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Genome-wide association study reveals a NAC transcription factor TaNAC074 linked to pre-harvest sprouting tolerance in wheat

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Abstract

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Twelve QTL associated with pre-harvest sprouting tolerance were identified using association analysis in wheat. Two markers were validated and a candidate gene TaNAC074 for Qgpf.cas-3B.2 was verified using Agrobacterium-mediated transformation.

Abstract

Pre-harvest sprouting (PHS) is a considerable global threat to wheat yield and quality. Due to this threat, breeders must identify quantitative trait loci (QTL) and genes conferring PHS-tolerance (PHST) to reduce the negative effects of PHS caused by low seed dormancy. In this study, we evaluated a panel of 302 diverse wheat genotypes for PHST in four environments and genotyped the panel with a high-density wheat 660 K SNP array. By using a genome-wide association study (GWAS), we identified 12 stable loci significantly associated with PHST (P < 0.0001), explaining 3.34 − 9.88% of the phenotypic variances. Seven of these loci co-located with QTL and genes reported previously. Five loci (Qgpf.cas-3B.2, Qgpf.cas-3B.3, Qgpf.cas-3B.4, Qgpf.cas-7B.2, and Qgpf.cas-7B.3), located in genomic regions with no known PHST QTL or genes, are likely to be new QTL conferring PHST. Additionally, two molecular markers were developed for Qgpf.cas-3A and Qgpf.cas-7B.3, and validated using a different set of 233 wheat accessions. Finally, the PHST-related function of candidate gene TaNAC074 for Qgpf.cas-3B.2 was confirmed by CAPS (cleaved amplified polymorphic sequences) marker association analysis in 233 wheat accessions and by expression and phenotypic analysis of transgenic wheat. Overexpression of TaNAC074 significantly reduced seed dormancy in wheat. This study contributes to broaden the genetic basis and molecular marker-assisted breeding of PHST.

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Data availability

The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request.

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Acknowledgements

The authors are thankful to the management and staff of the Liu lab and Key Laboratory of Plant Molecular Physiology, Beijing, China, for field management and technical assistance. The authors would like to thank Dr. Wim J.J. Soppe for assistance with English language editing of this manuscript. We also thank the reviewers and journal editors for thoughtful and constructive comments.

Funding

This work was supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (grant no.XDA24010104) and the National Natural Science Foundation of China (No.32001431; Joint Fund Projects, U20A2033; No. 31870305).

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Authors and Affiliations

  1. Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China

    Hao Jiang, Yu Fang, Si-tong Liu, Jun Wei, Fei-long Guo, Xing-ting Wu, Hong Cao & Yong-xiu Liu

  2. University of Chinese Academy of Sciences, Beijing, 100049, China

    Yu Fang, Si-tong Liu, Jun Wei, Fei-long Guo, Xing-ting Wu, Fei Lu & Yong-xiu Liu

  3. Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China

    Dong Yan & Li-feng Gao

  4. State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China

    Chang-bin Yin & Fei Lu

  5. CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China

    Fei Lu

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  1. Hao Jiang
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  2. Yu Fang
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  3. Dong Yan
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Contributions

HJ, YF, LG, and YL conceived the project; FL and LG provided materials; HJ, HC and YL acquired funding; HJ, YF, HC, CY and JW designed the plot layout and planned the study; HJ, YF, HC, CY, SL, XW, FG and JW performed field activities; HJ, YF, FG, HC, SL, XW and JW measured seed germination; HJ, YF and DY analyzed the data; HJ wrote a draft of the manuscript; LG and YL supervised the study. All authors reviewed, edited, and agreed to the published version of the manuscript.

Corresponding authors

Correspondence to Li-feng Gao or Yong-xiu Liu.

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Communicated by Steven S. Xu.

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Jiang, H., Fang, Y., Yan, D. et al. Genome-wide association study reveals a NAC transcription factor TaNAC074 linked to pre-harvest sprouting tolerance in wheat. Theor Appl Genet 135, 3265–3276 (2022). https://doi.org/10.1007/s00122-022-04184-y

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