, Volume 241, Issue 6, pp 1381–1394 | Cite as

Molecular characterization and transcriptome analysis of orange head Chinese cabbage (Brassica rapa L. ssp. pekinensis)

Original Article


Main conclusion

The orange head phenotype ofBr-orresulted from a large insertion in carotenoid isomerase (BrCRTISO) . Comparative transcriptome analysis revealed that the mutation affected the expression of abundant transcription factor genes. A new orange trait-specific marker was developed for marker-assisted breeding.

Orange head leaves are a desirable quality trait for Chinese cabbage. Our previous fine mapping identified BrCRTISO as the Br-or candidate gene for the orange Chinese cabbage mutant. Here, we examined the BrCRTISO gene from white and orange head Chinese cabbage. While BrCRTISO from the white control plant was able to complement the ArabidopsisAtcrtiso mutant phenotype, Brcrtiso with a large insertion from the orange head Chinese cabbage failed to rescue the Arabidopsis mutant phenotype. The results show that Brcrtiso was non-functional, concomitant with the accumulation of prolycopene in Br-or to yield orange head. Comparative transcriptome analysis by RNA-seq identified 372 differentially expressed genes between the control and Br-or mutant using two near-isogenic lines with white and orange inner leaves. The mutation in BrCRTISO specifically affected many genes in the functional groups involved in RNA, protein, transport, and signaling. Particularly, expressions of many transcription factor genes were dramatically altered in Br-or, suggesting a potential role of BrCRTISO or carotenoid metabolites in affecting transcription. A novel co-dominant gene-specific marker was developed that co-segregated with orange color phenotype and would be useful for marker-assisted selection with enhanced selection efficiency. Our study provides new insights into understanding of the molecular basis of Br-or in mediating head leaf color and depicts a global view of the effect of BrCRTISO on cellular processes in plant. It also provides a molecular tool to accelerate breeding new Chinese cabbage cultivars with unique health quality and visual appearance.


Chinese cabbage Orange head BrCRTISO Transcriptome Gene-specific marker 



Marker-assisted selection


Near-isogenic lines


Geranylgeranyl pyrophosphate


Phytoene synthase


Phytoene desaturase


ζ-Carotene desaturase


Carotenoid isomerase


Lycopene β-cyclase


Lycopene ε-cyclase


β-Carotene hydroxylase


ε-Carotene hydroxylase


Zeaxanthin epoxidase


Carotenoid cleavage dioxygenase


9-Cis-epoxycarotenoid dioxygenase

Supplementary material

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Supplementary material 1 (DOCX 828 kb)
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Supplementary material 2 (DOCX 16 kb)
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Supplementary material 3 (DOCX 33 kb)
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Supplementary material 4 (DOCX 21 kb)


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Copyright information

© Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  1. 1.College of Horticulture, State Key Laboratory of Crop Stress Biology for Arid AreaNorthwest A&F UniversityYanglingChina
  2. 2.Plant Breeding and Genetics Section, School of Integrative Plant ScienceCornell UniversityIthacaUSA
  3. 3.Boyce Thompson Institute for Plant ResearchCornell UniversityIthacaUSA
  4. 4.Australian Research Council Centre of Excellence in Plant Energy BiologyThe Australian National UniversityCanberraAustralia
  5. 5.Robert W. Holley Center for Agriculture and Health, USDA-ARSCornell UniversityIthacaUSA

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