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Development of 5123 intron-length polymorphic markers for large-scale genotyping applications in foxtail millet

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Title Development of 5123 intron-length polymorphic markers for large-scale genotyping applications in foxtail millet
 
Creator Muthamilarasan, Mehanathan
Venkata Suresh, B.
Pandey, Garima
Kumari, Kajal
Parida, Swarup K.
Prasad, Manoj
 
Subject comparative mapping
Foxtail Millet (Setaria italica L.)
intron-length polymorphism (ILP)
physical mapping
transferability
 
Description Accepted date: 5 September 2013
Generating genomic resources in terms of molecular markers is imperative in molecular breeding for crop improvement. Though development and application of microsatellite markers in large-scale was reported in the model crop foxtail millet, no such large-scale study was conducted for intron-length polymorphic (ILP) markers. Considering this, we developed 5123 ILP markers, of which 4049 were physically mapped onto 9 chromosomes of foxtail millet. BLAST analysis of 5123 expressed sequence tags (ESTs) suggested the function for ∼71.5% ESTs and grouped them into 5 different functional categories. About 440 selected primer pairs representing the foxtail millet genome and the different functional groups showed high-level of cross-genera amplification at an average of ∼85% in eight millets and five non-millet species. The efficacy of the ILP markers for distinguishing the foxtail millet is demonstrated by observed heterozygosity (0.20) and Nei's average gene diversity (0.22). In silico comparative mapping of physically mapped ILP markers demonstrated substantial percentage of sequence-based orthology and syntenic relationship between foxtail millet chromosomes and sorghum (∼50%), maize (∼46%), rice (∼21%) and Brachypodium (∼21%) chromosomes. Hence, for the first time, we developed large-scale ILP markers in foxtail millet and demonstrated their utility in germplasm characterization, transferability, phylogenetics and comparative mapping studies in 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.
The authors also thank Mr V.V. Satyanarayana, NIPGR,
for his timely assistance. 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 seeds.
 
Date 2015-12-21T07:05:30Z
2015-12-21T07:05:30Z
2014
 
Type Article
 
Identifier DNA Res., 21(1): 41-52
1340-2838
http://172.16.0.77:8080/jspui/handle/123456789/438
http://dnaresearch.oxfordjournals.org/content/21/1/41
10.1093/dnares/dst039
 
Language en_US
 
Publisher Oxford University Press