Identification of tomato root growth regulatory genes and transcription factors through comparative transcriptomic profiling of different tissues

Abstract

Tomato is an economically important vegetable crop and a model for development and stress response studies. Although studied extensively for understanding fruit ripening and pathogen responses, its role as a model for root development remains less explored. In this study, an Illumina-based comparative differential transcriptomic analysis of tomato root with different aerial tissues was carried out to identify genes that are predominantly expressed during root growth. Sequential comparisons revealed ~ 15,000 commonly expressed genes and ~ 3000 genes of several classes that were mainly expressed or regulated in roots. These included 1069 transcription factors (TFs) of which 100 were differentially regulated. Prominent amongst these were members of families encoding Zn finger, MYB, ARM, bHLH, AP2/ERF, WRKY and NAC proteins. A large number of kinases, phosphatases and F-box proteins were also expressed in the root transcriptome. The major hormones regulating root growth were represented by the auxin, ethylene, JA, ABA and GA pathways with root-specific expression of certain components. Genes encoding carbon metabolism and photosynthetic components showed reduced expression while several protease inhibitors were amongst the most highly expressed. Overall, the study sheds light on genes governing root growth in tomato and provides a resource for manipulation of root growth for plant improvement.

Supplementary information: The online version contains supplementary material available at 10.1007/s12298-021-01015-0.

Keywords: Lateral root; Phytohormones; Primary root; RNA sequencing; Transcription factors.

Fig. 1

Venn diagram showing the number of shared and uniquely expressed transcripts among various tomato tissues

Fig. 2

Comparison of genes that are differentially expressed in root with respect to other tissues of tomato. A Volcano plots representing the Log2 fold change (FC) of differentially expressed genes in comparisons of root versus other tissues. The Log₂FC and the p-value are plotted on the x-axis and the y-axis, respectively. The red points in the scatter-plot are significant with p-value ≥ 0.9 and the black points represent non significant with p-value < 0.9. B The comparison of genes that were differentially expressed genes with [Log₂|FC| (≤ − 2 and ≥ 2)] and p-value ≥ 0.9 in root compared with other tissues. C The Heat map and dendrogram represent the top 10 up- and down-regulated transcripts in comparisons of root versus other tissues. The red-green spectrum represents the scaled expression values and gray represents zero expression value (Color figure online)

Fig. 3

The GO terms under different functional categories enriched among the DEGs in the tomato root compared with other tissues. A Venn diagram representing shared and unique GO terms of up- and down-regulated genes in the comparisons of root versus other tissues. B GO enrichment (Sample number/Background number) of up-regulated genes under biological processes and molecular function categories in the tomato root compared with other tissues. The blue-red spectrum represents the GO enrichment values (Color figure online)

Fig. 4

The enriched KEGG pathways of up-regulated A and down-regulated B DEGs in tomato root in comparison to all other tissues. Gene ratio represents the ratio of the number of DEGs to the total gene number in a pathway. The dots size and color represent the number of DEGs mapped to the indicated pathway and the range of p-value, respectively (Color figure online)

Fig. 5

Functional categorization showing the proportion of differentially expressed regulatory genes [Log₂|FC|(≤ − 2 and ≥ 2) and p-value ≥ 0.9] identified in root. A Transcription factors and B Various kinases, phosphatases and F-box proteins. The green horizontal bar of the graph represents the proportions of different up-regulated genes, while the red horizontal bar represents the proportions of different down-regulated genes. The numbers on the left represent the percentage while the number of the right denote the total DEGs in that catagory that were mapped on the tomato genome in the root transcriptome (Color figure online)

Fig. 6

Expression profile of phytohormone signaling genes among various tissues. Schematic representation of hormonal pathways genes by heat map based on log₂(FPKM). Red, green and grey coloured squares indicate high, low and zero levels of gene expression respectively (Color figure online)

Fig. 7

Expression profile of cell wall related genes among various tissues. Schematic representation cell cycle and cell wall related transcripts by heatmap based on log₂(FPKM). Red, green and gray colour squares indicates high, low and zero levels of gene expression respectively (Color figure online)

Fig. 8

Real time PCR validation of randomly selected root-expressed genes among various tissues. The expression data were normalized with reference gene SlCAC. Error bars represent ± SE (n = 3). The expression data were analyzed and compared by one-way ANOVA and Duncan’s Multiple Range Test (DMRT) respectively. The statistically significant differences in expression level were indicated by different letters