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Gene co-expression modules behind the three-pistil formation in wheat

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Abstract

Multi-pistil trait in wheat is of great potential value in plant development research and crop breeding. Our previous studies identified the Pis1 locus that causes three pistils in wheat by genetic mapping using multiple DNA marker systems. However, there are still 26 candidate genes on the locus, and the causal gene remains to be found. In this study, we aimed to approach the molecular mechanism of multi-pistil formation. Comparative RNA sequencing (RNA-Seq) during the pistil formation was undertaken in four wheat lines: a three-pistil mutant TP, a single-pistil TILLING mutant of TP (SP), a three-pistil near-isogenic line CM28TP with the background of cultivar Chunmai 28 (CM28), and CM28. Electron microscopic analysis specified probable developmental stages of young spikes for the three-pistil formation. mRNA sequencing in the young spikes of the four lines represented 253 down-regulated genes and 98 up-regulated genes in both three-pistil lines, which included six potential genes for ovary development. Weighted gene co-expression analysis represented three-pistil trait-associated transcription factor-like genes, among which one hub gene, ARF5, was the most highlighted. ARF5 is on the Pis1 locus and an orthologue of MONOPTEROS which mediates tissue development in Arabidopsis. qRT-PCR validation implies that the deficiency of ARF5 underlies the three-pistil formation in wheat.

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Fig. 1

Data availability

The raw RNA sequencing data have been deposited in the National Center for Biotechnology Information (NCBI) Sequence Read Archive [Accession ID: PRJNA705852]. All other relevant supplementary data is provided within this manuscript as an additional file: Supplementary Figures S1–S7 and Tables S1–S7.

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Funding

This work was supported by the National Natural Science Foundation of China (Grant No. 32272066, 32060456), the Natural Science Foundation of Sichuan Province (Grant No. 2022NSFSC0160), and the Major science and technology special sub-project of the Sichuan Provincial Department of Science and Technology (Grant No. 2022ZDZX0014-4–4).

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Author notes

  1. Naoki Yamamoto, Zhenyong Chen, and Yuhuan Guo contributed equally to this work.

Authors and Affiliations

  1. Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong, 637009, Sichuan, China

    Naoki Yamamoto, Zhenyong Chen, Yuhuan Guo, Zhouyuan Yu, Yichao Wu & Zaijun Yang

  2. College of Environmental Science and Engineering, China West Normal University, Nanchong, 637009, Sichuan, China

    Wurina Tong

  3. School of Agricultural Science, Xichang University, Xichang, 615000, China

    Zhengsong Peng

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  1. Naoki Yamamoto
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  2. Zhenyong Chen
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  3. Yuhuan Guo
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  4. Wurina Tong
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  5. Zhouyuan Yu
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  6. Yichao Wu
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  7. Zhengsong Peng
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  8. Zaijun Yang
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Contributions

N. Y. and Z. C. contributed equally to this work. N. Y. and Z. C.: methodology and data analysis; Y. G.: methodology, W. T.: methodology; Z. Y.: methodology; Y. W.: methodology; Z. P.: supervision, reviewing, and editing; Z. Y.: supervision, data analysis, reviewing, and editing.

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Correspondence to Zaijun Yang.

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Yamamoto, N., Chen, Z., Guo, Y. et al. Gene co-expression modules behind the three-pistil formation in wheat. Funct Integr Genomics 23, 123 (2023). https://doi.org/10.1007/s10142-023-01052-w

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  • DOI: https://doi.org/10.1007/s10142-023-01052-w

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