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. 2024 Dec 10:15:1483635.
doi: 10.3389/fpls.2024.1483635. eCollection 2024.

Evolution and comparative transcriptome analysis of glucosinolate pathway genes in Brassica napus L

Shiying Liu  1   2 , Zexuan Wu  1   2 , Xingying Chen  1   2 , Zhuo Chen  1   2 , Yibing Shen  1   2 , Salman Qadir  1   2 , Huafang Wan  1   2 , Huiyan Zhao  1   2 , Nengwen Yin  1   2 , Jiana Li  1   2 , Cunmin Qu  1   2 , Hai Du  1   2
Affiliations

Evolution and comparative transcriptome analysis of glucosinolate pathway genes in Brassica napus L

Shiying Liu et al. Front Plant Sci. .

Abstract

Glucosinolates (GSLs) are important secondary metabolites abundantly distributed in Brassicaceae plants, whose degradation products benefit plant resistance but are regarded as disadvantageous factors for human health. Thus, reducing GSL content is an important goal in the breeding program in crops, such as Brassica napus. In this study, 1280 genes in the GSL pathway were identified from 14 land plant genomes, which are specifically distributed in Brassicaceae and are extensively expanded in B. napus. Most GSL pathway genes had many positive selection sites, especially the encoding genes of transcription factors (TFs) and structural genes involved in the GSL breakdown process. There are 344 genes in the GSL pathway in the B. napus genome, which are unequally distributed on the 19 chromosomes. Whole-genome duplication mainly contributed to the gene expansion of the GSL pathway in B. napus. The genes in GSL biosynthesis were regulated by various TFs and cis-elements in B. napus and mainly response to abiotic stress and hormone induction. A comparative transcriptome atlas of the roots, stems, leaves, flowers, siliques, and seeds of a high- (ZY821), and a low-GSL-content (ZS11) cultivar was constructed. The features of the two cultivars may be attributed to diverse expression differences in each organ at different stages, especially in seeds. In all, 65 differential expressed genes (DEGs) concentrated on the core structure pathway were inferred to mainly influence the GSL contents between ZY821 and ZS11. This study provides an important RNA-seq dataset and diverse gene resources for future manipulating GSLs biosynthesis and distribution in B. napus using molecular breeding methods.

Keywords: Brassica napus; evolution; glucosinolate; pathway; transcriptome.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
The distribution of glucosinolates (GSL) pathway genes in 14 representative land plants.
Figure 2
Figure 2
The chromosomal locations of GSL pathway genes in B. napus. (A) Chromosome positions of the 344 GSL pathway genes in B. napus. (B) The number of GSL pathway genes on each chromosome. Different colors represent the four major processes in GSL pathway. (C) The ratio of GSL pathway genes underwent different duplication events. HE, homologous exchange; SD, segmental duplication; SE, segmental exchange; TD, tandem duplication; WGD, whole genome duplication.
Figure 3
Figure 3
Cis-acting regulatory elements (CREs) and transcription factor (TF) binding site analysis in promoters of GSL pathway genes. (A) The TF gene families with potential binding sites in the promoter regions of GSL pathway genes. (B) The distribution of TF gene families with potential sites in the promoter regions of the four processes of GSL pathway. (C) The cis-elements related to hormone responsiveness in the promoter regions of GSL pathway genes. (D) The cis-elements related to stress responses in the promoter regions of GSL pathway genes. The X-axis represents the gene number.
Figure 4
Figure 4
Transcriptome analysis of Zhongshuang 11 (ZS11) and Zhongyou 821 (ZY821) at different developmental stages. (A) The samples of rapeseed Zhongshuang11 (ZS11) and Zhongyou 821 (ZY821) varieties used in spatio-temporal transcriptome. These samples include root (Ro), leaf (Le), stem (St), flower (Fl), silique (Si), and seed (Se), which harvested from seedling (S), bud (B), full-bloom (F), and seed developmental stages covering the entire life cycle of ZS11 and ZY821 respectively. DAF, days after flowering. (B) and (C) Principal component analysis (PCA) based on the expression profile of ZS11 and ZY821 respectively. (D) Gene expression grading for each sample of ZS11 and ZY821 varieties. LEG: low expression gene (FPKM<1), MEG: middle expression gene(1<fpkm10). The Y-axis represents the gene number. (E) Differentially expressed gene (DEG) of ZS11 and ZY821 (up indicates the expression in ZY821 is higher than in ZS11; down represent the expression in ZS11 is higher than in ZY821). (F) The k means clustering analysis of DEGs. (G) The KEGG pathway enrichment of 15 co-expression modules.
Figure 5
Figure 5
The DEGs between ZY821 and ZS11 in the AGSL and IGSL pathways. Pink box represents the DEGs have higher expression levels in ZY821 than in ZS11; Green box represents the expression levels of the DEGs in ZS11 higher than in ZY821; Gray box represents these with similar expression value in ZS11 and ZY821.
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