Open Access Research article

Novel genomes and genome constitutions identified by GISH and 5S rDNA and knotted1 genomic sequences in the genus Setaria

Meicheng Zhao123, Hui Zhi12, Andrew N Doust4, Wei Li2, Yongfang Wang2, Haiquan Li2, Guanqing Jia1, Yongqiang Wang35, Ning Zhang123 and Xianmin Diao123*

Author Affiliations

1 Institute of Crops Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China

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

3 College of Life Science, Hebei Normal University, Shijiazhuang 050012, China

4 Department of Botany, Oklahoma State University, Stillwater, Oklahoma 74078, USA

5 Institute of Cotton Research, Hebei Academy of Agricultural and Forestry Science, Shijiazhuang 050031, China

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BMC Genomics 2013, 14:244  doi:10.1186/1471-2164-14-244

Published: 11 April 2013



The Setaria genus is increasingly of interest to researchers, as its two species, S. viridis and S. italica, are being developed as models for understanding C4 photosynthesis and plant functional genomics. The genome constitution of Setaria species has been studied in the diploid species S. viridis, S. adhaerans and S. grisebachii, where three genomes A, B and C were identified respectively. Two allotetraploid species, S. verticillata and S. faberi, were found to have AABB genomes, and one autotetraploid species, S. queenslandica, with an AAAA genome, has also been identified. The genomes and genome constitutions of most other species remain unknown, even though it was thought there are approximately 125 species in the genus distributed world-wide.


GISH was performed to detect the genome constitutions of Eurasia species of S. glauca, S. plicata, and S. arenaria, with the known A, B and C genomes as probes. No or very poor hybridization signal was detected indicating that their genomes are different from those already described. GISH was also performed reciprocally between S. glauca, S. plicata, and S. arenaria genomes, but no hybridization signals between each other were found. The two sets of chromosomes of S. lachnea both hybridized strong signals with only the known C genome of S. grisebachii. Chromosomes of Qing 9, an accession formerly considered as S. viridis, hybridized strong signal only to B genome of S. adherans. Phylogenetic trees constructed with 5S rDNA and knotted1 markers, clearly classify the samples in this study into six clusters, matching the GISH results, and suggesting that the F genome of S. arenaria is basal in the genus.


Three novel genomes in the Setaria genus were identified and designated as genome D (S. glauca), E (S. plicata) and F (S. arenaria) respectively. The genome constitution of tetraploid S. lachnea is putatively CCC’C’. Qing 9 is a B genome species indigenous to China and is hypothesized to be a newly identified species. The difference in genome constitution and origin of S. verticillata and S. faberi is also discussed. The new genomes and the genome constitutions of Setaria species identified in this report provide useful information for Setaria germplasm management, foxtail millet breeding, grass evolution and the development of S. viridis and S. italica as a new model for functional genomics.

Setaria; GISH; Genome constitution; Phylogenetic relationships