16.marker.50

The mapping population comprised 188 F2 [(Scarlet Nantes × Camberley) × (Turkish × 2566B)] individuals, where (Scarlet Nantes × Camberley) and (Turkish × 2566B) designate two inbred lines derived from crosses of the four parental stocks noted, and the F2 population was derived from self-pollinating a single F1 plant. The mapping population is henceforth referred to as 70349 F2.

JoinMap 4.0 software was used for mapping. Scores of all DArT markers were converted into genotype codes using the AC/BD system for dominant markers segregating in F2 populations. The linkage groups (LGs) were obtained at a LOD threshold value >3.0. We used regression mapping algorithm and the Kosambi mapping function to calculate distances between marker loci. The DArT markers were named with the prefix ‘crPt’ where ‘cr’ stands for carrot, ‘P’ for PstI, and ‘t’ for TaqI, followed by numbers corresponding to their unique clone ID. Markers with more than 10 % of missing data were removed. Redundant markers were removed using the similarity loci function in JoinMap with a similarity threshold of 0.95. Each marker was tested against the expected segregation ratio using a Chi squared goodness of fit. The linkage map was first built with higher likelihood support for marker order following the second round of JoinMap. For the final map a third round of ordering of unmapped markers was performed using the fixed order function of markers as established at round two, allowing retention of the high likelihood support for markers as established at round two and providing the most likely position of all remaining informative markers.

LGs were anchored to chromosomes through physical co-localization of DArT sequences and currently available SNPs with known chromosome locations on the assembled carrot contigs.