Population genetics of foxtail millet and its wild ancestor

Chunfang Wang,Hui Zhi,Wei Li,Jinfeng Chen,Xianmin Diao,Haiquan Li,Yongfang Wang,Mingsheng Chen,Baohua Zhao,Lu Yang

doi:10.1186/1471-2156-11-90

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.

Highlights

IntroductionOnly a small fraction of flowering plants were domesticated
Nucleotide diversity and neutrality test We collected 50 cultivated foxtail millets and 34 wild green foxtails to represent the broad diversity of these two species (Table 1)
We can conclude that the level of genetic diversity of foxtail millet, which maintained 45% of its wild diversity, was mainly a result of its change in population size during domestication process, followed by mutation accumulated after divergence

Summary

Introduction

Only a small fraction of flowering plants were domesticated It will be of great benefit for future crop breeding and improvement if we have a better understanding of the domestication process. Elevated levels of linkage disequilibrium (LD) are observed in the genome of domesticated plants [3,6,12] This is caused by either the domestication bottleneck and/or reduction of effective recombination rate due to self-fertilization [5]. Studies that focus on the level and organization of genetic variation in these major crops are essential for our understanding of the process of domestication and are instructive for crop improvement or other research that is based on these population parameters, such as association mapping [2,12,14]

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Results

Discussion

Conclusion