Genetic Study on Clonal F1 and Double Cross Populations

This study focused on genetic analysis methods in clonal F₁ and double crosses. For linkage analysis, molecular markers were classified based on the number of distinguishable alleles at marker locus and the number of distinguishable genotypes in clonal F₁ progenies. Three recombination frequencies were estimated for different scenarios by maximum likelihood algorithm and Newton-Raphson method. Female, male and/or combined maps could be built using the estimates between markers. A combined algorithm of nearest neighbor and Two-opt algorithm of Traveling Salesman Problem was used for marker ordering. Extensive comparisons with software JoinMap4.1, OneMap and R/qtl shows that the new methodology can build more accurate linkage maps in shorter time. We also proposed a procedure to build the four haploids of the two parents. For QTL mapping, it was demonstrated that dominance effect between the female and male parents in clonal F₁ and double cross populations can cause the interactions between markers. We then developed an inclusive linear model that includes marker variables and marker interactions so as to completely control both additive effects and dominance effects. The linear model was finally used for background control in Inclusive Composite Interval Mapping (ICIM) of QTL. The efficiency of ICIM was demonstrated by extensive simulations and by comparisons with simple interval mapping, multiple-QTL models and composite interval mapping. The integrated software called GACD (Genetic Analysis of Clonal F₁ and Double cross populations) was developed for linkage analysis, map construction and QTL mapping in clonal F₁ and double cross populations, freely available from www.isbreeding.net.