16.marker.65

The F₄ population 74,146 was derived from a cross between USDA carrot inbred line B493, an orange-rooted line, and QAL (Queen Anne’s Lace), a wild-type white-rooted carrot from the United States. Plants were grown the summer of 2013 at the University of Wisconsin, Hancock Agricultural Research Station, and 213 roots were selected for phenotyping and genotyping.

Plants from this population were genotyped using Genotyping-By-Sequencing (GBS), as described by Elshire et al., which was carried out at the University of Wisconsin–Madison Biotechnology Center with minimal modification and half-sized reactions. The TASSEL-GBS pipeline version 4.3.7 was used to call SNPs.

Heterozygous SNPs, with an allele ratio expected to be 1:1, were eliminated if the ratio of the two alleles was <0.3 or >0.7, leaving 2999 high quality markers for linkage mapping. Genetic linkage analysis and map construction was executed in JoinMap 4. The 74,146 map was analyzed as an F₂ population. Markers ascertained to be the result of false double recombination events were identified using CheckMatrix version 248 and removed. The following parameters were used for the calculation: Haldane’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 was performed = 1, and third round = no. At LOD.10, with,10% missing data for marker and genotype, 616 markers were grouped into nine linkage groups.

QTL analysis was carried out using the R package R/qtl. For the single QTL model interval analyses, genotype probabilities were calculated with a step value of 1 over the entire linkage map. The “scanone” function used the normal phenotype model (model =“normal”) and the Haley-Knott regression method (method =“hk”) as parameters. After running 1000 permutations with an assumed genotyping error rate of 0.001, a LOD of 4.01 was set as the QTL significance threshold. Confidence intervals for each QTL were defined as the 1.5 LOD drop off flanking the peak of the QTL.