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Molecular Breeding

, Volume 14, Issue 4, pp 441–454 | Cite as

Comparison of identity by descent and identity by state for detecting genetic regions under selection in a sorghum pedigree breeding program

  • D. R. Jordan
  • Y. Z. Tao
  • I. D. Godwin
  • R. G. Henzell
  • M. Cooper
  • C. L. McIntyre
Article

Abstract

Seventy sorghum inbred lines which formed part of the Queensland Department of Primary Industries (QDPI) sorghum breeding program were screened with 104 previously mapped RFLP markers. The lines were related by pedigree and consisted of ancestral source lines, intermediate lines and recent releases from the program. We compared the effect of defining marker alleles using either identity by state (IBS) or identity by descent (IBD) on our capacity to trace markers through the pedigree and detect evidence of selection for particular alleles. Allelic identities defined using IBD were much more sensitive for detecting non-Mendelian segregation in this pedigree. Only one marker allele showed significant evidence of selection when IBS was used compared with ten regions with particular allelic identities when IBD was used. Regions under selection were compared with the location of QTLs for agronomic traits known to be under selection in the breeding program. Only two of the ten regions were associated with known QTLs that matched with knowledge of the agronomic characteristics of the ancestral lines. Some of the other regions were hypothesised to be associated with genes for particular traits based on the properties of the ancestral source lines.

Key words

Breeding Haplotype Pedigree QTL Sorghum RFLP 

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References

  1. Bink M.C.A.M., Uimari P., Sillanpaa M.J., Janss L.L.G. and Jansen R.C. 2002. Multiple QTL mapping in related plant populations via a pedigree-analysis approach. Theor. Appl. Genet. 104: 751–762.Google Scholar
  2. Crasta O.R., Xu W.W., Rosenow D.T., Mullet J., Nguyen H.T. 1999. Mapping of post-flowering drought resistance traits in grain sorghum: association between QTLs influencing premature senescence and maturity. Molecular and General Genetics 262: 579–588.Google Scholar
  3. De Koeyer D.L., Philips R.L., Stuthman D.D. 2001. Alleleic shifts and quantitative trait loci in a recurrent selection population of oat. Crop Science 41: 1228–1234.Google Scholar
  4. Duncan R.R., Bramel-Cox P.J., Miller F.R., Shands H.L. and Wiesner L.E. 1991. Contributions of introduced sorghum germplasm to hybrid development in the USA.. In: Use of plant introductions in cultivar development, Part 1, Proceedings of a symposium sponsored by Division C-1 of the Crop Sci Society of America in Las Vegas, Nevada, USA. (Crop Science Society of America, Inc.), pp. 69–102.Google Scholar
  5. Haldane J.B.S. and Waddington C.H. 1931. Inbreeding and linkage. Genetics 16: 357–374.Google Scholar
  6. Hayano-Saito Y., Tsuji T., Fujii K., Saito K., Iwasaki M., Saito A. 1998. Localisation of the rice stripe disease resistance gene, stv-bi,by graphical genotyping and linkage analyses with molecular markers. Theor. Appl. Genet. 96: 1044–1049.Google Scholar
  7. Lorenzen L.L., Boutin S., Young N., Specht J.E. and Shoemaker R.C. 1995. Soybean pedigree analysis using map-based molecular markers: I. Crop Science 35: 1326–1336.Google Scholar
  8. Newman L.H. 1912. Plant breeding in Scandinavia. Canadian Seed Growers Association, Ottawa, Canada.Google Scholar
  9. Panaud O., Chen X. and Mccouch S.R. 1996. Development of microsatellite markers and characterization of simple sequence length polymorphism (SSLP) in rice (Oryza sativa l). Molecular General Genetics 252: 597–607.Google Scholar
  10. Pestova E. and Roder M. 2002. Microsatelite analysis of wheat chromosome 2D allows the reconstruction of chromosomal inheritance in pedigrees of breeding programmes. Theor. Appl. Genet. 106: 84–91.Google Scholar
  11. Russell J.R., Ellis R.P., Thomas W.T.B., Waugh R., Provan J., Booth A., Fuller J., Lawrence P., Young G. and Powell W. 2000. A retrospective analysis of spring barley germplasm development from ‘foundation genotypes’ to currently successful cultivars. Molecular Breeding 6: 553–568.Google Scholar
  12. Sjakste T.G., Rashal I. and Roder M.S. 2003. Inheritance of microsatelite alleles in pedigrees of Latvian barley varieties and related European ancestors. Theor. Appl. Genet. 106: 539–549.Google Scholar
  13. Shoemaker R.C., Guffy R.D., Lorenzen L.L. and Specht J.E. 1992. Molecular genetic mapping of soybean: map utilization. Crop Science 32: 1091–1098.Google Scholar
  14. Subudhi P.K., Rosenow D.T. and Nguyen H.T. 2000. Quantitative trait loci for the stay green trait in sorghum (Sorghum bicolor L. Moench): consistency across genetic backgrounds and environments. Theor. Appl. Genet. 101: 733–741.Google Scholar
  15. Tao Y.Z., McIntyre C.L. and Henzell R.G. 1996. Applications of molecular markers to Australian sorghum breeding programs. I: Construction of a RFLP map using sorghum recombinant inbred lines. In Proceedings of the Third Australian Sorghum Conference, Tamworth, 20–22 February 1996.Google Scholar
  16. Tao Y.Z. Jordan D.R., Henzell R.G. and McIntyre C.L. 1998. Identification of genomic regions for rust resistance in sorghum. Euphytica 103: 287–292.Google Scholar
  17. Tao Y.Z., Henzell R.G., Jordan D.R., Butler D.G., Kelly A.M. and McIntyre C.L. 2000. Identification of genomic regions associated with stay green in sorghum by testing RILs in multiple environments. Theoretical and Applied Genetics 100: 1225–1232.Google Scholar
  18. Tao Y.Z., Hardy A., Drenth J., Henzell R.G., Franzmann B.A., Jordan D.R., Butler D.G. and McIntyre C.L. 2003. Identifications of two different mechanisms for sorghum midge resistance through QTL mapping. Theoretical and Applied Genetics 107: 116–122.Google Scholar
  19. Tao Y.Z., Manners J.M., Ludlow M.M. and Henzell R.G. 1993. DNA polymorphisms in grain sorghum (Sorghum bicolor (L.) Moench). Theor. Appl. Genet. 86: 679–688.Google Scholar
  20. Teakle D.S. and Pritchard A.J. 1971. Resistance of Krish sorghum to four strains of sugarcane mosaic virus in Queensland. Plant Disease Reporter 55: 596–598.Google Scholar
  21. Tuinstra M.R., Grote E.M., Goldsbrough P.B. and Ejeta G. 1997. Genetic analysis of post-flowering drought tolerance and components of grain development in Sorghum bicolor (L.) Moench. Molecular Breeding 3: 439–448.Google Scholar
  22. Xu W.W., Subudhi P.K., Crasta O.R., Rosenow D.T., Mullet J.E. and Nguyen H.T. 2000. Molecular mapping of QTLs conferring stay-green in grain sorghum (Sorghum bicolor L. Moench). Genome 43: 461–469.Google Scholar
  23. Young N.D. and Tanksley S.D. 1989. Restriction fragment length polymorphism maps and the concept of graphical genotypes. Theor. Appl. Genet. 77: 95–101.Google Scholar

Copyright information

© Minister of Public Works and Government Services Canada 2004

Authors and Affiliations

  • D. R. Jordan
    • 1
    • 3
  • Y. Z. Tao
    • 2
  • I. D. Godwin
    • 3
  • R. G. Henzell
    • 1
  • M. Cooper
    • 3
  • C. L. McIntyre
    • 2
  1. 1.Department of Primary Industries, Hermitage Research StationWarwick
  2. 2.CSIRO Plant IndustrySt Lucia
  3. 3.School of Land and Food SciencesThe University of QueenslandBrisbane

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