Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2022 Nov 21:13:1017672.
doi: 10.3389/fpls.2022.1017672. eCollection 2022.

Genetic dissection of the soybean dwarf mutant dm with integrated genomic, transcriptomic and methylomic analyses

Jian Song  1   2 , Xuewen Wang  3 , Lan Huang  4 , Zhongfeng Li  2 , Honglei Ren  2   5 , Jun Wang  6
Affiliations

Genetic dissection of the soybean dwarf mutant dm with integrated genomic, transcriptomic and methylomic analyses

Jian Song et al. Front Plant Sci. .

Abstract

Plant height affects crop production and breeding practices, while genetic control of dwarfism draws a broad interest of researchers. Dwarfism in soybean (Glycine max) is mainly unexplored. Here, we characterized a dwarf mutant dm screened from ethyl methanesulfonate (EMS) mutated seeds of the soybean cultivar Zhongpin 661(ZP). Phenotypically, dm showed shorter and thinner stems, smaller leaves, and more nodes than ZP under greenhouse conditions. Genetically, whole-genome sequencing and comparison revealed that 210K variants of SNPs and InDel in ZP relative to the soybean reference genome Williams82, and EMS mutagenesis affected 636 genes with variants predicted to have a large impact on protein function in dm. Whole-genome methylation sequencing found 704 differentially methylated regions in dm. Further whole-genome RNA-Seq based transcriptomic comparison between ZP and dm leaves revealed 687 differentially expressed genes (DEGs), including 263 up-regulated and 424 down-regulated genes. Integrated omics analyses revealed 11 genes with both differential expressions and DNA variants, one gene with differential expression and differential methylation, and three genes with differential methylation and sequence variation, worthy of future investigation. Genes in cellulose, fatty acids, and energy-associated processes could be the key candidate genes for the dwarf phenotype. This study provides genetic clues for further understanding of the genetic control of dwarfism in soybean. The genetic resources could help to inbreed new cultivars with a desirable dwarf characteristic.

Keywords: DNA variation; auxin; cellulose; dwarf; methylation; soybean; transcriptome.

PubMed Disclaimer

Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Phenotypic characterization of soybean dwarf mutant. (A) Two branches and three petioles on the fourth node of dwarf mutant (V6 stage), as indicated by white arrows. (B) Top view of branches from the fourth node (V6 stage), as indicated by black arrows. (C) Full view of dwarf mutant and control (R2 stage). Stem thickness was shown for the third node in the left rectangle; Branches of dwarf mutant was enlarged in the right rectangle, and branch apexes were indicated by white arrows. (D) leaf size of the ninth node (R5 stage), scale bar =5 cm. (E) Comparison of node number of M3 plants of the dwarf mutant and control, n=9,*** represents Student’s t-test P< 0.001.
Figure 2
Figure 2
SNPs and indels in gene models and on chromosomes. (A) Relative location of SNPs to gene model. (B) Relative location of indels to gene model. (C) Indels size-frequency distribution. (D) Distribution of mutated genes caused by SNPs (Nonsynonymous substitution and alternative splicing) and indels (codon insertion/deletion, frame shift and alternative splicing) on soybean chromosomes. (E) Distribution of SNPs and indels on soybean chromosomes.
Figure 3
Figure 3
Gene Ontology (GO) analysis of mutated genes with InDels and SNPs. (A) Venn graph shows the number of genes in three types of predicted effects from mutations. (B) GO terms enriched by Fisher test at significance level< 0.05 and 5 minimum number of mapping entry. (C) Hierarchy structure of enriched GO terms.
Figure 4
Figure 4
Categorization of differentially expressed genes between dwarf mutant and control. (A, C) GO enriched categories of up- and down-regulated DEGs, respectively. 470 out of 686 input genes were annotated with GO terms. (B, D) Directed acyclic graph (DAG) of biological process enriched by GO analysis of up- and down-regulated DEGs, respectively. DAG of the biological processes was reconstructed using top 10 enriched GO categories; the significant level of each category was labelled on map, each node for a GO term, and the color represents enrichment degree, the darker the higher enrichment.
Figure 5
Figure 5
Genome-wide methylation status in dwarf mutant and control. (A) Relative methylation level defined as the ratio of methylated cytosines to total cytosines in each context. (B) Ratio (%) of methylated cytosines in different contexts to total methylated cytosines; genome-wide methylated cytosine is set as 100%. mC, mCG, mCHG, mCHG represents methylated cytosine in C (genome-wide), CG, CHG, CHH context, respectively.
Figure 6
Figure 6
Integrative analysis among variants, transcriptome, and methylome. (A) Venn map showing the distribution of genes with nonsynonymous mutation in resequencing dataset, differentially expressed gene in transcriptome dataset and differentially methylated regions in methylome dataset. (B) Comparison of fiber contents between dwarf mutant and control.
Figure 7
Figure 7
CGI prediction and correlation between methylation and expression of differentially expressed genes (DEGs). (A) Number of DEGs and DEGs with CGI prediction. (B) Methylation frequency of up-regulated and down-regulated DEGs. *, **, *** represents significant level of Student’s t-test of 0.05, 0.01, 0.001, respectively. Enriched GO categories of correlated DEGs are listed.
Figure 8
Figure 8
Differences of Glyma.13G312990 between dwarf mutant and control at methylation, transcriptional and genomic level. M for the dm mutant, and c for the control cultivar ZP.
See this image and copyright information in PMC

Similar articles

See all similar articles

References

    1. Al Harrasi I., Al Yahyai R., Yaish M. W., Yang H. (2018). Differential DNA methylation and transcription profiles in date palm roots exposed to salinity. PloS One 13, e0191492. doi: 10.1371/journal.pone.0191492 - DOI - PMC - PubMed
    1. Bennetzen J. L., Wang X. W. (2018). Relationships between gene structure and genome instability in flowering plants. Mol. Plant 11, 407–413. doi: 10.1016/j.molp.2018.02.003 - DOI - PubMed
    1. Candaele J., Demuynck K., Mosoti D., Beemster G. T. S., Dirk I. (2014). Differential methylation during maize leaf growth targets developmentally regulated genes. Plant Physiol. 164, 1350–1364. doi: 10.1104/pp.113.233312 - DOI - PMC - PubMed
    1. Cheng W., Gao J. S., Feng X. X., Shao Q., Yang S. X., Feng X. Z. (2016). Characterization of dwarf mutants and molecular mapping of a dwarf locus in soybean. J. Integr. Agriculture. 15, 2228–2236. doi: 10.1016/S2095-3119(15)61312-0 - DOI
    1. Cokus S. J., Feng S., Zhang X., Chen Z., Merriman B., Haudenschild C. D., et al. . (2008). Shotgun bisulphite sequencing of the arabidopsis genome reveals DNA methylation patterning. Nature. 452, 215–219. doi: 10.1038/nature06745 - DOI - PMC - PubMed

LinkOut - more resources