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Development of eSSR-markers in Setaria italica and their applicability in studying genetic diversity, cross-transferability and comparative mapping in millet and non-millet species

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Title Development of eSSR-markers in Setaria italica and their applicability in studying genetic diversity, cross-transferability and comparative mapping in millet and non-millet species
 
Creator Kumari, Kajal
Muthamilarasan, Mehanathan
Misra, Gopal
Gupta, Sarika
Subramanian, Alagesan
Parida, Swarup K.
Chattopadhyay, Debasis
Prasad, Manoj
 
Subject Foxtail millet
Setaria italica
eSSR-Markers
Millet
Non-Millet
 
Description Accepted date: May 22, 2013
Foxtail millet (Setariaitalica L.) is a tractable experimental model crop for studying functional genomics of millets and bioenergy grasses. But the limited availability of genomic resources, particularly expressed sequence-based genic markers is significantly impeding its genetic improvement. Considering this, we attempted to develop EST-derived-SSR (eSSR) markers and utilize them in germplasm characterization, cross-genera transferability and in silico comparative mapping. From 66,027 foxtail millet EST sequences 24,828 non-redundant ESTs were deduced, representing ~16 Mb, which revealed 534 (~2%) eSSRs in 495 SSR containing ESTs at a frequency of 1/30 kb. A total of 447 pp were successfully designed, of which 327 were mapped physically onto nine chromosomes. About 106 selected primer pairs representing the foxtail millet genome showed high-level of cross-genera amplification at an average of ~88% in eight millets and four non-millet species. Broad range of genetic diversity (0.02-0.65) obtained in constructed phylogenetic tree using 40 eSSR markers demonstrated its utility in germplasm characterizations and phylogenetics. Comparative mapping of physically mapped eSSR markers showed considerable proportion of sequence-based orthology and syntenic relationship between foxtail millet chromosomes and sorghum (~68%), maize (~61%) and rice (~42%) chromosomes. Synteny analysis of eSSRs of foxtail millet, rice, maize and sorghum suggested the nested chromosome fusion frequently observed in grass genomes. Thus, for the first time we had generated large-scale eSSR markers in foxtail millet and demonstrated their utility in germplasm characterization, transferability, phylogenetics and comparative mapping studies in millets and bioenergy grass species.
This work was financially supported by the core grant of National Institute of Plant Genome Research (NIPGR), New Delhi, India. MM
acknowledges the award of Junior Research Fellowship from University Grants Commission, New Delhi. The funders had no role in study design, data
collection and analysis, decision to publish, or preparation of the manuscript.
 
Date 2015-11-06T04:56:04Z
2015-11-06T04:56:04Z
2013
 
Type Article
 
Identifier PLoS One, 8(6): e67742
1932-6203
http://172.16.0.77:8080/jspui/handle/123456789/336
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0067742
10.1371/journal.pone.0067742
 
Language en_US
 
Publisher PLOS