title: Linkage analysis in unconventional mating designs in line crosses.
abstract: Linkage estimation and genetic map construction with genotyped DNA markers in plants preferentially employ a few maximally informative early-generation or recombinant-inbred mating designs. Fitting their recombination models to unconventional designs adapted to cultivar development (series of backcrossing, selfing, haploid-doubling, random-intercrossing, and sib-mating steps) distorts single- and multipoint linkage estimates even with dense marker coverage. Two methods are provided for correct linkage estimation in unconventional designs: fitting a correct multigeneration model, or correcting the estimates produced by fitting a one-generation model with any conventional software. These methods also support calculation of multilocus genotype frequencies and QTL-genotype distributions and are available in software.
authors.affiliation: Department of Plant Pathology, 4024 Throckmorton Plant Sciences Center, Kansas State University, Manhattan, KS 66506, USA. jcn@ksu.edu
authors.forename: James C
authors.initials: JC
authors.lastname: Nelson
mesh_terms: D002874:Chromosome Mapping / Q000379:methods*; D032461:Chromosomes, Plant / Q000235:genetics; D003433:Crosses, Genetic; D018744:DNA, Plant / Q000235:genetics*; D008040:Genetic Linkage; D005819:Genetic Markers; D005838:Genotype; D008957:Models, Genetic; D010944:Plants / Q000235:genetics*; D040641:Quantitative Trait Loci; D011995:Recombination, Genetic; D012984:Software
chemical_list: D018744:DNA, Plant; D005819:Genetic Markers