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

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Title Genome-wide development and use of microsatellite markers for large-scale genotyping applications in foxtail millet [Setaria italica (L.)]
 
Creator Pandey, Garima
Misra, Gopal
Kumari, Kajal
Gupta, Sarika
Parida, Swarup K.
Chattopadhyay, Debasis
Prasad, Manoj
 
Subject foxtail millet (Setaria italica L.)
microsatellite
comparative mapping
physical mapping
transferability
 
Description Accepted date: 9 January 2013
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.
Grateful thanks are due to the
Director, National Institute of Plant Genome Research
(NIPGR), New Delhi, India for providing facilities.
Ms Garima Pandey acknowledges the award of
Junior Research Fellowship from University Grants
Commission, New Delhi. We are also thankful to the
National Bureau of Plant Genetic Resources, New
Delhi/Hyderabad/Akola, India and Tamil Nadu
Agricultural University, India for providing the
seed material. We thank Mr Mehanathan
Muthamilarasan, NIPGR, New Delhi for critically
reading the manuscript. Computational resources
under BTISNET program (DISC facility) are gratefully
acknowledged.
 
Date 2015-11-09T11:09:19Z
2015-11-09T11:09:19Z
2013
 
Type Article
 
Identifier DNA Res., 20(2): 197-207
1340-2838
http://172.16.0.77:8080/jspui/handle/123456789/352
http://dnaresearch.oxfordjournals.org/content/20/2/197.long
10.1093/dnares/dst002
 
Language en_US
 
Publisher Oxford University Press