Abstract
Main conclusionGenome-wide identification, classification, expression analyses, and functional characterization of GRAS genes in oil crop, Brassica napus, indicate their importance in root development and stress response.GRAS proteins are a plant-specific transcription factor gene family involved in tissues development and stress response. We classified 87 putative GRAS genes in the Brassica napus genome (BnGRASs) into 13 subfamilies by phylogenetic analysis. The C-terminal GRAS domains of Brassica napus (B. napus) proteins were less conserved among subfamilies, but were conserved within each subfamily. A series of analyses revealed that 89.7% of the BnGRASs did not have intron insertions, and 24 specific-motifs were found at the N-terminal. A highly conserved microRNA 171 (miRNA171) target was observed specifically in the HAM subfamily across land plants. A total of 868 pairs of interaction proteins were predicted, the primary of which were transcription factors involved in transcriptional regulation and signal transduction. Integrated comparative analysis of GRAS genes across 26 species of algae, mosses, ferns, gymnosperms, and angiosperms revealed that this gene family originated in early mosses and was classified into 19 subfamilies, 14 of which may have originated prior to bryophyte evolution. RNA-Seq analysis demonstrated that most BnGRASs were widely expressed in different tissues/organs at different stages in B. napus, and 24 BnGRASs were highly/specifically expressed in roots. Results from a qRT-PCR analysis suggested that two BnGRASs belonging to SCR and LISCL subfamilies potentially have important roles in the stress response of roots.
Highlights
GRAS proteins are an important family of transcription factors (TF) in plants (Silverstone et al 1998)
Given that B. napus was hybridised by B. rapa and B. oleracea about 7500 years ago, these results suggest that genomic heterogeneous doubling was the main driving force for the large expansion of GRAS genes in B. napus genome, which tended to retain the genes from B. rapa
Our results showed that the BnGRAS86 and BnGRAS25 obviously respond to drought and salt stress, suggesting that they may be good genes for analyzing the mechanisms of GRAS gene regulation of B. napus abiotic stress response
Summary
GRAS proteins are an important family of transcription factors (TF) in plants (Silverstone et al 1998). GRAS transcription factor functions vary and include microspore and root development (Morohashi et al 2003), signal transduction (Bolle et al 2000), stem cell maintenance (Stuurman et al 2002; Li et al 2003), and stress response. Genome-wide analyses in a range of plants, such as Chinese cabbage (Brassica rapa), tomato (Solanum lycopersicum), and woad (Isatis indigotica) (Song et al 2014; Huang et al 2015; Zhang et al 2016), have generally divided the GRAS gene family into eight subfamilies: DELLA, SCARECROW (SCR), LATERAL SUPPRESSOR (LS), HAIRY MERISTEM (HAM), phytochrome A signal transduction 1 (PAT1), SCL4/7, SHORT-ROOT (SHR), and SCARECROW-LIKE9 (SCL9) (Lee et al 2008; Guo et al 2017). The classification of this gene family is not yet uniform
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