Functional characterization of a novel Brassica LEAFY homolog from Indian mustard: Expression pattern and gain-of-function studies

Clone and Function Verification of the OPR gene in Brassica napus Related to Linoleic Acid Synthesis

BACKGROUND

Fatty acid composition and content affect rapeseed oil quality. Fatty acid synthesis-related genes in rapeseed have been studied globally by researchers. Nevertheless, rapeseed oil is mainly composed of seven different fatty acids (FA), and each fatty acid was regulated by different genes. Furthermore, different FA affect each other, which needs continuous and in-depth research to obtain more clear results in Brassica napus.

RESULTS

In this paper, broad-scale miRNA expression profiles were constructed and 21 differentially expressed miRNAs were detected. GO enrichment analysis showed that most up-regulated proteins were involved in transcription factor activity and catalytic activity. KEGG pathway enrichment analysis indicated that 20 pathways involving 36 target genes were enriched, of which the bna00592 pathway may be involved in fatty acid metabolism. The results were verified using a quantitative real-time PCR (RT-qPCR) analysis, we found that the target gene of bna-miR156b > c > g was the OPR (12-oxo-phytodienoic acid reductase). Four copies of OPR gene were found, and the over-expression vectors (pCAMBIA1300-35 s-OPR and pCAMBIA1300-RNAi-OPR) were constructed to verify their functions. In T1 and T2 generation, the content of linoleic acid (LA) increased significantly in OE but deceased in OPRi.

CONCLUSIONS

This is the first study to provide four copies of the OPR gene that regulates LA metabolism, can be used for the molecular mechanism of LA and optimizing fatty acid profiles in oilseed for breeding programs.

Homeologs of Brassica SOC1, a central regulator of flowering time, are differentially regulated due to partitioning of evolutionarily conserved transcription factor binding sites in promoters

Evolution of Brassica genome post-polyploidization reveals asymmetrical genome fractionation and copy number variation. Herein, we describe the impact of promoter divergence among SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1) homeologs on expression and function in Brassica spp. SOC1, a regulated floral pathway integrator, is conserved as 3 redundant homeologs in diploid Brassicas. Even with high sequence identity within coding regions (92.8-100%), the spatio-temporal expression patterns of 9 SOC1 homologs in B. juncea and B. nigra indicates regulatory divergence. While LF and MF2 SOC1 homeologs are upregulated during floral transition, MF1 is barely expressed. Also, MF2 homeolog levels do not decline post-flowering, unlike LF. To investigate the underlying source of divergence, we analyzed the sequence and phylogeny of all reported (22) and isolated (21) upstream regions of Brassica SOC1. Full length upstream regions (4712-19189 bp) reveal 5 ubiquitously conserved ancestral Blocks, harboring binding sites of 18 TFs (TFBSs) characterized in Arabidopsis thaliana. The orthologs of these TFBSs are differentially conserved among Brassica SOC1 homeologs, imparting expression divergence. No crucial TFBSs are exclusively lost from LF_SOC1 promoter, while MF1_SOC1 has lost NF-Y binding site crucial for SOC1 activation by CONSTANS. MF2_SOC1 homeologs have lost important TFBSs (SEP3, AP1 and SMZ), responsible for SOC1 repression post-flowering. BjuAALF_SOC1 promoter (proximal 2 kb) shows ubiquitous reporter expression in B. juncea cv. Varuna transgenics, while BjuAAMF1_SOC1 promoter shows absence of reporter expression, validating the impact of TFBS divergence. Conservation of the original primary protein sequence is discovered in B. rapa homeologs (46) of 18 TFs. Co-regulation pattern of these TFs appeared similar for B. rapa LF and MF2 SOC1 homeologs; MF1 shows significant variation. Strong regulatory association is recorded for AP1, AP2, SEP3, FLC and CONSTANS/NF-Y, highlighting their importance in homeolog-specific SOC1 regulation. Correlation of B. juncea AP1, AP2 and FLC expression with SOC1 homeologs also complies with the TFBS differences. We thus conclude that redundant SOC1 loci contribute differentially to cumulative expression of SOC1 due to divergent selection of ancestral TFBSs.

Transcriptome and digital gene expression analysis unravels the novel mechanism of early flowering in Angelica sinensis

Angelica sinensis (Oliv.) Diels is a widely used medicinal plant mainly originated in Gansu, China. Angelica sinensis is greatly demanded in the clinical practice of Chinese medicine due to its broad pharmacological activities of hematopoietic and anti-inflammatory properties. But, the percentage of early flowering in Angelica sinensis arrives to 20%~30%, which severely affects its quality and quantity. Here, transcriptome profiling and digital gene expression analysis were applied to study the mechanism of early flowering in Angelica sinensis. A total of 49,183,534 clean reads were obtained and assembled into 68,262 unigenes, and 49,477 unigenes (72.5%) could be annotated to a minimum of one database in the Nr, Nt, Swiss-Pro, GO, COG and KEGG. Taking the above transcriptome data as a reference, digital gene expression result showed that 5,094 genes expression level were significant changed during early flowering. These annotated genes offered much information promoting that the biosynthesis of secondary metabolites pathway, the hormone signal transduction pathway, and the transcription regulation system may be closely related to the early flowering phenomenon of Angelica sinensis. Further expression patterns of key genes contribute to early flowering were analyzed using quantitative real-time PCR. The transcriptome result offered important gene expression information about early flowering in Angelica sinensis.

Natural variation in Brassica FT homeologs influences multiple agronomic traits including flowering time, silique shape, oil profile, stomatal morphology and plant height in B. juncea

Natural structural variants of regulatory proteins causing quantitative phenotypic consequences have not been reported in plants. Herein, we show that 28 natural structural variants of FT homeologs, isolated from 6 species of Brassica, differ with respect to amino-acid substitutions in regions critical for interactions with FD and represent two evolutionarily distinct categories. Analysis of structural models of selected candidates from Brassica juncea (BjuFT_AAMF1) and Brassica napus (BnaFT_CCLF) predicted stronger binding between BjuFT and Arabidopsis thaliana FD. Over-expression of BjuFT and BnaFT in wild type and ft-10 mutant backgrounds of Arabidopsis validated higher potency of BjuFT in triggering floral transition. Analysis of gain-of-function and artificial miRNA mediated silenced lines of B. juncea implicated Brassica FT in multiple agronomic traits beyond flowering, consistent with a pleiotropic effect. Several dependent and independent traits such as lateral branching, silique shape, seed size, oil-profile, stomatal morphology and plant height were found altered in mutant lines. Enhanced FT levels caused early flowering, which in turn was positively correlated to a higher proportion of desirable fatty acids (PUFA). However, higher FT levels also resulted in altered silique shape and reduced seed size, suggesting trait trade-offs. Modulation of FT levels for achieving optimal balance of trait values and parsing pair-wise interactions among a reportoire of regulatory protein homeologs in polyploid genomes are indeed future areas of crop research.

Highly preserved roles of Brassica MIR172 in polyploid Brassicas: ectopic expression of variants of Brassica MIR172 accelerates floral transition

Functional characterization of regulatory genes governing flowering time is a research priority for breeding earliness in crop Brassicas. Highly polyploid genomes of Brassicas pose challenges in unraveling homeolog gene function. In Arabidopsis, five MIR172 paralogs control flowering time and floral organ identity by down-regulating AP2 and AP2-like genes. The impact of homeolog diversification on MIR172 loci, however, needs to be examined in morphologically diverse Brassicas. Herein, we analyze fractionation status and phylogeny of MIR172 and target AP2 from Brassicas and compare functionality of MIR172 variants representing distinct sub-genomes and progenitor genomes. Copy number analysis revealed higher retention of MIR172 loci relative to AP2 in diploid and amphi-diploid Brassica species. Dendrogram of 87 MIR172 sequences from Brassicaceae showed five major clusters corresponding to MIR172a-MIR172e which further separated into sub-genome and progenitor genome specific clades. Similar groupings were observed in the phylogeny of 11 Brassica AP2 and AP2-like genes. Over-expression of a pair of natural variants for each of MIR172b, MIR172d and MIR172e representing sub-genomes, progenitor genomes and species of Brassicas displayed floral acceleration in all transgenic lines indicating a strong selection pressure on MIR172. All gain-of-function lines, except 35S::MIR172e and 35S::MIR172e' displayed floral organ defects implying altered target spectrum of MIR172e relative to MIR172b and MIR172d. Expression of MIR172e caused marginal earliness in flowering time in B. juncea. In conclusion, this study demonstrates tightly preserved role of homeologs and natural variants of MIR172 family in mediating flowering in Brassicas and suggests their deployment for introgression of early flowering trait.