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

Publisher: Springer-Verlag [etc.] Country of Publication: Germany NLM ID: 1250576 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1432-2048 (Electronic) Linking ISSN: 00320935 NLM ISO Abbreviation: Planta Subsets: MEDLINE

Original Publication: Berlin, New York, Springer-Verlag [etc.]

Gene Expression Regulation, Plant*; Brassica/*genetics ; Gene Expression Profiling/*methods ; Mutation/*genetics; Arabidopsis/genetics ; Base Sequence ; Breeding ; Carotenoids/metabolism ; Down-Regulation/genetics ; Genes, Plant ; Genetic Complementation Test ; Metabolic Networks and Pathways ; Molecular Sequence Data ; Phenotype ; Phylogeny ; Plant Leaves/genetics ; Plant Leaves/metabolism ; Plant Proteins/genetics ; Plant Proteins/metabolism ; Reproducibility of Results ; Sequence Analysis, RNA ; Up-Regulation/genetics

Main Conclusion: The orange head phenotype of Br - or resulted 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 Arabidopsis Atcrtiso 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.

Plant J. 2011 Apr;66(1):212-29. (PMID: 21443633)
BMC Genomics. 2009 Nov 18;10:540. (PMID: 19922663)
Plant Cell. 2014 Feb;26(2):585-601. (PMID: 24510723)
Planta. 2014 Nov;240(5):1063-74. (PMID: 25139277)
Plant J. 2004 Mar;37(6):914-39. (PMID: 14996223)
Nat Genet. 2011 Aug 28;43(10):1035-9. (PMID: 21873998)
Arch Biochem Biophys. 2013 Nov 15;539(2):102-9. (PMID: 23851381)
Plant Physiol. 2009 Jul;150(3):1611-8. (PMID: 19429606)
Genome Biol. 2010;11(10):R106. (PMID: 20979621)
Plant Cell. 2010 Aug;22(8):2660-79. (PMID: 20798329)
Bioinformatics. 2009 May 1;25(9):1105-11. (PMID: 19289445)
Science. 2012 Jun 29;336(6089):1711-5. (PMID: 22745430)
Mol Biol Evol. 2013 Dec;30(12):2725-9. (PMID: 24132122)
Plant Physiol. 2012 Aug;159(4):1511-23. (PMID: 22718775)
Plant Cell Physiol. 2001 May;42(5):462-8. (PMID: 11382811)
Trends Plant Sci. 2010 Oct;15(10):573-81. (PMID: 20674465)
Plant Cell. 2006 Dec;18(12):3594-605. (PMID: 17172359)
Annu Rev Plant Biol. 2006;57:405-30. (PMID: 16669768)
Plant Sci. 2013 Jul;208:58-63. (PMID: 23683930)
New Phytol. 2011 Apr;190(1):89-100. (PMID: 21175633)
Trends Plant Sci. 2010 May;15(5):247-58. (PMID: 20304701)
Proc Natl Acad Sci U S A. 2012 Nov 13;109(46):19021-6. (PMID: 23112190)
Gene. 2005 Jan 3;344:171-80. (PMID: 15656983)
Theor Appl Genet. 2014 Jan;127(1):179-91. (PMID: 24121567)
Cell Res. 2007 May;17(5):471-82. (PMID: 17486124)
Phytochemistry. 2007 Apr;68(8):1112-9. (PMID: 17391716)
Plant Physiol. 2007 Oct;145(2):389-401. (PMID: 17704236)
Plant Cell. 2014 Jun 6;26(6):2524-2537. (PMID: 24907342)
Mol Plant. 2015 Jan;8(1):68-82. (PMID: 25578273)
Proc Natl Acad Sci U S A. 2012 Apr 3;109(14):5535-40. (PMID: 22431637)
Plant Cell. 1999 Dec;11(12):2283-90. (PMID: 10590158)
Plant Cell. 2009 Jan;21(1):39-53. (PMID: 19174535)
Nature. 2008 Jun 19;453(7198):1094-7. (PMID: 18463635)
Protoplasma. 2010 Sep;245(1-4):3-14. (PMID: 20411284)
Plant Cell. 2002 Feb;14(2):321-32. (PMID: 11884677)
Biochem Biophys Res Commun. 2014 Mar 7;445(2):457-62. (PMID: 24530916)
Plant J. 2008 Mar;53(5):717-30. (PMID: 17988221)
Plant Cell. 2002 Feb;14(2):333-42. (PMID: 11884678)
Plant Physiol. 2007 Nov;145(3):1073-85. (PMID: 17873090)
Arabidopsis Book. 2012;10:e0158. (PMID: 22582030)
Bioinformatics. 2007 Nov 1;23(21):2947-8. (PMID: 17846036)
Trends Plant Sci. 2010 May;15(5):266-74. (PMID: 20303820)
Electrophoresis. 2007 Jun;28(12):2080-94. (PMID: 17486657)
Proc Natl Acad Sci U S A. 2014 Apr 1;111(13):E1300-9. (PMID: 24639533)
J Integr Plant Biol. 2008 Jul;50(7):778-85. (PMID: 18713388)
Cold Spring Harb Protoc. 2011 Aug 01;2011(8):940-9. (PMID: 21807852)
Trends Plant Sci. 2003 Nov;8(11):554-60. (PMID: 14607101)

0 (Plant Proteins)
36-88-4 (Carotenoids)

Date Created: 20150218 Date Completed: 20160404 Latest Revision: 20181113

20221213

10.1007/s00425-015-2262-z

25686795