Abstract
Grain size is an important trait for crops. The endogenous hormones brassinosteroids (BRs) play key roles in grain size and mass. In this study, we identified an ethyl methylsulfonate (EMS) mutant wheat line, SM482gs, with increased grain size, 1000-grain weight, and protein content, but decreased starch content, compared with the levels in the wild type (WT). Comparative transcriptomic analysis of SM482gs and WT at four developmental stages [9, 15, 20, and 25 days post-anthesis (DPA)] revealed a total of 264, 267, 771, and 1038 differentially expressed genes (DEGs) at these stages. Kyoto Encyclopedia of Genes and Genomes (KEGG) database analysis showed that some DEGs from the comparison at 15 DPA were involved in the pathway of “brassinosteroid biosynthesis,” and eight genes involved in BR biosynthesis and signal transduction were significantly upregulated in SM482gs during at least one stage. This indicated that the enhanced BR signaling in SM482gs might have contributed to its increased grain size via network interactions. The expression of seed storage protein (SSP)-encoding genes in SM482gs was upregulated, mostly at 15 and 20 DPA, while most of the starch synthetase genes showed lower expression in SM482gs at all stages, compared with that in WT. The expression patterns of starch synthase genes and seed storage protein-encoding genes paralleled the decreased level of starch and increased storage protein content of SM482gs, which might be related to the increased seed weight and wrinkled phenotype.
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Data availability
The raw sequencing data were deposited in the NCBI SRA database with accession numbers SRP115001/SRR5908629 (https://www.ncbi.nlm.nih.gov/Traces/study/?acc=SRP115001).
Abbreviations
- BR:
-
Brassinosteroid
- EMS:
-
Ethyl methanesulfonate
- WT:
-
Wild type
- DPA:
-
Days post-anthesis
- DEG:
-
Differentially expressed gene
- GO:
-
Gene ontology
- KEGG:
-
Kyoto encyclopedia of genes and genomes
- HMW-GS:
-
High-molecular-weight glutenin subunit
- LMW-GS:
-
Low-molecular-weight glutenin subunit
- RT-qPCR:
-
Real-time quantitative reverse transcription polymerase chain reaction
- RNA-Seq:
-
Ribonucleic acid sequencing
- TPM:
-
Transcripts per million
- AGPase:
-
Adenosine diphosphate glucose pyrophosphorylase
- SS:
-
Starch synthase
- SBE:
-
Starch branching enzyme
- DBE:
-
Starch debranching enzyme
- GBSS:
-
Granule-bound starch synthase
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Funding
This work was supported by the National Key Research and Development Program of China (2017YFD0100900), the Key Research and Development Program of Sichuan Province (2018NZDZX0002), Sichuan Science and Technology Program (2020YFH0140), the International Science & Technology Cooperation Project of Chengdu, Sichuan Province, China (2019-GH02-00078-Hz), and the Technological Innovation Project of Chengdu, Sichuan Province, China (2018-YF05-00059-SN).
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XJZ carried out analysis of RNA sequencing, qRT-PCR and wrote this article. NL and JJD analyzed the bioinformatics. QY carried out material preparation. JYL and HPT contribute to the material planting, the succession of mutant material and management. QTJ conceived and designed the experiments. PFQ, MD, JM, JRW, GYC, XJL, YMW, and YLZ partially participated in its design and revised the manuscript. All authors read and approved the final manuscript.
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Supplementary Information
Figure S1. Hierarchical clustering heatmap of Pearson’s correlation coefficients between samples. The biological replicates of each sample are indicated as “1, 2.” The color scale represents the values of Pearson’s correlation coefficients.
Figure S2. GO terms of all DEGs of the SM482gs mutant compared with WT in different grain developmental stages. (A) GO terms of all upregulated DEGs in different comparisons. (B) GO terms of all downregulated DEGs in different comparisons. W: WT, M: SM482gs mutant. p≤0.05.
Figure S3. KEGG pathway enrichment of DEGs of the SM482gs mutant compared with WT in different grain developmental stages. W: WT, M: SM482gs mutant. p≤0.05.
Table S1. Top ten biological processes (BP) enriched among the down- and upregulated DEGs of the SM482gs mutant as compared with WT in different grain developmental stages. W: WT, M: SM482gs mutant.
Table S2. Top ten KEGG pathways enriched among the down- and upregulated DEGs of the SM482gs mutant as compared with WT in different grain developmental stages. W: WT, M: SM482gs mutant.
Table S3. Functional classification of DEGs in each k-means cluster. The numbers represent the numbers of genes.
Table S4. NCBI and transcript IDs of starch synthetase genes, BR-related homologous genes from Triticum species, rice, Arabidopsis, and storage protein genes.
Table S5. The detailed information and primers of genes analyzed for RT-qPCR.
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Zhong, X., Lin, N., Ding, J. et al. Genome-wide transcriptome profiling indicates the putative mechanism underlying enhanced grain size in a wheat mutant. 3 Biotech 11, 54 (2021). https://doi.org/10.1007/s13205-020-02579-6
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DOI: https://doi.org/10.1007/s13205-020-02579-6