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Title: A gene-derived SNP-based high resolution linkage map of carrot including the location of QTL conditioning root and leaf anthocyanin pigmentation

item CAVAGNARO, PABLO - University Of Wisconsin
item IORIZZO, MASSIMO - University Of Wisconsin
item YILDIZ, MEHTAP - Yuzuncu Yil Centennial University
item Senalik, Douglas
item PARSONS, JOSHUA - University Of Wisconsin
item ELLISON, SHELBY - University Of Wisconsin
item Simon, Philipp

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/11/2014
Publication Date: 12/16/2014
Publication URL:
Citation: Cavagnaro, P.F., Iorizzo, M., Yildiz, M., Senalik, D.A., Parsons, J., Ellison, S., Simon, P.W. 2014. A gene-derived SNP-based high resolution linkage map of carrot including the location of QTL conditioning root and leaf anthocyanin pigmentation. Biomed Central (BMC) Genomics. 15:1118.

Interpretive Summary: One of the original colors of carrots, when they were first developed as a root crop 1100 years ago, was purple, due to anthocyanin pigments. Purple carrots are still grown today on a relatively limited scale for both niche vegetable markets and as a raw product for pigment extraction. One gene has been described in previous research to account for purple carrot color. In this study we evaluated three diverse genetic sources of purple carrots and found that two additional genes control presence or absence of purple color, and that four genes control the intensity of color. An additional gene was discovered to control the type of anthocyanins. The genetic map developed for this study represents the most detailed and complete for carrot to date. This research is of interest to plant geneticists, biochemists, and molecular biologists, and to vegetable growers and processors.

Technical Abstract: Background: Purple carrots accumulate large quantities of anthocyanins in their roots and leaves. These flavonoid pigments possess antioxidant activity and are implicated in providing health benefits. The lack of informative and saturated linkage maps associated with well characterized populations segregating for anthocyanin pigmentation have been limited. To investigate the genetic architecture conditioning anthocyanin pigmentation we scored root and petiole color visually and quantified root anthocyanin pigments by high performance liquid chromatography in segregating F2, F3 and F4 generations in a mapping population, mapped quantitative loci for these traits onto a dense gene-derived single nucleotide polymorphism (SNP)-based linkage map, and performed comparative trait mapping with two unrelated populations. Results: Root pigmentation, scored visually by the presence or absence of purple coloration, segregated in a pattern consistent with a two gene model in an F2, and progeny testing of 46 additional F3-F4 families confirmed the proposed genetic model. Purple petiole pigmentation was conditioned by a single dominant gene that co-segregates with one of the genes conditioning root pigmentation. Root total pigment estimate (RTPE) was scored as the percentage of the root with purple color. All five anthocyanin glycosides previously reported in carrot, as well as RTPE, varied quantitatively in the F2 population. For the purpose of QTL analysis, a high resolution gene-derived SNP-based linkage map of carrot was constructed with 894 markers covering 635.1 cM with a 1.3 cM map resolution. Significant QTL for all anthocyanin pigments and for RTPE were mapped. A total of 15 QTL mapped to six chromosomes. Eight QTL with the largest phenotypic effect mapped to two regions of chromosome 3 with co-localized QTL for several anthocyanin glycosides and for RTPE. A single dominant gene conditioning anthocyanin acylation was identified and mapped. Comparative mapping with other carrot populations segregating for purple color indicated that genetic control of anthocyanin pigmentation is controlled by at least three genes, in contrast to monogenic control reported previously. Conclusions: Two regions of chromosome 3 with co-localized QTL for all anthocyanin pigments and for root pigment content, largely condition anthocyanin accumulation in roots and leaves. The loci controlling root and petiole anthocyanin pigmentation differ across diverse carrot genetic backgrounds.