Zhaomiao Lin

Occurrence of perfect and imperfect grains of six japonica rice cultivars as affected by nitrogen fertilization

This study aims to quantify nitrogen (N) effect on occurrence of perfect rice kernel (PRK) and imperfect grains which includes white-belly rice kernel (WBRK), white-core rice kernel (WCRK), green rice kernel (GRK), opaque rice kernel (ORK), and other imperfect grains (OTHERS). Two-year field experiments involving six japonica rice cultivars and seven N treatments were performed. The structural differences between white-belly and white-core tissues were compared using scanning electron microscope. Averaged over cultivars, grain yield increased progressively with N rate. PRK increased with N rate in 2008, but decreased with increased N rate in 2009. WBRK and WCRK decreased as N rate increased for both years. High N input resulted in higher occurrence of GRK and OTHERS for both years. Most starch granules in white-belly tissues are intact and surrounded by globular protein bodies, with many air spaces between them; while in white-core tissues, starch granules are easily broken into many single granules and no protein bodies are visible. Our results suggest that N has suppressing influence on chalky grains but favorable effect on other imperfect grains, and indicate different mechanism between WBRK and WCRK.

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

BackgroundGrain 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.ResultsWe 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.ConclusionsUsing 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.

Endosperm structure of white-belly and white-core rice grains shown by scanning electron microscopy.

Abstract: White-belly and white-core are the major two types of grain chalkiness in japonica rice. This study aims to compare the morphological features of white-belly and white-core using a scanning electron microcope (SEM). A japonica rice cultivar Wuyujing3 and its mutants were used as materials. Nearly 1000 SEM images were observed, and 12 representative photos were selected. SEM images showed contrasting differences between white-belly and white-core in endosperm microstructure including the shape of endosperm cell, the size distribution of starch granules, and the amount of protein bodies. White-belly and white-core also varied markedly in morphological features of the cracked compound starch granules. Our findings should help to advance our understanding of the multi-faceted nature of grain chalkiness from the perspective of starch and protein accumulation, and should be of value for future work on rice grain chalkiness.

Physicochemical and Sensory Properties of japonica Rice Varied with Production Areas in China

Northeast of China and Jiangsu Province are major production areas of japonica rice in China. Rice from northeast of China is well-known for its good-eating and appearance quality, and that from Jiangsu Province is viewed as inferior. However, little is known concerning the difference in physicochemical and sensory properties of rice between the major two production areas. Analysis of 16 commercial rice samples showed marked differences in physicochemical properties, including chalky grain rate, contents of amylose and protein and pasting properties between the two main areas. Northeastern rice contained more short-chain amylopectin as compared with Jiangsu rice. However, Jiangsu rice is comparable to northeastern rice in terms of sensory quality including overall acceptability and textural properties of springiness, stickiness and hardness as evaluated by trained panel. Our results indicated the limitation of conventional index of physicochemical properties, and suggested the necessity of identification of new factors controlling rice sensory property. In addition, the taste analyzer from Japan demonstrates limitation in distinguishing the differences between northeastern and Jiangsu rice, and therefore needs localization to fit China.

Chalky part differs in chemical composition from translucent part of japonica rice grains as revealed by a notched‐belly mutant with white‐belly

Abstract BACKGROUND Chalkiness has a deleterious influence on rice appearance and milling quality. We identified a notched‐belly mutant with a high percentage of white‐belly, and thereby developed a novel comparison system that can minimize the influence of genetic background and growing conditions. Using this mutant, we examined the differences in chemical composition between chalky and translucent endosperm, with the aim of exploring relations between occurrence of chalkiness and accumulation of starch, protein and minerals. RESULTS Comparisons showed a significant effect of chalkiness on chemical components in the endosperm. In general, occurrence of chalkiness resulted in higher total starch concentration and lower concentrations of the majority of the amino acids measured. Chalkiness also had a positive effect on the concentrations of As, Ba, Cd, Cr, Mn, Na, Sr and V, but was negatively correlated with those of B, Ca, Cu, Fe and Ni. By contrast, no significant chalkiness effect on P, phytic acid‐P, K, Mg or Zn was observed. In addition, substantial influence of the embryo on endosperm composition was detected, with the embryo showing a negative effect on total protein, amino acids such as Arg, His, Leu, Lys, Phe and Tyr, and all the 17 minerals measured, excluding Ca, Cu, P and Sr. CONCLUSION An inverse relation between starch and protein as well as amino acids was found with respect to chalkiness occurrence. Phytic acid and its colocalized elements K and Mg were not affected by chalkiness. The embryo exerted a marked influence on chemical components of the endosperm, in particular minerals, suggesting the necessity of examining the role of the embryo in chalkiness formation.

Analysis of Variations in White-Belly and White-Core Rice Kernels Within a Panicle and the Effect of Panicle Type

Abstract This study aims to investigate the variation in occurrence of white-belly rice kernel (WBRK) and white-core rice kernel (WCRK) among different positions within a panicle. Twenty-four M4 mutants involved in four panicle types, namely the compact, intermediate, loose, and chicken foot panicle were used. They derived from a japonica rice cultivar Wuyujing 3. Considerable differences in morphological characters existed among the four types of panicle, especially in panicle length, the secondary branch number and ratio of grain number to total branch length. Marked differences were found in WBRK and WCRK among different positions within a panicle for all types of panicle. In general, grains located on the primary rachis and top rachis branches had higher WBRK and WCRK percentage than those on the secondary rachis and bottom rachis branches. WCRK exhibited larger variation among grain positions than WBRK did. Moreover, there was a significant difference in WCRK/WBRK among grain positions within a panicle, with primary rachis and top rachis branches having higher values than the secondary and bottom rachis. In addition, panicle type showed no significant effect on the pattern of WBRK and WCRK occurrence within a panicle. The results indicated the difference in mechanism of WBRK and WCRK formation in grain position within a panicle, and are valuable for breeding and agronomic practices aimed at lowering chalky grain rate.

Complementary Proteome and Transcriptome Profiling in Developing Grains of a Notched-Belly Rice Mutant Reveals Key Pathways Involved in Chalkiness Formation

Rice grain chalkiness is a highly complex trait involved in multiple metabolic pathways and controlled by polygenes and growth conditions. To uncover novel aspects of chalkiness formation, we performed an integrated profiling of gene activity in the developing grains of a notched-belly rice mutant. Using exhaustive tandem mass spectrometry-based shotgun proteomics and whole-genome RNA sequencing to generate a nearly complete catalog of expressed mRNAs and proteins, we reliably identified 38,476 transcripts and 3,840 proteins. Comparison between the translucent part and chalky part of the notched-belly grains resulted in only a few differently express genes (240) and differently express proteins (363), thus making it possible to focus on ‘core’ genes or common pathways. Several novel key pathways were identified as of relevance to chalkiness formation, in particular the shift of C and N metabolism, the down-regulation of ribosomal proteins and the resulting low abundance of storage proteins especially the 13 kDa prolamin subunit, and the suppressed photosynthetic capacity in the pericarp of the chalky part. Further, genes and proteins as transporters for carbohydrates, amino acid/peptides, proteins, lipids and inorganic ions showed an increasing expression pattern in the chalky part of the notched-belly grains. Similarly, transcripts and proteins of receptors for auxin, ABA, ethylene and brassinosteroid were also up-regulated. In summary, this joint analysis of transcript and protein profiles provides a comprehensive reference map of gene activity regarding the physiological state in the chalky endosperm.