Understanding epistasis in linkage analysis : the Kap and lks2 loci in the Oregon Wolfe Barley poputlation Public Deposited

http://ir.library.oregonstate.edu/concern/undergraduate_thesis_or_projects/th83m371s

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  • An organisms' genotype may not be reflected in its phenotype. For example, epistasis - the interaction of non-allelic genes can cause deviations from expected phenotypic ratios. The epistatic interaction between the hooded (Kap) and short-awned (lks2) loci in barley (Hordeum vulgare) precludes the localization of the Kap locus, based on phenotypic data, when alleles at both loci are segregating. In individuals that are homozygous for the recessive allele of lks2, the expression of the hooded phenotype is masked, resulting in the expression of the short-awned, rather than the hooded, phenotype. Two strategies were employed to determine the location of the Kap locus in an experimental population of barley, the Oregon Wolfe Barleys, and to determine the Kap locus genotype of a doubled haploid line in the population. The first strategy capitalized on the availability of molecular marker data in the population and involved inferring the Kap locus genotypes of the short-awned individuals based on the genotypes from flanking DNA markers. The second strategy confirmed the predicted genotypes by mapping a barley homeobox gene (hvknox3) believed to represent the hooded (Kap) locus. The hvknox3 locus mapped to BIN 4 of barley chromosome 4 (4H), which is the reported map position of the Kap locus. The Kap-predict and hvknox3 genotypes were compared and found to be the same, except for OWB line 52. To test the alternative hypotheses regarding the Kap genotype of OWB 52, this line was crossed with a known dominant hooded line, OWB 62. Putative F 1's were checked with hvknox3 primers and true F1 heterozygotes were allowed to self-pollinate and to produce seed. F2 seed were planted and the phenotypic assessment of the F2 population will be completed by August 2000.
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