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Originally published as Genetics Published Articles Ahead of Print on November 19, 2005.

Genetics, Vol. 172, 1325-1335, February 2006, Copyright © 2006
doi:10.1534/genetics.105.044271

Constructing the Parental Linkage Phase and the Genetic Map Over Distances <1 cM Using Pooled Haploid DNA

Dario Gasbarra1 and Mikko J. Sillanpää

University of Helsinki, Helsinki FIN-00014, Finland

1 Corresponding author: Department of Mathematics and Statistics, University of Helsinki, P.O. Box 68 (Gustaf Hällströmin katu 2b), Room 316, Helsinki FIN-00014, Finland.
E-mail: dag{at}rolf.helsinki.fi

A new statistical approach for construction of the genetic linkage map and estimation of the parental linkage phase based on allele frequency data from pooled gametic (sperm or egg) samples is introduced. This method can be applied for estimation of recombination fractions (over distances <1 cM) and ordering of large numbers (even hundreds) of closely linked markers. This method should be extremely useful in species with a long generation interval and a large genome size such as in dairy cattle or in forest trees; the conifer species have haploid tissues available in megagametophytes. According to Mendelian expectation, two parental alleles should occur in gametes in 1:1 proportions, if segregation distortion does not occur. However, due to mere sampling variation, the observed proportions may deviate from their expected value in practice. These deviations and their dependence along the chromosome can provide information on the parental linkage phase and on the genetic linkage map. Usefulness of the method is illustrated with simulations. The role of segregation distortion as a source of these deviations is also discussed. The software implementing this method is freely available for research purposes from the authors.