TY - JOUR
T1 - Development of novel microRNA-based genetic markers in foxtail millet for genotyping applications in related grass species
AU - Yadav, Chandra
AU - Muthamilarasan, Mehanathan
AU - Pandey, Garima
AU - Khan, Yusuf
AU - Prasad, Manoj
N1 - Funding Information:
Acknowledgments The authors’ work in this area was supported by the core grant of NIPGR. Mr. Mehanathan Muthamilarasan and Ms. Garima Pandey acknowledge the award of Research Fellowships from University Grants Commission, New Delhi, India.
Publisher Copyright:
© 2014, Springer Science+Business Media Dordrecht.
PY - 2014/12/6
Y1 - 2014/12/6
N2 - DNA markers are important in molecular breeding, and, hence, considering its prominence, a variety of DNA-based molecular markers have been explored and developed for expediting crop improvement programs. microRNA (miRNA)-based molecular marker is a type of functional markers exploited predominantly in animal sciences, but reported in very few plants. Considering the efficacy, stability and transferability potential of the miRNA-based markers, the present study was conducted to develop these markers in the model crop foxtail millet. The pre-miRNA sequences of foxtail millet and other related grasses including rice, maize, wheat, sorghum and Brachypodium were retrieved and aligned for identifying the conserved regions. One hundred and seventy-six primer pairs were designed for these consensus sequences, and all these 176 miRNA-based markers were mapped onto foxtail millet genome. Of the 176 markers, 66 were chosen for further experimentations based on representing the nine chromosomes of foxtail millet and presence of highly conserved regions. All the 66 markers showed 100 % amplification in five cultivars of foxtail millet. Moreover, all the markers showed a higher level of cross-genera transferability potential with an average of ~67 % in millets and non-millet species. This is the first report on the development of novel miRNA-based markers in foxtail millet. Promisingly, these markers would serve as novel genotyping tool for various molecular breeding approaches aiming at crop improvement in millets and non-millet species.
AB - DNA markers are important in molecular breeding, and, hence, considering its prominence, a variety of DNA-based molecular markers have been explored and developed for expediting crop improvement programs. microRNA (miRNA)-based molecular marker is a type of functional markers exploited predominantly in animal sciences, but reported in very few plants. Considering the efficacy, stability and transferability potential of the miRNA-based markers, the present study was conducted to develop these markers in the model crop foxtail millet. The pre-miRNA sequences of foxtail millet and other related grasses including rice, maize, wheat, sorghum and Brachypodium were retrieved and aligned for identifying the conserved regions. One hundred and seventy-six primer pairs were designed for these consensus sequences, and all these 176 miRNA-based markers were mapped onto foxtail millet genome. Of the 176 markers, 66 were chosen for further experimentations based on representing the nine chromosomes of foxtail millet and presence of highly conserved regions. All the 66 markers showed 100 % amplification in five cultivars of foxtail millet. Moreover, all the markers showed a higher level of cross-genera transferability potential with an average of ~67 % in millets and non-millet species. This is the first report on the development of novel miRNA-based markers in foxtail millet. Promisingly, these markers would serve as novel genotyping tool for various molecular breeding approaches aiming at crop improvement in millets and non-millet species.
KW - Cereals
KW - Cross-transferability
KW - Foxtail millet (Setaria italica L.)
KW - Millets
KW - Phylogenetics
KW - microRNA-based markers
UR - http://www.scopus.com/inward/record.url?scp=84914819896&partnerID=8YFLogxK
U2 - 10.1007/s11032-014-0137-9
DO - 10.1007/s11032-014-0137-9
M3 - Article
SN - 1380-3743
VL - 34
SP - 2219
EP - 2224
JO - Molecular Breeding
JF - Molecular Breeding
IS - 4
ER -