2016 Integ NG full map

Genetic maps of three populations were used to establish a consensus map suitable for guiding the construction of superscaffolds and pseudomolecules. Each linkage map consisted of a “full” dataset including all the segregating markers mapped in each population and a “bin” data set, consisting of markers representing unique recombination events.

This is the "full" data set map, the "bin" data set map can be found here.

Before merging the data from each population for map integration, the co-linearity of common markers was inspected using MapChart 2.2, and markers that were inconsistent were removed. In total, the three linkage maps shared 567 markers in the full dataset and 228 markers in the bin dataset. Both the “full” set and the “bin” dataset were used to generate a “full” and a “bin” integrated map using JoinMap 4.0 software. Population-specific locus genotype scores were then integrated into one dataset in each Linkage Group (LG) using the Combine Groups for Mapping Integration Module, followed by locus ordering by the Regression Mapping Module of JoinMap. The following parameters were used for the calculation: Kosambi's mapping function, LOD ≥ 3.0, REC frequency ≤0.4, goodness of fit jump threshold for removal of loci = 5.0, number of added loci after which a ripple is performed = 1, and third round = yes. Markers in common were used as anchor points. The integrated maps resulted in 2,073 markers for the full dataset and 918 markers for the bin dataset, covering 622 cM and 616 cM, respectively.

The maps that were used to generate this integrated map are:

• 70349 NG full map
• 70796 NG full map
• 80592 NG full map