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Fine mapping of a quantitative trait locus conferring resistance to maize rough dwarf disease

Theoretical and Applied Genetics volume 129, pages 2333–2342 (2016)Cite this article

Abstract

Key message

A QTL qMrdd8 that confers resistance to MRDD was fine mapped into an interval of 347 kb; one SNP and two InDels identified in the interval were significantly associated with resistance to MRDD.

Abstract

Maize rough dwarf disease (MRDD) is highly prevalent in the summer maize-growing areas in China, and leads to significant yield losses in maize (Zea mays L.). In this study, the quantitative trait locus (QTL) qMrdd8, which confers resistance to MRDD, was fine mapped. Initially, qMrdd8 was consistently identified in the interval between the simple sequence repeat markers umc1617 and phi121 in three F2 sub-populations derived from a cross between the resistant recombinant inbred line NL203 and the susceptible line B73. Subsequently, qMrdd8 was fine mapped into an interval of 347 kb defined by the markers IDRQ2 and IDRQ20 using a recombinant-derived progeny test strategy. Based on single nucleotide polymorphism (SNP) genotypes identified using the MaizeSNP50 BeadChip, a long haplotype including qMrdd8 was identified in four resistant inbred lines. One SNP, the 2549-bp insertion/deletion polymorphism (InDel) InDel25, and the 2761-bp InDel27, which all were significantly associated with resistance to MRDD in a set of 226 maize inbred lines (P < 0.05), were detected within qMrdd8. Furthermore, two candidate genes, CG1 and CG2, were detected in the interval using RNA sequencing (RNA-Seq), and InDel25 was localized within the candidate gene CG1. In conclusion, the fine mapping of qMrdd8 will be helpful in cloning the resistance gene, and the three polymorphic markers identified in this study could be used to improve MRDD resistance via a marker-assisted selection approach.

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Acknowledgments

We thank Jianhua Yuan, Qingchang Meng, Yanping Chen, and Xiaoming Kong for their assistance in evaluation of resistance to MRDD. This research was jointly funded by the Pilot Project of Breeding of the Seven Major Crops (2016YFD0101803), the International Science & Technology Cooperation Program of China (2014DFG1690), the National Hi-Tech Research Program and Development Program of China (2012AA101104), and the Chinese Academy of Agriculture Science (CAAS) Innovation Project.

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    Affiliations

    1. Institute of Crop Science, Chinese Academy of Agricultural Sciences, No. 12 Zhongguancun South Street, Haidian District, Beijing, 100081, China

      Changlin Liu, Jinge Hua, Degui Zhang, Zhuanfang Hao, Hongjun Yong, Chuanxiao Xie, Mingshun Li, Shihuang Zhang, Jianfeng Weng & Xinhai Li

    2. Northeast Agricultural University, Harbin, 150000, Heilongjiang, China

      Chang Liu

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    1. Changlin Liu
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    3. Chang Liu
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    Correspondence to Jianfeng Weng or Xinhai Li.

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    We claim that the experiments described herein comply with the ethical standards in China.

    Conflict of interest

    A patent regarding the polymorphisms SNP7, InDel25, and InDel27 and tightly linked markers has been applied for at the State Intellectual Property Office of the People’s Republic of China.

    Additional information

    C. Liu and J. Hua contributed equally to this article.

    Communicated by T. Lubberstedt.

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    Liu, C., Hua, J., Liu, C. et al. Fine mapping of a quantitative trait locus conferring resistance to maize rough dwarf disease. Theor Appl Genet 129, 2333–2342 (2016). https://doi.org/10.1007/s00122-016-2770-7

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    • DOI: https://doi.org/10.1007/s00122-016-2770-7

    Keywords

    • Quantitative Trait Locus
    • Inbred Line
    • Quantitative Trait Locus Mapping
    • Disease Score
    • Maize Inbred Line