51 Linkage analysis and map construction in genetic populations of clonal F1 and double cross

          Zhang, L., H. Li, J. Wang. 2015. Linkage analysis and map construction in genetic populations of clonal F1 and double cross. G3-Genes Genom Genet. 5(3):427-439.

Abstract: In this study, we considered four categories of molecular markers based on the number of distinguishable alleles at the marker locus and the number of distinguishable genotypes in clonal F₁ progenies. For two marker loci, there are nine scenarios which allow the estimation of female, male and/or combined recombination frequencies. In a double cross population derived from four inbred lines, five categories of markers are classified, and another five scenarios are present for recombination frequency estimation. Theoretical frequencies of identifiable genotypes were given for each scenario, from which the maximum likelihood estimates of one or more of the three recombination frequencies could be estimated. If there was no analytic solution, Newton-Raphson method was used to acquire a numerical solution. We then proposed to use an algorithm in Travelling Salesman Problem to determine the marker order. Finally, we proposed a procedure to build the two haploids of the female parent and the two haploids of the male parent in clonal F₁. Once the four haploids were built, clonal F₁ hybrids can be exactly regarded as a double cross population. Efficiency of the proposed methods was demonstrated in simulated clonal F₁ populations and one actual maize double cross. Extensive comparisons with software JoinMap4.1, OneMap and R/qtl shows that the methodology proposed in this paper can build more accurate linkage maps in shorter time.

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