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Construction of a high-resolution linkage map and chromosomal localization of the loci determining major qualitative traits in onion (Allium cepa L.)

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Abstract

A yellow inbred line (SP3B) and a red doubled haploid line (H6) were used to produce a F2 mapping population of onion (Allium cepa L.). Initially, insertion/deletion and cleaved amplified polymorphic sequence markers were developed based on polymorphisms in the reference transcriptome. To improve efficiency of marker development, RNA-seq was carried out to identify single nucleotide polymorphisms (SNPs) between parental lines. High-quality SNPs were selected via customized screening process, and 344 high resolution melting (HRM) markers were developed. In addition, 161 HRM markers were developed based on the SNPs detected using genotyping-by-sequencing. A linkage map consisting of 652 molecular markers distributed in eight linkage groups was constructed. The total length of the linkage map was 749.8 cM, and the average interval between markers was 1.91 cM, the highest resolution among onion linkage maps reported so far. All eight linkage groups were assigned to onion chromosomes by identifying the common homologous loci in other linkage maps. Four major loci (C, I, R, and L) determining onion bulb colors were located on separate chromosomes. Analysis of ‘Santero’, a F1 cultivar resistant to downy mildew, revealed that the length of the chromosome fragment introgressed from Allium roylei, harboring the resistance gene estimated at 27.6 cM at the end of chromosome 3. The high-resolution linkage map constructed in this study and chromosomal locations of major qualitative loci will be used to design an effective selection strategy for onion breeding programs.

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Acknowledgements

This study was supported by the Korea Institute of Planning and Evaluation for Technology in Food, Agriculture and Forestry (IPET) through the Agriculture, Food and Rural Affairs Research Center Support Program (Vegetable Breeding Research Center), and funded by the Ministry of Agriculture, Food and Rural Affairs (710011-03) and Golden Seed Project (Center for Horticultural Seed Development, No 213007-05-4-SBB10). The authors thank Ji-wha Hur, Jeong-Ahn Yoo, and Su-jung Kim for their dedicated technical assistance.

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

    Youngcho Cho, Bongju Kim & Sunggil Kim

  2. JENONG S&T Co. Ltd., JeJu, 63309, Republic of Korea

    Youngcho Cho & Bongju Kim

  3. Department of Horticulture, Institute of Agricultural Science and Technology, Jeonbuk National University, Jeonju, 54896, Republic of Korea

    Jundae Lee

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  1. Youngcho Cho
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Supplementary Fig.

 1. Development of an HRM marker based on the SNP between red and yellow DFR-A alleles. A. Organization of red and yellow DFR-A alleles and a homologous pseudogene, DFR-B. Arrow-shaped boxes indicate genic regions and 5’-to-3’ directions. Exons and introns are denoted by filled and empty boxes, respectively. The location of triplet codons displaying normal and premature stop codons is shown above the exon 3. The SNP used to develop an HRM marker is shown on the vertical lines in the 5’ upstream regions. Horizontal arrows indicate primer-binding positions. Similar colors of rectangular boxes indicate homologous sequences. B. Normalized melting peaks (upper) and curves (bottom) of the HRM marker. (TIFF 274 kb)

Supplementary Fig.

 2. Development of an HRM marker based on the SNP between two active ANS alleles. A. Organization of two ANS alleles segregating in the mapping population. Arrow-shaped boxes indicate genic regions and 5’-to-3’ directions. Exons and intron are denoted by filled and empty boxes, respectively. The SNP used to develop an HRM marker is shown on the vertical lines at the 5’ upstream regions. Horizontal arrows indicate primer-binding positions. B. Normalized melting peaks (upper) and curves (bottom) of the HRM marker. (TIFF 269 kb)

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Cho, Y., Kim, B., Lee, J. et al. Construction of a high-resolution linkage map and chromosomal localization of the loci determining major qualitative traits in onion (Allium cepa L.). Euphytica 217, 17 (2021). https://doi.org/10.1007/s10681-020-02746-z

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