Genetic Diversity, Linkage Disequilibrium and Association Mapping
Maize, at all levels of resolution, is one of the most diverse crop species. Large insertions and deletions are common between maize inbreds, and include tandem repeat clusters, abundant retroelement and transposons. At the gene level, single nucleotide polymorphisms are common, especially in introns and untranslated regions of genes. Depending on choice of experimental population and region in the genome, linkage disequilibrium between polymorphic sites could decay very rapidly, or persist for hundreds of Kb. Appropriately chosen germplasm collections may be used for genetic association mapping (also called linkage disequilibrium mapping), either with candidate genes, or by scanning the whole genome with thousands of markers at high density. This approach, in favorite circumstances, could provide high resolution. The power of association mapping is variable, and has not been thoroughly investigated. Rapid advances in genome sequencing and high density genotyping are making this approach to relating genotype with phenotype increasingly attractive.
KeywordsLinkage Disequilibrium Association Mapping Maize Genome Oleic Acid Content Heterotic Group
Unable to display preview. Download preview PDF.
- Ananiev, E.V., Phillips, R.L., and Rines, H.W. (1998b). Complex structure of knob DNA on maize chromosome 9. Retrotransposon invasion into heterochromatin. Genetics 149, 2025–2037.Google Scholar
- Bruggmann, R., Bharti, A., Gundlach, H., Lai, J., Young, S., Pontaroli, A., Wei, F., Haberer, G., Fuks, G., Du, C., Raymond, C., Estep, M., Liu, R., Bennetzen, J., Chan, A., Rabinowicz, P., Quackenbush, J., Barbazuk, W., Wing, R., Birren, B., Nusbaum, C., Rounsley, S., Mayer, K., and Messing, J. (2006). Uneven chromosome contraction and expansion in the maize genome. Genome Res. 16, 1241–1251.PubMedCrossRefGoogle Scholar
- Buckner, B., San Miguel, P., Janick-Buckner, D., and Bennetzen, J.L. (1998). The y1 Gene of Maize codes for Phytoene Synthase. Genetics 143, 479–488.Google Scholar
- Fengler, K., Allen, S.M., Li, B., and Rafalski, A. (2007). Distribution of genes, recombination, and repetitive elements in the maize genome. The Plant Genome [A Supplement to Crop Science], 83–95.Google Scholar
- Hartl, D. (2000). A Primer of Population Genetics. (Sunderland, MA, USA.: Sinauer Associates).Google Scholar
- Longley, A.E. (1939). Knob positions on corn chromosomes. J. Agric. Res. 59, 475–490Google Scholar
- McClintock, B. (1978). Significance of chromosome constitutions in tracing the origin and migration of races of maize in the Americas. In: Maize Breeding and Genetics. Walden, D.B., ed., 159–184. In in: Maize Breeding and Genetics, D.B. Walden, ed (New York: Wiley), pp. 159–184.Google Scholar
- Nagaki, K., Song, J., Stupar, R.M., Parokonny, A.S., Yuan, Q., Ouyang, S., Liu, J., Hsiao, J., Jones, K.M., Dawe, R.K., Buell, C.R., and Jiang, J. (2003). Molecular and cytological analyses of large tracks of centromeric DNA reveal the structure and evolutionary dynamics of maize centromeres. Genetics 163, 759–770.PubMedGoogle Scholar
- Remington, D.L., Thornsberry, J.M., Matsuoka, Y., Wilson, L.M., Whitt, S.R., Doebley, J., Kresovich, S., Goodman, M.M., and Buckler, E.S.t. (2001). Structure of linkage disequilibrium and phenotypic associations in the maize genome. Proc Natl Acad Sci U S A 98, 11479–11484.PubMedCrossRefGoogle Scholar
- Tochtrop, C., and Buckner, B. (2000). Sequence analysis of a recessive allele of the y1 gene of maize. In Maize Genetics Conference Abstracts, pp. P96.Google Scholar
- Yamasaki, M., Tenaillon, M.I., Bi, I.V., Schroeder, S.G., Sanchez-Villeda, H., Doebley, J.F., Gaut, B.S., and McMullen, M.D. (2005). A large-scale screen for artificial selection in maize identifies candidate agronomic loci for domestication and crop improvement. Plant Cell 17, 2859–2872.PubMedCrossRefGoogle Scholar
- Yu, J., Pressoir, G., Briggs, W.H., Vroh, B.I., Yamasaki, M., Doebley, J.F., McMullen, M.D., Gaut, B.S., Nielsen, D.M., Holland, J.B., Kresovich, S., and Buckler, E.S. (2006). A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet. 38, 203–208.PubMedCrossRefGoogle Scholar