Open Access Research article

Development of highly polymorphic simple sequence repeat markers using genome-wide microsatellite variant analysis in Foxtail millet [Setaria italica (L.) P. Beauv.]

Shuo Zhang1, Chanjuan Tang1, Qiang Zhao2, Jing Li14, Lifang Yang1, Lufeng Qie14, Xingke Fan14, Lin Li14, Ning Zhang3, Meicheng Zhao1, Xiaotong Liu1, Yang Chai1, Xue Zhang14, Hailong Wang14, Yingtao Li14, Wen Li15, Hui Zhi1*, Guanqing Jia1* and Xianmin Diao14*

Author Affiliations

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

2 National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China

3 National Center for Plant Gene Research, State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China

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

5 College of Agronomy, Shanxi Agricultural University, Jinzhong 030801, China

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BMC Genomics 2014, 15:78  doi:10.1186/1471-2164-15-78

Published: 28 January 2014



Foxtail millet (Setaria italica (L.) Beauv.) is an important gramineous grain-food and forage crop. It is grown worldwide for human and livestock consumption. Its small genome and diploid nature have led to foxtail millet fast becoming a novel model for investigating plant architecture, drought tolerance and C4 photosynthesis of grain and bioenergy crops. Therefore, cost-effective, reliable and highly polymorphic molecular markers covering the entire genome are required for diversity, mapping and functional genomics studies in this model species.


A total of 5,020 highly repetitive microsatellite motifs were isolated from the released genome of the genotype 'Yugu1’ by sequence scanning. Based on sequence comparison between S. italica and S. viridis, a set of 788 SSR primer pairs were designed. Of these primers, 733 produced reproducible amplicons and were polymorphic among 28 Setaria genotypes selected from diverse geographical locations. The number of alleles detected by these SSR markers ranged from 2 to 16, with an average polymorphism information content of 0.67. The result obtained by neighbor-joining cluster analysis of 28 Setaria genotypes, based on Nei’s genetic distance of the SSR data, showed that these SSR markers are highly polymorphic and effective.


A large set of highly polymorphic SSR markers were successfully and efficiently developed based on genomic sequence comparison between different genotypes of the genus Setaria. The large number of new SSR markers and their placement on the physical map represent a valuable resource for studying diversity, constructing genetic maps, functional gene mapping, QTL exploration and molecular breeding in foxtail millet and its closely related species.

Microsatellite marker; SSR development; Polymorphism; Setaria italica