Theoretical and Applied Genetics

, Volume 118, Issue 4, pp 821–829 | Cite as

Development and genetic mapping of SSR markers in foxtail millet [Setaria italica (L.) P. Beauv.]

  • Xiaoping Jia
  • Zhongbao Zhang
  • Yinghui Liu
  • Chengwei Zhang
  • Yunsu Shi
  • Yanchun Song
  • Tianyu Wang
  • Yu Li
Original Paper

Abstract

SSR markers are desirable markers in analysis of genetic diversity, quantitative trait loci mapping and gene locating. In this study, SSR markers were developed from two genomic libraries enriched for (GA)n and (CA)n of foxtail millet [Setaria italica (L.) P. Beauv.], a crop of historical importance in China. A total of 100 SSR markers among the 193 primer pairs detected polymorphism between two mapping parents of an F2 population, i.e. “B100” of cultivated S. italica and “A10” of wild S. viridis. Excluding 14 markers with unclear amplifications, and five markers unlinked with any linkage group, a foxtail millet SSR linkage map was constructed by integrating 81 new developed SSR markers with 20 RFLP anchored markers. The 81 SSRs covered nine chromosomes of foxtail millet. The length of the map was 1,654 cM, with an average interval distance between markers of 16.4 cM. The 81 SSR markers were not evenly distributed throughout the nine chromosomes, with Ch.8 harbouring the least (3 markers) and Ch.9 harbouring the most (18 markers). To verify the usefulness of the SSR markers developed, 37 SSR markers were randomly chosen to analyze genetic diversity of 40 foxtail millet accessions. Totally 228 alleles were detected, with an average 6.16 alleles per locus. Polymorphism information content (PIC) value for each locus ranged from 0.413 to 0.847, with an average of 0.697. A positive correlation between PIC and number of alleles and between PIC and number of repeat unit were found [0.802 and 0.429, respectively (P < 0.01)]. UPGMA analysis revealed that the 40 foxtail millet cultivars could be grouped into five clusters in which the landraces’ grouping was largely consistent with ecotypes while the breeding varieties from different provinces in China tended to be grouped together.

Notes

Acknowledgments

We thank Dr M. Gale of John Innes Center for providing seeds of the mapping population, Dr K. Devos of the University of Georgia at Athens for providing RFLP data and advice, and Prof. Ping Lu for providing seeds of foxtail millet accessions. We also thank two anonymous reviewers for valuable suggestions and careful corrections. This research was supported by the Basic Research Program (grant no. 2005CCA02500) and National Research Program for Public Will (grant no. 2005DIA4J019) of the Ministry of Science and Technology of China, and National Natural Science Foundation (grant no. 30571168).

Supplementary material

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References

  1. Anderson JA, Churchill GA, Autrique JE, Tanksley SD, Sorrells ME (1993) Optimizing parental selection for genetic linkage maps. Genome 36:181–186PubMedCrossRefGoogle Scholar
  2. Bassam BJ, Caetano-Anolles G, Gresshoff PM (1991) Fast and sensitive silver staining of DNA in polyacrylamide gels. Anal Biochem 196:80–83PubMedCrossRefGoogle Scholar
  3. Bell CJ, Ecker JR (1994) Assignment of 30 microsatellite loci to the linkage map of Arabidopsis. Genomics 19:137–144PubMedCrossRefGoogle Scholar
  4. Bhattramakki D, Dong J, Chabra AK, Hart GE (2000) An integrated SSR and RFLP linkage map of Sorghum bicolor (L.) Moench. Genome 43:988–1002PubMedCrossRefGoogle Scholar
  5. Castiglioni P, Ajmone-Marsan P, van Wijk R, Motto M (1999) AFLP markers in a molecular linkage map of maize: codominant scoring and linkage group distribution. Theor Appl Genet 99:425–431CrossRefGoogle Scholar
  6. Cregan PB, Mudge J, Fickus EW, Marek LF, Danesh D, Denny R, Mathews BF, Jarvik T, Young ND (1999) Targeted isolation of simple sequence repeat markers through the use of bacterial artificial chromosomes. Theor Appl Genet 98:919–928CrossRefGoogle Scholar
  7. De Wet JMJ, Oestry-Stidd LL, Cubero JL (1979) Origins and evolution of foxtail millet. J Agric Trop Bot Appl 26:53–63Google Scholar
  8. Devos KM, Wang ZM, Beales CJ, Sasaki T, Gale MD (1998) Comparative genetic maps of foxtail millet (Setaria italica) and rice (Oryza sativa). Theor Appl Genet 96:63–68CrossRefGoogle Scholar
  9. Devos KM, Pittaway TS, Reynolds A, Gale MD (2000) Comparative mapping reveals a complex relationship between the pearl millet genome and those of foxtail millet and rice. Theor Appl Genet 100:190–198CrossRefGoogle Scholar
  10. Doust AN, Devos KM, Gadberry MD, Gale MD, Kellogg EA (2004) Genetic control of branching in foxtail millet. Proc Natl Acad Sci U S A 101:9045–9050PubMedCrossRefGoogle Scholar
  11. Doust AN, Devos KM, Gadberry MD, Gale MD, Kellogg EA (2005) The genetic basis for inflorescence variation between foxtail and green millet (Poaceae). Genetics 169:1659–1672PubMedCrossRefGoogle Scholar
  12. Edwards KJ, Barker JHA, Daly A, Jones C, Karp A (1996) Microsatellite libraries enriched for several microsatellite sequences in plants. Biotechniques 20:758PubMedGoogle Scholar
  13. Fisher PJ, Gardner RC, Richardson TE (1996) Single locus microsatellites isolated using 5’-anchored PCR. Nucleic Acids Res 24:4369–4371PubMedCrossRefGoogle Scholar
  14. Fukunaga K, Kato M (2003) Mitochondrial DNA variation in foxtail millet, Setaria italica (L.) P. Beauv. Euphytica 129:7–13CrossRefGoogle Scholar
  15. Fukunaga K, Domon E, Kawase M (1997) Ribosomal DNA variation in foxtail millet, Setaria italica (L.) P. Beauv., and a survey of variation from Europe and Asia. Theor Appl Genet 95:751–756CrossRefGoogle Scholar
  16. Fukunaga K, Wang ZM, Kato K, Kawase M (2002) Geographical variation of nuclear genome RFLPs and genetic differentiation in foxtail millet, Setaria italica (L.) P. Beauv. Genet Resour Crop Evol 49:95–101CrossRefGoogle Scholar
  17. Hayden MJ, Sharp PJ (2001) Targeted development of informative microsatellite (SSR) markers. Nucleic Acids Res 29(8):e44PubMedCrossRefGoogle Scholar
  18. Jia XP, Shi YS, Song YC, Wang GY, Wang TY, Li Y (2007) Development of EST-SSR in foxtail millet (Setaria italica). Genet Resour Crop Evol 54:233–236CrossRefGoogle Scholar
  19. Jusuf M, Pernes J (1985) Genetic variability of foxtail millet (Setaria italica (L.) P. Beauv.): Electrophoretic study of five isoenzyme systems. Theor Appl Genet 71:385–391CrossRefGoogle Scholar
  20. Kawase K, Sakamoto S (1984) Variation, geographical distribution and genetical analysis of esterase isozymes in foxtail millet, Setaria italica (L.) P. Beauv. Theor Appl Genet 67:529–533CrossRefGoogle Scholar
  21. Kawase M, Sakamoto S (1987) Geographical distribution of landrace groups classified by pollen sterility in foxtail millet (Setaria italica L. P. Beauv). Japanese J Breed 37:1–9Google Scholar
  22. Kosambi DD (1944) The estimation of map distance from recombination values. Ann Eugen 12:172–175Google Scholar
  23. Küster H (1984) Neolithic plant remains from Eberdingenhochdorf, southern Germany. In: Van Zeist WV, Casparoe WA (eds) Plants and ancient man (studies in palaeoethnobotany). A.A. Bakame, Rotterdam, pp 307–311Google Scholar
  24. Lander ES, Green P, Abrahamson J, Barlow A, Daly MJ, Lincoln SE, Newburg L (1987) MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174–181PubMedCrossRefGoogle Scholar
  25. Le Thierry d’ Ennequin M, Panaud O, Toupance B, Sarr A (2000) Assessment of relationships between Setaria italica and its wild relative S. viridis using AFLP markers. Theor Appl Genet 100:1061–1066CrossRefGoogle Scholar
  26. Li Y, Wu SZ (1996) Traditional maintenance and multiplication of foxtail millet (Setaria italica (L.) P. Beauv.) landraces in China. Euphytica 87:33–38CrossRefGoogle Scholar
  27. Li HW, Li CH, Pao WK (1945) Cytological and genetic studies of interspecific cross of the cultivated foxtail millet, Setaria italica P. Beauv. and the green foxtail millet, S. viridis L. J Am Soc Agron 37:32–54Google Scholar
  28. Li Y, Cao YS, Wu SZ, Zhang XZ (1995) A diversity analysis of foxtail millet (Setaria italica (L.) P. Beauv.) landraces of Chinese origin. Genet Resour Crop Evol 43:377–384CrossRefGoogle Scholar
  29. Li Y, Jia J, Wang Y, Wu S (1998) Intraspecific and interspecific variation in Setaria revealed by RAPD analysis. Genet Resour Crop Evol 45:279–285CrossRefGoogle Scholar
  30. Maguire TL, Edwards KJ, Saenger P, Henry R (2000) Characterisation and analysis of microsatellite loci in a mangrove species, Avicennia marina (Forsk.) Vierh. (Avicenniaceae). Theor Appl Genet 101:279–285CrossRefGoogle Scholar
  31. Marinoni D, Akkak A, Bounous G, Edwards KJ, Botta R (2003) Development and characterization of microsatellite markers in Castanea sativa (Mill.). Mol Breed 11:127–136CrossRefGoogle Scholar
  32. Matsuoka YS, Mitchell E, Kresovich S, Goodman M, Doebley J (2002) Microsatellites in Zea—variability, patterns of mutations, and use for evolutionary studies. Theor Appl Genet 104:436–450PubMedCrossRefGoogle Scholar
  33. McCouch SR, Teytelman L, Xu Y, Lobos KB, Clare K, Walton M, Fu B, Maghirang R, Li Z, Xing Y, Zhang Q, Kono I, Yano M, Fjellstrom R, DeClerck G, Schneider D, Cartinhour S, Ware D, Stein L (2002) Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Res 9:199–207PubMedCrossRefGoogle Scholar
  34. Merdinoglu DG, Butterlin L, Bevilacqua V, Chiquet AF (2005) Development and characterization of a large set of microsatellite markers in grapevine (Vitis vinifera L.) suitable for multiplex PCR. Mol Breed 15:349–366CrossRefGoogle Scholar
  35. Nei M, Li WH (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci U S A 76:5269–5273PubMedCrossRefGoogle Scholar
  36. Panaud O, Chen SR, McCouch R (1996) Development of microsatellite markers and characterization of simple sequence length polymorphism (SSLP) in rice (Oryza sativa L.). Mol Gen Genet 252:597–607PubMedGoogle Scholar
  37. Pandey M, Gailing O, Fischer D, Hattemer HH, Finkeldey R (2004) Characterization of microsatellite markers in sycamore (Acer pseudoplatanus L.). Mol Ecol Notes 4:253–255CrossRefGoogle Scholar
  38. Pejic I, Ajmone-Marsan P, Morgante M, Kozumplick V (1998) Comparative analysis of genetic similarity among maize inbred lines detected by RFLPs, RAPDs, SSRs, and AFLPs. Theor Appl Genet 97:1248–1255CrossRefGoogle Scholar
  39. Powel W, Morgante M, Andre C, Hanafey M, Vogel J (1996) The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Mol Breed 2:225–238CrossRefGoogle Scholar
  40. Prasad M, Varshney RK, Royj K (2000) The use of microsatellites for detecting DNA polymorphism, genotype identification and genetic diversity in wheat. Theor Appl Genet 100:584–592Google Scholar
  41. Rohlf JF (1995) NTSYS-pc: numerical taxonomy and multivariate analysis system, Version 2.11. Exeter Software, SetauketGoogle Scholar
  42. Russell JR, Fuller JD, Macaulay M (1997) Direct evaluation of levels of genetic variation among barley accessions detected by RFLPs, AFLPs, SSRs and RAPDs. Theor Appl Genet 93:714–723CrossRefGoogle Scholar
  43. Sargent DJ, Hadonou AM, Simpson DW (2003) Development and characterization of polymorphic microsatellite markers from Fragaria viridis, a wild diploid strawberry. Mol Ecol Notes 3:550–552CrossRefGoogle Scholar
  44. Schmidt T, Jung C, Metzla M (1991) Distribution and evolution of two satellite DNAs in the genus Beta. Theor Appl Genet 82:793–799CrossRefGoogle Scholar
  45. Schontz D, Rether B (1998) Genetic variability in foxtail millet, Setaria italica (L.) P. Beauv. using a heterologous rDNA probe. Plant Breed 117:231–234CrossRefGoogle Scholar
  46. Schontz D, Rether B (1999) Genetic variability in foxtail millet, Setaria italica (L.) P. Beauv.: identification and classification of lines with RAPD markers. Plant Breed 118:190–192CrossRefGoogle Scholar
  47. Sivaraman L, Ranjekar PK (1984) Novel molecular features of millet genomes. Indian J Biochem Biophys 21:299–303PubMedGoogle Scholar
  48. Smulders MJM, Bredemeijer G, Rus-Kortekaas W, Arens P, Vosman B (1997) Use of short microsatellites from database sequence to generate polymorphism among Lycopersicon esculentum cultivars and accessions of other Lycopersicon species. Theor Appl Genet 97:264–272CrossRefGoogle Scholar
  49. Tautz D, Renz M (1984) Simple sequences are ubiquitous components of eukaryotic genomes. Nucleic Acids Res 12:4127–4138PubMedCrossRefGoogle Scholar
  50. Thomas MR, Scott NS (1993) Microsatellite repeats in grapevine reveal DNA polymorphisms when analysed as sequence tagged sites (STSs). Theor Appl Genet 86:985–990Google Scholar
  51. Toth G, Gaspari Z, Jurka J (2000) Microsatellites in different eukaryotic genome, survey and analysis. Genome Res 10:1967–1981CrossRefGoogle Scholar
  52. Ueno S, Tsumura Y, Washitani I (2003) Development of microsatellite markers in Primula sieboldii E. Morren, a threatened Japanese perennial herb. Conserv Genet 4:809–811CrossRefGoogle Scholar
  53. Viruel MA, Hormaza JI (2004) Development, characterization and variability analysis of microsatellites in lychee (Litchi chinensis Sonn., Sapindaceae). Theor Appl Genet 108:896–902PubMedCrossRefGoogle Scholar
  54. Wang ZM, Devos KM, Liu CJ, Wang RQ, Gale MD (1998) Construction of RFLP-based maps of foxtail millet. Theor Appl Genet 96:31–36CrossRefGoogle Scholar
  55. Xu Y, Zhu L, Xiao J (1997) Chromosomal regions associated with segregation distortion of molecular markers in F2, backcross, doubled haploid, and recombinant inbred populations in rice (Oryza sativa L.). Mol Genet Genomics 253:535–545CrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2009

Authors and Affiliations

  • Xiaoping Jia
    • 1
  • Zhongbao Zhang
    • 1
  • Yinghui Liu
    • 1
  • Chengwei Zhang
    • 1
  • Yunsu Shi
    • 1
  • Yanchun Song
    • 1
  • Tianyu Wang
    • 1
  • Yu Li
    • 1
  1. 1.Institute of Crop ScienceChinese Academy of Agricultural Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)BeijingPeople’s Republic of China

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