Abstract
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.
References
Bennetzen JL, Schmutz J, Wang H, Percifield R, Hawkins J, Pontaroli AC, Estep M, Feng L, Vaughn JN, Grimwood J, Jenkins J, Barry K, Lindquist E, Hellsten U, Deshpande S, Wang X, Wu X, Mitros T, Triplett J, Yang X, Ye CY, Mauro-Herrera M, Wang L, Li P, Sharma M, Sharma R, Ronald PC, Panaud O, Kellogg EA, Brutnell TP, Doust AN, Tuskan GA, Rokhsar D, Devos KM (2012) Reference genome sequence of the model plant Setaria. Nature Biotechnol 30:555–561
Dai X, Zhao PX (2011) psRNATarget: a plant small RNA target analysis server. Nucleic Acids Res 39:W155–W159
Fu SW, Chen L, Man YG (2011) miRNA Biomarkers in breast cancer detection and management. J Cancer 2:116–122
Fu D, Ma B, Mason AS, Xiao M, Wei L, An Z (2013) MicroRNA-based molecular markers: a novel PCR-based genotyping technique in Brassica species. Plant Breed 132:375–381
Gascuel O (1997) BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. Mol Biol Evol 14:685–695
Grady WM, Tewari M (2010) The next thing in prognostic molecular markers: microRNA signatures of cancer. Gut 59:706–708
Gupta S, Kumari K, Muthamilarasan M, Subramanian A, Prasad M (2013) Development and utilization of novel SSRs in foxtail millet [Setaria italica (L.) P. Beauv.]. Plant Breed 132:367–374
Jaccard P (1908) Nouvelles recherches sur la distribution florale. Bull Soc Vaud Sci Nat 44:223–270
Khan Y, Yadav A, Suresh VB, Muthamilarasan M, Yadav CB, Prasad M (2014) Comprehensive genome-wide identification and expression profiling of foxtail millet [Setaria italica (L.)] miRNAs in response to abiotic stress and development of miRNA database. Plant Cell Tiss Organ. doi:10.1007/s11240-014-0480-x
Kozomara A, Griffiths-Jones S (2014) miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acid Res 42:D68–D73
Kumari K, Muthamilarasan M, Misra G, Gupta S, Subramanian A, Parida SK, Chattopadhyay D, Prasad M (2013) 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. PLoS ONE 8:e67742
Lata C, Prasad M (2013) Setaria genome sequencing: an overview. J Plant Biochem Biotechnol 22:257–260
Lata C, Gupta S, Prasad M (2013) Foxtail millet, a model crop for genetic and genomic studies in bioenergy grasses. Crit Rev Biotechnol 33:328–343
Mondal TK, Ganie SA (2014) Identification and characterization of salt responsive miRNA-SSR markers in rice (Oryza sativa). Gene 535:204–209
Muthamilarasan M, Theriappan P, Prasad M (2013) Recent advances in crop genomics for ensuring food security. Curr Sci 105:155–158
Muthamilarasan M, Venkata Suresh B, Pandey G, Kumari K, Parida SK, Prasad M (2014) Development of 5123 intron-length polymorphic markers for large-scale genotyping applications in foxtail millet. DNA Res 21:41–52
Pandey G, Misra G, Kumari K, Gupta S, Parida SK, Chattopadhyay D, Prasad M (2013) Genome-wide development and use of microsatellite markers for large-scale genotyping applications in foxtail millet [Setaria italica (L.)]. DNA Res 20:197–207
Perrier X, Flori A, Bonnot F (2003) Data analysis methods. In: Hamon P, Seguin M, Perrier X, Glaszmann JC (eds) Genetic diversity of cultivated tropical plants. Science Publishers, Montpellier, pp 43–76
Suresh BV, Muthamilarasan M, Misra G, Prasad M (2013) FmMDb: a versatile database of foxtail millet markers for millets and bioenergy grasses research. PLoS ONE 8:e71418
Untergrasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M, Rozen SG (2012) Primer3—new capabilities and interfaces. Nucleic Acids Res 40:e115
Voorrips RE (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 93:77–78
Zhang G, Liu X, Quan Z, Cheng S, Xu X, Pan S, Xie M, Zeng P, Yue Z, Wang W, Tao Y, Bian C, Han C, Xia Q, Peng X, Cao R, Yang X, Zhan D, Hu J, Zhang Y, Li H, Li H, Li N, Wang J, Wang C, Wang R, Guo T, Cai Y, Liu C, Xiang H, Shi Q, Huang P, Chen Q, Li Y, Wang J, Zhao Z, Wang J (2012) Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential. Nature Biotechnol 30:549–554
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.
Author information
Authors and Affiliations
Corresponding author
Additional information
Chandra Bhan Yadav and Mehanathan Muthamilarasan have contributed equally to this work.
Electronic supplementary material
Below is the link to the electronic supplementary material.
11032_2014_137_MOESM1_ESM.pptx
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)
11032_2014_137_MOESM4_ESM.doc
Supplementary Table S3. Chromosomal distribution and physical density of miRNA-based markers on the nine chromosomes of foxtail millet. (DOC 32 kb)
11032_2014_137_MOESM5_ESM.xls
Supplementary Table S4. Amplification and polymorphic potential of 66 miRNA-based markers in foxtail millet. (XLS 37 kb)
11032_2014_137_MOESM6_ESM.xls
Supplementary Table S5. Cross-genera transferability of 66 miRNA-based markers from foxtail millet to related grass species. (XLS 42 kb)
Rights and permissions
About this article
Cite this article
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). https://doi.org/10.1007/s11032-014-0137-9
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11032-014-0137-9