16.marker.48-49

An F₂ population derived from a heterozygous P₁p₁ F₁ intercross between B1896 (true-breeding p₁p₁ yellow-rooted F₄M inbred derived from the cross PI 173687 × B493), and B7262 (P₁P₁ purple exterior with orange inner phloem and xylem inbred from the same cross) was self-pollinated to produce population 10117. A total of 370 SSR primer pairs (156 GSSRs, 144 BSSRs, 70 ESSRs) and 21 AFLP primer combinations were evaluated. Of the 370 SSR markers initially evaluated for polymorphism and mode of segregation in the F₂ population, 44 (11.9 %) were polymorphic, presented unambigous band patterns, and had segregation ratios consistent with single loci. Only these SSR markers, of which 36 were codominant and 8 were dominant, were included in the linkage analysis. Twenty-one AFLP primer combinations amplified 891 bands of which 283 (31.8 %) were polymorphic in the F₂ population. A total of 17 anthocyanin genes (10 structural and seven regulatory genes) were initially screened and eight polymorphic genes used for mapping. The genotypes of polymorphic markers were recorded according to the symbols required by Mapmaker/EXP version 3.0 as follows: homozygous maternal “A”, homozygous paternal “B”, heterozygous “H”, not A “C”, not B “D”, and missing data “−”. The degree of marker segregation distortion in the F₂ was determined by marker data comparison against the expected 3:1 and 1:2:1 ratio for dominant and codominant markers, respectively, using Chi square tests, where significant distortion was declared at P < 0.01. Because the parental allelic phase was unknown, codominant markers were double-scored by switching the presumed allelic origin. All markers were entered into Mapmaker/EXP version 3.0 for analysis. Markers were grouped with the two-point “group” command at LOD = 4.0 and a maximum recombination frequency value of 0.25. Markers within a group were ordered using the Order command with LOD of 3.0. The remaining markers were then located with the Ripple command. The groups were mapped using the Kosambi mapping function.

Carrot linkage maps for both parental lines were constructed using 279 marker data points. These included 2 phenotypic loci (P₁ and Y₂), 237 AFLPs, 40 SSRs, 1 SCAR, 5 anthocyanin biosynthesis structural genes (F3H, FLS1, LDOX2, PAL3, and UFGT), and 3 anthocyanin transcription factors (DcEFR1, DcMYB3, and DcMYB5) with 45 of them (15.7 %) being codominant markers. Additionally, 24 markers (22 AFLPs and 2 SSRs) were unlinked. Based on known chromosome location of molecular (SSR) and phenotypic (Y2) markers, LGs were assigned to their respective chromosomes. Anthocyanin biosynthesis genes and transcription factors we mapped only occurred on carrot chromosomes 2, 3, 4, 7, and 8, and these linkage data and maps are summarized in Table 4 and Fig. 5, respectively.