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Here we propose a simple method to deal with this problem by taking information from multiple linked markers into account.
This program follows the approach of Haley et al. [ 4] and uses information of multiple linked markers, which may or may not be fixed for alternative alleles in the breeds.
Rannala and Reeve (2004) extended their former likelihood approach for disease mapping (Rannala and Reeve 2001) to estimate allele age of a mutant under neutrality using multiple linked markers, and employed Markov Chain Monte Carlo to generate the posterior distribution of allele age of the mutant.
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Further information about likely candidates can be derived from haplotype analysis (the analysis of multiple closely linked markers).
Segregation distortion was observed for multiple tightly linked markers in 16 regions throughout the genome [Additional file 2].
Second, many of the anchored scaffolds contained just one mapped marker, or contained multiple tightly linked markers whose map order was questionable due to insufficient recombination.
Also, due to the small population size and insufficient recombination, many anchored scaffolds contained just one mapped marker, or contained multiple tightly linked markers whose map order was undefined, which made orientation of some scaffolds impossible.
Although this study dealt with two QTLs coupled with linked markers, the same principle can be readily extended to the situation of multiple QTL.
Hence, these markers were considered as tightly linked markers and used for introgressing BPH31 in the background of Jaya.
M1, M2, M5 and M6 are linked markers for negative selection of linked segments of target genes.
Regions of linkage were identified by binning neighboring markers and counting linked markers within the bins.
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