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

DNA Research

Volumn 21, Issue 1, 2014, Pages 41-52

  Muthamilarasan, Mehanathan ^a   Venkata Suresh, B ^a   Pandey, Garima ^a   Kumari, Kajal ^a   Parida, Swarup Kumar ^a   Prasad, Manoj ^a  

^a NATIONAL INSTITUTE OF PLANT GENOME RESEARCH   (India)

Author keywords

comparative mapping; foxtail millet (Setaria italica L.); intron length polymorphism (ILP); physical mapping; transferability

Indexed keywords

COMPARATIVE MAPPING; FOXTAIL MILLET (SETARIA ITALICA L.); INTRON-LENGTH POLYMORPHISM (ILP); PHYSICAL MAPPING; TRANSFERABILITY;

CHROMOSOMES, PLANT; COMPUTER SIMULATION; GENETIC MARKERS; GENOTYPING TECHNIQUES; INTRONS; POLYMORPHISM, GENETIC; SETARIA PLANT; SYNTENY;

EID: 84894545931     PISSN: 13402838     EISSN: 17561663     Source Type: Journal    
DOI: 10.1093/dnares/dst039     Document Type: Article

References (38)

1. Doust, A.N., Kellogg, E.A., Devos, K.M. and Bennetzen, J.L. 2009, Foxtail millet: a sequence-driven grass model system, Plant Physiol., 149, 137-41.
2. Lata, C., Gupta, S. and Prasad, M. 2013, Foxtail millet: a model crop for genetic and genomic studies in bioenergy grasses, Crit. Rev. Biotechnol., 33, 328-43.
3. Li, P. and Brutnell, T.P. 2011, Setaria viridis and Setaria italica, model genetic systems for Panicoid grasses, J. Exp. Bot., 62, 3031-7.
4. Lata, C. and Prasad, M. 2013, Setaria genome sequencing: an overview, J. Plant Biochem. Biotechnol., 22, 257-60.
5. Muthamilarasan, M., Theriappan, P. and Prasad, M. 2013, Recent advances in crop genomics for ensuring food security, Curr. Sci., 105, 155-8.
6. Bennetzen, J.L., Wang, J.S.H., Percifield, R., et al. 2012, Reference genome sequence of the model plant Setaria, Nat. Biotech., 30, 555-61.
7. Zhang, G., Liu, X., Quan, Z., et al. 2012, Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential, Nat. Biotech., 30, 549-54.
8. Pandey, G., Misra, G., Kumari, K., et al. 2013, Genomewide development and use of microsatellite markers for large-scale genotyping applications in foxtail millet [Setaria italica (L.)], DNA Res., 20, 197-207.
9. Kumari, K., Muthamilarasan, M., Misra, G., et al. 2013, Development of eSSR-markers in Setaria italica and their applicability in studying genetic diversity, crosstransferability and comparative mapping in millet and non-millet species, PLoS ONE, 8, e67742.
10. Suresh, V.B., Muthamilarasan, M. and Prasad, M. 2013, FmMDb: a versatile database of foxtail millet markers for millets and bioenergy grasses research, PLoS ONE, 8, e71418.
11. Botstein, D., White, R.L., Skolnick, M. andDavis,R.W. 1980, Construction of a genetic linkage map in man using restriction fragment length polymorphisms, Am. J. Hum. Genet., 32, 314-31.
12. Williams, J.G., Kubelik, A.R., Livak, K.J., Rafalski, J.A. and Tingey, S.V. 1990, DNA polymorphisms amplified by arbitrary primers are useful as genetic markers, Nucleic Acids Res., 18, 6531-5.
13. Vos, P., Hogers, R., Bleeker, M., et al. 1995, AFLP: a new technique for DNA fingerprinting, Nucleic Acids Res., 23, 4407-14.
14. Becker, J.and Heun, M.1995, Barley microsatellites: allele variation and mapping, Plant Mol. Biol., 27, 835-45.
15. Kruglyak, L. 1997, The use of a genetic map of biallelic markers in linkage studies, Nat. Genet., 17, 21-4.
16. Choi, H.K., Kim, D., Uhm, T., et al. 2004, A sequencebased genetic map of Medicago truncatula and comparison of marker colinearity with M. sativa, Genetics, 166, 1463-502.
17. Yang, L., Jin, G., Zhao, X., Zheng, Y., Xu, Z. and Wu,W. 2007, PIP: a database for potential intron polymorphism markers, Bioinformatics, 23, 2174-7.
18. Wang, X., Zhao, X., Zhu, J. and Wu,W. 2005,Genome-wide investigation of intron length polymorphisms and their potential as molecular markers in rice (Oryza sativa L.), DNA Res., 12, 417-27.
19. Braglia, L., Manca, A., Mastromauro, F. and Breviario, D. 2010, cTBP: a successful intron length polymorphism (ILP)-based genotyping method targeted to well defined experimental needs, Diversity, 2, 572-85.
20. Gupta, S., Kumari, K., Das, J., Lata, C., Puranik, S. and Prasad, M. 2011, Development and utilization of novel intron length polymorphic markers in foxtail millet [Setaria italica (L.) P. Beauv.], Genome, 54, 586-602.
21. Saghai-Maroof, M.A., Biyaschev, R.M., Yang, G.P., Zhang, Q. and Allard, R.W. 1994, Extraordinary polymorphism microsatellite DNA in barley, species diversity, chromosomal location and population dynamics, Proc. Natl Acad. Sci. USA, 91, 5466-70.
22. Voorrips, R.E. 2002,MapChart: software for the graphical presentation of linkage maps and QTLs, J. Hered., 93, 77-8.
23. Rotmistrovsky, K., Jang,W. and Schuler, G.D. 2004, Aweb server for performing electronic PCR, Nucleic Acids Res., 32, W108-12.
24. Roldán-Ruiz, I., Van Eeuwijk, F.A., Gilliland, T.J., et al. 2001, A comparative study of molecular and morphological methods of describing relationships between perennial ryegrass (Lolium perenne L.) varieties, Theor. Appl. Genet., 103, 1138-50.
25. Jaccard, P. 1908, Nouvelle recherches sur la distribution florale, Bull. Soc. Vaud. Sci. Nat., 44, 223-70.
26. Rohlf, F.J. 1997, NTSYS-pc numerical taxonomy and multivariance analysis system. Version 2.02e, Exeter Software: Setauket, NY. http://www.exetersoftware. com/cat/ntsyspc/ntsyspc.html.
27. Nei, M. 1973, Analysis of genetic diversity in subdivided populations, Proc. Natl Acad. Sci. USA, 70, 3321-3.
28. Liu, K. and Muse, M. 2005, PowerMarker: an integrated analysis environment for genetic marker analysis, Bioinformatics, 21, 2128-9.
29. Krzywinski, M., Schein, J., Birol, I., et al. 2009, Circos, an information aesthetic for comparative genomics, Genome Res., 19, 1639-45.
30. Palumbi, S.R. 1995, Nucleic acids II: the polymerase chain reaction. In: Hillis, D. and Moritz, C. (eds), Molecular systematics, 2nd edition. Sinauer Associates Inc.: Sunderland, MA, pp. 205-47.
31. Ferreira,A.O.,Cardoso, H.G.,Macedo, E.S., Breviario, D.and Arnholdt-Schmitt, B. 2009, Intron polymorphism pattern in AOX1b of wild St John's wort (Hypericum perforatum) allows discrimination between individual plants, Physiol. Plant., 137, 520-31.
32. Choudhary, S., Sethy, N.K.,Shokeen, B.andBhatia, S.2009, Development of chickpea EST-SSR markers and analysis of allelic variation across related species, Theor. Appl. Genet., 118, 591-608.
33. Gupta, S. and Prasad, M. 2009,Development and characterization of genic SSR markers in Medicago truncatula and their transferability in leguminous and nonleguminous species, Genome, 52, 761-71.
34. Ming, H., Xie, F-M., Chen, L-V., Zhao, X-Q., Jojee, L. and Madonna, D. 2010, Comparative analysis of genetic diversity and structure in rice using ILP and SSR markers, Rice Sci., 17, 257-68.
35. Devos, K.M.,Wang, Z.M., Beales, J., Sasaki, T. andGale, M.D. 1998, Comparative genetic maps of foxtail millet (Setaria italica) and rice (Oryza sativa), Theor. Appl. Genet., 96, 63-8.
36. Devos, K.M. and Gale, M.D. 2000, Genome relationships: the grassmodel incurrent research, PlantCell,12,637-46.
37. Devos, K.M. 2005, Updating the crop circle, Curr. Opin. Plant Biol., 8, 155-62.
38. Srinivasachary, D.M.M., Gale, M.D. and Devos, K.M. 2007, Comparative analyses reveal high levels of conserved colinearity between the finger millet and rice genomes, Theor. Appl. Genet., 115, 489-99.