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Identification of a candidate gene for the I locus determining the dominant white bulb color in onion (Allium cepa L.)

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Abstract

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Through a map-based cloning approach, a gene coding for an R2R3-MYB transcription factor was identified as a causal gene for the I locus controlling the dominant white bulb color in onion.

Abstract

White bulb colors in onion (Allium cepa L.) are determined by either the C or I loci. The causal gene for the C locus was previously isolated, but the gene responsible for the I locus has not been identified yet. To identify candidate genes for the I locus, an approximately 7-Mb genomic DNA region harboring the I locus was obtained from onion and bunching onion (A. fistulosum) whole genome sequences using two tightly linked molecular markers. Within this interval, the AcMYB1 gene, known as a positive regulator of anthocyanin production, was identified. No polymorphic sequences were found between white and red AcMYB1 alleles in the 4,860-bp full-length genomic DNA sequences. However, a 4,838-bp LTR-retrotransposon was identified in the white allele, in the 79-bp upstream coding region from the stop codon. The insertion of this LTR-retrotransposon created a premature stop codon, resulting in the replacement of 26 amino acids with seven different residues. A molecular marker was developed based on the insertion of this LTR-retrotransposon to genotype the I locus. A perfect linkage between bulb color phenotypes and marker genotypes was observed among 5,303 individuals of segregating populations. The transcription of AcMYB1 appeared to be normal in both red and white onions, but the transcription of CHS-A, which encodes chalcone synthase and is involved in the first step of the anthocyanin biosynthesis pathway, was inactivated in the white onions. Taken together, an aberrant AcMYB1 protein produced from the mutant allele might be responsible for the dominant white bulb color in onions.

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Data availability

Nucleotide sequences of AcMYB1 alleles are accessible at NCBI database under the accession numbers of PP095636 and PP095637. Detailed information of the onion genome sequence (DHW30006) is available at NCBI under the BioProject number of PRJNA912256. The raw sequences of RNA-Seq reads are available upon request.

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Acknowledgments

This study was supported by the Korea Institute of Planning and Evaluation for Technology in Food, Agriculture and Forestry (No. 322067-03-3-HD020) and the BK21 FOUR funded by the Ministry of Education of Korea and National Research Foundation of Korea. The authors thank Ji-wha Hur, Jeong-Ahn Yoo, and Su-jung Kim for their dedicated technical assistance.

Funding

This study was funded by Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, Forestry and Fisheries, 322067-03-3-HD020, Sunggil Kim.

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Authors and Affiliations

  1. Department of Horticulture, Biotechnology Research Institute, Chonnam National University, Gwangju, 61186, Republic of Korea

    Geonjoong Kim & Sunggil Kim

  2. Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea

    Heejung Cho

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  1. Geonjoong Kim
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Contributions

Geonjoong Kim performed experiments and drafted the manuscript. Heejung Cho assembled the draft whole genome sequence of onion (DHW30006). Sunggil Kim organized and coordinated this research project and edited the final manuscript.

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Correspondence to Sunggil Kim.

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The authors have no conflicts of interest relevant to this study to disclose.

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All experiments performed in this study were in compliance with the current laws of the Republic of Korea.

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Communicated by Sandra Elaine Branham.

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Supplementary Information

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Supplementary Fig. 1. Pedigree of the F2 and F4 populations used in this study. (TIF 69 KB)

122_2024_4626_MOESM2_ESM.tif

Supplementary Fig. 2. Dot plot showing the alignment of 7.52-Mb bunching onion and 6.87-Mb onion sequences (DHW30006) containing the I locus. Blue and red colors indicate parallel and antiparallel orientations of alignments, respectively. (TIF 133 KB)

122_2024_4626_MOESM3_ESM.tif

Supplementary Fig. 3. Alignment of AcMYB1 and two homologs (Ace03g21065 and AfisC3G03591) identified from the whole genome sequences of onion (DHW30006) and bunching onion, respectively. A. Alignment of cDNA sequences of the three genes encoding R2R3-MYB transcription factors. B. Alignment of deduced amino acid sequences of the three genes encoding R2R3-MYB transcription factors. (TIF 399 KB)

122_2024_4626_MOESM4_ESM.tif

Supplementary Fig. 4. Phylogenetic tree of the reverse transcriptase (RT) domains of Ivana-AcMYB1 and 16 families from the Ty1/copia superfamily. An LTR-retrotransposon (Athila) from the Ty3/gypsy superfamily is used as an outgroup. The REXdb identification numbers of the LTR-retrotransposons are shown as taxon names. Detailed information on the LTR-retrotransposons is provided in Supplementary Table 5. (TIF 63 KB)

122_2024_4626_MOESM5_ESM.tif

Supplementary Fig. 5. Bulb color phenotypes of F4 individuals with three distinct genotypes of the I locus. Three representative bulbs were selected for each genotype from the WR15-5 population. (TIF 333 KB)

122_2024_4626_MOESM6_ESM.tif

Supplementary Fig. 6. Phylogenetic tree of R2R3-MYB transcription factors isolated from onion and other plant species. Detailed information about each protein is provided in Supplementary Table 4. (TIF 81 KB)

Supplementary file7 (XLSX 63 KB)

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Kim, G., Cho, H. & Kim, S. Identification of a candidate gene for the I locus determining the dominant white bulb color in onion (Allium cepa L.). Theor Appl Genet 137, 118 (2024). https://doi.org/10.1007/s00122-024-04626-9

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