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Conserved co-functional network between maize and Arabidopsis aid in the identification of seed defective genes in maize

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Abstract

Background

The biological pathways related to Arabidopsis seed development have been well studied and functional genes involved in it have been discovered. However, functional studies about maize seed development were more limited compared to Arabidopsis.

Objective

Therefore, transferring knowledge from Arabidopsis into maize would facilitate functional studies about maize seed development.

Method

In this study, public transcriptome data of the two species related to seed development were obtained. Co-expression network in each species was compared by integrating orthology information.

Results

This conserved co-functional network contained 4510 maize and 4808 Arabidopsis genes, respectively. Most of these genes were expressed in throughout embryo, early or later endosperm/seed. These conserved co-functional genes were significantly enriched for members of PPR protein family, which was consistent with that PPR proteins play an important role in maize seed development. Spatial-temporally co-functional genes were discovered in the seed coat and embryo. Furthermore, 66 well-studied genes involved in Arabidopsis seed development were co-functional with 319 maize genes and one maize gene (GRMZM2G036050) was further confirmed using an EMS-induced seed defective mutant by bulked segregating RNA sequencing (BSR) analysis.

Conclusions

Altogether, these results showed the potential of this approach to support functional studies in maize seed development by transferring knowledge from Arabidopsis.

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Stating in the method section.

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Funding

This research was funded by GDAS’ Project of Science and Technology Development (Grant No. 2020GDASYL-20200103058), Research and Development Plan in Key Areas of Guangdong Province (2019B020238001).

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Author notes

  1. **angbo Zhang, Yang Cui and Juxuan Wang co-first authors.

Authors and Affiliations

  1. Guangdong Sugarcane Genetic Improvement Engineering Center, Institute of Bioengineering, Guangdong Academy of Sciences, Guangzhou, 510316, China

    **angbo Zhang, Yonghong Huang & Yongwen Qi

  2. Sciences Rice and Sorghum Institude, Sichuan Academy of Agricultural, Deyang, 618000, China

    Yang Cui

  3. Yunnan Yingmao Sugar Industry (Group) Co. LTD, Kunming, 650228, China

    Juxuan Wang

Authors
  1. **angbo Zhang
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  2. Yang Cui
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Contributions

YQ and XZ designed the research; XZ, YC, and JW analyzed data; XZ wrote the paper; YH polished English writing. all authors have read and approved the manuscript.

Corresponding author

Correspondence to Yongwen Qi.

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**angbo Zhang, Yang Cui, Juxuan Wang, and Yongwen Qi declare that they have no confict of interest.

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Zhang, X., Cui, Y., Wang, J. et al. Conserved co-functional network between maize and Arabidopsis aid in the identification of seed defective genes in maize. Genes Genom 43, 433–446 (2021). https://doi.org/10.1007/s13258-021-01067-2

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