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Physical information of 2705 PCR-based molecular markers and the evaluation of their potential use in wheat

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Abstract

Genetic information of polymerase chain reaction (PCR)-based markers, one of the main tools of genetics and genomics research in wheat, have been well documented in wheat. However, the physical position in relation to these markers has not yet been systematically characterized. Aim of this study was to characterize the physical information of thousands of widely used molecular markers. We first assigned 2705 molecular markers to wheat physical map, of which 86.1% and 84.7% were the best hits to chromosome survey sequencing (CSS) project (CSS-contigs) and International Wheat Genome Sequencing Consortium Reference Sequence v1.0 (IWGSC RefSeq v1.0), respectively. Physical position of 96.2% markers were predicated based on BLAST analysis, were in accordance with that of the previous nullisomic/aneuploidy/linkage analysis. A suggestive high-density physical map with 4643 loci was constructed, spanning 14.01 Gb (82.4%) of the wheat genome, with 3.02 Mb between adjacent markers. Both forward and reverse primer sequences of 1166 markers had consistent best hits to IWGSC RefSeq v1.0 based on BLAST analysis, and the corresponding allele sizes were characterized. A detailed physical map with 1532 loci was released, spanning 13.93 Gb (81.9%) of the wheat genome, with 9.09 Mb between adjacent markers. Characteristic of recombination rates in different chromosomal regions was discussed. In addition, markers with multiple sites were aligned to homoeologous sites with a consistent order, confirming that a collinearity existed among A, B and D subgenomes. This study facilitates the integration of physical and genetical information of molecular markers, which could be of value for use in genetics and genomics research such as gene/QTL map-based cloning and marker-assisted selection.

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Acknowledgements

This research was supported by the Shandong Provincial Science Foundation for Outstanding Youth (ZR2017JL017), National Natural Science Foundation of China (31701505, 31671673, 31871612), Yantai Key Research and Development Plan (2017ZH052), Shandong Provincial Science Foundation (ZR2018PC016), the Open Project Programme (CSBAAKF2018003) of State Key Laboratory of Crop Stress Biology for Arid Areas, NWAFU, the Key Research Programme of the Chinese Academy of Sciences (KFZD-SW-110) and Shandong key research and development plan (2017NC210012).

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Author notes

  1. Chunhua Zhao, Han Sun and Chunhui Guan contributed equally to this work.

Authors and Affiliations

  1. College of Agriculture, Ludong University, Yantai, 264025, Shandong, People’s Republic of China

    Chunhua Zhao, Han Sun, Chunhui Guan, Junpeng Cui, Qianqian Zhang, Mengmeng Liu, Mengna Zhang, Qifan Guo, Yuzhu Hou, Mingjie Xiang, Xiaomin Jiang, Xiulong Luo, Yongzhen Wu & Fa Cui

  2. State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy (Academy of Agriculture Sciences), North West Agricultural and Forestry University, Yangling, 712100, Shanxi, People’s Republic of China

    Dejun Han

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  1. Chunhua Zhao
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Correspondence to Yongzhen Wu or Fa Cui.

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Zhao, C., Sun, H., Guan, C. et al. Physical information of 2705 PCR-based molecular markers and the evaluation of their potential use in wheat. J Genet 98, 69 (2019). https://doi.org/10.1007/s12041-019-1114-1

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  • DOI: https://doi.org/10.1007/s12041-019-1114-1

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