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Journal of Zhejiang University SCIENCE B

, Volume 14, Issue 7, pp 570–577 | Cite as

Diversity arrays technology (DArT) for studying the genetic polymorphism of flue-cured tobacco (Nicotiana tabacum)

Article

Abstract

Diversity arrays technology (DArT) is a microarray-based marker system that achieves high throughput by reducing the complexity of the genome. A DArT chip has recently been developed for tobacco. In this study, we genotyped 267 flue-cured cultivars/landraces, including 121 Chinese accessions over five decades from widespread geographic regions in China, 103 from the Americas, and 43 other foreign cultivars, using the newly developed chip. Three hundred and thirty polymorphic DArT makers were selected and used for a phylogenetic analysis, which suggested that the 267 accessions could be classified into two subgroups, which could each be further divided into 2–4 sections. Eight elite cultivars, which account for 83% of the area of Chinese tobacco production, were all found in one subgroup. Two high-quality cultivars, HHDJY and Cuibi1, were grouped together in one section, while six other high-yield cultivars were grouped into another section. The 330 DArT marker clones were sequenced and close to 95% of them are within non-repetitive regions. Finally, the implications of this study for Chinese flue-cured tobacco breeding and production programs were discussed.

Key words

Nicotiana tabacum Diversity arrays technology (DArT) Genetic diversity Flue-cured tobacco 

CLC number

S336 

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Supplementary material

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References

  1. Agarwal, M., Shrivastava, N., Padh, H., 2008. Advances in molecular marker techniques and their applications in plant sciences. Plant Cell Rep., 27(4):617–631. [doi:10.1007/s00299-008-0507-z]PubMedCrossRefGoogle Scholar
  2. Akbari, M., Wenzl, P., Caig, V., Carling, J., Xia, L., Yang, S., Uszynski, G., Mohler, V., Lehmensiek, A., Kuchel, H., et al., 2006. Diversity arrays technology (DArT) for high-throughput profiling of the hexaploid wheat genome. Theor. Appl. Genet., 113(8):1409–1420. [doi:10.1007/s00122-006-0365-4]PubMedCrossRefGoogle Scholar
  3. Alsop, B.P., Farre, A., Wenzl, P., Wang, J., Zhou, M., Romagosa, I., Kilian, A., Steffenson, B.J., 2011. Development of wild barley-derived DArT markers and their integration into a barley consensus map. Mol. Breed., 27(1):77–92. [doi:10.1007/s11032-010-9415-3]CrossRefGoogle Scholar
  4. Botstein, D., White, R.L., Skolnick, M., Davis, R.W., 1980. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am. J. Hum. Genet., 32(3):314–331.PubMedGoogle Scholar
  5. Conesa, A., Gotz, S., Garcia-Gomez, J.M., Terol, J., Talon, M., Robles, M., 2005. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics, 21(18):3674–3676. [doi:10.1093/bioinformatics/bti610]PubMedCrossRefGoogle Scholar
  6. Edwards, K.D., Bombarely, A., Story, G.W., Allen, F., Mueller, L.A., Coates, S.A., Jones, L., 2010. TobEA: an atlas of tobacco gene expression from seed to senescence. BMC Genomics, 11(1):142. [doi:10.1186/1471-2164-11-142]PubMedCrossRefGoogle Scholar
  7. Fricano, A., Bakaher, N., del Corvo, M., Piffanelli, P., Donini, P., Stella, A., Ivanov, N.V., Pozzi, C., 2012. Molecular diversity, population structure, and linkage disequilibrium in a worldwide collection of tobacco (Nicotiana tabacum L.) germplasm. BMC Genet., 13(1):18. [doi:10.1186/1471-2156-13-18]PubMedCrossRefGoogle Scholar
  8. Hubisz, M.J., Falush, D., Stephens, M., Pritchard, J.K., 2009. Inferring weak population structure with the assistance of sample group information. Mol. Ecol. Resour., 9(5): 1322–1332. [doi:10.1111/j.1755-0998.2009.02591.x]PubMedCrossRefGoogle Scholar
  9. Jaccoud, D., Peng, K., Feinstein, D., Kilian, A., 2001. Diversity arrays: a solid state technology for sequence information independent genotyping. Nucleic Acids Res., 29(4):E25. [doi:10.1093/nar/29.4.e25]PubMedCrossRefGoogle Scholar
  10. Liu, G., 2011. Practical Guide to Leaf Tobacco Production Techniques in China. China National Leaf Tobacco Corporation, Beijing (in Chinese).Google Scholar
  11. Lu, X.P., Gui, Y.J., Xiao, B.G., Li, Y., Tong, Z.J., Liu, Y., Bai, X.F., Wu, W.R., Xia, L., Huttner, E., et al., 2013. Development of DArT markers for linkage map of flue-cured tobacco. Chin. Sci. Bull., 58(6):641–648.CrossRefGoogle Scholar
  12. Moon, H.S., Nicholson, J.S., Heineman, A., Lion, K., Hoeven, R., Hayes, A.J., Lewis, R.S., 2009a. Changes in genetic diversity of US flue-cured tobacco germplasm over seven decades of cultivar development. Crop Sci., 49(2): 498–508. [doi:10.2135/cropsci2008.05.0253]CrossRefGoogle Scholar
  13. Moon, H.S., Nifong, J.M., Nicholson, J.S., Heineman, A., Lion, K., Hoeven, R., Hayes, A.J., Lewis, R.S., 2009b. Microsatellite-based analysis of tobacco (Nicotiana tabacum L.) genetic resources. Crop Sci., 49(6):2149–2159. [doi:10.2135/cropsci2009.01.0024]CrossRefGoogle Scholar
  14. Ren, N., Timko, M.P., 2001. AFLP analysis of genetic polymorphism and evolutionary relationships among cultivated and wild Nicotiana species. Genome, 44(4):559–571. [doi:10.1139/g01-060]PubMedGoogle Scholar
  15. Sambrook, J., Russell, D.W., 2001. Molecular Cloning: A Laboratory Manual, 3rd Ed. Huang, P.T. et al., translator, 2002. Science Press, Beijing, p.547–610 (in Chinese).Google Scholar
  16. Tajima, F., 1983. Evolutionary relationship of DNA sequences in finite populations. Genetics, 105(2):437–460.PubMedGoogle Scholar
  17. Tinker, N.A., Kilian, A., Wight, C.P., Heller-Uszynska, K., Wenzl, P., Rines, H.W., Bjornstad, A., Howarth, C.J., Jannink, J.L., Anderson, J.M., et al., 2009. New DArT markers for oat provide enhanced map coverage and global germplasm characterization. BMC Genomics, 10(1):39. [doi:10.1186/1471-2164-10-39]PubMedCrossRefGoogle Scholar
  18. Watterson, G.A., 1975. On the number of segregating sites in genetical models without recombination. Theor. Popul. Biol., 7(2):256–276. [doi:10.1016/0040-5809(75)90020-9]PubMedCrossRefGoogle Scholar
  19. Wenzl, P., Carling, J., Kudrna, D., Jaccoud, D., Huttner, E., Kleinhofs, A., Kilian, A., 2004. Diversity arrays technology (DArT) for whole-genome profiling of barley. PNAS, 101(26):9915–9920. [doi:10.1073/pnas.0401076101]PubMedCrossRefGoogle Scholar
  20. Yang, B.C., Xiao, B.G., Chen, X.J., Shi, C.H., 2007. Assessing the genetic diversity of tobacco germplasm using intersimple sequence repeat and inter-retrotransposon amplification polymorphism markers. Ann. Appl. Biol., 150(3): 393–401. [doi:10.1111/j.1744-7348.2007.00139.x]CrossRefGoogle Scholar
  21. Ye, J., Fang, L., Zheng, H., Zhang, Y., Chen, J., Zhang, Z., Wang, J., Li, S., Li, R., Bolund, L., 2006. WEGO: a web tool for plotting GO annotations. Nucleic Acids Res., 34(Web Sever):W293–W297. [doi:10.1093/nar/gkl031]PubMedCrossRefGoogle Scholar
  22. Zhang, H.Y., Liu, X.Z., He, C.S., Yang, Y.M., 2006. Genetic diversity among flue-cured tobacco (Nicotiana tabacum L.) revealed by amplified fragment length polymorphism. Bot. Stud., 47(3):223–229.Google Scholar
  23. Zhao, J.H., Zhang, J.S., Wang, Y., Wang, R.G., Wu, C., Fan, L.J., Ren, X.L., 2011. DNA methylation polymorphism in flue-cured tobacco and candidate markers for tobacco mosaic virus resistance. J. Zhejiang Univ.-Sci. B (Biomed. & Biotechnol.), 12(11):935–942. [doi:10.1631/jzus.B1000 417]CrossRefGoogle Scholar

Copyright information

© Zhejiang University and Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  1. 1.Department of AgronomyZhejiang UniversityHangzhouChina
  2. 2.Yunnan Academy of Tobacco Agricultural Sciences and China Tobacco Breeding Research Center at YunnanYuxiChina

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