Metabolomic analysis of pathways related to rice grain chalkiness by a notched-belly mutant with high occurrence of white-belly grains

Zhaomiao Lin,Yutong Jiang,Zunxin Wang,Yanfeng Ding,Ganghua Li,Danny Alexander,Zhenghui Liu,Xincheng Zhang,Shaohua Wang

doi:10.1186/s12870-017-0985-7

Zhaomiao Lin, Yutong Jiang + Show 7 more

Open Access

https://doi.org/10.1186/s12870-017-0985-7

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Abstract

BackgroundGrain 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.ResultsWe 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.ConclusionsGenerally, 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\t 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.

Highlights

Grain chalkiness is a highly undesirable trait deleterious to rice appearance and milling quality
By subjecting the translucent (Tr) upper part and chalky (Ch) bottom part of developing grains produced in the greenhouse to three analytical platforms (UPLC/MS/MS optimized for basic species, UPLC/MS/MS optimized for acidic species, and GC/MS optimized for small, volatile, and thermally stable molecules), we identified 214 rice grain metabolites (Additional file 1)
We investigated the dynamics of metabolomic changes in translucent and chalky endosperm with a interval of five days through seed development, i.e., 5, 10, 15, and 20 day after anthesis (DAA)

Summary

Introduction

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. Grain chalkiness is a highly undesirable trait, with detrimental effects on rice appearance. By molecular marker-based QTL analyses of numerous mapping populations, more than 140 QTLs were identified across all 12 chromosomes for the chalkiness trait, Lin et al BMC Plant Biology (2017) 17:39 mostly among Asian cultivars [2]. Li et al [6] studied the function of Chalk, which encodes V-PPase with inorganic pyrophosphate hydrolysis and H+-translocation activity They found that Chalk could disturb pH homeostasis in the endomembrane trafficking system, resulting in an abnormal decrease in protein body number and size, causing aberrant shape and spatial arrangements of starch granules and protein bodies

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