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Construction of a sequence-based bin map and map** of QTLs for downy mildew resistance at four developmental stages in Chinese cabbage (Brassica rapa L. ssp. pekinensis)

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Abstract

Specific-locus amplified fragment sequencing is a high-resolution method for genetic map**, genoty**, and single nucleotide polymorphism (SNP) marker discovery. Previously, a major QTL for downy mildew resistance, BraDM, was mapped to linkage group A08 in a doubled-haploid population derived from Chinese cabbage lines 91–112 and T12–19. The aim of the present study was to improve the linkage map and identify the genetic factors involved in downy mildew resistance. We detected 53,692 high quality SLAFs, of which 7230 were polymorphic, and 3482 of the polymorphic markers were used in genetic map construction. The final map included 1064 bins on ten linkage groups and was 858.98 cM in length, with an average inter-locus distance of 0.81 cM. We identified six QTLs that are involved in downy mildew resistance. The four major QTLs, sBrDM8, yBrDM8, rBrDM8, and hBrDM8, for resistance at the seedling, young plant, rosette, and heading stages were mapped to A08, and are identical to BraDM. The two minor resistance QTLs, rBrDM6 (A06) and hBrDM4 (A04), were active at the rosette and heading stages. The major QTL sBrDM8 defined a physical interval of ~228 Kb on A08, and a serine/threonine kinase family gene, Bra016457, was identified as the possible candidate gene. We report here the first high-density bin map for Chinese cabbage, which will facilitate map** QTLs for economically important traits and SNP marker development. Our results also expand knowledge of downy mildew resistance in Chinese cabbage and provide three SNP markers (A08-709, A08-028, and A08-018) that we showed to be effective when used in MAS to breed for downy mildew resistance in B. rapa.

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Acknowledgments

This work was supported by grants from the Program of National Natural Science Foundation (No. 31171959), the National Plan for Science and Technology Support (2014BAD01B09), and the earmarked fund for Modern Agroindustry Technology Research System (CARS-25-A-11).

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    Authors and Affiliations

    1. Bei**g Vegetable Research Center (BVRC), Bei**g Academy of Agriculture and Forestry Science (BAAFS), Bei**g, 100097, People’s Republic of China

      Shuancang Yu, Tongbing Su, Shenghua Zhi, Fenglan Zhang, Weihong Wang, Deshuang Zhang, **uyun Zhao & Yangjun Yu

    2. Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Bei**g, People’s Republic of China

      Shuancang Yu, Tongbing Su, Shenghua Zhi, Fenglan Zhang, Weihong Wang, Deshuang Zhang, **uyun Zhao & Yangjun Yu

    3. Bei**g Key Laboratory of Vegetable Germplasm Improvement, Bei**g, 100097, People’s Republic of China

      Shuancang Yu, Tongbing Su, Shenghua Zhi, Fenglan Zhang, Weihong Wang, Deshuang Zhang, **uyun Zhao & Yangjun Yu

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    1. Shuancang Yu
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    Correspondence to Fenglan Zhang.

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    Shuancang Yu and Tongbing Su have been contributed equally to this work.

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    Supplementary Table 1 Detailed information about the marker bins and SLAFs (XLSX 1672 kb)

    11032_2016_467_MOESM2_ESM.xlsx

    Supplementary Table 2 Test of SNP Markers in the BC2 population and PCR primer sequences for amplification of the markers. (XLSX 11 kb)

    Supplementary material 3 (DOCX 129 kb)

    Supplementary material 4 (DOCX 164 kb)

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    Yu, S., Su, T., Zhi, S. et al. Construction of a sequence-based bin map and map** of QTLs for downy mildew resistance at four developmental stages in Chinese cabbage (Brassica rapa L. ssp. pekinensis). Mol Breeding 36, 44 (2016). https://doi.org/10.1007/s11032-016-0467-x

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