Open Access Research article

Population genetics of foxtail millet and its wild ancestor

Chunfang Wang124, Jinfeng Chen3, Hui Zhi12, Lu Yang3, Wei Li2, Yongfang Wang2, Haiquan Li2, Baohua Zhao4, Mingsheng Chen3* and Xianmin Diao12*

Author Affiliations

1 The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, the Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China

2 Institute of Millet Crops, Hebei Academy of Agricultural and Forestry Science, Shijiazhuang 050031, China

3 State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China

4 College of Life Sciences, Hebei Normal University, Shijiazhuang 050012, China

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BMC Genetics 2010, 11:90  doi:10.1186/1471-2156-11-90

Published: 11 October 2010



Foxtail 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.


In 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.


The 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.