Strigolactone insensitivity affects differential shoot and root transcriptome in barley

Abstract

Strigolactones (SLs) are plant hormones that play a crucial role in regulating various aspects of plant architecture, such as shoot and root branching. However, the knowledge of SL-responsive genes and transcription factors (TFs) that control the shaping of plant architecture remains elusive. Here, transcriptomic analysis was conducted using the SL-insensitive barley mutant hvd14.d (carried mutation in SL receptor DWARF14, HvD14) and its wild-type (WT) to unravel the differences in gene expression separately in root and shoot tissues. This approach enabled us to select more than six thousand SL-dependent genes that were exclusive to each studied organ or not tissue-specific. The data obtained, along with in silico analyses, found several TFs that exhibited changed expression between the analyzed genotypes and that recognized binding sites in promoters of other identified differentially expressed genes (DEGs). In total, 28 TFs that recognize motifs over-represented in DEG promoters were identified. Moreover, nearly half of the identified TFs were connected in a single network of known and predicted interactions, highlighting the complexity and multidimensionality of SL-related signalling in barley. Finally, the SL control on the expression of one of the identified TFs in HvD14- and dose-dependent manners was proved. Obtained results bring us closer to understanding the signalling pathways regulating SL-dependent plant development.

Keywords: Hordeum vulgare; Barley; DWARF14; Root; Shoot; Strigolactones; Transcriptome.

Fig. 1

The phenotype of 3-week-old seedlings of Sebastian (wild-type) and hvd14.d (SL-insensitive mutant). A Differences in root and shoot between both genotypes. B Mutant hvd14.d exhibited a semi-dwarf phenotype and C produced significantly higher tillers than Sebastian. D Despite the shorter seminal roots of hvd14.d, the E total root length of both genotypes is similar. F Mutant hvd14.d developed more lateral roots than Sebastian, but G the length of lateral roots in both genotypes is similar. Asterisks indicate statistically significant differences between samples in a paired Student’s t-test (***correspond to p-values of p < 0.001; white arrows indicate tillers). LRs, lateral roots

Fig. 2

Overview of differentially expressed genes (DEGs) identified in shoot and root tissues when compared SL-insensitive barley mutant hvd14.d and its parent variety Sebastian (wild-type). SL_C—SL-related common genes; SL_S—SL-specific shoot DEGs; SL_R—SL-specific root DEGs

Fig. 3

Protein-network analysis of SL-dependent TFs, performed using STRING Database. A Three networks of SL-dependent TFs of known or predicted interactions were identified. B Gene ontology enrichment analyses revealed the biological processes in which identified SL-dependent TFs might be involved; fdr, false discovery rate. Protein-protein interactions are presented as known interactions (experimentally determined: pink lines; from curated databases: light-blue line); predicted interactions (based on: gene co-occurrence: dark-blue; gene neighbourhood: dark-green), based on the co-expression (black) or text mining (light-green)

Fig. 4

Analysis of HORVU.MOREX.r2.1HG0041130 gene expression in tissues of 2-week-old seedlings of Sebastian and hvd14.d plants in response to GR24 treatment. A Relative level of expression of the HORVU.MOREX.r2.1HG0041130 gene in control (non-treated) plants B 30 min, C 1 h, and D 3 h after treatment with 1 plant treated with mock (0.01% acetone), 1 µM and 10 µM of GR24^5DS. Statistical analyses were performed using the t-test (*p < .05; **p < .01; ***p < .001) comparing A hvd14.d vs Sebastian or SL-treated vs mock-treated plants. Mean value with standard deviation were presented