Allelic Diversity for Candidate Genes and Association Studies: Methods and Results

Conference paper

Abstract

The increasing ease with which molecular markers can be generated makes it possible for plant geneticists to use these genomic technologies for better exploitation of the available genetic variation in breeding populations. Identifying markers based on conventional bi-parental mapping populations is most likely not the best way to implement a marker assisted selection (MAS) program, although this approach is useful for introgression of alleles from wild germplasm. Instead, association mapping may be used in a more practical approach, by measuring both phenotypes and markers directly on the plants in the breeding nursery. Conventional quantitative trait loci (QTL) mapping enables one to identify chromosomal regions of 5–20 cM containing genes underlying the trait of interest. However, that still leaves several hundred potential candidate genes. Association mapping enables the exploitation of the wider genetic diversity and incorporate a larger number of recombinations. Synthetic populations used for genetic improvement of self-incompatible crops including many forage and turf species, present a useful tool for incorporating association mapping and genotype building using molecular markers. This is particularly true for traits that have not previously been selected for, since linkage disequilibrium (LD) is less likely to have been built up. We show some preliminary data from a experiment to illustrate population structure, LD and associations with candidate genes in synthetic populations not previously selected for this trait. Some recent research on association analysis in perennial ryegrass and clovers are also reviewed. We also briefly describe genomic selection (GS) that can predict the breeding values of lines in a population by analyzing phenotypes and high-density marker scores as a way to incorporate MAS into the breeding process.

Keywords

Association mapping Genomic selection Linkage disequilibrium Quantitative trait loci 

References

  1. Andersen, J.R., Lübberstedt, T. 2003. Functional markers in plants. Trends Plant Sci. 8:554–560.PubMedCrossRefGoogle Scholar
  2. Auzanneau, J., Huyghe, C., Julier, B., Barre, P. 2007. Linkage disequilibrium in synthetic varieties of perennial ryegrass. Theor. Appl. Genet. 115:837–847.CrossRefGoogle Scholar
  3. Cogan, N.O.I., Ponting, R.C., Vecchies, A.C., Drayton, M.C., George, J., Dobrowolski, M.P., Sawbridge, T.I., Spangenberg, G.C., Smith, K.F., Forster, J.W. 2006. Gene-associated single nucleotide polymorphism (SNP) discovery in perennial ryegrass (Lolium perenne L.). Mol. Genet. Genom. 276:101–112.CrossRefGoogle Scholar
  4. Cogan, N.O.I., Drayton, M.C., Ponting, R.C., Vecchies, A.C., Bannan, N.R., Sawbridge, T.I., Smith, K.F., Spangenberg, G.C., Forster, J.W. 2007. Validation of in silico-predicted genic SNPs in white clover (Trifolium repens L.), an outbreeding alloplyploid species. Mol. Genet. Genom. 277:413–425.CrossRefGoogle Scholar
  5. Dracatos, P.M., Cogan, N.O.I., Dobrowolski, M.P., Sawbridge, T.I., Spangenberg, G.C., Smith, K.F., Forster, J.W. 2008. Discovery and genetic mapping of single nucleotide polymorphisms in candidate genes for pathogen defence response in perennial ryegrass (Lolium perenne L.). Theor. Appl. Genet.117:203–219.PubMedCrossRefGoogle Scholar
  6. Heffner, E.L., Sorrells, M.E., Jannink, J.-L. 2009. Genomic selection for crop improvement. Crop Sci. 49:1–12.CrossRefGoogle Scholar
  7. Isobe, S., Kölliker, R., Hisano, H., Sasamoto, S., Wada, T., Klimenko, I., Okumura, K., Tabata, S. 2009. Construction of a consensus linkage map for red clover (Trifolium pratense L.). BMC Plant Biol. 9:57.Google Scholar
  8. Gupta, P.K., Rustgi, S., Kulwal, P.L. 2005. Linkage disequilibrium and association studies in higher plants: Present status and future prospects. Plant Mol. Biol. 57:461–485.PubMedCrossRefGoogle Scholar
  9. Mackay, T.F.C. 2001. The genetic architecture of quantitative traits. Ann. Rev. Genet. 33:303–339.Google Scholar
  10. Meuwissen, T.H.E., Hayes, B.J., Goddard, M.E. 2001. Prediction of total genetic value using genome-wide dense marker maps. Genetics 157:1819–1829.PubMedGoogle Scholar
  11. Ponting, R.C., Drayton, M.C., Cogan, N.O.I., Dobrowolski, M.P., Spangenberg, G.C., Smith, K.F., Forster, J.W. 2007. SNP discovery, validation, haplotype structure and linkage disequilibrium in full-length herbage nutritive quality genes of perennial ryegrass (Lolium perenne L.). Mol. Genet. Genom. 278:585–597.CrossRefGoogle Scholar
  12. Rafalski, A., Morgante, M. 2004. Corn and humans: Recombination and linkage disequilibrium in two genomes of similar size. Trends Genet. 20:103–111.PubMedCrossRefGoogle Scholar
  13. Skøt, L., Humphreys, J., Humphreys, M.O., Thorogood, D., Gallagher, J., Sanderson, R., Armstead, I.P., Thomas, I.D. 2007. Association of candidate genes with flowering time and water-soluble carbohydrate content in Lolium perenne L. Genetics 177:535–547.PubMedCrossRefGoogle Scholar
  14. Smith, K.F., Dobrowolski, M.P., Cogan, N.O.I., Spangenberg, G.C., Forster, J.W. 2009. Utilizing linkage disequilibrium and association mapping to implement candidate gene based markers in perennial ryegrass breeding (pp. 335–340). In: Yamada, T., Spangenberg, G. (eds.), Molecular Breeding of Forage and Turf. Springer Science + Business, New York.Google Scholar
  15. Spangenberg, G.S., Forster, J.W., Edwards, D., John, U., Mouradov, A., Emmerling, M., Batley, J., Felitti, S., Cogan, N.O.I., Smith, K.F., Dobrowolski, M.P. 2005. Future directions in the molecular breeding of forage and turf (pp. 83–97). In: Humphreys, M.O. (ed.), Molecular breeding for the genetic improvement of forage crops and turf. Wageningen Academic Publishers, The Netherlands.Google Scholar
  16. Wong, C.K., Bernardo, R. 2008. Genomewide selection in oil palm: Increasing selection gain per unit time and cost with small populations. Theor. Appl. Genet. 116:815–824.PubMedCrossRefGoogle Scholar
  17. Wu, R., Zeng, Z.-B. 2001. Joint linkage and linkage disequilibrium mapping in natural populations. Genetics 157:899–909.PubMedGoogle Scholar
  18. Wu, R., Ma, C.-X., Casella, G. 2002. Joint linkage and linkage disequilibrium mapping of quantitative trait loci in natural populations. Genetics 160:779–792.PubMedGoogle Scholar
  19. Xing, Y., Frei, U., Schejbel, B., Asp, T., Lübberstedt, T. 2008. Nucleotide diversity and linkage disequilibrium in 11 expressed resistance candidate genes in Lolium perenne. BMC Plant Biol. 7:43.CrossRefGoogle Scholar
  20. Yamada, T., Spangenberg, G. (eds.) 2009. Molecular Breeding of Forage and Turf (pp. 1–352). Springer Science + Business Media, New York.Google Scholar
  21. Yang, Y., Zhang, J., Hoh, J., Matsuda, F., Xu, P., Lathrop, M., Ott, J. 2003. Efficiency of single-nucleotide polymorphism haplotype estimation from pooled DNA. Proc. Natl. Acad. Sci. USA 100:7225–7230.PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2010

Authors and Affiliations

  1. 1.Field Center for Northern Biosphere, Hokkaido UniversitySapporoJapan
  2. 2.Aberystwyth University, Institute of Biological, Environmental and Rural SciencesAberystwyth CeredigionUK

Personalised recommendations