Metabolomic analysis of pathways related to rice grain chalkiness by a notched-belly mutant with high occurrence of white-belly grains.
Grain chalkiness is a highly undesirable trait deleterious to rice appearance and milling quality. The physiological and molecular foundation of chalkiness formation is still partially understood, because of the complex interactions between multiple genes and growing environments.



We report the untargeted metabolomic analysis of grains from a notched-belly mutant (DY1102) with high percentage of white-belly, which predominantly occurs in the bottom part proximal to the embryo. Metabolites in developing grains were profiled on the composite platforms of UPLC/MS/MS and GC/MS. Sampling times were 5, 10, 15, and 20 days after anthesis, the critical time points for chalkiness formation. A total of 214 metabolites were identified, covering most of the central metabolic pathways and partial secondary pathways including amino acids, carbohydrates, lipids, cofactors, peptides, nucleotides, phytohormones, and secondary metabolites. A comparison of the bottom chalky part and the upper translucent part of developing grains of DY1102 resulted in 180 metabolites related to chalkiness formation.



Generally, in comparison to the translucent upper part, the chalky endosperm had lower levels of metabolites regarding carbon and nitrogen metabolism for synthesis of storage starch and protein, which was accompanied by perturbation of pathways participating in scavenging of reactive oxygen species, osmorugulation, cell wall synthesis, and mineral ion homeostasis. Based on these results, metabolic mechanism of chalkiness formation is discussed, with the role of embryo highlighted.
College of Agronomy, Nanjing Agricultural University/Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing, 210095, People's Republic of China.|Crops Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350013, People's Republic of China.
Zhaomiao
Z
Lin
College of Agronomy, Nanjing Agricultural University/Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing, 210095, People's Republic of China.
Xincheng
X
Zhang
College of Agronomy, Nanjing Agricultural University/Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing, 210095, People's Republic of China.
Zunxin
Z
Wang
College of Agronomy, Nanjing Agricultural University/Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing, 210095, People's Republic of China.
Yutong
Y
Jiang
College of Agronomy, Nanjing Agricultural University/Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing, 210095, People's Republic of China. liuzh@njau.edu.cn.|Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, 210095, People's Republic of China. liuzh@njau.edu.cn.
Zhenghui
Z
Liu
Metabolon Inc, Durham, NC, 27713, USA.
Danny
D
Alexander
College of Agronomy, Nanjing Agricultural University/Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing, 210095, People's Republic of China.
Ganghua
G
Li
College of Agronomy, Nanjing Agricultural University/Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing, 210095, People's Republic of China.
Shaohua
S
Wang
College of Agronomy, Nanjing Agricultural University/Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing, 210095, People's Republic of China.
Yanfeng
Y
Ding
D002523:Edible Grain / Q000033:anatomy & histology / Q000235:genetics* / Q000378:metabolism; D008401:Gas Chromatography-Mass Spectrometry; D018506:Gene Expression Regulation, Plant / Q000235:genetics* / Q000502:physiology; D055432:Metabolomics; D012275:Oryza / Q000033:anatomy & histology / Q000235:genetics* / Q000378:metabolism*; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D053719:Tandem Mass Spectrometry
D010940:Plant Proteins
Grain chalkiness; Metabolomic analysis; Notched-belly mutants; Rice; White-belly