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Integrating GWAS and transcriptomics to identify genes involved in seed dormancy in rice

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Abstract

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Several QTLs and genes responsible for seed dormancy were detected and SNP candidates were shown to cause changes in seed germination.

Abstract

Seed dormancy is a key agricultural trait to prevent pre-harvest sprouting in crop plants such as rice (Oryza sativa L.), wheat (Triticum aestivum), and barley (Hordeum vulgare L.). However, our knowledge of seed dormancy is hampered by the complexities of studying a trait that changes over time after seed harvest, and is complicated by interactions between phytohormones, seed coat components and the environment. Here, we have conducted a genome-wide association study using a panel of 311 natural accessions of cultivated rice, examining a total of 519,158 single nucleotide polymorphisms (SNPs). Eight quantitative trait loci (QTLs) were found to associate with seed dormancy in the whole panel and five in the Japonica and Indica subpanel; expression of candidate genes within 100 kb of each QTL was examined in two published, germination-specific transcriptomic datasets. Ten candidate genes, differentially expressed within the first four days post-imbibition, were identified. Five of these genes had previously been associated with awn length, heading date, yield, and spikelet length phenotypes. Two candidates were validated using Quantitative Reverse Transcription (qRT)-PCR. In addition, previously identified genes involved in hormone signaling during germination were found to be differentially expressed between a japonica and an indica line; SNPs in the promoter of Os9BGlu33 were associated with germination index, with qRT-PCR validation. Collectively, our results are useful for future characterization of seed dormancy mechanism and crop improvement, and suggest haplotypes for further analysis that may be of use to boost PHS resistance in rice.

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Data Availability

The association mapping population data can be found in Rice SNP-Seek database (Wang et al. 2018), and transcriptome data can be found in the Gene Expression Omnibus (GEO) database, with the accession number SRP277875 and GSE115371 (Narsai et al. 2017; Yang et al. 2020).

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Acknowledgements

We would like to thank Mr. Zhijing Luo and Ms. Mingjiao Chen for their assistance in rice growth, and Dr. Natalie Betts for her valuable suggestions on the article.

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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

    Jin Shi, Jianxin Shi, Wanqi Liang & Dabing Zhang

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

    Dabing Zhang

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  1. Jin Shi
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  2. Jianxin Shi
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Contributions

Dabing Zhang and Wanqi Liang designed the study. Jin Shi performed the experiments and bioinformatic analysis. Jianxin Shi helped to revise the manuscript. All authors contributed to the article and approved the submitted version. This work was supported by the National Natural Science Foundation of China (grant nos. 31861163002 and 31700276), and the Innovative Research Team, Ministry of Education, and 111 Project (grant no. B14016).

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Correspondence to Dabing Zhang.

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Shi, J., Shi, J., Liang, W. et al. Integrating GWAS and transcriptomics to identify genes involved in seed dormancy in rice. Theor Appl Genet 134, 3553–3562 (2021). https://doi.org/10.1007/s00122-021-03911-1

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