Population genetics of foxtail millet and its wild ancestor

Wang, Chunfang and Chen, Jinfeng and Zhi, Hui and Yang, Lu and Li, Wei and Wang, Yongfang and Li, Haiquan and Zhao, Baohua and Chen, Mingsheng and Diao,, Xianmin (2010) Population genetics of foxtail millet and its wild ancestor. BMC Genetics, 11 (1). pp. 1-13.

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Abstract

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. Results: 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 r/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

Item Type: Article
Author Affiliation: he 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
Subjects: Crop Improvement
Crop Improvement > Genetics/Genomics
Crop Improvement > Plant Breeding
Divisions: Millet
Depositing User: Mr T L Gautham
Date Deposited: 27 Apr 2011 04:53
Last Modified: 27 Apr 2011 04:53
Official URL: http://www.biomedcentral.com/content/pdf/1471-2156...
URI: http://eprints.icrisat.ac.in/id/eprint/1890

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