Genome-wide development and use of microsatellite markers for large-scale genotyping applications in foxtail millet [setaria italica (L.)]

DNA Research

Volumn 20, Issue 2, 2013, Pages 197-207

  Pandey, Garima ^a   Misra, Gopal ^a   Kumari, Kajal ^a   Gupta, Sarika ^a   Parida, Swarup Kumar ^a   Chattopadhyay, Debasis ^a   Prasad, Manoj ^a  

^a NATIONAL INSTITUTE OF PLANT GENOME RESEARCH   (India)

Author keywords

Comparative mapping; Foxtail millet (Setaria Italica L.); Microsatellite; Physical mapping; Transferability

Indexed keywords

ARABIDOPSIS; ARTICLE; BIOENERGY; BRACHYPODIUM; CHROMOSOME; CHROMOSOME 8; CHROMOSOME 9; COMPARATIVE GENOMIC HYBRIDIZATION; COMPUTER MODEL; DINUCLEOTIDE REPEAT; DNA POLYMORPHISM; FOXTAIL MILLET; GENE AMPLIFICATION; GENE FREQUENCY; GENE TRANSFER; GENETIC ASSOCIATION; GENETIC LINKAGE; GENETIC VARIABILITY; GENOTYPE; MAIZE; MICROSATELLITE MARKER; PANICUM VIRGATUM; PHYLOGENY; PLANT GENETICS; QUANTITATIVE TRAIT LOCUS; RICE; SORGHUM; TRINUCLEOTIDE REPEAT;

CHROMOSOME MAPPING; CHROMOSOMES, PLANT; GENETIC MARKERS; GENOME, PLANT; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; MICROSATELLITE REPEATS; PENNISETUM; PHYLOGENY; POLYMORPHISM, GENETIC; SEQUENCE ANALYSIS, DNA; SETARIA PLANT; TRINUCLEOTIDE REPEATS;

PANICUM VIRGATUM; PENNISETUM GLAUCUM; POACEAE; SETARIA (PLANT); SETARIA ITALICA; ZEA MAYS;

EID: 84879139179     PISSN: 13402838     EISSN: 17561663     Source Type: Journal    
DOI: 10.1093/dnares/dst002     Document Type: Article

References (36)

1. Devos, K.M. and Gale, M.D. 2000, Genome relationships: The grass model in current research, Plant Cell, 12, 637-46.
2. 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.
3. Lata, C., Gupta, S. and Prasad, M. 2012, Foxtail millet: A model crop for genetic and genomic studies in bioenergy grasses, Crit. Rev. Biotechnol. DOI: 10.3109/07388551.2012.716809. (September 18, 2012).
4. Li, P. and Brutnell, T.P. 2011, Setaria viridis and Setaria italica, model genetic systems for Panicoid grasses, J. Exp. Bot., 62, 3031-37.
5. Bennetzen, J.L., Wang, J.S.H., Percifield, R., et al. 2012, Reference genome sequence of the model plant Setaria, Nature Biotech., 30, 555-61.
6. 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. Biotechnol., 30, 549-54.
7. Mitros, T.K., Bennetzen, J.L., Schmutz, J. and Rokhsar, D.S. 2010, The foxtail millet genome and its relationship amongst the grasses. In: Plant and Animal Genomes XVIII Conference, January 9-13, San Diego, CA. W328 (abstract).
8. Delseny, M., Laroche, M. and Penon, P. 1983, Detection of sequences with Z-DNA forming potential in higher plants, Biochem. Biophys. Res. Commun., 116, 113-20.
9. Tautz, D. and Renz, M. 1984, Simple sequences are ubiquitous repetitive components of eukaryotic genomes, Nucleic Acids Res., 12, 4127-38.
10. Varshney, R.K., Graver, A. and Sorrells, M.E. 2005, Genic microsatellite markers in plants: Features and applications, Trends Biotechnol., 23, 48-55.
11. Parida, S.K., Rajkumar, K.A., Dalal, V., Singh, N.K. and Mohapatra, T. 2006, Unigene derived microsatellite markers for the cereal genomes, Theor. Appl. Genet., 112, 808-17.
12. Parida, S.K., Kalia, S.K., Sunita, K., et al. 2009, Informative genomic microsatellite markers for efficient genotyping applications in sugarcane, Theor. Appl. Genet., 118, 327-38.
13. Parida, S.K., Yadav, D.K. and Mohapatra, T. 2010, Microsatellites in Brassica unigenes: Relative abundance, marker design and use in comparative physical mapping and genome analysis, Genome, 53, 55-67.
14. Lin, H.S., Chiang, C.Y., Chang, S.B. and Kuoh, C.S. 2011, Development of simple sequence repeats (SSR) markers in Setaria italica (Poaceae) and cross-amplification in related species, Int. J. Mol. Sci., 12, 7835-45.
15. Gupta, S., Kumari, K., Sahu, P.P., Vidapu, S. and Prasad, M. 2012, Sequence based novel genomic microsatellite markers for robust genotyping purposes in foxtail millet [Setaria italica (L.) P. Beauv], Plant Cell Rep., 31, 323-37.
16. Jia, X.P., Shi, Y.S., Song, Y.C., Wang, G.Y., Wang, T.Y. and Li, Y. 2007, Development of EST-SSR in foxtail millet (Setaria italica), J. Genet. Res. Crop Evol., 54, 233-6.
17. Singh, H., Deshmukh, R.K., Singh, A., Singh, A.K. and Gaikwad, K. 2010, Highly variable SSR markers suitable for rice genotyping using agarose gels, Mol. Breed., 25, 359-64.
18. Sayama, T., Hwang, T.-Y., Komatsu, K., et al. 2011, Development and application of a whole-genome simple sequence repeat panel for high-throughput genotyping in soybean, DNA Res., 18, 107-15.
19. Sonah, H., Deshmukh, R.K., Sharma, A., et al. 2011, Genome-wide distribution and organization of microsatellites in plants: An insight into marker development in Brachypodium, PLoS One, 6, e21298. doi:10.1371/journal. pone.0021298 ma1.
20. Voorrips, R.E. 2002, MapChart: Software for the graphical presentation of linkage maps and QTLs, J. Hered., 93, 77-8.
21. Jaccard, P. 1908, Nouvelle recherches sur la distribution florale, Bull Soc. Vaud. Sci. Nat., 44, 223-70.
22. Rohlf, F.J. 1997, NTSYS-pc numerical taxonomy and multivariance analysis system. Version 2.02e, Exeter Software, Setauket, NY.
23. Kalia, R.K., Rai, M.K., Kalia, S., Singh, R. and Dhawan, A.K. 2011, Microsatellites markers: An overview of the recent progress in Plants, Euphytica, 177, 309-34.
24. Morgante, M. and Olivieri, A.M. 1993, PCR-amplified microsatellites as markers in plant genetics, Plant J., 3, 175-82.
25. Sharma, P.C., Grover, A. and Kahl, G. 2007, Mining microsatellites in eukaryotic genomes, Trends Biotechnol., 25, 490-8.
26. Yasodha, R. 2011, Characterization of microsatellites in the tribe bambuseae, Gene Conserv., 10, 51-64.
27. Sharma, M.K., Sharma, R., Cao, P., et al. 2012, A genome-wide survey of switchgrass genome structure and organization, PLoS One, 7, e33892. doi:10.1371/journal.pone.0033892.
28. Temnykh, S., Declerk, G., Lukashover, A., Lipovich, L., Cartinhour, S. and McCouch, S. 2001, Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): Frequency, lengthvariation, transposon associations and genetic marker potential, Genome Res., 11, 1441-52.
29. Wei, L., Hui, Z., Yong-fang, W., Hai-quan, L. and Xianmin, D. 2012, Assesment of genetic relationship of foxtail millet with its wild ancestor and close relatives by ISSR markers, J. Int. Agri., 11, 556-66.
30. Hirano, R., Naito, K., Fukunaga, K., Watanabe, K.N., Ohsawa, R. and Kawase, M. 2011, Genetic structure of landraces in foxtail millet (Setaria italica (L.) P. Beauv.) revealed with transposon display and interpretation to crop evolution of foxtail millet, Genome, 54, 1-9.
31. Jones, E.S., Dupal, M.P., Kollier, R., Drayton, M.C. and Forster, J.W. 2001, Development and characterization of simple sequence repeat (SSR) markers for perennial ryegrass (Lolium perenne. L.), Theor. Appl.Genet., 102, 405-15.
32. Chen, S.Y., Lin, Y.T., Lin, C.W., Chen, W.Y., Yang, C.H. and Ku, H.M. 2010, Transferability of rice SSR markers to bamboo, Euphytica, 175, 23-33.
33. Gautami, B., Ravi, K., Narasu, M.L., Hoisington, D.A. and Varshney, R.K. 2009, Novel set of groundnut SSRs for genetic diversity and inter-specific transferability, Int. J. Integr. Biol., 7, 100-6.
34. Devos, K.M., Wang, Z.M., Beales, J., Sasaki, T. and Gale, M.D. 1998, Comparative genetic maps of foxtail millet (Setaria italica) and rice (Oryza sativa), Theor. Appl. Genet., 96, 63-8.
35. Devos, K.M. 2005, Updating the crop circle, Curr. Opin. Plant Biol., 8, 155-62.
36. 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.