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Intronic Sequence Variations in a Gene with Peroxidase Domain Alter Bolting Time in Cabbage (Brassica oleracea var. capitata)

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Abstract

Cabbage (Brassica oleracea var. capitata) is the most popular leafy vegetable; however, its quality as a vegetable depends on its growth stage. Premature bolting triggered by low temperatures leads to a reduction of yield and quality of cabbage. Late bolting is preferred by growers to increase market value, whereas early bolting plants are ideal for quality seed production. Herein, we reported a gene BolPrx.2 annotated as Q9FLC0 in the SwissPort, involved in bolting time variation in cabbage and designed molecular markers to characterize early- and late-bolting cabbage populations and lines. The BolPrx.2 gene encodes a peroxidase domain and has been identified as a candidate showed almost similar effect as the previously reported MADS-box domain-containing FLC genes for controlling bolting time. An insertion/deletion (InDel) variation in intron1 has been identified as a causal factor for variation between late- and early-bolting inbred lines. By using this InDel, we designed molecular markers for characterizing the bolting time variation and validated them with 141 F2 generation plants. These markers predicted about 84% of the variation within the population and commercial lines. Therefore, it could be a potential genetic tool to predict bolting time variation and support marker-assisted back crossing (MABC) programs for developing desired bolting types of cabbage cultivars.

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Funding

This research was supported by the Golden Seed Project (Center for Horticultural Seed Development, No. 213007-05-2-SB110), the Ministry of Agriculture, the Food and Rural Affairs (MAFRA), the Ministry of Oceans and Fisheries (MOF), the Rural Development Administration (RDA), and Korea Forest Service (KFS), Korea.

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Authors and Affiliations

  1. Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam, 57922, Republic of Korea

    Md. Abuyusuf, Ujjal Kumar Nath, Hoy-Taek Kim, Manosh Kumar Biswas, Jong-In Park & Ill-Sup Nou

  2. Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh

    Ujjal Kumar Nath

  3. University-Industry Cooperation Foundation, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam, 57922, Republic of Korea

    Hoy-Taek Kim

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  1. Md. Abuyusuf
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  4. Manosh Kumar Biswas
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Contributions

The work presented here was carried out in collaboration among all authors. MA carried out the experiments and prepared the tables, figures, and manuscript draft. UKN collected primary data regarding genes and wrote, edited, and finalized the manuscript. JIP formulated the experimental concept and provided the plant materials. HTK conducted greenhouse experiments and took care of the plant populations. MKB performed in silico analyses and helped with cloning. ISN designed and participated in all the experiments and assisted in improving the technical sites for the project. All authors have read and approved the final manuscript.

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Correspondence to Jong-In Park or Ill-Sup Nou.

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Electronic Supplementary Material

ESM 1

Supplementary Table S1. Primer list of 8 genes of BolFLC, BolPrxs, BolATL73 and BolCYP. Supplementary Table S2. Nucleotide and amino acid similarities of BolPrx.2 gene with reported FLC gene and other flowering pathway genes in Brassica oleracea, respectively. (DOC 89 kb)

Supplementary Fig. S1

Validation of 20 commercial inbred early- and late-bolting cabbage lines with InDel marker of BolPrx.2 gene matched 85%, the heterozygous lines (lanes: 10, 13, and 16) are not matched with the phenotypes. Here, P1= late-bolting parent (BN4730), P2= early-bolting parent (BN7115), F1= (BN4730 × BN7115), M=100 bp DNA marker, red color numbered (10 early-bolting lines): lane 1, 2, 4, 7, 9, 11, 12, 15,17 are 17FLE1, 17FLE2, 17FLE3, 17FLE4, 17FLE5, 17FLE6, 17FLE7, 17FLE8, 17FLE9, and 17FLE10, respectively and black color numbered (10 late-bolting lines): lanes 3, 5, 6, 8, 10, 13, 14, 16 ,19 and 20 are 17FLL1, 17FLL2, 17FLL3, 17FLL4, 17FLL5, 17FLL6, 17FLL7, 17FLL8, 17FLL9, and 17FLL10, respectively. (PPT 493 kb)

Additional file 1.

List of the genes and their sequences used for constructing of phylogenetic tree. (DOC 46 kb)

Additional file 2.

Sequence alignment of the total sequences of the gene BolPrx.2 cloned from late bolting line (BN4730) and early bolting line (BN7115) aligned with reference sequence of BolPrx.2 gene collected from Brassica database (http://brassicadb.org/brad/index.php). Blue and black colour regions are the introns and exons of the gene, respectively. Gray highlighted codons indicate the start and stop codon of the gene; yellow, pink, and green highlighted portion indicate the deletion, insertion and SNPs variations in the late bolting line. (DOC 41 kb)

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Abuyusuf, M., Nath, U.K., Kim, HT. et al. Intronic Sequence Variations in a Gene with Peroxidase Domain Alter Bolting Time in Cabbage (Brassica oleracea var. capitata). Plant Mol Biol Rep 36, 725–737 (2018). https://doi.org/10.1007/s11105-018-1113-z

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