B493 × Z007 F₃

In order to better characterize the effect that Or alleles have on conditioning the accumulation of carotenoids in roots, we analyzed an F₃ family fixed homozygous recessive for y and y₂, derived from a cross between an orange carrot and a white wild carrot, segregating for the two known Or alleles, which we name Or_c and Or_w. QTL mapping across three different environments revealed that the accumulation of several carotenoids was associated with the Or_c allele, with consistent patterns across environments. A second QTL on chromosome 7, harboring a carotene hydroxylase gene homologous to Lut5 in Arabidopsis, was also associated with the accumulation of several carotenoids. Two alleles for this gene, which we name CH_c and CH_w, were discovered to be segregating in this population.

2,571 markers across 460 samples clustered into 9 linkage groups and the resulting linkage map has a minimum of 75 markers on chromosome 7 to a maximum of 476 on chromosome 3. The average spacing of markers ranged from a maximum of one marker every 0.9 cM on chromosomes 7 and 9 to a minimum of one marker every 0.4 cM on chromosome 6. The physical spacing of markers ranged from 75 kb on chromosome 4 to 482 kb on chromosome 7. In total, the linkage map was 1384 cM in length.