Genome-wide analysis and functional characterization of the DELLA gene family associated with stress tolerance in B. napus

Abstract

Background: Brassica napus is an essential crop for oil and livestock feed. Eventually, this crop's economic interest is at the most risk due to anthropogenic climate change. DELLA proteins constitute a significant repressor of plant growth to facilitate survival under constant stress conditions. DELLA proteins lack DNA binding domain but can interact with various transcription factors or transcription regulators of different hormonal families. Significant progress has been made on Arabidopsis and cereal plants. However, no comprehensive study regarding DELLA proteins has been delineated in rapeseed.

Results: In our study, we have identified 10 BnaDELLA genes. All of the BnaDELLA genes are closely related to five AtDELLA genes, suggesting a relative function and structure. Gene duplication and synteny relationship among Brassica. napus, Arabidopsis. thaliana, Brassica rapa, Brassica oleracea, and Brassica nigra genomes were also predicted to provide valuable insights into the BnaDELLA gene family evolutionary characteristics. Chromosomal mapping revealed the uneven distribution of BnaDELLA genes on eight chromosomes, and site-specific selection assessment proposes BnaDELLA genes purifying selection. The motifs composition in all BnaDELLA genes is inconsistent; however, every BnaDELLA gene contains 12 highly conserved motifs, encoding DELLA and GRAS domains. The two known miRNAs (bna-miR6029 and bna-miR603) targets BnaC07RGA and BnaA09GAI, were also predicted. Furthermore, quantitative real-time PCR (qRT-PCR) analysis has exhibited the BnaDELLA genes diverse expression patterns in the root, mature-silique, leaf, flower, flower-bud, stem, shoot-apex, and seed. Additionally, cis-acting element prediction shows that all BnaDELLA genes contain light, stress, and hormone-responsive elements on their promoters. The gene ontology (GO) enrichment report indicated that the BnaDELLA gene family might regulate stress responses. Combine with transcriptomic data used in this study, we detected the distinct expression patterns of BnaDELLA genes under biotic and abiotic stresses.

Conclusion: In this study, we investigate evolution feature, genomic structure, miRNAs targets, and expression pattern of the BnaDELLA gene family in B. napus, which enrich our understanding of BnaDELLA genes in B. napus and suggests modulating individual BnaDELLA expression is a promising way to intensify rapeseed stress tolerance and harvest index.

Keywords: Abiotic stress; Brassica napus; DELLA; Genome-wide; Gibberellins.

Fig. 1

The cladogram of DELLA proteins from A. thaliana (At:5), B. napus (Bna: 10), B. rapa (Bra: 5), B. oleracea (Bol: 4), B. juncea (Bju: 9), and B. nigra (Bni: 4) were conducted in MEGA X [86] using the neighbor-joining method, missing data with gaps were eliminated by complete deletion option. The DELLA proteins are cluster into three groups, which are indicated by the different colors. The bootstrap test (1000 replicates) is shown next to the branches

Fig. 2

Exon and intron location of the BnaDELLAs. Blue double-sided wedge represents exon, and upstream/downstream regions are indicated as cyan-colored boxes. The scale can estimate the length of the exon at base

Fig. 3

The length of the 20 motifs ranged from 6 to 50 amino acid residues and represented by different colors and numbers, p- values of the motifs on each protein is less than 1e⁻⁵

Fig. 4

Schematic representation of DELLA genes distribution on B. napus chromosomes. Chromosome number is indicated on the side of each chromosome

Fig. 5

Synteny analysis of the BnaDELLA family in B. napus. Cyan-colored line genes belong to Group I, and green-colored line genes belong to group II, yellow-colored line genes belong to Group III. These colored genes lines indicate duplicated BnaDELLA gene pairs, while gray lines in the background represent synteny blocks in the B. napus genome. The distribution density of BnaDELLAs present at the bottom of each chromosome

Fig. 6

Synteny analysis of BnaDELLAs between A. thaliana, B. rapa, B. oleracea, and B. nigra. Black lines indicate the syntenic DELLA gene pairs between denoted species. While in the background, gray line represents collinear blocks

Fig. 7

cis-acting element prediction in the BnaDELLAs. A The values in the circle indicated the count of cis-acting element in the promoter of BnaDELLAs; B The different colored block lines represent the different types and positions of cis-acting elements in each BnaDELLA gene

Fig. 8

qRT-PCR analysis of the selected BnaDELLAs expression in different organs. The relative abundance of the selected BnaDELLAs was normalized with respect to the reference gene (Actin). The x-axis corresponds to different organs. Values on the y axis are denoted as the mean ± SD of three biological replicates (listed in Table S5.2). Asterias on vertical bar shows significant difference at * P < 0.05, ** P < 0.01, *** P < 0.001

Fig. 9

Heatmap of the expression profile of BnaDELLAs under different abiotic and biotic conditions including, MA (Cold shock at chilling 4 °C and freezing − 4 °C temperatures), CA (4 degree Celsius 12 h following cold acclimation 14 days 4 degree Celsius), FA (-4 degree Celsius 12 h following cold acclimation 14 days 4 degree Celsius), DT (Drought treated), HT (Heat treatment), ABA, salinity, and Sclerotinia sclerotiorum. The color scale reflects the data of the expression being processed with normalization of log2 (listed in Table S7), and different colors denote different expression levels