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The influence of the Or and Carotene Hydroxylase genes on carotenoid accumulation in orange carrots [Daucus carota (L.)]

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Abstract

Key message

The Or and CH genes are necessary for the accumulation of high amounts of β-carotene and other carotenoid pigments in carrot roots, in addition to the Y and Y2 genes.

Abstract

Carrot taproot color results from the accumulation of various carotenoid and anthocyanin pigments. Recently, the Or gene was identified as a candidate gene associated with the accumulation of β-carotene and other provitamin A carotenoids in roots. The specific molecular mechanisms involved with this process, as well as the interactions between Or and the other genes involved in this process are not well understood. 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 Orc and Orw. QTL mapping across three different environments revealed that the accumulation of several carotenoids was associated with the Orc 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 CHc and CHw, were discovered to be segregating in this population. Our study provides further evidence that Or and CH are likely involved with controlling the accumulation of β-carotene and may be involved with modulating carotenoid flux in carrot, demonstrating that both were important domestication genes in carrot.

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Availability of data and material

All phenotypic and genotypic data necessary to confirm the conclusions presented in this article are available as supplementary material. The unfiltered VCF file is available at https://doi.org/10.6084/m9.figshare.14067131.v1.

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Acknowledgements

The authors would like to thank Dr. Tom Horejsi for field assistance, Dr. Jeffrey Endelman for providing code for marker binning, as well as Nathan Bosch, Elise Leeder, Priya Beejan, and Erin Lalor for assistance with sample collection and preparation for HPLC phenotyping. The authors would also like to thank the University of Wisconsin Biotechnology center DNA sequencing facility for providing genotyping-by-sequencing library preparation and sequencing services.

Funding

This study was funded by the National Institute of Food and Agriculture, U. S. Department of Agriculture (NIFA-USDA), under award number 2016–51181-25400. K.C. was supported by a University of Wisconsin–Madison Science and Medicine Graduate Research Scholars Fellowship and NIFA-USDA under award number 2016–51181-25400. S.E. was supported by NIFA-USDA under award number 2016–51181-25400.

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Authors and Affiliations

  1. Department of Horticulture, University of WI – Madison, 1575 Linden Dr., Madison, WI, 53706, United States of America

    Kevin M. Coe, Shelby Ellison, Douglas Senalik, Julie Dawson & Philipp Simon

  2. Vegetable Crop Unit, U.S. Department of Agriculture – ARS, Dept. of Horticulture, University of WI – Madison, 1575 Linden Dr., Madison, WI, 53706, United States of America

    Douglas Senalik & Philipp Simon

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  1. Kevin M. Coe
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  2. Shelby Ellison
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  3. Douglas Senalik
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  4. Julie Dawson
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  5. Philipp Simon
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Contributions

KC, SE, JD, and PS conceived and designed this study. KC and SE collected phenotypic and genotypic data, KC, SE, JD, and DS ran analyses. KC, JD, and PS wrote the paper. JD, SE, DS, and PS provided comments about the paper.

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Correspondence to Philipp Simon.

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Communicated by Richard G. F. Visser.

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Coe, K.M., Ellison, S., Senalik, D. et al. The influence of the Or and Carotene Hydroxylase genes on carotenoid accumulation in orange carrots [Daucus carota (L.)]. Theor Appl Genet 134, 3351–3362 (2021). https://doi.org/10.1007/s00122-021-03901-3

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  • DOI: https://doi.org/10.1007/s00122-021-03901-3

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