Identification of Genes/Proteins Related to Submergence Tolerance by Transcriptome and Proteome Analyses in Soybean

Abstract

Flooding can lead to yield reduction of soybean. Therefore, identification of flooding tolerance genes has great significance in production practice. In this study, Qihuang 34, a highly-resistant variety to flooding stress, was selected for submergence treatments. Transcriptome and proteome analyses were conducted, by which twenty-two up-regulated differentially expressed genes (DEGs)/differentially expressed proteins (DEPs) associated with five KEGG pathways were isolated. The number of the DEGs/DEPs enriched in glycolysis/gluconeogenesis was the highest. Four of these genes were confirmed by RT-qPCR, suggesting that glycolysis/gluconeogenesis may be activated to generate energy for plant survival under anaerobic conditions. Thirty-eight down-regulated DEGs/DEPs associated with six KEGG pathways were identified under submergence stress. Eight DEGs/DEPs enriched in phenylpropanoid biosynthesis were assigned to peroxidase, which catalyzes the conversion of coumaryl alcohol to hydroxy-phenyl lignin in the final step of lignin biosynthesis. Three of these genes were confirmed by RT-qPCR. The decreased expression of these genes led to the inhibition of lignin biosynthesis, which may be the cause of plant softening under submergence stress for a long period of time. This study revealed a number of up-/down-regulated pathways and the corresponding DEGs/DEPs, by which, a better understanding of the mechanisms of submergence tolerance in soybean may be achieved.

A Comprehensive Transcriptomics Analysis Reveals Long Non-Coding RNA to Be Involved in the Key Metabolic Pathway in Response to Waterlogging Stress in Maize

“…Many studies have been conducted to investigate the transcriptomes of PCgenes in response to WS condition in plants such as Arabidopsis, rice, maize, cotton, and soybean [7,9,11,69,70]. However, there are few investigations centered on lncRNAs responding to WS.…”

Peer Review #1 of "Genome-wide characterization and expression analysis of soybean trihelix gene family (v0.1)"

“…The expression data was obtained from the public RNA-seq data published in Phytozome v12.1 (Libault et al, 2010;Goodstein et al, 2011). The RNA-seq data was obtained from NCBI Sequence Read Archive (SRA) with the accession number: SRP181976 (Lin et al, 2019). The expression values (Fragments per kilobase for a million reads, FPKM) for each gene were log2 transformed before generating the heatmap.…”

“…Previous studies showed that the maize trihelix genes could respond to flood stress (Du et al, 2016). Considering that many soybean trihelix genes processed the anaerobic responsive element (ARE) in their promoters, we analyzed our previous transcriptome data of the soybean cultivar Qihuang34 submerged for 3, 6, 12 and 24 hours at the seedling stage (Lin et al, 2019) (Table S6).…”

“…Note: The genes written in red and black color were up-and down-regulated, respectively. The RNA-seq data was obtained from NCBI Sequence Read Archive (SRA) (SRP181976) (Lin et al, 2019). Log2FC, Log2FoldChange.…”

Review: Proteomic Techniques for the Development of Flood-Tolerant Soybean

“…Proteomic study of the soybean radicle collected from these categories showed that RNA binding/processing-related proteins and flooding stress indicator proteins correlated with flood-tolerant index [ 31 ]. Lin et al [ 105 ] reported that Qihuang 34 was a flood-tolerant cultivar, which was indicated with the highest survival ratio of seedling, and metabolic pathways relevant to carbon metabolism, mitogen-activated protein kinase signaling, fatty acid degradation, as well as isoflavonoid biosynthesis were enriched via differently changed genes and proteins under flooding. In addition, it was shown that glycolysis was activated for ATP production for plant survival; however, decreased lignin caused plant softening under submergence for a long period of time [ 105 ].…”