title: 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).
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.
authors.affiliation: Vegetable and Fruit Improvement Center, Department of Horticultural Sciences, Texas A&M University, TX, 77845, USA.
authors.forename: Sunggil
authors.initials: S
authors.lastname: Kim
authors.forename: Kil Sun
authors.initials: KS
authors.lastname: Yoo
authors.forename: Leonard M
authors.initials: LM
authors.lastname: Pike
mesh_terms: D000429:Alcohol Oxidoreductases / Q000235:genetics*; D000872:Anthocyanins / Q000096:biosynthesis*; D001483:Base Sequence; D001947:Breeding; D017931:DNA Primers; D018076:DNA, Complementary / Q000235:genetics; D040461:Gene Components; D020868:Gene Silencing; D005819:Genetic Markers / Q000235:genetics*; D009154:Mutation / Q000235:genetics; D019697:Onions / Q000235:genetics*; D010858:Pigmentation / Q000235:genetics*; D016133:Polymerase Chain Reaction; D011401:Promoter Regions, Genetic / Q000235:genetics; D017422:Sequence Analysis, DNA; D017385:Sequence Homology
chemical_list: D000872:Anthocyanins; D017931:DNA Primers; D018076:DNA, Complementary; D005819:Genetic Markers; D000429:Alcohol Oxidoreductases; C056570:dihydroflavanol 4-reductase