Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2013 Apr;20(2):197-207.
doi: 10.1093/dnares/dst002. Epub 2013 Feb 3.

Genome-wide development and use of microsatellite markers for large-scale genotyping applications in foxtail millet [Setaria italica (L.)]

Garima Pandey  1 , Gopal Misra, Kajal Kumari, Sarika Gupta, Swarup Kumar Parida, Debasis Chattopadhyay, Manoj Prasad
Affiliations

Genome-wide development and use of microsatellite markers for large-scale genotyping applications in foxtail millet [Setaria italica (L.)]

Garima Pandey et al. DNA Res. 2013 Apr.

Abstract

The availability of well-validated informative co-dominant microsatellite markers and saturated genetic linkage map has been limited in foxtail millet (Setaria italica L.). In view of this, we conducted a genome-wide analysis and identified 28 342 microsatellite repeat-motifs spanning 405.3 Mb of foxtail millet genome. The trinucleotide repeats (∼48%) was prevalent when compared with dinucleotide repeats (∼46%). Of the 28 342 microsatellites, 21 294 (∼75%) primer pairs were successfully designed, and a total of 15 573 markers were physically mapped on 9 chromosomes of foxtail millet. About 159 markers were validated successfully in 8 accessions of Setaria sp. with ∼67% polymorphic potential. The high percentage (89.3%) of cross-genera transferability across millet and non-millet species with higher transferability percentage in bioenergy grasses (∼79%, Switchgrass and ∼93%, Pearl millet) signifies their importance in studying the bioenergy grasses. In silico comparative mapping of 15 573 foxtail millet microsatellite markers against the mapping data of sorghum (16.9%), maize (14.5%) and rice (6.4%) indicated syntenic relationships among the chromosomes of foxtail millet and target species. The results, thus, demonstrate the immense applicability of developed microsatellite markers in germplasm characterization, phylogenetics, construction of genetic linkage map for gene/quantitative trait loci discovery, comparative mapping in foxtail millet, including other millets and bioenergy grass species.

PubMed Disclaimer

Figures

Figure 1.
Figure 1.
Analysis of simple sequence repeats from foxtail millet genome. (A) Relative frequency, proportion (%) and number of selected microsatellite repeat-motif types. (B) Different classes of selected microsatellite repeats.
Figure 2.
Figure 2.
Frequency and relative distribution of long and hypervariable class I and variable class II microsatellite repeats in the foxtail millet genome.
Figure 3.
Figure 3.
Representative gel showing amplification profiles of one microsatellite marker SiGMS 3261 and its fragment length polymorphism among foxtail millet and related species. The amplicons are resolved in 2% agarose gel along with 100 bp DNA size standard.
Figure 4.
Figure 4.
Genetic relationships among 9 millet and 4 non-millet grass species based on 58 foxtail millet microsatellite markers using neighbor-joining clustering. Nine millet species, including foxtail millet, were clearly differentiated from the four non-millet grass species, and expected genetic relationships among species under study were also evident.
Figure 5.
Figure 5.
Genome relationships of foxtail millet with other grass species. Syntenic relationship of foxtail millet genome with (A) sorghum, (B) maize and (C) rice chromosomes using 15 573 physically mapped foxtail millet microsatellite markers. Maximum syntenic relationships of foxtail millet chromosomes with sorghum chromosomes based on microsatellite markers were apparent.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Devos K.M., Gale M.D. Genome relationships: the grass model in current research. Plant Cell. 2000;12:637–46. - PMC - PubMed
    1. Doust A.N., Kellogg E.A., Devos K.M., Bennetzen J.L. Foxtail millet: a sequence-driven grass model system. Plant Physiol. 2009;149:137–41. - PMC - PubMed
    1. Lata C., Gupta S., Prasad M. Foxtail millet: a model crop for genetic and genomic studies in bioenergy grasses. Crit. Rev. Biotechnol. 2012 DOI:10.3109/07388551.2012.716809. (September 18, 2012) - DOI - PubMed
    1. Li P., Brutnell T.P. Setaria viridis and Setaria italica, model genetic systems for Panicoid grasses. J. Exp. Bot. 2011;62:3031–37. - PubMed
    1. Bennetzen J.L., Wang J.S.H., Percifield R., et al. Reference genome sequence of the model plant Setaria. Nature Biotech. 2012;30:555–61. - PubMed

Publication types

Substances