Dataset Information

Proteomic analysis of proteins related to rice grain chalkiness using iTRAQ based on a notched-belly mutant with white-belly

ABSTRACT: 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.

INSTRUMENT(S): TripleTOF 5600

ORGANISM(S): Oryza Sativa (rice)

TISSUE(S): Plant Cell, Endosperm

DISEASE(S): Wounds And Injuries

SUBMITTER: Zhaomiao Lin

LAB HEAD: Zhenghui Liu

PROVIDER: PXD001030 | Pride | 2014-06-17

REPOSITORIES: Pride

ACCESS DATA

Dataset's files

Source:

Items per page:

1 - 5 of 61

Publications

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.

Lin Zhaomiao Z Zhang Xincheng X Yang Xiaoyu X Li Ganghua G Tang She S Wang Shaohua S Ding Yanfeng Y Liu Zhenghui Z

BMC plant biology 20140612

<h4>Background</h4>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.<h4>Results</h4>We identified a notched-belly mutant (DY1 ...[more]

PMID: 24924297

Similar Datasets

Project description:Transcriptomic analyses are particularly powerful in research when they are based on detailed underlying knowledge of developmental processes, morphological/anatomical features and biochemical/metabolic processes. Our work is based on our detailed knowledge of grain development and provides an invaluable resource for both Brachypodium grain development specifically and for comparative analyses to other species, including cereal crops. Grain development includes several transition points in addition to being preceded and succeeded by the fundamental developmental switches of fertilization and germination. Such complex process requires a larger sets of genes expressed in a highly-controlled manner. We have selected eight stages of developmental in Brachypodium distachyon encompassing these transitions and conducted comprehensive transcriptomic analyses to generate a valuable resource of the developmental transitions and the distinctive biological processes that are activated and/or repressed during grain development and germination. Comparison of the data generated in this project to other grasses, including the important crop species, and beyond will also shed light on the conservation and/or diversification in gene expression and function in an evolutionary context. Brachypodium distachyon grains (Bd-21 accession) were germinated on moist filter paper after stratification at 4°C for 48h. Five-day old seedlings were transferred to 9cm square pots with a 2:2:1 multipurpose compost: vermiculite: sand mix and grown under controlled environment conditions with a 18h photoperiod at 20°-22°C and light intensity of 180-200 umol/m/s. Tissue samples were collected from eight distinct developmental stages; pre-anthesis ovaries, young grains (1-3 DAA), middle length grains (3-8 DAA), full length grains (8-15 DAA), mature grains (15-20 DAA), mature grains without embryo, germinating grains and seedlings at 3-4 days after germination (Fig.1). Tissues were frozen in liquid nitrogen immediately after collection and were kept at -80°C until further analyses. Total RNA was isolated from frozen tissue samples using the Spectrum Plant Total RNA Kit (Sigma-Aldrich) following the manufacturer’s instructions. Three biological replicates were used for each stage of development. The RNA samples were treated with DNase I (New England Biolabs) in order to eliminate DNA contamination and their concentration was determined using a NanoDrop spectrophotometer (Thermo Fisher Scientific).

			Action	DRS
	ShuiDao_all.dat	Other
	shuidao-1.mgf	Mgf
	shuidao-1.wiff	Wiff
	shuidao-1.wiff.scan	Wiff
	shuidao-10.mgf	Mgf