Plant & Animal Genomes XIII Conference

January 15-19, 2005
Town & Country Convention Center
San Diego, CA

A New Approach Of QTL Mapping Analysis Of Selective DNA Pooling Experiments

Zeev Frenkel¹ , Lior Cohen¹ , Ehud Lipkin² , Moris Soller² , Abraham Korol¹

¹  Institute of Evolution, University of Haifa, Haifa 31905, Israel

²  Deptartment of Genetics, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel

Selective DNA pooling is an exceedingly cost-effective means of carrying out an initial scan for marker-QTL linkage in suitable populations, e.g., in a daughter design. A few analytical approaches have been proposed for QTL detection using data on several families. One of the problems in such analysis is the heterogeneity of the families with respect to QTL effects, heterozygosity at putative QTLs, different information content of different marker loci (polymorphism of the sires, shared alleles of the sires and their dam populations), and varying proportion of shared marker loci among families when data come form different labs. No less important are the limitations caused by lack of analytical tools for this design and very restrictive assumptions employed in QTL detection tests. We developed an analytical system for QTL analysis in a selective DNA pooling design, allowing for a number of sub-pools pools in the trait distribution tails in each family. Our system allows, for the first time, QTL detection based on permutation tests rather than using asymptotic distributions of test statistics, and estimation of QTL position and effect ( including confidence intervals for corresponding parameters, based on re-sampling techniques, either jackknife or bootstrap). Likewise, our approach allows for classification of the families into two groups, heterozygous and homozygous for the detected QTL. No less important are the possibilities for dealing with situations involving linked QTLs within targeted genomic regions. The proposed method is illustrated on simulated data and on cattle productivity data.