Construction and Analysis of High-Density Linkage Map Using High-Throughput Sequencing Data
A: The single-linkage clustering algorithm was used to partition the marker loci into linkage groups based on a pairwise modified independence LOD score for the recombination frequency. B and B': The ordering module combines Gibbs sampling, spatial sampling, and simulated annealing algorithm to order markers and estimate map distances. C: The error correction module identified singletons according to parental contribution of genotypes and eliminated them from the data using k-nearest neighbor algorithm. To order markers correctly, the processes of ordering and error correction were carried out iteratively. D: Heat maps and haplotype maps were constructed to evaluate map quality.