Development and Characterization of SSR Markers in Proso Millet Based on Switchgrass Genomics

Santosh G. Rajput, Tammy Plyler-Harveson, Dipak K. Santra

Panhandle Research and Extension Center, University of Ne-braska-Lincoln, Scottsbluff, USA.

DOI: 10.4236/ajps.2014.51023                

Abstract

Proso millet (Panicummiliaceum) has highwater use efficiency (WUE), a short growing-season, and is highly adapted to a semi-arid climate. Genomic resources for proso millet are very limited. Large numbers of DNA markers and other genomic tools in proso millet can readily be developed by using genomic resources in related grasses. The objectives of the present report were to 1) test and characterize switchgrass SSR markers for use in proso millet, and 2) elucidate repeat-motifs in proso millet based on new SSR marker analysis. A total of 548 SSR markers were tested on 8 proso millet genotypes. Out of these, 339 amplified SSR markers in proso millet. This showed that 62% of the switchgrass SSR markers were transferable to proso millet. Of these 339 markers, 254 were highly polymorphic among the 8 proso genotypes. The resolving power of these 254 polymorphic SSR markers ranged from 0.25-14.75 with an average of 2.71. The 254 polymorphic SSR markers amplified 984 alleles in the ranges of 50 bp to 1300 bp. The majority of the SSR markers (221 of 254) amplified dinucleotide repeats. Based on SSR marker analysis, AG/GA was the most abundant repeat-motifs in proso millet. Switchgrass genomic information seems to be the most useful for developing DNA markers in proso millet. Markers developed in this study will be helpful for linkage map construction, mapping agronomic traits and future molecular breeding efforts in proso millet.

Keywords

Millet; Minor Crops; Comparative Genomics; Molecular Breeding

Conflicts of Interest

The authors declare no conflicts of interest.

References

[1]	[1] A. Lawler, “Bridging East and West: Millet on the Move,” Science, Vol. 325, No. 5943, 2009, pp. 942-943. http://dx.doi.org/10.1126/science.325_942
[2]	G. W. Wiegrefe, “How to Prduceproso Millet (A Farmer’s Guide),” Pierre, South Dakota, 1990.
[3]	D. D. Baltensperger, “Progress with Proso, Pearl and Other Millets,” In: J. Janick and A. Whipkey, Eds., Trends in New Crops and New Uses, ASHS Press, Alexandria, 2002, pp. 100-103.
[4]	E. A. Oelke, E. S. Oplinger, D. H. Putnam, B. R. Durgan, J. D. Doll and D. J. Undersander Millets, “Alternative Field Crops Manual,” University of Wisconsin, Cooperative Extension and University of Minnesota, Center for Alternative Plants & Animal Products and Minnesota Extension Service, 1990.
[5]	M. Brink and G. Belay, “Cereals and Pulses,” Plant Resources of Tropical Africa, 2006, pp. 122-125.
[6]	D. J. Lyon, P. A. Burgener, K. L. De Boer, R. M. Harveson, G. L. Hein, G. W. Hergert, T. L. Holman, L. A. Nelson, J. J. Johnson, T. Nleya, J. M. Krall, D. C. Nielsen and M. F. Vigil, “Producing and Marketing of Proso Millet in Great Plains,” 2008. http://ianrpubs.unl.edu/live/ec137/build/ec137.pdf
[7]	USDA-NASS Quick Stats. http://quickstats.nass.usda.gov/results/962608D8-F138-3CC7-9705-068D2A399631
[8]	D. K. Santra and D. Rose, “Alternative Uses of Proso Millet,” University of Nebraska-Lincoln NebGude G2218, 2013.
[9]	AGMRC, 2012. http://www.agmrc.org/commodities__products/grains__oilseeds/proso-millet/
[10]	H. K. M. Ribu and K. W. Hilu, “Detection of Interspecific and Intraspecific Variation in Panicummillets through Random Amplified Polymorphic DNA,” Theoretical and Applied Genetics, Vol. 88, 1994, pp. 412-416.
[11]	D. Karam, P. Westra, S. J. Nissen, S. M. Ward and J. E. F. Figueiredo, “Genetic Diversity Among Proso Millet (Panicummiliaceum L.) Biotypes Assessed by AFLP Technique,” Planta Daninha, Vol. 22, No. 2, 2004, pp. 167-174. http://dx.doi.org/10.1590/S0100-83582004000200001
[12]	D. Karam, P. Westra, S. J. Niessen, M. W. Sarah and J. E. F. Figueiredo, “Assessment of Silver-Stained AFLP Markers for Studying DNA Polymorphism in Proso Millet (Panicummiliaceum L.),” Revista Brasileira de Botanica, Vol. 29, No. 4, 2006, pp. 609-615.
[13]	W. Powell, M. Morgante and C. Andre, “The Comparison of RFLP, RAPD, AFLP and SSR (Microsatellite) Markers for Germplasm analysis,” Molecular Breeding, Vol. 2, No. 3, 1996, pp. 225-238. http://dx.doi.org/10.1007/BF00564200
[14]	P. K. Gupta and R. K. Varshney, “The Development and Use of Microsatellite Markers Fore Genetic Analysis and Plant Breeding with Emphasis on Bread Wheat,” Euphytica, Vol. 113, No. 3, 2000, pp. 163-185. http://dx.doi.org/10.1023/A:1003910819967
[15]	X. Hu, J. Wang, P. Lu and H. Zhang, “Assessment of Genetic Diversity in Broomcorn Millet Panicummiliaceum L.) Using SSR Markers,” Journal of Genetics and Genomics, Vol. 36, No. 8, 2009, pp. 491-500. http://dx.doi.org/10.1016/S1673-8527(08)60139-3
[16]	C. Young-II, J.-W. Chung, G.-A. Lee, K.-H. Ma, A. Dixit, J.-G. Gwag and Y.-J. Park, “Development and Characterization of Twenty-Five New Polymorphic Microsatellite Markers in Proso Millet (Panicummiliaceum L.),” Genes & Genomics, Vol. 32, No. 3, 2010, pp. 267-273. http://dx.doi.org/10.1007/s13258-010-0007-8
[17]	M. C. Saha, J. D. Cooper, M. A. RoufMian, K. Chekhovskiy and G. D. May, “Tall Fescue Genomic SSR Markers: Development and Transferability across Multiple Grass Species,” Theoretical and Applied Genetics, Vol. 113, No. 8, 2006, pp. 1449-1458. http://dx.doi.org/10.1007/s00122-006-0391-2
[18]	L. Zane, L. Bargelloni and T. Patarnello, “Strategies for Microsatellite Isolation: A Review,” Molecular Ecology, Vol. 11, No. 1, 2002, pp. 1-16. http://dx.doi.org/10.1046/j.0962-1083.2001.01418.x
[19]	S. H. Dwivedi, H. Upadhyaya, S. Senthilvel, C. Hash, K. Fukunaga, X. Diao, D. K. Santra, D. Baltensperger and M. Prasad, “Millets: Genetic and Genomic Resources,” Plant Breeding Review, Vol. 6, 2012, pp. 247-375.
[20]	S. L. Dillon, P. K. Lawrence and R. J. Henry, “The New Use of Sorghum bicolor-Derived SSR Markers to Evaluate Genetic Diversity in 17 Australian Sorghum Species,” Plant Genetic Resources: Characterization and Utilization, Vol. 3, No. 1, 2005, pp. 19-28. http://dx.doi.org/10.1079/PGR200454
[21]	C. C. Tan, Y. Q. Wu, T. Charles, A. Michael, T. Chuck and T. Samuels, “Development of Simple Sequence Repeat Markers for Bermuda Grass from Its Expressed Sequence Tag Sequences and Preexisting Sorghum SSR Markers,” Molecular Breeding, Vol. 29, No. 1, 2012, pp. 23-30. http://dx.doi.org/10.1007/s11032-010-9521-2
[22]	E. C. Bess, A. N. Doust and E. A. Kellogg, “A Naked Grass in the ‘Bristle Clade’: A Phylogenetic and Developmental Study of Panicum Section Bulbosa (Paniceae: Poaceae),” International Journal of Plant Sciences, Vol. 166, No. 3, 2005, pp. 371-381. http://dx.doi.org/10.1086/428701
[23]	L. Liu, Y. Wu, Y. Wang and T. Samuels, “A High-Density Simple Sequence Repeat-Based Genetic Linkage Map of Switchgrass,” Genes Genomes and Gentics, Vol. 2, No. 3, 2012, pp. 357-370.
[24]	M. Okada, C. Lanzatella, M. C. Saha, J. Bouton, R. Wu and C. M. Tobias, “Complete Switchgrass Genetic Maps Reveal Subgenome Collinearity, Preferential Pairing and Multilocus Interactions,” Genetics, Vol. 185, No. 3, 2010, pp. 745-760. http://dx.doi.org/10.1534/genetics.110.113910
[25]	Y. W. Wang, T. D. Samuels and Y. Q. Wu, “Development of 1,030 Genomic SSR Markers in Switchgrass,” Theoretical and Applied Genetics, Vol. 122, No. 4, 2011, pp. 677-686. http://dx.doi.org/10.1007/s00122-010-1477-4
[26]	J. J. Doyle and J. L. Doyle, “A Rapid DNA Isolation Procedure from Small Amount of Fresh Leaf Tissue,” Phytochemical Bulletin, Vol. 19, 1987, pp. 11-15.
[27]	A. Prevost and M. J. Wilkinson, “A New System of Comparing PCR Primers Applied to ISSR Fingerprinting of Potato Cultivars,” Theoretical and Applied Genetics, Vol. 98, No. 1, 1999, pp. 107-112. http://dx.doi.org/10.1007/s001220051046
[28]	J. Yu, M. La Rota, R. Kantety and M. Sorrells, “EST Derived SSR Markers for Comparative Mapping in Wheat and Rice,” Molecular Genetics and Genomics, Vol. 271, No. 6, 2004, pp. 742-751. http://dx.doi.org/10.1007/s00438-004-1027-3
[29]	A. L. S. Azevedo, P. P. Costa, J. C. Machado, M. A. Machado, A. V. Pereira and F. J. da Silva Lédo, “Cross Species Amplification of Pennisetumglaucum Microsatellite Markers in Pennisetumpurpureum and Genetic Diversity of Napier Grass Accessions,” Crop Science, Vol. 52, No. 4, 2012, pp. 1776-1785. http://dx.doi.org/10.2135/cropsci2011.09.0480
[30]	M. L. Wang, N. A. Barkley, J.-K. Yu, R. E. Dean, M. L. Newman, M. E. Sorrells and G. A. Pederson, “Transfer of Simple Sequence Repeat (SSR) Markers from Major Cereal Crops to Minor Grass Species for Germplasm Characterization and Evaluation,” Plant Genetic Resources: Characterization and Utilization, Vol. 3, No. 1, 2005, pp. 45-57. http://dx.doi.org/10.1079/PGR200461
[31]	R. K. Varshney, A. Graner and M. E. Sorrells, “Genic Microsatellite Markers in Plants: Features and Applications,” Trends in Biotechnology, Vol. 23, No. 1, 2005, pp. 48-55. http://dx.doi.org/10.1016/j.tibtech.2004.11.005
[32]	H. V. Hunt, H. M. Moots, R. A. Graybosch, H. Jones, M. Parker, O. Romanova, M. K. Jones, C. J. Howe and K. Trafford, “Waxy Phenotype Evolution in the Allotetraploid Cereal Broomcorn Millet: Mutations at the GBSSI Locus in Their Functional and Phylogenetic Context,” Molecular Biology and Evolution, Vol. 30, No. 1, 2013, pp. 109-122. http://dx.doi.org/10.1093/molbev/mss209
[33]	H. W. Cai, M. Inoue, N. Yuyama, W. Takahashi, M. Hirata and T. Sasaki, “Isolation, Characterization and Mapping of Simple Sequence Repeat Markers in Zoysiagrass (Zoysiaspp.),” Theoretical and Applied Genetics, Vol. 112, No. 1, 2005, pp. 158-166. http://dx.doi.org/10.1007/s00122-005-0118-9
[34]	M. Feldman, B. Liu, G. S. Segal, A. Abbo, A. Levy and J. M. Vega, “Rapid Elimination of Low-Copy DNA Sequences in Polyploid Wheat: A Possible Mechanism for Differentiation of Homoeologous Chromosomes,” Genetics, Vol. 147, No. 3, 1997, pp. 1381-1387.
[35]	Y. Chi, Y. Cheng, J. Vanitha, N. Kumar, R. Ramamoorthy, S. Ramachandran and S.-Y. Jiang, “Expansion Mechanisms and Functional Divergence of the Glutathione S-Transferase Family in Sorghum and Other Higher Plants,” DNA Research, Vol. 18, No. 1, 2011, pp. 1-16. http://dx.doi.org/10.1093/dnares/dsq031
[36]	T. Fukao, E. Yeung and J. Bailey-Serres, “The Submergence Tolerance Regulator SUB1A Mediates Crosstalk between Submergence and Drought Tolerance in Rice,” Plant Cell, Vol. 23, No. 1, 2011, pp. 412-427. http://dx.doi.org/10.1105/tpc.110.080325
[37]	A. Cuadrado and N. Jouve, “Similarities in the Chromosomal Distribution of AG and AC Repeats within and between Drosophila, Human and Barley Chromosomes,” Cytogenetic and Genome Research, Vol. 119, No. 1-2, 2007, pp. 91-99. http://dx.doi.org/10.1159/000109624
[38]	C. S. Reddy, B. A. Prasad, B. P. M. Swamy, K. Kaladhar and N. Sarla, “ISSR Markers Based on GA and AG Repeats Reveal Genetic Relationship among Rice Varieties Tolerant to Drought, Flood or Salinity,” Journal of Zhejiang University Science, Vol. 2, 2009, pp. 133-141.
[39]	L. Cardle, L. Ramsay, D. Milbourne, M. Macaulay, D. Marshall and R. Waugh, “Computational and Experimental Characterization of Physically Clustered Simple Sequence Repeats in Plants,” Genetics, Vol. 156, 2000, pp. 847-854.
[40]	P. Y. Danin, N. Reis, G. Tzuri and N. Katzir, “Devolopment and Characterization of Microsatellites Markers in Cucumis,” Theoretical and Applied Genetics, Vol. 102, 2001, pp. 61-72.