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Complementary Proteome and Transcriptome Profiling in Developing Grains of a Notched-Belly Rice Mutant Reveals Key Pathways Involved in Chalkiness Formation.
- Source :
-
Plant & cell physiology [Plant Cell Physiol] 2017 Mar 01; Vol. 58 (3), pp. 560-573. - Publication Year :
- 2017
-
Abstract
- Rice grain chalkiness is a highly complex trait involved in multiple metabolic pathways and controlled by polygenes and growth conditions. To uncover novel aspects of chalkiness formation, we performed an integrated profiling of gene activity in the developing grains of a notched-belly rice mutant. Using exhaustive tandem mass spectrometry-based shotgun proteomics and whole-genome RNA sequencing to generate a nearly complete catalog of expressed mRNAs and proteins, we reliably identified 38,476 transcripts and 3,840 proteins. Comparison between the translucent part and chalky part of the notched-belly grains resulted in only a few differently express genes (240) and differently express proteins (363), thus making it possible to focus on 'core' genes or common pathways. Several novel key pathways were identified as of relevance to chalkiness formation, in particular the shift of C and N metabolism, the down-regulation of ribosomal proteins and the resulting low abundance of storage proteins especially the 13 kDa prolamin subunit, and the suppressed photosynthetic capacity in the pericarp of the chalky part. Further, genes and proteins as transporters for carbohydrates, amino acid/peptides, proteins, lipids and inorganic ions showed an increasing expression pattern in the chalky part of the notched-belly grains. Similarly, transcripts and proteins of receptors for auxin, ABA, ethylene and brassinosteroid were also up-regulated. In summary, this joint analysis of transcript and protein profiles provides a comprehensive reference map of gene activity regarding the physiological state in the chalky endosperm.<br /> (© The Author 2017. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists.)
- Subjects :
- Down-Regulation genetics
Edible Grain genetics
Edible Grain metabolism
Endosperm metabolism
Gene Expression Regulation, Plant genetics
Mutation
Oryza embryology
Oryza genetics
Phenotype
Photosynthesis
Plant Proteins genetics
Plant Proteins metabolism
Prolamins metabolism
Proteomics methods
RNA, Messenger analysis
Ribosomal Proteins
Seeds growth & development
Sequence Analysis, RNA
Starch metabolism
Transcriptome
Up-Regulation genetics
Gene Expression Profiling
Gene Expression Regulation, Plant physiology
Oryza metabolism
Proteome metabolism
Seeds metabolism
Subjects
Details
- Language :
- English
- ISSN :
- 1471-9053
- Volume :
- 58
- Issue :
- 3
- Database :
- MEDLINE
- Journal :
- Plant & cell physiology
- Publication Type :
- Academic Journal
- Accession number :
- 28158863
- Full Text :
- https://doi.org/10.1093/pcp/pcx001