Estimation of Long-Term Effective Population Sizes Through the History of Durum Wheat Using Microsatellite Data

Abstract

Estimation of long-term effective population size (N e ) from polymorphism data alone requires an independent knowledge of mutation rate. Microsatellites provide the opportunity to estimate N e because their high mutation rate can be estimated from observed mutations. We used this property to estimate N e in allotetraploid wheat Triticum turgidum at four stages of its history since its domestication. We estimated the mutation rate of 30 microsatellite loci. Allele-specific mutation rates were predicted from the number of repeats of the alleles. Effective population sizes were calculated from the diversity parameter ϭ 4N e . We demonstrated from simulations that the unbiased estimator of based on Nei's heterozygosity is the most appropriate for estimating N e because of a small variance and a relative robustness to variations in the mutation model compared to other estimators. We found a N e of 32,500 individuals with a 95% confidence interval of [20,739; 45,991] in the wild ancestor of wheat, 12,000 ([5790; 19,300]) in the domesticated form, 6000 ([2831; 9556]) in landraces, and 1300 ([689; 2031]) in recent improved varieties. This decrease illustrates the successive bottlenecks in durum wheat. No selective effect was detected on our loci, despite a complete loss of polymorphism for two of them.

Genetic diversity in red clover (Trifolium pratense L.) revealed by morphological and microsatellite (SSR) markers

“…The breeding schemes and the synthetic structure of the cultivars with several parental families maintain a large within cultivar variation, at least for neutral markers, as observed in alfalfa (Flajoulot et al 2005). We found higher genetic diversity than other studies based on RAPD markers (Kongkiatngam et al 1995(Kongkiatngam et al , 1996Ulloa et al 2003) and isozyme markers (Mosjidis and Klingler 2006), probably because microsatellite markers display high mutation rates, and are thus expected to reveal fairly high amounts of polymorphisms especially when used at the species level (Thuillet et al 2005). But Kölliker et al (2006) found higher mean values of diversity than those reported here, which is probably related to the nature of the populations, the use of more SSR loci and the analysis of more individuals per population.…”

Genomics of Origin, Domestication and Evolution of Phaseolus vulgaris

“…However, the genetic diversity reduction using sequence data was about two-fold, 13-fold and three-fold higher than those in a comparable sample of P. vulgaris genotypes using AFLP data (45 %; Rossi et al 2009), SSR data (7 %; ) and chloroplast (cp)SSR data (26 %; Desiderio et al 2013), respectively. This is clear evidence of the crucial role of marker mutation rates for describing the diversity of plant populations (Thuillet et al 2005). In particular, the loss of diversity detected with cpSSRs is intermediate between the SSRs and AFLPs, as is their mutation rate (Provan et al 1999;Marshall et al 2002).…”

Elite durum wheat genetic map and recombination rate variation in a multiparental connected design

“…They contain large gaps partly due to absence of polymorphism between genitors inside some genomic regions partly due to the low polymorphism level of the elite pool. Indeed, based on microsatellite and sequence polymorphism data sets, Thuillet et al (2005) and Haudry et al (2007) have reported a low level of polymorphism between breeding varieties resulting from drastic bottlenecks occurred during durum wheat domestication and modern breeding. To overcome it and to increase the density of markers, a genetic map based on multiple segregating populations could be used (Piquemal et al 2005).…”