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Discovery of DNA polymorphisms via genome-resequencing and development of molecular markers between two barley cultivars

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Abstract

Key message

Genome resequencing uncovers genome-wide DNA polymorphisms that are useful for the development of high-density InDel markers between two barley cultivars.

Abstract

Discovering genomic variations and developing genetic markers are crucial for genetics studies and molecular breeding in cereal crops. Although InDels (insertions and deletions) have become popular because of their abundance and ease of detection, discovery of genome-wide DNA polymorphisms and development of InDel markers in barley have lagged behind other cereal crops such as rice, maize and wheat. In this study, we re-sequenced two barley cultivars, Golden Promise (GP, a classic British spring barley variety) and Hua30 (a Chinese spring barley variety), and mapped clean reads to the reference Morex genome, and identified in total 13,933,145 single nucleotide polymorphisms (SNPs) and 1,240,456 InDels for GP with Morex, 11,297,100 SNPs and 781,687 InDels for Hua30 with Morex, and 13,742,399 SNPs and 1,191,597 InDels for GP with Hua30. We further characterized distinct types, chromosomal distribution patterns, genome location, functional effect, and other features of these DNA polymorphisms. Additionally, we revealed the functional relevance of these identified SNPs/InDels regarding different flowering times between Hua30 and GP within 17 flowering time genes. Furthermore, we developed a series of InDel markers and validated them experimentally in 43 barley core accessions, respectively. Finally, we rebuilt population structure and phylogenetic tree of these 43 barley core accessions. Collectively, all of these genetic resources will facilitate not only the basic research but also applied research in barley.

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Data availability

The genome-resequencing dataset generated is available in the NCBI database under BioProject ID PRJNA825118. The other data associated with this study is available from the corresponding author on reasonable request.

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Acknowledgements

The authors would like to thank Mr. Ting Luo and Ms. Mingjiao Chen for their assistance with barley cultivation.

Funding

This research was funded by the National Natural Science Foundation of China (31970803 and 32130006), China-Germany Mobility Program (M-0141), the Innovative Research Team, Ministry of Education, and 111 Project (B14016), the Australian Research Council Discovery Project (grant no. DP210100956.).

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  1. Yueya Zhang and Jin Shi contributed equally to this work.

Authors and Affiliations

  1. Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China

    Yueya Zhang, Jin Shi, Chaoqun Shen, Vinh-Trieu To, Qi Shi, Jianxin Shi & Dabing Zhang

  2. School of Agriculture, Food, and Wine, University of Adelaide, Adelaide, South Australia, 5064, Australia

    Dabing Zhang & Weiwei Chen

  3. Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China

    Lingzhen Ye

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  1. Yueya Zhang
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Contributions

DBZ and WWC conceived and designed the project. YYZ drafted the manuscript. JS performed bioinformatic analysis. YYZ, CQS, VTT and QS performed the experiments. LZY provided materials for 40 barley varieties. JXS, WWC and DBZ revised the manuscript. All authors read and approved the manuscript.

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Correspondence to Dabing Zhang or Weiwei Chen.

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Zhang, Y., Shi, J., Shen, C. et al. Discovery of DNA polymorphisms via genome-resequencing and development of molecular markers between two barley cultivars. Plant Cell Rep 41, 2279–2292 (2022). https://doi.org/10.1007/s00299-022-02920-8

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