Analysis of Hormone Regulation on Seed Germination of Coix Based on Muli-Omics Analysis

Abstract

Seed germination is an important stage of growth and reproduction and plays an important role in the life cycle of spermatophyte. It is co-determined by both genetic and environmental factors, and plant hormone regulation may be a highly conservative mechanism. Coix lachryrma-jobi (coix) is a grain with balanced nutrition for medicine and food and has substantial production value. It is an important part of agricultural production, and the efficiency of seed germination after sowing is a key link. In this study, coix species "small white shell Xingren" was used as the experimental material, and changes in gene expression levels and metabolite enrichment in seeds were identified by transcriptome and metabonomic analysis before and after seed germination. A total of 599 metabolites, including those from amino acid metabolism, sugar metabolism, and fatty acid metabolism, were significantly increased in germinating coix. Simultaneously, 10,929 differentially expressed genes (DEGs) were identified, and functional clusters of genes were also significantly clustered in hormone-signaling and glucose and fatty acid metabolism. In addition, this study found that a considerable number of hormone-signaling genes were significantly up-regulated during seed germination, activating multiple metabolic processes. The results of our conjoint analysis of multi omics showed that glucose and fatty acid metabolism played an important role in seed germination under hormone regulation.

Keywords: coix lachryrma-jobi (coix); hormone-signaling; metabolome; seed germination; transcriptome.

Figure 1

Gene expression analysis during seed germination. (a), Expression density of genes using the transcript per million mapped read (TPM) value. The abscissa is the sample name, and the ordinate is the TPM value. The box chart for each region is divided into five statistics (top to bottom are the maximum, upper quartile, median, lower quartile, and minimum). (b), Identification of differentially expressed genes (DEGs) between treatments. The volcano plot presents the expression of the DEGs in different treatments, the yellow dots represent up-regulated genes, and the blue dots represent down-regulated genes. (c), The GOs classification of all DEGs of germinated seeds and controls. The abscissa is the number of differentially expressed genes in different GOs, and the ordinate is the type of GO enrichment.

Figure 2

The KEGG pathways of all DEGs of germinated seeds and controls. The abscissa is the percent of differentially expressed genes in different KEGG, and the ordinate is the type of KEGG enrichment.

Figure 3

Statistical description of metabolic analysis of coix seed germination. (a), Principal Component Score (PCA) analysis of metabolome sequencing results. The X-axis represents the first principal component (PC1), and the Y-axis represents the second principal component (PC2). (b), Statistical description of metabolic analysis of coix seed germination. (c), The KEGG pathways of all DEGs of germinated seeds and controls. The abscissa is the type of KEGG enrichment, and the ordinate is the percent of differentially expressed genes in different KEGG.

Figure 4

Differential metabolites and differentially expressed genes related to GABA synthesis pathway. In the box plot, the abscissa represents the sample and the ordinate represents the enrichment content for the differentially enriched metabolites. Blue is the test result of non-germinated seeds, and red is the test result of germinated seeds.

Figure 5

Hormone regulatory pathways change during seed germination. Analysis of metabolite accumulation in hormone metabolism pathway shows that red indicates up-regulation and enrichment, and green indicates down-regulation and enrichment. The column chart shows some differentially expressed genes in the pathway, with the gene name in italic font.