Rate and Pattern of Mutation at Microsatellite Loci in Maize

Abstract

Microsatellites are important tools for plant breeding, genetics, and evolution, but few studies have analyzed their mutation pattern in plants. In this study, we estimated the mutation rate for 142 microsatellite loci in maize (Zea mays subsp. mays) in two different experiments of mutation accumulation. The mutation rate per generation was estimated to be 7.7 x 10(-4) for microsatellites with dinucleotide repeat motifs, with a 95% confidence interval from 5.2 x 10(-4) to 1.1 x 10(-3). For microsatellites with repeat motifs of more than 2 bp in length, no mutations were detected; so we could only estimate the upper 95% confidence limit of 5.1 x 10(-5) for the mutation rate. For dinucleotide repeat microsatellites, we also determined that the variance of change in the number of repeats (sigma(m)2) is 3.2. We sequenced 55 of the 73 observed mutations, and all mutations proved to be changes in the number of repeats in the microsatellite or in mononucleotide tracts flanking the microsatellite. There is a higher probability to mutate to an allele of larger size. There is heterogeneity in the mutation rate among dinucleotide microsatellites and a positive correlation between the number of repeats in the progenitor allele and the mutation rate. The microsatellite-based estimate of the effective population size of maize is more than an order of magnitude less than previously reported values based on nucleotide sequence variation.

Pros and cons of using genomic SSRs and EST-SSRs for resolving phylogeny of the genus Gossypium

“…Another reason is that the high portion of trinucleotide repeats in coding regions may be due to the exertion of selection pressure for selecting particular single amino acid stretches (Morgante et al 2002). Also the most informative SSRs contained C10 repeats which are in agreement with the previous studies (Vigouroux et al 2002;Qureshi et al 2004;Kantartzi et al 2009). It was also observed that position of the SSR loci on the chromosome has no effect on the corresponding PIC values (Lacape et al 2003(Lacape et al , 2007.…”

“…Most diploid species were wild except A-genome species. Wild species were not domesticated suggesting selection pressure for accumulating particular type of alleles was not applied is the reason for escalation in PIC values (Vigouroux et al 2002;Qureshi et al 2004). …”

Population genetics of cobia (Rachycentron canadum) in the Gulf of Thailand and Andaman Sea: fisheries management implications

“…The long-term effective population size (Ne) was obtained by assuming Long-term effective population size (Ne) was estimated by assuming the average mutation rate of the microsatellites in cobia to be 1 9 10 -4 mutation/generation/locus. The number of immigrants per generation (Nm) was estimated by multiplying h by M divided by 4 a Migration from the other sample group Aquacult Int (2013) 21: 197-217 209 the average mutation rate of the microsatellites in cobia to be 1 9 10 -4 mutation/generation/locus (Schug et al 1997;Vigouroux et al 2002;Whittaker et al 2003;Yue et al 2007). The number of immigrants per generation (Nm) was estimated by multiplying h by M divided by 4.…”

Estimating dispersal from short distance spatial autocorrelation

“…Mutation has virtually no effect at normal rates, but when the rate is 10 À3 , spatial autocorrelations at the smallest distances are decreased by an average of seven percent. The critical range, of 10 À2 down to 10 À3 , is spanned by microsatellite loci in animals (eg Bruford et al, 1992;Jarne and Lagoda, 1996) and plants (Udupa and Baum, 2001;Thuillet et al, 2002;Vigouroux et al, 2002), as well as some other hypervariable markers. For loci with more than a few alleles, mutation at a rate of 10 À2 causes 30-40% reductions in values for the finest scale autocorrelation.…”