Dataset Information

Transcriptomic profiling of two Pak Choi varieties with contrasting anthocyanin contents provides an insight into structural and regulatory genes in anthocyanin biosynthetic pathway.

ABSTRACT:

Background

The accumulation of anthocyanin in horticultural crops not only improves their stress tolerances but also their nutritional values. Many key regulatory and structural genes in anthocyanin biosynthesis have been identified in model plants, but limited information is available for non-model plant species featured with colored leaves. In this study, two Pak Choi varieties with green or purple leaves were selected to analyze the anthocyanin biosynthesis through RNA-Seq.

Results

A total of 2475 unigenes were differentially expressed between these tested varieties, including 1303 down-regulated and 1172 up-regulated genes in the purple-leafed one. The reliability of the RNA-Seq was further confirmed by using real-time quantitative PCR. Kyoto Encyclopedia of Genes and Genomes enrichment analysis of the differentially expressed genes revealed 'flavonoid biosynthesis' was the only enriched pathway in the purple-leafed variety: In the pathway of phenylpropanoid metabolism, Bra017210, Bra039777, and Bra021637 were expressed at higher levels in the purple-leafed variety;?among the early anthocyanin biosynthetic genes, Bra037747 transcripts were only detected in the purple-leafed variety but not in the green-leafed one; among the late anthocyanin biosynthetic genes, Bra027457, Bra013652, Bra019350, Bra003021, Bra035004, and Bra038445 were all up-regulated in purple-leafed variety; and genes encoding anthocyanin-related transcription factors, such as Bra016164, and genes encoding anthocyanin transportation, such as GST F12, were also identified as up-regulated ones in the purple-leafed variety.

Conclusions

The current result provided a valuable insight into the anthocyanin accumulation in the purple-leafed variety of Pak Choi and a bioinformatic resource for further functional identification of key allelic genes determining the difference of anthocyanin content between Pak Choi varieties.

SUBMITTER: Zhang L

PROVIDER: S-EPMC5387373 | biostudies-literature | 2017 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Transcriptomic profiling of two Pak Choi varieties with contrasting anthocyanin contents provides an insight into structural and regulatory genes in anthocyanin biosynthetic pathway.

Zhang Lu L Xu Bin B Wu Tao T Yang Yanfang Y Fan Lianxue L Wen Muxuan M Sui Jiaxin J

BMC genomics 20170411 1

<h4>Background</h4>The accumulation of anthocyanin in horticultural crops not only improves their stress tolerances but also their nutritional values. Many key regulatory and structural genes in anthocyanin biosynthesis have been identified in model plants, but limited information is available for non-model plant species featured with colored leaves. In this study, two Pak Choi varieties with green or purple leaves were selected to analyze the anthocyanin biosynthesis through RNA-Seq.<h4>Results ...[more]

PMID: 28399809

Similar Datasets

Project description:Lonicera japonica Thunb., belonging to the Caprifoliaceae family, is an important traditional Chinese medicinal plant. The L. japonica flower (LJF) is widely used in medicine, cosmetics, drinks, and food due to its medicinal and sweet-smelling properties. Considerable efforts have been devoted to investigating the pharmacological activities of LJF; however, the regulatory mechanism of the floral scents remains unknown. We previously selected and bred an elite variety of L. japonica var. chinensis Thunb. called 'Yujin2', which has a strong aroma and is used in functional drinks and cosmetics. In order to reveal the regulatory mechanism of the floral scents of LJF, volatile metabolomic and transcriptomic analyses of the LJF at the silver flowering stage of 'Yujin2' (strong aroma) and 'Fengjin1' (bland odor) were performed. Our results revealed that a total of 153 metabolites and 9,523 genes were differentially regulated in LJF between 'Yujin2' and 'Fengjin1'. The integrated analysis of omics data indicated that the biosynthetic pathways of terpenoids (i.e., monoterpenoids, including geraniol and alpha-terpineol; sesquiterpenoids, including farnesol, farnesal, and alpha-farnesene; triterpenoid squalene), tryptophan and its derivatives (methyl anthranilate), and fatty acid derivatives, were major contributors to the stronger aroma of 'Yujin2' compared to 'Fengjin1'. Moreover, several genes involved in the terpenoid biosynthetic pathway were characterized using quantitative real-time PCR. These results provide insights into the metabolic mechanisms and molecular basis of floral scents in LJF, enabling future screening of genes related to the floral scent regulation, such as alpha-terpineol synthase, geranylgeranyl diphosphate synthase, farnesyl pyrophosphate synthase, anthranilate synthase, as well as transcription factors such as MYB, WRKY, and LFY. The knowledge from this study will facilitate the breeding of quality-improved and more fragrant variety of L. japonica for ornamental purpose and functional beverages and cosmetics.

Project description:Purple Broccoli (Brassica oleracea L. var italica) attracts growing attention as a functional food. Its purple coloration is due to high anthocyanin amounts. Light represents a critical parameter affecting anthocyanins biosynthesis. In this study, 'Purple Broccoli', a light-responding pigmentation cultivar, was assessed for exploring the mechanism underlying light-induced anthocyanin biosynthesis by RNA-Seq. Cyanidin, delphinidin and malvidin derivatives were detected in broccoli head samples. Shading assays and RNA-seq analysis identified the flower head as more critical organ compared with leaves. Anthocyanin levels were assessed at 0, 7 and 11 days, respectively, with further valuation by RNA-seq under head-shading and light conditions. RNA sequences were de novo assembled into 50,329 unigenes, of which 38,701 were annotated against four public protein databases. Cluster analysis demonstrated that anthocyanin/phenylpropanoid biosynthesis, photosynthesis, and flavonoid biosynthesis in cluster 8 were the main metabolic pathways regulated by light and had showed associations with flower head growth. A total of 2,400 unigenes showed differential expression between the light and head-shading groups in cluster 8, including 650 co-expressed, 373 specifically expressed under shading conditions and 1,377 specifically expressed under normal light. Digital gene expression (DGE) analysis demonstrated that light perception and the signal transducers CRY3 and HY5 may control anthocyanin accumulation. Following shading, 15 structural genes involved in anthocyanin biosynthesis were downregulated, including PAL, C4H, 4CL, CHS, CHI, F3H and DFR. Moreover, six BoMYB genes (BoMYB6-1, BoMYB6-2, BoMYB6-3, BoMYB6-4, BoMYBL2-1 and BoMYBL2-2) and three BobHLH genes (BoTT8_5-1, BoTT8_5-2 and BoEGL5-3) were critical transcription factors controlling anthocyanin accumulation under light conditions. Based on these data, a light-associated anthocyanin biosynthesis pathway in Broccoli was proposed. This information could help improve broccoli properties, providing novel insights into the molecular mechanisms underpinning light-associated anthocyanin production in purple vegetables.

Dataset Information

Transcriptomic profiling of two Pak Choi varieties with contrasting anthocyanin contents provides an insight into structural and regulatory genes in anthocyanin biosynthetic pathway.

Background

Results

Conclusions

Publications

Transcriptomic profiling of two Pak Choi varieties with contrasting anthocyanin contents provides an insight into structural and regulatory genes in anthocyanin biosynthetic pathway.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets