Integrated analysis of transcriptomic and proteomic data reveals novel regulators of soybean (Glycine max) hypocotyl development

Xueliang Zhang; Zhikang Shen; Xiaohu Sun; Min Chen; Naichao Zhang

doi:10.1071/FP23013

RESEARCH ARTICLE (Open Access)

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Integrated analysis of transcriptomic and proteomic data reveals novel regulators of soybean (Glycine max) hypocotyl development

Xueliang Zhang ^A ^# , Zhikang Shen

^B ^C ^# , Xiaohu Sun ^C , Min Chen

^B ^C ^* and Naichao Zhang

^A ^*

+ Author Affiliations

- Author Affiliations

^A School of Life Sciences, Henan University, Kaifeng, China.

^B Sanya Institute, Henan University, Sanya, China.

^C State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng, China

^* Correspondence to: chenmin@henu.edu.cn, naichao.zhang@henu.edu.cn

^# These authors contributed equally to this paper

Handling Editor: Gayatri Venkataraman

Functional Plant Biology 50(12) 1086-1098 https://doi.org/10.1071/FP23013

Submitted: 12 January 2023 Accepted: 5 October 2023 Published: 23 October 2023

© 2023 The Author(s) (or their employer(s)). Published by CSIRO Publishing. This is an open access article distributed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC BY-NC-ND)

Abstract

Hypocotyl elongation directly affects the seedling establishment and soil-breaking after germination. In soybean (Glycine max), the molecular mechanisms regulating hypocotyl development remain largely elusive. To decipher the regulatory landscape, we conducted proteome and transcriptome analysis of soybean hypocotyl samples at different development stages. Our results showed that during hypocotyl development, many proteins were with extreme high translation efficiency (TE) and may act as regulators. These potential regulators include multiple peroxidases and cell wall reorganisation related enzymes. Peroxidases may produce ROS including H₂O₂. Interestingly, exogenous H₂O₂ application promoted hypocotyl elongation, supporting peroxidases as regulators of hypocotyl development. However, a vast variety of proteins were shown to be with dramatically changed TE during hypocotyl development, including multiple phytochromes, plasma membrane intrinsic proteins (PIPs) and aspartic proteases. Their potential roles in hypocotyl development were confirmed by that ectopic expression of GmPHYA1 and GmPIP1-6 in Arabidopsis thaliana affected hypocotyl elongation. In addition, the promoters of these potential regulatory genes contain multiple light/gibberellin/auxin responsive elements, while the expression of some members in hypocotyls was significantly regulated by light and exogenous auxin/gibberellin. Overall, our results revealed multiple novel regulatory factors of soybean hypocotyl elongation. Further research on these regulators may lead to new approvals to improve soybean hypocotyl traits.

Keywords: aquaporins, cell walls, growth regulation, hydrogen peroxide, hypocotyl development, phytochrome, proteomics, seed storage proteins, translation efficiency.

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