PXD001030

PXD001030 is an original dataset announced via ProteomeXchange.

Title	Proteomic analysis of proteins related to rice grain chalkiness using iTRAQ based on a notched-belly mutant with white-belly
Description	Grain chalkiness is a complex trait adversely affecting appearance and milling quality, and therefore has been one of principal targets for rice improvement. Eliminating chalkiness from rice has been a daunting task due to the complex interaction between genotype and environment and the lack of molecular markers. In addition, the molecular mechanisms underlying grain chalkiness formation are still imperfectly understood. We identified a notched-belly mutant (DY1102) with high percentage of white-belly, which only occurs in the bottom part proximal to the embryo. Using this mutant, a novel comparison system that can minimize the effect of genetic background and growing environment was developed. An iTRAQ-based comparative display of the proteins between the bottom chalky part and the upper translucent part of grains of DY1102 was performed. A total of 113 proteins responsible for chalkiness formation was identified. Among them, 70 proteins are up-regulated and 43 down-regulated. Approximately half of these differentially expressed proteins involved in central metabolic or regulatory pathways including carbohydrate metabolism (especially cell wall synthesis) and protein synthesis, folding and degradation, providing proteomic confirmation of the notion that chalkiness formation involves diverse but delicately regulated pathways. Protein metabolism was the most abundant category, accounting for 27.4% of the total differentially expressed proteins. In addition, down regulation of PDIL 2-3 and BiP was detected in the chalky tissue, indicating the important role of protein metabolism in grain chalkiness formation. Using this novel comparison system, our comprehensive survey of endosperm proteomics in the notched-belly mutant provides a valuable proteomic resource for the characterization of pathways contributing to chalkiness formation at molecular and biochemical levels.
HostingRepository	PRIDE
AnnounceDate	2014-07-24
AnnouncementXML	Submission_2014-07-24_05:20:06.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Zhaomiao Lin
SpeciesList	scientific name: Rice(O. sativa); NCBI TaxID: 4530;
ModificationList	iTRAQ8plex-116 reporter+balance reagent acylated residue
Instrument	TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2014-06-03 02:23:40	ID requested
1	2014-06-17 00:48:21	announced
⏵ 2	2014-07-24 05:20:07	announced	Updated project metadata.

Lin Z, Zhang X, Yang X, Li G, Tang S, Wang S, Ding Y, Liu Z, Proteomic analysis of proteins related to rice grain chalkiness using iTRAQ and a novel comparison system based on a notched-belly mutant with white-belly. BMC Plant Biol, 14():163(2014) [pubmed]

curator keyword: Biological

submitter keyword: Rice, Grain chalkiness, iTRAQ, White-belly, Notched-belly mutants

Zhenghui Liu
contact affiliation	College of Agronomy, Nanjing Agricultural University
contact email	liuzh@njau.edu.cn
lab head
Zhaomiao Lin
contact affiliation	Nanjing Agricultural University
contact email	2012201020@njau.edu.cn
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD001030
     1. Label: PRIDE project
     2. Name: Proteomic analysis of proteins related to rice grain chalkiness using iTRAQ based on a notched-belly mutant with white-belly