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Transcriptome profiling of transgenic rice seeds lacking seed storage proteins (globulin, prolamin, and glutelin) by RNA-Seq analysis

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Abstract

Major seed storage proteins in rice (Oryza sativa) are composed of glutelin, prolamin, and globulin. We previously generated four SSP-RNAi lines with reduced levels of globulin (Glb-RNAi); prolamin (Pro-RNAi); prolamin and globulin (PGb-RNAi); and glutelin, prolamin, and globulin (GPGb-RNAi). To identify the genes and molecular events associated with SSP deletion, we profiled the levels of seed transcripts in these four SSP-RNAi lines during seed development. We identified 2951 differentially expressed genes (DEGs) with a fold change of ≥ 2 or ≤ − 2 relative to the wild type (cv. Ilmi). Gene ontology (GO) analysis showed that most DEGs were associated with the functional categories “regulation of transcription, DNA-dependent”, “regulation of RNA metabolic process”, and “integral to membrane”. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis demonstrated that the DEGs also functioned in “metabolism”, “folding, sorting and degradation”, and “transport and catabolism”. We identified 105 transcription factor (TF) genes and belonging to 25 TF gene families in our list of DEGs. Specifically, which are expected to affect expression of SSP-related genes, the expressions of TF genes, such as zinc finger protein, basic helix–loop–helix protein 008, and MYB transcription factor 55/61L, were decreased, and the expression levels of C2H2-type zinc finger protein, basic helix–loop–helix protein 073, and zinc finger protein were increased by RNA-Seq data and real-time quantitative PCR. Furthermore, it was confirmed in four SSP-RNAi lines that the expression levels of lipid transfer proteins were reduced. These results provide important information about the effect of SSPs-related genes on seed development.

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Acknowledgements

This work was supported by grants from the National Institute of Agricultural Science (RDA PJ014838) and the Next-Generation BioGreen 21 Program (RDA PJ013159 and RDA PJ013149), South Korea. This study was supported by Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (2020R1I1A1A01069882) to KC.

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  1. Sewon Kim and Kyoungwon Cho contributed equally to this work.

Authors and Affiliations

  1. National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, 54874, South Korea

    Sewon Kim & Jong-Yeol Lee

  2. Department of Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, 61186, South Korea

    Kyoungwon Cho

  3. Division of Horticultural Biotechnology, Hankyong National University, Anseong, 17579, South Korea

    Sun-Hyung Lim

  4. Department of Biochemistry, School of Medicine, Dongguk University, Gyeongju, 38066, South Korea

    Tae-Won Goo

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  1. Sewon Kim
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Correspondence to Jong-Yeol Lee.

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Kim, S., Cho, K., Lim, SH. et al. Transcriptome profiling of transgenic rice seeds lacking seed storage proteins (globulin, prolamin, and glutelin) by RNA-Seq analysis. Plant Biotechnol Rep 15, 77–93 (2021). https://doi.org/10.1007/s11816-020-00655-0

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