Population genetics of foxtail millet and its wild ancestor

Abstract

BackgroundFoxtail millet (Setaria italica (L.) P. Beauv.), one of the most ancient domesticated crops, is becoming a model system for studying biofuel crops and comparative genomics in the grasses. However, knowledge on the level of genetic diversity and linkage disequilibrium (LD) is very limited in this crop and its wild ancestor, green foxtail (Setaria viridis (L.) P. Beauv.). Such information would help us to understand the domestication process of cultivated species and will allow further research in these species, including association mapping and identification of agricultural significant genes involved in domestication.ResultsIn this study, we surveyed DNA sequence for nine loci across 50 accessions of cultivated foxtail millet and 34 of its wild progenitor. We found a low level of genetic diversity in wild green foxtail (θ = 0.0059), θ means Watterson's estimator of θ. Despite of a 55% loss of its wild diversity, foxtail millet still harbored a considerable level of diversity (θ = 0.0027) when compared to rice and sorghum (θ = 0.0024 and 0.0034, respectively). The level of LD in the domesticated foxtail millet extends to 1 kb, while it decayed rapidly to a negligible level within 150 bp in wild green foxtail. Using coalescent simulation, we estimated the bottleneck severity at k = 0.6095 when ρ/θ = 1. These results indicated that the domestication bottleneck of foxtail millet was more severe than that of maize but slightly less pronounced than that of rice.ConclusionsThe results in this study establish a general framework for the domestication history of foxtail millet. The low level of genetic diversity and the increased level of LD in foxtail millet are mainly caused by a population bottleneck, although gene flow from foxtail millet to green foxtail is another factor that may have shaped the pattern of genetic diversity of these two related gene pools. The knowledge provided in this study will benefit future population based studies in foxtail millet.

Genome-Wide Association Analysis of the Anthocyanin and Carotenoid Contents of Rose Petals

“…The value of heterozygosity is in fact the percentage of polymorphic SNPs; thus, it is not surprising that the value is somewhat lower than that found with 24 SSR markers in garden roses (Vukosavljev et al, 2013). Unlike many other cultivated plant species (Kilian et al, 2007; Gil-Ariza et al, 2009; Wang et al, 2010; Gross et al, 2014), we did not see a reduction over time when we considered the year of release of the variety. This may corroborate observations on the sensitivity of rose for inbreeding depression, which makes selfing unsuitable as a breeding strategy (Pipino et al, 2011).…”

Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential

“…Comparisons between genetic maps of foxtail millet, rice and pearl millet have shed light on the chromosomal relationships between these grasses 4,5 . Genetic variations of foxtail millet have also been studied in some genomic regions 6 and population of foxtail millet has been investigated using single-nucleotide polymorphism (SNP), simple sequence repeat and other markers 7,8 . Evolutionary relationships between foxtail millet and its wild ancestor green millet have been studied using polymorphisms in single genes 9 or genomic regions 6 .…”

“…Genetic variations of foxtail millet have also been studied in some genomic regions 6 and population of foxtail millet has been investigated using single-nucleotide polymorphism (SNP), simple sequence repeat and other markers 7,8 . Evolutionary relationships between foxtail millet and its wild ancestor green millet have been studied using polymorphisms in single genes 9 or genomic regions 6 . Small collections of other resources, including simple sequence repeats 10 and expressed sequence tags (ESTs) 11 , have also been developed.…”

Domestication

“…However, these estimates are based on a modest number of accessions and markers so should probably be expanded and verified. Foxtail millet retains about 45 % of the genetic diversity of its wild ancestor green millet (Wang et al 2010), and pearl millet retains 67-74 % of the wild diversity (Clotault et al 2012;Oumar et al 2008). In contrast, landraces of maize harbor almost as much variation as is found in teosinte (83 %; Hufford et al 2012).…”