title: Transcriptome analysis of grain-filling caryopses reveals involvement of multiple regulatory pathways in chalky grain formation in rice.
abstract: BACKGROUND
  Grain endosperm chalkiness of rice is a varietal characteristic that negatively affects not only the appearance and milling properties but also the cooking texture and palatability of cooked rice. However, grain chalkiness is a complex quantitative genetic trait and the molecular mechanisms underlying its formation are poorly understood.
  
  
  RESULTS
  A near-isogenic line CSSL50-1 with high chalkiness was compared with its normal parental line Asominori for grain endosperm chalkiness. Physico-biochemical analyses of ripened grains showed that, compared with Asominori, CSSL50-1 contains higher levels of amylose and 8 DP (degree of polymerization) short-chain amylopectin, but lower medium length 12 DP amylopectin. Transcriptome analysis of 15 DAF (day after flowering) caryopses of the isogenic lines identified 623 differential expressed genes (P < 0.01), among which 324 genes are up-regulated and 299 down-regulated. These genes were classified into 18 major categories, with 65.3% of them belong to six major functional groups: signal transduction, cell rescue/defense, transcription, protein degradation, carbohydrate metabolism and redox homeostasis. Detailed pathway dissection demonstrated that genes involved in sucrose and starch synthesis are up-regulated, whereas those involved in non-starch polysaccharides are down regulated. Several genes involved in oxidoreductive homeostasis were found to have higher expression levels in CSSL50-1 as well, suggesting potential roles of ROS in grain chalkiness formation.
  
  
  CONCLUSIONS
  Extensive gene expression changes were detected during rice grain chalkiness formation. Over half of these differentially expressed genes are implicated in several important categories of genes, including signal transduction, transcription, carbohydrate metabolism and redox homeostasis, suggesting that chalkiness formation involves multiple metabolic and regulatory pathways.
authors.affiliation: Institute of Crop Sciences, Chinese Academy of Agriculture Sciences, Beijing, 100081, China.
authors.forename: Xiaolu
authors.initials: X
authors.lastname: Liu
authors.forename: Tao
authors.initials: T
authors.lastname: Guo
authors.forename: Xiangyuan
authors.initials: X
authors.lastname: Wan
authors.forename: Haiyang
authors.initials: H
authors.lastname: Wang
authors.forename: Mingzhu
authors.initials: M
authors.lastname: Zhu
authors.forename: Aili
authors.initials: A
authors.lastname: Li
authors.forename: Ning
authors.initials: N
authors.lastname: Su
authors.forename: Yingyue
authors.initials: Y
authors.lastname: Shen
authors.forename: Bigang
authors.initials: B
authors.lastname: Mao
authors.forename: Huqu
authors.initials: H
authors.lastname: Zhai
authors.forename: Long
authors.initials: L
authors.lastname: Mao
authors.forename: Jianmin
authors.initials: J
authors.lastname: Wan
mesh_terms: D056625:Endosperm / Q000235:genetics; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks / Q000235:genetics*; D006706:Homeostasis; D020411:Oligonucleotide Array Sequence Analysis; D012275:Oryza / Q000033:anatomy & histology* / Q000201:enzymology / Q000235:genetics* / Q000648:ultrastructure; D010084:Oxidation-Reduction; D010368:Pectins / Q000378:metabolism; D010641:Phenotype; D010788:Photosynthesis / Q000235:genetics; D018515:Plant Leaves / Q000235:genetics; D011134:Polysaccharides / Q000096:biosynthesis; D019655:Quantitative Trait, Heritable; D017382:Reactive Oxygen Species / Q000378:metabolism; D015203:Reproducibility of Results; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012639:Seeds / Q000235:genetics*; D013213:Starch / Q000096:biosynthesis / Q000648:ultrastructure; D013395:Sucrose / Q000378:metabolism
chemical_list: D011134:Polysaccharides; D017382:Reactive Oxygen Species; D013395:Sucrose; C007916:hemicellulose; D010368:Pectins; D013213:Starch