To visualize the impact of resistance markers on the overall dataset, a second PCA excluding data from the targets encoding resistance markers was built (data not shown).
Finally, a comprehensive map including all the markers was built, by adding all the remaining markers at the most likely location with Mapcomp command and optimized with Flip command (or details on commands, see Carthagene user guide at [ 34].
First, a single consensus marker map was built by integrating the available genetic maps, based on common markers designated with common names between the maps, using the ConsMap command of the software.
By using all the markers from this group, a 1000 1 framework map (a map whose likelihood is at least 1000-fold higher than the next possible highest likelihood using the same markers in alternate orders) was built under a haploid model.
Then, the consensus map was built using bridge markers as framework markers (Table 1, Table S2).
In addition to the Goodwin project, a second major upscale redevelopment is getting under way at the former Colt Armory complex, whose star-spangled blue onion dome overlooking Interstate 91 has been a marker for travelers since the highway was built in the late 50's.
The Beagle probability model was built at each marker by running the Beagle software (Beagle 3.3.2; http://faculty.washington.edu/browning/beagle/beagle.html, Browning [ 3], Browning and Browning [ 12]) and fitting all the chromosome markers at one time.
The map developed in the present study was built with 1,375 markers including 1.268 microsatellites, 105 SNPs and two genes, which makes it more portable to other strains and families.
A framework map of quail chromosome 1 was built, comprising 60 markers with an average number of informative meioses of 505 (from 79 to 835), for a genetic length of 287.4 cM and with an average between-marker distance of 4.9 ± 3.9 cM.
Second, the initial draft of the consensus map was built from the 'bPb' DArT markers only.
