Carrot (Daucus carota L.) molecular markers: investigations into Daucus phylogeny, chloroplast DNA inheritance and genetic mapping

Restriction Fragment Length Polymorphisms (RFLPs), Random Amplified Polymorphic DNAs (RAPDs), Amplified Fragment Length Polymorphisms (AFLPs), and Selective Amplification of Microsatellite Polymorphic Loci (SAMPL) were identified in carrot, Daucus carota L. These markers were then used for specific investigations into the Daucus genome. RFLPs of the chloroplast (cp) and the mitochondria (mt) were used to delineate the phylogeny of several Daucus species and carrots. In general, there was good agreement of the molecular data with that of classical taxonomy although mt variation tended to be broader than that of the cp. A cp RFLP mutation (BP10U) was identified within cultivated carrot (ssp. sativus) and its inheritance studied. Chloroplast inheritance in carrot is much debated and our results indicate that inheritance is maternal in cultivated carrot. Occasional paternal inheritance, if any, could not be ruled out with the experiments done so far. Also, the occurrence of this mutation among other carrot lines was studied. All the inbreds having this mutation were male fertile. However, this marker did not seem to be associated with any particular phenotype. Results indicated that the mutation could have had more than one source of origin. The above mentioned nuclear marker systems were used to construct a linkage map of carrot using up to 103 F2s from a cross between inbreds B9304 and YC7262. A 113- point linkage map was constructed. This map had 99 AFLPs, six RFLPs, two RAPDs, three phenotypic loci and three SAMPL. At LOD score 4.0 and maximum recombination of 0.25, markers fell into 11 linkage groups although carrot has nine chromosomes. Association of markers with genes segregating for root phloem color, xylem color (known to be correlated with carotene content) and sugar type was found. The closest markers to these genes, all of which were AFLPs, were as follows: P6B15 was 1.7 cM from P1 (purple phloem), P1B34 was 2.1 cM from Y2 (yellow xylem) and P3B30XA was 8.1 cM from Rs (high reducing sugar). Map-based cloning of P1 and Y2 may now be possible although the physical distances of these markers from the genes are not known.