2015 HM3

A Br1091 plant was crossed with a HM plant to generate the Br1091 × HM1 F₂ population from a single F₁ plant. A SFF plant was crossed to a second HM plant to generate the SFF × HM2 F2 population from a single F1 plant. HM1 and HM2 were siblings derived from a self-pollinated HM selection. A third HM plant was self-pollinated to generate the HM3 population. This population had undergone five generations of selfing before the final self-pollination to produce the population, and it was still segregating for resistance.

This linkage map is for the HM3 population.

Linkage maps were constructed with JoinMap 3.0 software. Markers and genotypes with more than 10% missing data and markers that significantly deviated from expected segregation ratios using a Chi-square test (P < 0.01) were removed. For linkage groups with clusters of markers with significant segregation distortion (P < 0.0005), all markers were used to generate the linkage map. Linkage groups were obtained at a LOD threshold >3.0. The regression mapping algorithm was used with Haldane’s mapping function to calculate distances between markers. Haldane’s mapping function was chosen because it provided a more accurate marker placement according to the carrot physical map than the Kosambi’s mapping function. Each marker was coded twice, once for each parental phase. The linkage groups were properly phased by using marker scores for individuals related to the parents. The marker order was further examined using CheckMatrix (http://www.atgc.org/XLinkage, Truco et al. 2013) for inconsistencies, and markers with more than one inconsistent score were removed. To remove redundant markers in the Br1091 × HM1 population, a genetic bin map was developed. For each linkage group, pair-wise recombination values among all markers were calculated. Adjacent markers with zero recombination among them were assigned to the same genetic bin. In addition, adjacent markers with “false” recombination due to missing data were considered to belong to the same genetic bin. The marker with the least number of missing data points was chosen to represent each genetic bin. SNPs and SSRs with known chromosome locations were used to anchor the linkage groups. After being assigned to chromosomes, linkage groups were oriented and numbered following the chromosome orientation and classification of Iovene et al. (2011).