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Development of a PCR-based marker utilizing a deletion mutation in the dihydroflavonol 4-reductase (DFR) gene responsible for the lack of anthocyanin production in yellow onions (Allium cepa)

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Abstract

Bulb color in onions (Allium cepa) is an important trait, but the mechanism of color inheritance is poorly understood at the molecular level. A previous study showed that inactivation of the dihydroflavonol 4-reductase (DFR) gene at the transcriptional level resulted in a lack of anthocyanin production in yellow onions. The objectives of the present study were the identification of the critical mutations in the DFR gene (DFR-A) and the development of a PCR-based marker for allelic selection. We report the isolation of two additional DFR homologs (DFR-B and DFR-C). No unique sequences were identified in either DFR homolog, even in the untranslated region (UTR). Both genes shared more than 95% nucleotide sequence identity with the DFR-A gene. To obtain a unique sequence from each gene, we isolated the promoter regions. Sequences of the DFR-A and DFR-B promoters differed completely from one another, except for an approximately 100-bp sequence adjacent to the 5′UTR. It was possible to specifically amplify only the DFR-A gene using primers designed to anneal to the unique promoter region. The sequences of yellow and red DFR-A alleles were the same except for a single base-pair change in the promoter and an approximately 800-bp deletion within the 3′ region of the yellow DFR-A allele. This deletion was used to develop a co-dominant PCR-based marker that segregated perfectly with color phenotypes in the F2 population. These results indicate that a deletion mutation in the yellow DFR-A gene results in the lack of anthocyanin production in yellow onions.

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Acknowledgements

The authors thank members of Vegetable and Fruit Improvement Center for their dedicated support of this research. We gratefully acknowledge the proofreading by Dr. Marla Binzel. This work was supported by produce industry member contributions to the Vegetable and Fruit Improvement Center and U.S. Department of Agriculture grant (CSREES 2001-34402-10543, “Designing Foods for Health”).

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  1. Vegetable and Fruit Improvement Center, Department of Horticultural Sciences, Texas A&M University, TX, 77845, USA

    Sunggil Kim, Kil Sun Yoo & Leonard M. Pike

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  1. Sunggil Kim
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  2. Kil Sun Yoo
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  3. Leonard M. Pike
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Correspondence to Leonard M. Pike.

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Communicated by I. Paran

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Kim, S., Yoo, K.S. & Pike, L.M. Development of a PCR-based marker utilizing a deletion mutation in the dihydroflavonol 4-reductase (DFR) gene responsible for the lack of anthocyanin production in yellow onions (Allium cepa). Theor Appl Genet 110, 588–595 (2005). https://doi.org/10.1007/s00122-004-1882-7

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