deeply understand genetic variation of genomes. However, patterns of rate variation of microsatellite loci are still poorly understood in plant species. Furthermore, how their mutation rates vary in di-, tri-, and tetra-nucleotide repeats within the species is largely uninvestigated across related plant genomes.ResultsGenome-wide variation of mutation rates was first investigated by means of the composite population parameter θ (θ = 4Nμ, where N is the effective population size and μ is the mutation rate per locus per generation) in four subspecies of Asian cultivated rice O. sativa and its three related species, O. rufipogon, O. glaberrima, and O. officinalis. On the basis of three data sets of microsatellite allele frequencies throughout the genome, population mutation rate (θ) was estimated for each locus. Our results reveal that the variation of population mutation rates at microsatellites within each studied species or subspecies of cultivated rice can be approximated with a gamma distribution. The mean population mutation rates of microsatellites do not significantly differ in motifs of di-, tri-, and tetra-nucleotide repeats for the studied rice species. The shape parameter was also estimated for each subspecies of rice as well as other related rice species. Of them, different subspecies of O. sativa possesses similar shape parameters (α) of the gamma distribution, while other species extensively vary in their population mutation rates.ConclusionThrough the analysis of genome-wide microsatellite data, the population mutation rate can be approximately fitted with a gamma distribution in most of the studied species. In general, different population histories occurred along different lineages may result in the observed variation of population mutation rates at microsatellites among the studied Oryza species.

Highlights

Mutation rate (μ) per generation per locus is an important parameter in the models of population genetics
The gamma distribution of population mutation rates at di, tri, and tetra-nucleotide microsatellite loci The estimates of population mutation rate were computed for each locus in all rice species where genotypes are available
We found that the histograms can be fitted for most species and/or subspecies with a gamma distribution except O. officinalis (Figure 2)

Summary

Introduction

Mutation rate (μ) per generation per locus is an important parameter in the models of population genetics. Patterns of rate variation of microsatellite loci are still poorly understood in plant species. How their mutation rates vary in di-, tri-, and tetra-nucleotide repeats within the species is largely uninvestigated across related plant genomes. DNA sequence motifs of 1–6 nucleotide bases in Microsatellites are composed of tandemly repeated, sim- length. These loci are ubiquitously found throughout (page number not for citation purposes). There are growing interests in using such microsatellite data, as they make it possible to take mutation rate variation into consideration by analyzing multiple loci across related species rather than a single locus from a single species

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