Comparative transcriptome and flavonoids components analysis reveal the structural genes responsible for the yellow seed coat color of Brassica rapa L.
Background Seed coat color is an important horticultural trait in Brassica crops, which is divided into two categories: brown/black and yellow. Seeds with yellow seed coat color have higher oil quality, higher protein content and lower fiber content. Yellow seed coat color is therefore considered a...
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PeerJ Inc.
2021-03-01
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| author | Yanjing Ren Ning Zhang Ru Li Xiaomin Ma Lugang Zhang |
| author_facet | Yanjing Ren Ning Zhang Ru Li Xiaomin Ma Lugang Zhang |
| author_sort | Yanjing Ren |
| collection | DOAJ |
| description | Background Seed coat color is an important horticultural trait in Brassica crops, which is divided into two categories: brown/black and yellow. Seeds with yellow seed coat color have higher oil quality, higher protein content and lower fiber content. Yellow seed coat color is therefore considered a desirable trait in hybrid breeding of Brassica rapa, Brassica juncea and Brassica napus. Methods Comprehensive analysis of the abundance transcripts for seed coat color at three development stages by RNA-sequencing (RNA-seq) and corresponding flavonoids compounds by liquid chromatography-tandem mass spectrometry (LC-MS/MS) were carried out in B. rapa. Results We identified 41,286 unigenes with 4,989 differentially expressed genes between brown seeds (B147) and yellow seeds (B80) at the same development stage. Kyoto Encyclopedia of Genes and Genomes enrichment analysis identified 19 unigenes associated with the phenylpropanoid, flavonoid, flavone and flavonol biosynthetic pathways as involved in seed coat color formation. Interestingly, expression levels of early biosynthetic genes (BrCHS, BrCHI, BrF3H, BrF3’H and BrFLS) in the flavonoid biosynthetic pathway were down-regulated while late biosynthetic genes (BrDFR, BrLDOX and BrBAN) were hardly or not expressed in seeds of B80. At the same time, BrTT8 and BrMYB5 were down-regulated in B80. Results of LC-MS also showed that epicatechin was not detected in seeds of B80. We validated the accuracy of our RNA-seq data by RT-qPCR of nine critical genes. Epicatechin was not detected in seeds of B80 by LC-MS/MS. Conclusions The expression levels of flavonoid biosynthetic pathway genes and the relative content of flavonoid biosynthetic pathway metabolites clearly explained yellow seed color formation in B. rapa. This study provides a foundation for further research on the molecular mechanism of seed coat color formation. |
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| spelling | doaj.art-0ee2fc6ecd5d4e8291a8fa5a5e4148292023-12-03T00:40:49ZengPeerJ Inc.PeerJ2167-83592021-03-019e1077010.7717/peerj.10770Comparative transcriptome and flavonoids components analysis reveal the structural genes responsible for the yellow seed coat color of Brassica rapa L.Yanjing Ren0Ning Zhang1Ru Li2Xiaomin Ma3Lugang Zhang4Academy of Agriculture and Forestry Sciences, Qinghai University, Xining, ChinaState Key Laboratory of Crop Stress Biology for Arid Area, Northwest A&F University, Yangling, ChinaState Key Laboratory of Crop Stress Biology for Arid Area, Northwest A&F University, Yangling, ChinaState Key Laboratory of Crop Stress Biology for Arid Area, Northwest A&F University, Yangling, ChinaState Key Laboratory of Crop Stress Biology for Arid Area, Northwest A&F University, Yangling, ChinaBackground Seed coat color is an important horticultural trait in Brassica crops, which is divided into two categories: brown/black and yellow. Seeds with yellow seed coat color have higher oil quality, higher protein content and lower fiber content. Yellow seed coat color is therefore considered a desirable trait in hybrid breeding of Brassica rapa, Brassica juncea and Brassica napus. Methods Comprehensive analysis of the abundance transcripts for seed coat color at three development stages by RNA-sequencing (RNA-seq) and corresponding flavonoids compounds by liquid chromatography-tandem mass spectrometry (LC-MS/MS) were carried out in B. rapa. Results We identified 41,286 unigenes with 4,989 differentially expressed genes between brown seeds (B147) and yellow seeds (B80) at the same development stage. Kyoto Encyclopedia of Genes and Genomes enrichment analysis identified 19 unigenes associated with the phenylpropanoid, flavonoid, flavone and flavonol biosynthetic pathways as involved in seed coat color formation. Interestingly, expression levels of early biosynthetic genes (BrCHS, BrCHI, BrF3H, BrF3’H and BrFLS) in the flavonoid biosynthetic pathway were down-regulated while late biosynthetic genes (BrDFR, BrLDOX and BrBAN) were hardly or not expressed in seeds of B80. At the same time, BrTT8 and BrMYB5 were down-regulated in B80. Results of LC-MS also showed that epicatechin was not detected in seeds of B80. We validated the accuracy of our RNA-seq data by RT-qPCR of nine critical genes. Epicatechin was not detected in seeds of B80 by LC-MS/MS. Conclusions The expression levels of flavonoid biosynthetic pathway genes and the relative content of flavonoid biosynthetic pathway metabolites clearly explained yellow seed color formation in B. rapa. This study provides a foundation for further research on the molecular mechanism of seed coat color formation.https://peerj.com/articles/10770.pdfBrassica rapaTranscriptomeLC-MS/MSSeed coat colorFlavonoid biosynthesis pathway |
| spellingShingle | Yanjing Ren Ning Zhang Ru Li Xiaomin Ma Lugang Zhang Comparative transcriptome and flavonoids components analysis reveal the structural genes responsible for the yellow seed coat color of Brassica rapa L. PeerJ Brassica rapa Transcriptome LC-MS/MS Seed coat color Flavonoid biosynthesis pathway |
| title | Comparative transcriptome and flavonoids components analysis reveal the structural genes responsible for the yellow seed coat color of Brassica rapa L. |
| title_full | Comparative transcriptome and flavonoids components analysis reveal the structural genes responsible for the yellow seed coat color of Brassica rapa L. |
| title_fullStr | Comparative transcriptome and flavonoids components analysis reveal the structural genes responsible for the yellow seed coat color of Brassica rapa L. |
| title_full_unstemmed | Comparative transcriptome and flavonoids components analysis reveal the structural genes responsible for the yellow seed coat color of Brassica rapa L. |
| title_short | Comparative transcriptome and flavonoids components analysis reveal the structural genes responsible for the yellow seed coat color of Brassica rapa L. |
| title_sort | comparative transcriptome and flavonoids components analysis reveal the structural genes responsible for the yellow seed coat color of brassica rapa l |
| topic | Brassica rapa Transcriptome LC-MS/MS Seed coat color Flavonoid biosynthesis pathway |
| url | https://peerj.com/articles/10770.pdf |
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