Development and utilization of novel SSRs in foxtail millet [Setaria italica (L.) P. Beauv.]

Plant Breeding

Volumn 132, Issue 4, 2013, Pages 367-374

  Gupta, Sarika ^a   Kumari, Kajal ^a   Muthamilarasan, Mehanathan ^a   Subramanian, Alagesan ^b   Prasad, Manoj ^a  

^a NATIONAL INSTITUTE OF PLANT GENOME RESEARCH   (India)

^b TAMIL NADU AGRICULTURAL UNIVERSITY   (India)

Author keywords

Foxtail millet (Setaria italica L.); Genetic diversity; Microsatellite; Molecular markers; SSRs; Transferability

Indexed keywords

POACEAE; SETARIA ITALICA;

EID: 84881377543     PISSN: 01799541     EISSN: 14390523     Source Type: Journal    
DOI: 10.1111/pbr.12070     Document Type: Article

References (60)

1. Bell, C. J., and J. R. Ecker, 1994: Assignment of 30 microsatellite loci to the linkage map of Arabidopsis. Genomics 19, 137-144.
2. Bennetzen, J. L., J. Schmutz, H. Wang, R. Percifield, J. Hawkins, A. C. Pontaroli, M. Estep, L. Feng, J. N. Vaughn, J. Grimwood, J. Jenkins, K. Barry, E. Lindquist, U. Hellsten, S. Deshpande, X. Wang, X. Wu, T. Mitros, J. Triplett, X. Yang, C. Y. Ye, M. Mauro-Herrera, L. Wang, P. Li, M. Sharma, R. Sharma, P. C. Ronald, O. Panaud, E. A. Kellogg, T. P. Brutnell, A. N. Doust, G. A. Tuskan, D. Rokhsar, and K. M. Devos, 2012: Reference genome sequence of the model plant Setaria. Nature Biotech. 30, 555-561.
3. Bhattramakki, D., J. Dong, K. Chhabra, and G. E. Hart, 2000: An integrated SSR and RFLP linkage map of Sorghum bicolor (L.) Moench. Genome 43, 988-1002.
4. Bohn, M., H. F. Utz, and A. E. Melchinger, 1999: Genetic similarities among winter wheat cultivars determined on the basis of RFLPs, AFLPs, and SSRs and their use for predicting progeny variance. Crop Sci. 39, 228-237.
5. Chen, M., P. SanMiguel, A. C. de Oliveira, S. S. Woo, H. Zhang, R. A. Wing, and J. L. Bennetzen, 1997: Microcollinearity in sh2-homologous regions of the maize, rice, and sorghum genomes. Proc. Natl Acad. Sci. USA 94, 3431-3435.
6. Cordeiro, G. M., T. L. Maguire, K. J. Edwards, and R. J. Henry, 1999: Optimization of a microsatellite enrichment technique in Saccharum spp. Plant Mol. Biol. Rep. 17, 225-229.
7. Devos, K. M., Z. M. Wang, J. Beales, T. Sasaki, and M. D. Gale, 1998: Comparative genetic maps of foxtail millet (Setaria italica) and rice (Oryza sativa). Theor. Appl. Genet. 96, 63-68.
8. Doust, A. N., E. A. Kellogg, K. M. Devos, and J. L. Bennetzen, 2009: Foxtail millet: a sequence-driven grass model system. Plant Physiol. 149, 137-141.
9. Edwards, K. J., J. H. A Barker, A. Daly, C. Jones, and A. Karp, 1996: Microsatellite libraries enriched for several microsatellite sequences in plants. Biotechniques 20, 758-760.
10. Gupta, S., and M. Prasad, 2009: Development and characterization of genic SSR markers in Medicago truncatula and their transferability in leguminous and non-leguminous species. Genome 52, 761-771.
11. Gupta, P. K., and R. K. Varshney, 2000: The development and use of microsatellites markers for genetic analysis and plant breeding with emphasis on bread wheat. Euphytica 113, 163-185.
12. Gupta, S., K. Kumari, J. Das, C. Lata, S. Puranik, and M. Prasad, 2011: Development and utilization of novel intron length polymorphic markers in foxtail millet [Setaria italica (L.) P. Beauv.]. Genome 54, 586-602.
13. Gupta, S., K. Kumari, P. P. Sahu, S. Vidapu, and M. Prasad, 2012: Sequence-based novel genomic microsatellite markers for robust genotyping purposes in foxtail millet [Setaria italica (L.) P. Beauv.]. Plant Cell Rep. 31, 323-337.
14. Hirata, M., H. W. Cai, M. Inoue, N. Yuyama, Y. Miura, T. Komatsu, T. Takamizo, and M. Fujimori, 2006: Development of simple sequence repeat (SSR) markers and construction of an SSR-based linkage map in Italian ryegrass (Lolium multiflorum Lam.). Theor. Appl. Genet. 113, 270-279.
15. Hokanson, S. C., A. K. Szewc-Mcfadden, W. F. Lamboy, and J. R. Mcferson, 1998: Microsatellite (SSR) markers reveal genetic identities, genetic diversity and relationships in a Malus domestica borkh. core subset collection. Theor. Appl. Genet. 67, 671-683.
16. Huang, X., and A. Madan, 1999: CAP3: a DNA sequence assembly program. Genome Res. 9, 868-877.
17. Ince, A. G., M. Karaca, and A. N. Onus, 2010: CAPS-microsatellites: use of CAPS method to convert non-polymorphic microsatellites into useful markers. Mol. Breed 25, 491-499.
18. Jaccard, P., 1908: Nouvelle recherches sur la distribution florale. Bulletin de la Société Vaudoise des Sciences Naturelles 44, 223-270.
19. Jia, X. P., Y. S. Shi, Y. C. Song, G. Y. Wang, T. Y. Wang, and Y. Li, 2007: Development of EST-SSR in foxtail millet (Setaria italica). J. Genet. Resour. Crop Evo. 54, 233-236.
20. Jia, X., Z. Zhang, Y. Liu, C. Zhang, Y. Shi, Y. Song, T. Wang, and Y. Li, 2009: Development and genetic mapping of SSR markers in foxtail millet [Setaria italica (L.) P. Beauv.]. Theor. Appl. Genet. 118, 821-829.
21. Jones, E. S., M. P. Dupal, R. Kolliker, M. C. Drayton, and J. W. Forster, 2001: Development and characterization of simple sequence repeat (SSR) markers for perennial ryegrass (Lolium perenne L.). Theor. Appl. Genet. 102, 405-415.
22. Jones, K. C., K. F. Levine, and J. D. Banks, 2002: Characterization of 11 polymorphic tetra-nucleotide microsatellites for forensic applications in California elk (Cervus elaphus canadensis). Mol. Ecol. Notes 2, 425-427.
23. Kalia, R. K., M. K. Rai, S. Kalia, R. Singh, and A. K. Dhawan, 2011: Microsatellites markers: an overview of the recent progress in plants. Euphytica 177, 309-334.
24. Kantety, R. V., L. R. Mauricio, D. E. Matthews, E. Mark, and M. E. Sorrells, 2002: Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat. Plant Mol. Biol. 48, 501-510.
25. Koelliker, R., E. S. Jones, M. C. Drayton, M. P. Dupal, and J. W. Forster, 2001: Development and characterization of simple sequence repeat (SSR) markers for white clover (Trifolium repens L.). Theor. Appl. Genet. 102, 416-424.
26. König, J., D. Kopahnke, B. J. Steffenson, N. Przulj, T. Romeis, M. S. Röder, F. Ordon, and D. Perovic, 2012: Genetic mapping of a leaf rust resistance gene in the former Yugoslavian barley landrace MBR1012. Mol. Breed 30, 1253-1264.
27. Lata, C., and M. Prasad, 2012: Validation of an allele-specific marker associated with dehydration stress tolerance in a core set of foxtail millet accessions. Plant Breed, DOI:10.1111/j.1439-0523.2012.01983.x.
28. Lata, C., S. Gupta, and M. Prasad, 2012: Foxtail millet: a model crop for genetic and genomic studies in bioenergy grasses. Crit. Rev. Biotechnol, DOI:10.3109/07388551.2012.716809
29. Lin, H.-S., C.-Y. Chiang, S.-B. Chang, and C.-S. Kuoh, 2011: Development of Simple Sequence Repeats (SSR) Markers in Setaria italica (Poaceae) and Cross-Amplification in Related Species. Int. J. Mol. Sci. 12, 7835-7845.
30. Lin, H.-S., G.-I. Liao, C.-Y. Chiang, C.-S. Kuoh, and S.-B. Chang, 2012: Genetic diversity of foxtail millet (Setaria italica) germplasm as determined by agronomic traits and microsatellite markers. Aust. J. Crop Sci. 6, 342-349.
31. Liu, Z., G. Bai, D. Zhang, C. Zhu, X. Xia, R. Cheng, and Z. Shi, 2011: Genetic diversity and population structure of elite foxtail millet [Setaria italica (L.) P. Beauv.] germplasm in China. Crop Sci. 51, 1655-1663.
32. Merdinoglu, D. G., L. Butterlin, V. Bevilacqua, and A. F. Chiquet, 2005: Development and characterization of a large set of microsatellite markers in grapevine (Vitis vinifera L.) suitable for multiplex PCR. Mol. Breed 15, 349-366.
33. Nei, M., 1973: Analysis of genetic diversity in subdivided populations. Proc. Natl Acad. Sci. USA 70, 3321-3323.
34. Panaud, O., S. R. Chen, and R. McCouch, 1996: Development of microsatellite markers and characterization of simple sequence length polymorphism (SSLP) in rice (Oryza sativa L.). Mol. Gen. Genet. 252, 597-607.
35. Parida, S. K., S. K. Kalia, S. Kaul, V. Dalal, G. Hemaprabha, A. Selvi, A. Pandit, A. Singh, K. Gaikwad, T. R. Sharma, P. S. Srivastava, N. K. Singh, and T. Mohapatra, 2009: Informative genomic microsatellite markers for efficient genotyping applications in sugarcane. Theor. Appl. Genet. 118, 327-338.
36. Pejic, I., P. Ajmone-Marsan, M. Morgante, V. Kozumplick, P. Castiglioni, G. Taramino, and M. Motto, 1998: Comparative analysis of genetic similarity among maize inbred lines detected by RFLPs, RAPDs, SSRs, and AFLPs. Theor. Appl. Genet. 97, 1248-1255.
37. Perovic, D., J. Förster, P. Devaux, D. Hariri, M. Guilleroux, K. Kanyuka, R. Lyons, J. Weyen, D. Feuerhelm, U. Kastirr, P. Sourdille, M. Röder, and F. Ordon, 2009: Mapping and diagnostic marker development for Soil-borne cereal mosaic virus resistance in bread wheat. Mol. breed 23, 641-653.
38. Pestova, F., M. W. Ganal, and M. S. Roder, 2000: Isolation and mapping of microsatellite markers specific for the D-genome of bread wheat. Genome 43, 689-697.
39. Powell, W., G. C. Machray, and J. Provan, 1996: Polymorphism revealed by simple sequence repeats. Trends Plant Sci. 1, 215-222.
40. Prasad, M., R. K. Varshney, J. K. Roy, H. S. Balyan, and P. K. Gupta, 2000: The use of microsatellites for detecting DNA polymorphism, genotype identification and genetic diversity in wheat. Theor. Appl. Genet. 100, 584-592.
41. Rohlf, F. J., 1997: NTSYS-pc. Numerical taxonomy and multivariance analysis system version 2.02e. Exeter Software, New York, USA http://www.exetersoftware.com/cat/ntsyspc/ntsyspc.html. (last accessed on September 15, 2012).
42. Roldán-Ruiz, I., F. A. Van Eeuwijk, T. J. Gilliland, P. Dubreuil, J. Dillmann, M. Lalemand, M. De Loose, and C. P. Baril, 2001: A comparative study of molecular and morphological methods of describing relationships between perennial ryegrass (Lolium perenne L.) varieties. Theor. Appl. Genet. 103, 1138-1150.
43. Russel, J., J. Fuller, G. Young, B. Thomas, G. Taramino, M. Macaulay, R. Waugh, and W. Powell, 1997: Discriminating between barley genotypes using microsatellite markers. Genome 40, 442-450.
44. Saghai-Maroof, M. A., R. M. Biyaschev, G. P. Yang, Q. Zhang, and R. W. Allard, 1994: Extraordinary polymorphism microsatellite DNA in barley: species diversity, chromosomal location and population dynamics. Proc. Natl Acad. Sci. USA 91, 5466-5470.
45. Saha, M. C., J. D. Cooper, M. A. Rouf Mian, K. Chekhovskiy, and G. D. May, 2006: Tall fescue genomic SSR markers: development and transferability across multiple grass species. Theor. Appl. Genet. 113, 1449-1458.
46. Sambrook, J., E. F. Fritsch, and T. Maniatis, 1989: Molecular Cloning: A Laboratory Manual. Cold Spring Harbour Laboratory, Cold Spring Harbour, New York.
47. Sargent, D. J., A. M. Hadonou, and D. W. Simpson, 2003: Development and characterization of polymorphic microsatellite markers from Fragaria viridis, a wild diploid strawberry. Mol. Ecol. Notes 3, 550-552.
48. Sharopova, N., M. D. McMullen, L. Schultz, S. Schroeder, H. Sanchez-Villeda, J. Gardiner, D. Bergstrom, K. Houchins, S. Melia-Hancock, T. Musket, N. Duru, M. Polacco, K. Edwards, T. Ruff, J. C. Register, C. Brouwer, R. Thompson, R. Velasco, E. Chin, M. Lee, W. Woodman-Clikeman, M. J. Long, E. Liscum, K. Cone, G. Davis, and E. H. Coe Jr, 2002: Development and mapping of SSR markers for maize. Plant Mol. Biol. 48, 463-481.
49. Shokeen, B., N. K. Sethy, S. Kumar, and S. Bhatia, 2007: Isolation and characterization of microsatellite markers for analysis of molecular variation in the medicinal plant Madagascar periwinkle (Catharanthus roseus (L.) G. Don.). Plant Sci. 172, 441-451.
50. Temnykh, S., G. DeClerck, A. Lukashova, L. Lipovich, S. Cartinhour, and S. McCouch, 2001: Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations and genetic marker potential. Genome Res. 11, 1441-1452.
51. Tsuruta, S. I., M. Hashiguchi, M. Ebina, T. Matsuo, T. Yamamoto, M. Kobayashi, M. Takahara, H. Nakagawa, and R. Akashi, 2005: Development and characterization of simple sequence repeat markers in Zoysia japonica Steud. Grassland Sci. 51, 249-257.
52. Tyrka, M., D. Perovic, A. Wardynska, and F. Ordon, 2008: A new diagnostic SSR marker for selection of the Rym4/Rym5 locus in barley breeding. J. Appl. Genet. 49, 127-134.
53. Wang, Z. M., K. M. Devos, C. J. Liu, R. Q. Wang, and M. D. Gale, 1998: Construction of RFLP-based maps of foxtail millet, Setaria italica (L.) P. Beauv. Theor. Appl. Genet. 96, 31-36.
54. Wang, M. L., N. A. Barkley, J. K. Yu, R. E. Dean, M. L. Newman, M. E. Sorrells, and G. A. Pederson, 2005: Transfer of simple sequence repeat (SSR) markers from major cereal crops to minor grass species for germplasm characterization and evaluation. Plant Genet. Resour. 3, 45-57.
55. Wang, Y. W., T. D. Samuels, and Y. Q. Wu, 2011: Development of 1, 030 genomic SSR markers in switchgrass. Theor. Appl. Genet. 122, 677-686.
56. Yeh, F. C., and T. J. B. Boyle, 1997: Population genetic analysis of co-dominant and dominant markers and quantitative traits. Belg. J. Bot. 129, 157.
57. Yu, F., B.-H. Wang, S.-P. Feng, J.-Y. Wang, W.-G. Li, and Y.-Y. Wu, 2011: Development, characterization, and cross-species/genera transferability of SSR markers for rubber tree (Hevea brasiliensis). Plant Cell Rep. 30, 335-344.
58. Zane, L., L. Bargelloni, and T. Patarnello, 2002: Strategies for microsatellite isolation: a review. Mol. Ecol. 11, 1-16.
59. Zhang, G., X. Liu, Z. Quan, S. Cheng, X. Xu, S. Pan, M. Xie, P. Zeng, Z. Yue, W. Wang, Y. Tao, C. Bian, C. Han, Q. Xia, X. Peng, R. Cao, X. Yang, D. Zhan, J. Hu, Y. Zhang, H. Li, H. Li, N. Li, J. Wang, C. Wang, R. Wang, T. Guo, Y. Cai, C. Liu, H. Xiang, Q. Shi, P. Huang, Q. Chen, Y. Li, J. Wang, Z. Zhao, and J. Wang, 2012: Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential. Nature Biotech. 30, 549-554.
60. Zhao, W., G.-A. Lee, S.-W. Kwon, K.-H. Ma, M.-C. Lee, and Y.-L. Park, 2012: Development and use of novel SSR markers for molecular genetic diversity in Italian millet (Setaria italica L.). Genes Genomics 34, 51-57.