title: 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.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.forename: Zhaomiao
authors.initials: Z
authors.lastname: Lin
authors.forename: Xincheng
authors.initials: X
authors.lastname: Zhang
authors.forename: Xiaoyu
authors.initials: X
authors.lastname: Yang
authors.forename: Ganghua
authors.initials: G
authors.lastname: Li
authors.forename: She
authors.initials: S
authors.lastname: Tang
authors.forename: Shaohua
authors.initials: S
authors.lastname: Wang
authors.forename: Yanfeng
authors.initials: Y
authors.lastname: Ding
authors.affiliation: College of Agronomy, Nanjing Agricultural University/Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing 210095, PR China. liuzh@njau.edu.cn.
authors.forename: Zhenghui
authors.initials: Z
authors.lastname: Liu
mesh_terms: D000687:Amylopectin / Q000378:metabolism; D015536:Down-Regulation / Q000235:genetics; D056625:Endosperm / Q000378:metabolism / Q000648:ultrastructure; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D007553:Isotope Labeling; D009154:Mutation / Q000235:genetics*; D012275:Oryza / Q000196:embryology / Q000235:genetics / Q000378:metabolism* / Q000648:ultrastructure; D010940:Plant Proteins / Q000378:metabolism*; D040901:Proteomics / Q000379:methods*; D012639:Seeds / Q000378:metabolism* / Q000648:ultrastructure; D013213:Starch / Q000378:metabolism; D015854:Up-Regulation / Q000235:genetics
chemical_list: D010940:Plant Proteins; D013213:Starch; D000687:Amylopectin