Plant & Animal Genomes XIV Conference Plant & Animal Genomes XIV ConferenceJanuary 14-18, 2006
Town & Country Convention Center
San Diego, CA
Currently, there are no publicly available genetic linkage mapping software packages that are sufficiently robust to accommodate large numbers of markers (>1000) and/or complex pedigree structure. To address this need, we designed, developed, and implemented a series of programs. The newly developed software uses a customized CRIMAP (publicly available linkage mapping program) as an engine, and combines many enhancements to increase the capacity and efficiency for linkage mapping. Given the dense coverage of markers on chromosomes, a step-wise strategy of “framing-splitting-filtering-merging” was developed and implemented, and was observed to greatly improve the efficiency of linkage map construction, and theoretically makes it possible to place any number of markers into the same linkage map. Through the implementation of a divide-and-conquer algorithm, the complex pedigree and their genotypes can be greatly simplified into smaller and much more manageable families, with options that allow the user flexibility in specifying family size and the number of generations to consider. A novel layered algorithm was developed and implemented in the formation and verification of linkages groups, handling conflicting linkages among markers, and subsequent assignment of linkage groups to chromosomes. Several other algorithms are developed to quickly identify marker haplotype groups, markers that have not been mapped yet, and the merging of two sub-maps. Together with other helpful accessory utilities, this software package was successfully used to construct dense linkage map for 6,000 markers genotyped on more than 10,000 animals from complex pedigree.