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Development of novel microRNA-based genetic markers in foxtail millet for genotyping applications in related grass species

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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.

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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.

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Correspondence to Manoj Prasad.

Additional information

Chandra Bhan Yadav and Mehanathan Muthamilarasan have contributed equally to this work.

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Supplementary Fig. S1. An un-rooted Neighbor-Joining tree for the 18 grass species. All the 66 tested miRNA-based markers have the ability to distinguish the investigated millet and non-millet species into three distinct groups. (PPTX 61 kb)

Supplementary Table S1. List of plant materials used in the present study. (DOC 41 kb)

Supplementary Table S2. Details of 176 miRNA-based markers developed in foxtail millet. (XLS 75 kb)


Supplementary Table S3. Chromosomal distribution and physical density of miRNA-based markers on the nine chromosomes of foxtail millet. (DOC 32 kb)


Supplementary Table S4. Amplification and polymorphic potential of 66 miRNA-based markers in foxtail millet. (XLS 37 kb)


Supplementary Table S5. Cross-genera transferability of 66 miRNA-based markers from foxtail millet to related grass species. (XLS 42 kb)

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Yadav, C.B., Muthamilarasan, M., Pandey, G. et al. Development of novel microRNA-based genetic markers in foxtail millet for genotyping applications in related grass species. Mol Breeding 34, 2219–2224 (2014).

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