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Identification and characterization of mRNAs and lncRNAs of a barley shrunken endosperm mutant using RNA-seq

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Abstract

Barley shrunken endosperm mutants have been extensively reported. However, knowledge of the underlying molecular mechanisms of these mutants remains limited. Here, a pair of near isogenic lines (normal endosperm: Bowman and shrunken endosperm: sex1) was subjected to transcriptome analysis to identify mRNAs and lncRNAs related to endosperm development to further dissect its mechanism of molecular regulation. A total of 2123 (1140 up- and 983 down-regulated) unique differentially expressed genes (DEGs) were detected. Functional analyses showed that these DEGs were mainly involved in starch and sucrose metabolism, biosynthesis of secondary metabolites, and plant hormone signal transduction. A total of 343 unique target genes were identified for 57 differentially expressed lncRNAs (DE lncRNAs). These DE lncRNAs were mainly involved in glycerophospholipid metabolism, starch and sucrose metabolism, hormone signal transduction, and stress response. In addition, key lncRNAs were identified by constructing a co-expression network of the target genes of DE lncRNAs. Transcriptome results suggested that mRNA and lncRNA played a critical role in endosperm development. The shrunken endosperm in barley seems to be closely related to plant hormone signal transduction, starch and sucrose metabolism, and cell apoptosis. This study provides a foundation for fine mapping, elucidates the molecular mechanism of shrunken endosperm mutants, and also provides a reference for further studies of lncRNAs during the grain development of plants.

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Acknowledgements

This work is supported by the National Natural Science Foundation of China (31970243 and 31971937), the International Science and Technology Cooperation and Exchanges Program of Science and Technology Department of Sichuan Province (2017HH0076), and the Key Projects of Scientific and Technological Activities for Overseas Students of Sichuan Province. We thank MogoEdit Bianji Company (http://www.mogoedit.com/) for editing the English text of this manuscript. We thank the anonymous referees for critical reading and revising of this manuscript.

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  1. Yaya Zou and Huaping Tang have contributed equally to this paper.

Authors and Affiliations

  1. State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China

    Yaya Zou, Huaping Tang, Ting Li, Min Sun, Xiangru Qu, Jieguang Zhou, Congcong Yang, Yang Mu, Qiantao Jiang, Yaxi Liu, Guoyue Chen, Youliang Zheng, Yuming Wei, Xiujin Lan & Jian Ma

  2. College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China

    Guangdeng Chen

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Fig. S1

Functional categories of DEGs. The (a) GO and (b) KEGG enrichment analysis of DEGs between Bowman and sex1 at 15 DAF. Electronic supplementary material 1 (TIF 8026 kb)

Fig. S2

Functional categories of DEGs. The (a) GO and (b) KEGG enrichment analysis of DEGs between Bowman and sex1 at 20 DAF. Electronic supplementary material 2 (TIF 8238 kb)

Fig. S3

Characterization of all lncRNAs and mRNAs. (a) Venn diagrams of coding potential prediction of lncRNAs by CPC, CPAT, CNCI and pfam. (b) Classification of lncRNAs. X axis indicates different types of lncRNA, Y axis indicates the corresponding number of lncRNA. Distributions of lncRNAs and mRNAs in transcript length (c, d), and exon number (e, f), respectively. Electronic supplementary material 3 (TIF 12861 kb)

Fig. S4

Functional categories of the target genes of DE lncRNAs between Bowman and sex1 at 15 DAF. The (a) COG classify, (b) GO and (c) KEGG enrichment analysis. Electronic supplementary material 4 (TIF 11789 kb)

Fig. S5

Functional categories of the target genes of DE lncRNAs between Bowman and sex1 at 20 DAF. The (a) COG classify, (b) GO and (c) KEGG enrichment analysis. Electronic supplementary material 5 (TIF 12021 kb)

Fig. S6

The network map of DE lncRNAs and their target genes. Electronic supplementary material 6 (TIF 12304 kb)

Fig. S7

Functional analysis of MSTRG.79382.1. The (a) COG analysis, (b) GO annotation and (c) KEGG enrichment analysis of MSTRG.79382.1. Electronic supplementary material 7 (TIF 11757 kb)

Table S1

Primers used for qRT-PCR for selected DEGs and DE lncRNAs. Electronic supplementary material 8 (XLSX 9 kb)

Table S2

Summary of Illumina RNA-seq reads for 24 samples (dataset A and dataset B). Electronic supplementary material 9 (XLSX 12 kb)

Table S3

DEGs in dataset A and dataset B. Electronic supplementary material 10 (XLSX 65 kb)

Table S4

GO analysis of DEGs at 10, 15 and 20 DAF. Electronic supplementary material 11 (XLSX 22 kb)

Table S5

KEGG enrichment annotation of DEGs at 10, 15 and 20 DAF. Electronic supplementary material 12 (XLSX 22 kb)

Table S6

Details of classification of lncRNA. Electronic supplementary material 13 (XLSX 58 kb)

Table S7

Summary of 10 known lncRNAs. Electronic supplementary material 14 (XLSX 9 kb)

Table S8

Summary of DE lncRNAs and their target genes. Electronic supplementary material 15 (XLSX 17 kb)

Table S9

COG classification of target genes DE lncRNAs at 10, 15 and 20 DAF. Electronic supplementary material 16 (XLSX 14 kb)

Table S10

GO analysis of target genes of DE lncRNAs at 10, 15 and 20 DAF. Electronic supplementary material 17 (XLSX 15 kb)

Table S11

KEGG enrichment annotation of target genes of DE lncRNAs at 10, 15 and 20 DAF. Electronic supplementary material 18 (XLSX 14 kb)

Table S12

DE lncRNA and target gene co-expression network analysis. Electronic supplementary material 19 (XLSX 21 kb)

Table S13

Functional analysis of MSTRG.79382.1. Electronic supplementary material 20 (XLSX 15 kb)

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Zou, Y., Tang, H., Li, T. et al. Identification and characterization of mRNAs and lncRNAs of a barley shrunken endosperm mutant using RNA-seq. Genetica 148, 55–68 (2020). https://doi.org/10.1007/s10709-020-00087-2

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