High day- and night-time temperatures affect grain growth dynamics in contrasting rice genotypes

Rice grain yield and quality are predicted to be highly vulnerable to global warming. Five genotypes including heat-tolerant and susceptible checks, a heat-tolerant near-isogenic line and two hybrids were exposed to control (31 °C/23 °C, day/night), high night-time temperature (HNT; 31 °C/30 °C), high day-time temperature (HDT; 38 °C/23 °C) and high day- and night-time temperature (HNDT; 38 °C/30 °C) treatments for 20 consecutive days during the grain-filling stage. Grain-filling dynamics, starch metabolism enzymes, temporal starch accumulation patterns and the process of chalk formation were quantified. Compensation between the rate and duration of grain filling minimized the impact of HNT, but irreversible impacts on seed-set, grain filling and ultimately grain weight were recorded with HDT and HNDT. Scanning electron microscopy demonstrated irregular and smaller starch granule formation affecting amyloplast build-up with HDT and HNDT, while a quicker but normal amylopast build-up was recorded with HNT. Our findings revealed temporal variation in the starch metabolism enzymes in all three stress treatments. Changes in the enzymatic activity did not derail starch accumulation under HNT when assimilates were sufficiently available, while both sucrose supply and the conversion of sucrose into starch were affected by HDT and HNDT. The findings indicate differential mechanisms leading to high day and high night temperature stress-induced loss in yield and quality. Additional genetic improvement is needed to sustain rice productivity and quality under future climates.

High-resolution QTL mapping for grain appearance traits and co-localization of chalkiness-associated differentially expressed candidate genes in rice

BACKGROUND

Grain appearance quality is a main determinant of market value in rice and one of the highly important traits requiring improvement in breeding programs. The genetic basis of grain shape and endosperm chalkiness have been given significant attention because of their importance in affecting grain quality. Meanwhile, the introduction of NGS (Next Generation Sequencing) has a significant part to play in the area of genomics, and offers the possibility for high-resolution genetic map construction, population genetics analysis and systematic expression profile study.

RESULTS

A RIL population derived from an inter-subspecific cross between indica rice PYZX and japonica rice P02428 was generated, based on the significant variations for the grain morphology and cytological structure between these two parents. Using the Genotyping-By-Sequencing (GBS) approach, 2711 recombination bin markers with an average physical length of 137.68 kb were obtained, and a high-density genetic map was constructed. Global genetic mapping of QTLs affecting grain shape and chalkiness traits was performed across four environments and the newly identified stable loci were obtained. Twelve important QTL clusters were detected, four of which were coincident with the genomic regions of cloned genes or fine mapped QTL reported. Eight novel QTL clusters (including six for grain shape, one for chalkiness, and one for both grain shape and chalkiness) were firstly obtained and highlighted the value and reliability of the QTL analysis. The important QTL cluster on chromosome 5 affects multiple traits including circularity (CS), grain width (GW), area size of grain (AS), percentage of grains with chalkiness (PGWC) and degree of endosperm chalkiness (DEC), indicating some potentially pleiotropic effects. The transcriptome analysis demonstrated an available gene expression profile responsible for the development of chalkiness, and several DEGs (differentially expressed genes) were co-located nearby the three chalkiness-related QTL regions on chromosomes 5, 7, and 8. Candidate genes were extrapolated, which were suitable for functional validation and breeding utilization.

CONCLUSION

QTLs affecting grain shape (grain width, grain length, length-width ratio, circularity, area size of grain, and perimeter length of grain) and chalkiness traits (percentage of grains with chalkiness and degree of endosperm chalkiness) were mapped with the high-density GBS-SNP based markers. The important differentially expressed genes (DEGs) were co-located in the QTL cluster regions on chromosomes 5, 7 and 8 affecting PGWC and DEC parameters. Our research provides a crucial insight into the genetic architecture of rice grain shape and chalkiness, and acquired potential candidate loci for molecular cloning and grain quality improvement.

Relationship between chalkiness and the structural and thermal properties of rice starch after shading during grain-filling stage

Chalkiness is a major concern in rice production and its acceptance and is increased by shade stress. However, the relationship between rice chalkiness and the structural and thermal properties of starch is unclear. Here, we investigated the effect of shade stress on rice starch properties. The chalky grain rate and chalkiness degree significantly decreased with the amylose content, Mn, and ΔH and increased with surface area- and volume-weighted mean diameters, branching degree, ratio of 1022/995 cm^-1, and molecular weight polydispersity. Shade stress significantly increased the volume- and surface area-weighted mean diameters and Mw and decreased the amylose content, A chain proportion of amylopectin, Mn, and regularity of starch. These effects led to an increase in the molecular weight polydispersity and branching degree and a decrease in the crystallinity degree and 1045/1022 cm^-1 ratio, thereby reducing starch ΔH and uniformity. These factors contributed to increased chalkiness of rice under shade stress.

Multiple strategies for heat adaptation to prevent chalkiness in the rice endosperm

Heat-induced chalkiness of rice grains is a major concern for rice production, particularly with respect to climate change. Although the formation of chalkiness in the endosperm is suppressed by nitrogen, little is known about the cell-specific dynamics of this process. Here, using picolitre pressure-probe electrospray-ionization mass spectrometry together with transmission electron microscopy and turgor measurements, we examine heat-induced chalkiness in single endosperm cells of intact rice seeds produced under controlled environmental conditions. Exposure to heat stress decreased turgor pressure and increased the cytosolic accumulation of sugars, glutathione, and amino acids, particularly cysteine. Heat stress also led to a significant enlargement of the protein storage vacuoles but with little accumulation of storage proteins. Crucially, this heat-induced partial arrest of amyloplast development led to formation of chalkiness. Whilst increased nitrogen availability also resulted in increased accumulation of amino acids, there was no decrease in turgor pressure. The heat-induced accumulation of cysteine and glutathione was much less marked in the presence of nitrogen, and storage proteins were produced without chalkiness. These data provide important information on the cell dynamics of heat acclimation that underpin the formation of chalkiness in the rice endosperm. We conclude that rice seeds employ multiple strategies to mitigate the adverse effects of heat stress in a manner that is dependent on nitrogen availability, and that the regulation of protein synthesis may play a crucial role in optimizing organelle compartmentation during heat adaption.

QTL analysis for chalkiness of rice and fine mapping of a candidate gene for qACE9

BACKGROUND

An ideal appearance is of commercial value for rice varieties. Chalkiness is one of the most important appearance quality indicators. Therefore, clarification of the heredity of chalkiness and its molecular mechanisms will contribute to reduction of rice chalkiness. Although a number of QTLs related to chalkiness were mapped, few of them have been cloned so far.

RESULTS

In this study, using recombinant inbred lines (RILs) of PA64s and 9311, we identified 19 QTLs associated with chalkiness on chromosomes 1, 4, 6, 7, 9 and 12, which accounted for 5.1 to 30.6 % of phenotypic variations. A novel major QTL qACE9 for the area of chalky endosperm (ACE) was detected in Hainan and Hangzhou, both mapped in the overlapping region on chromosome 9. It was further fine mapped to an interval of 22 kb between two insertion-deletion (InDel) markers IND9-4 and IND9-5 using a BC4F2 population. Gene prediction analysis identified five putative genes, among which only one gene (OsAPS1), whose product involved in starch synthesis, was detected two nucleotide substitutions causing amino acid change between the parents. Significant difference was found in apparent amylose content (AAC) between NILqACE9 and 9311. And starch granules were round and loosely packed in NILqACE9 compared with 9311 by scanning electron microscopy (SEM) analysis.

CONCLUSIONS

OsAPS1 was selected as a novel candidate gene for fine-mapped qACE9. The candidate gene not only plays a critical role during starch synthesis in endosperm, but also determines the area of chalky endosperm in rice. Further cloning of the QTL will facilitate the improvement of quality in hybrid rice.

The Usefulness of Known Genes/Qtls for Grain Quality Traits in an Indica Population of Diverse Breeding Lines Tested using Association Analysis

BACKGROUND

A number of studies reported major genes/QTLs for rice grain shapes, chalkiness and starch physicochemical properties. For these finely mapped QTLs or cloned genes to make an impact in practical breeding, it is necessary to test their effects in different genetic backgrounds. In this study, two hundred nineteen markers for 20 starch synthesis genes, 41 fine mapped grain shape and related traits QTLs/genes, and 54 chalkiness QTLs/genes plus 15 additional markers and a large indica population of 375 advanced lines were used to identify marker-trait associations under 6 environments that can be used directly in breeding for grain quality traits.

RESULTS

The significant associations detected by the QK model were used to declare the usefulness of the targeted genes/QTLs. A total of 65 markers were detected associations with grain quality trait at least in one environment. More phenotypic variations could be explained by haplotype than single marker, as exemplified by the starch biosynthesising genes. GBSSI was the major gene for AC and explained up to 55 % of the phenotypic variation, which also affected GC and accounted up to 11.31 % of the phenotypic variation. SSIIa was the major gene for chalkiness and explained up to 17 and 21 % of variation of DEC and PGWC, respectively. In addition, RMw513 and RM18068 were associated with DEC in 6 environments as well. Four markers (RGS1, RM15206, RMw513 and Indel1) tightly linked to GS3, gw5, and qGL7-2 were the most important ones for grain shapes. Allelic combinations between SSIIa and RMw513 revealed more variations in DEC.

CONCLUSIONS

The validated markers for genes/QTLs with major effects could be directly used in breeding for grain quality via marker-assisted selection. Creating desirable allelic combinations by gene pyramiding might be an effective approach for the development of high quality breeding lines in rice.

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.

Dry cultivation and cultivar affect starch synthesis and traits to define rice grain quality in various panicle parts

A pot experiment was conducted to explore the effects of high-quality (Huanghuazhan, HH), drought-resistant (IR, IRAT109) and drought-susceptible cultivars (ZS, Zhenshan97) under flooding irrigation and dry cultivation (D) on the starch accumulation and synthesis, physicochemical traits of starch granules and rice grain quality at the upper (U) and lower panicle. Under D treatment, IR and ZS had lower rice quality, especially the appearance and cooking quality. DHH-U had the highest appearance, nutritional and cooking quality among all cultivars under D treatment, which could be ascribed to the synthesis of more short-branch chain amylopectin and correspondingly higher starch granule tightness. DHH-U also maintained ordered carbohydrate structure, crystalline regions, and many hydrophilic and hydrophobic functional groups in starch granules before pasting. It could prevent the polymerization of small molecules to avoid the formation of macromolecules after pasting. Overall, these findings may facilitate the improvement of grain quality in rice dry cultivation.

Bin-based genome-wide association studies reveal superior alleles for improvement of appearance quality using a 4-way MAGIC population in rice

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4-way Multiparental population covered the limitations of the biparental structure.

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The combination of SNP and bin-GWAS showed a powerful tool for QTL mapping.

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qPGWC8.2 harbored a novel predicted gene for rice chalkiness quality.

Introduction

The multiparental population provides us the chance to identify superior alleles controlling a trait for genetic improvement. Genome wide association studies at bin level (bin-GWAS) are expected to be more power in QTL mapping than GWAS at SNP level (SNP-GWAS).

Objectives

This study is to estimate genetic effects of QTL conferring grain appearance quality in rice by SNP-GWAS and bin-GWAS, compare their power in QTL mapping and identify the superior alleles of all detected QTL from 4 parents for genetic improvement.

Methods

A 4-way MAGIC population and its four founders were cultivated in two environments to dissect the genetic basis of rice grain appearance quality. Both SNP-GWAS and bin-GWAS were conducted for QTL mapping. Multiple comparison among 4 parental bin/alleles was used to identify the superior alleles.

Results

A total of 16 and 20 QTL associated with grain appearance quality were identified by SNP- and bin-GWAS, respectively. A minor chalkiness QTL qPGWC8.2/qDEC8 was assigned to a 30-kb genomic region, in which OsMH_08T0121900 is the potential candidate gene because its encoded protein, glucan endo-1,3-beta-glucosidase precursor is involved in the starch and sucrose metabolism pathway. The superior parental alleles for GS3, GL3.1, GW5, GW7, and Chalk5 and two QTLs were almost carried by the high-quality parents Cypress and Yuejingsimiao (YJSM), while the poor-quality parent Guichao-2 (GC2) always carried the inferior alleles. The top five recombinant inbred lines with the highest quality of grain shape and chalkiness traits all carried gene combinations of superior alleles.

Conclusions

Both SNP- and bin-GWAS methods are encouraged for joint QTL mapping with MAGIC population. qPGWC8.2/qDEC8 is a novel candidate gene strongly associated with chalkiness. The superior alleles of GS3, GW5, GL3.1, GW7, Chalk5 and qPGWC8.2 were identified, and the pyramiding of these superior alleles is helpful to improve rice appearance quality.

Dynamic formation and transcriptional regulation mediated by phytohormones during chalkiness formation in rice

BACKGROUND

Rice (Oryza sativa L.) Chalkiness, the opaque part in the kernel endosperm formed by loosely piled starch and protein bodies. Chalkiness is a complex quantitative trait regulated by multiple genes and various environmental factors. Phytohormones play important roles in the regulation of chalkiness formation but the underlying molecular mechanism is still unclear at present.

RESULTS

In this research, Xiangzaoxian24 (X24, pure line of indica rice with high-chalkiness) and its origin parents Xiangzaoxian11 (X11, female parent, pure line of indica rice with high-chalkiness) and Xiangzaoxian7 (X7, male parent, pure line of indica rice with low-chalkiness) were used as materials. The phenotype, physiological and biochemical traits combined with transcriptome analysis were conducted to illustrate the dynamic process and transcriptional regulation of rice chalkiness formation. Impressively, phytohormonal contents and multiple phytohormonal signals were significantly different in chalky caryopsis, suggesting the involvement of phytohormones, particularly ABA and auxin, in the regulation of rice chalkiness formation, through the interaction of multiple transcription factors and their downstream regulators.

CONCLUSION

These results indicated that chalkiness formation is a dynamic process associated with multiple genes, forming a complex regulatory network in which phytohormones play important roles. These results provided informative clues for illustrating the regulatory mechanisms of chalkiness formation in rice.

Measurement of Rice Grain Dimensions and Chalkiness, and Rice Grain Elongation Using Image Analysis

Measurements of rice grain dimensions, percent grain chalkiness, and grain elongation used to be tedious and slow due to the manual nature of measurements (e.g., use of calipers to measure grains one at a time) and the subjective nature of scoring based on visual inspection (i.e., chalkiness). Recent developments in imaging technologies have enabled more high-throughput means for measuring physical traits (i.e., grain dimensions and chalkiness) in raw grains and grain elongation by comparing ratio between raw versus cooked rice. The digital images of rice grains are captured through computer scanning and analyzed using software that can calculate area and pixel value statistics of user-defined parameters. The improvements in throughput made possible by the use of imaging technologies will allow faster quality grading of rice varieties. Market quality is usually defined based on the rice grain physical traits (grain size and shape), degree of chalkiness, and the ability of rice to elongate on cooking. In this chapter, the routine methods to measure the physical traits of rice and grain elongation using image analysis are described.

Reduction of pyruvate orthophosphate dikinase activity is associated with high temperature-induced chalkiness in rice grains

Global warming affects both rice (Oryza sativa) yields and grain quality. Rice chalkiness due to high temperature during grain filling would lower the grain quality. The biochemical and molecular mechanisms responsible for the increased occurrence of chalkiness under high temperature are not fully understood. Previous research suggested that cytosolic pyruvate orthophosphate dikinase (cyPPDK, EC 2.7.9.1) in rice modulates carbon metabolism. The objective of this study was to determine the relationship between cyPPDK and high temperature-induced chalkiness. High temperature treatments were applied during the grain filling of two rice cultivars (9311 and TXZ-25) which had different sensitivity of chalkiness to high temperature. Chalkiness was increased significantly under high temperature treatment, especially for TXZ-25. A shortened grain filling duration and a decreased grain weight in both cultivars were caused by high temperature treatment. A reduction in PPDK activities due to high temperature was observed during the middle and late grain filling periods, accompanied by down regulated cyPPDK mRNA and protein levels. The temperature effects on the developmental regulation of PPDK activity were confirmed at transcription, translation and post-translational levels. PPDK activities were insensitive to variation in PPDK levels, suggesting the rapid phosphorylation mechanism of this protein. The two varieties showed similar responses to the high temperature treatment in both PPDK activities and chalkiness. We concluded that high temperature-induced chalkiness was associated with the reduction of PPDK activity.

Dry cultivation with ratoon system impacts rice quality using rice flour physicochemical traits, fatty and amino acids contents

A field experiment was conducted to explore the impact on rice quality using high-quality (HH) or drought-resistant (HY) cultivars under flooding irrigation (F) or dry cultivation (D) in ratooning rice system by evaluating the metabolism or physicochemical traits of starch, fatty acids, and amino acids affecting grain quality. Compared to FHY and DHY in the main or ratoon season, DHH in ratoon season (DHHR) exhibited a higher appearance and processing quality but lower cooking quality. DHHR mainly synthesized long branch chain amylopectin to construct the crystalline regions with increased crystallinity, crystallites size, interplanar spacing, dislocation density, Asp and Thr in brown and head rice. Also, it accumulated more of C16:0, C18:0, C18:1, C18:2, and C18:3 but reduced glutelin in head rice. An increase in functional groups and diversity was seen in brown and head rice, respectively. Overall, these traits improved the processing, appearance, and pasting quality of DHHR.

Foliar application of selenium affecting pollen viability, grain chalkiness, and transporter genes in cadmium accumulating rice cultivar: A pot study

Under Cadmium (Cd) stress, rice grain quality and quantity are compromised, affecting human health. Application of Selenium (Se) mitigating Cd stress in rice was already reported, but its role in rescuing Cd induced damage in the reproductive parts in rice plants has not been studied before. To investigate the underlying mechanism, Se mediated alleviation of Cd-stress induced damage to pollen viability, germination rate, and grain chalkiness were studied. A grain Cd accumulating rice genotype was selected and treated with 10 μM Cd and sprayed with 5 μM Se during tillering, elongating and heading stages. A significant reduction in pollen viability, germination percentage, and accumulation of higher amount of ROS in the reproductive parts were observed in Cd treated plants. However, Se supplementation (i.e. Cd + Se), decreased the ROS accumulation in anther, pistil, pollen and enhanced the pollen viability and germination percentage. Cd translocation was prevented from flag leaf to grains, under Se treatment. As a result, a significantly higher seed setting rate, and yield were observed. Additionally, Se improved grain nutrient content and grain quality. Therefore, the recent study suggests that the use of foliar spray of Se could be a cost-effective strategy to prevent Cd-induced yield loss and quality in rice.

Fine mapping of qWCR7, a grain chalkiness QTL in rice

Chalkiness is one of the key determinants of rice quality and is a highly undesirable trait for breeding and marketing. In this study, qWCR7, a major quantitative trait locus (QTL) of white-core rate (WCR), was genetically validated using a BC3F2 segregation population and further fine mapped using a near isogenic line (NIL) population, of which both were derived from a cross between the donor parent DL208 and the recurrent parent ZS97. qWCR7 was finally narrowed to a genomic interval of ~ 68 kb, containing seven annotated genes. Among those, two genes displayed markedly different expression levels in endosperm of NILs. Transcriptome analysis showed that the synthesis and accumulation of metabolites played a key role in chalkiness formation. The contents of storage components and expression levels of related genes were detected, suggesting that starch and storage protein were closely related to white-core trait. Our findings have laid the foundation of map-based cloning of qWCR7, which may have potential value in quality improvement during rice breeding.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-021-01260-x.

Regulation of OsPIL15 on rice quality

The phytochrome-interacting factor-like gene OsPIL15 negatively regulates grain size and 1000-grain weight, but its regulatory effect on rice quality traits is unknown. Here, knock-down, knock-out, and over-expression of OsPIL15 transgenic rice lines were used to investigate the effects of OsPIL15 on rice yield and quality traits. The results showed that knock-down or knock-out of OsPIL15 increased grain length and width, chalkiness, amylose content, glutenin and globulin content, and total protein content but reduced amylopectin content, total starch content, prolamin and albumin content, and gel consistency. Over-expression of OsPIL15 showed the opposite results, except for the reduction of prolamin content. Although OsPIL15 changed the grain size and weight, it had no effect on grain length/width ratio, brown rice rate, and milled rice rate. KEGG pathway enrichment analysis of differentially expressed genes between transgenic lines and wild type showed that OsPIL15 mainly regulated genes related to ribosome, metabolic pathways, and biosynthesis of secondary metabolites. Gene expression analysis showed that RNAi transgenic lines decreased OsCIN2 and OsSUS1 expression and increased OsGBSSI, OsSSI, OsAPGL2, and OsAPGL3 expression level, while over-expression of OsPIL15 increased OsCIN2, OsSUS1, OsSUS6, and OsSSI and decreased OsSSIIa, OsSSIIc, and OsAPGL2 expression level. These results revealed that OsPIL15 plays an important role in rice grain development. In addition to grain shape, OsPIL15 also regulates chalkiness, starch content, protein content, and gel consistency.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-022-01311-x.

Transcriptome and Metabolome Analyses Reveals the Pathway and Metabolites of Grain Quality Under Phytochrome B in Rice (Oryza sativa L.)

BACKGROUND

Grain size and chalkiness is a critical agronomic trait affecting rice yield and quality. The application of transcriptomics to rice has widened the understanding of complex molecular responsive mechanisms, differential gene expression, and regulatory pathways under varying conditions. Similarly, metabolomics has also contributed drastically for rice trait improvements. As master regulators of plant growth and development, phys influence seed germination, vegetative growth, photoperiodic flowering, shade avoidance responses. OsPHYB can regulate a variety of plant growth and development processes, but little is known about the roles of rice gene OsPHYB in modulating grain development.

RESULTS

In this study, rice phytochrome B (OsPHYB) was edited using CRISPR/Cas9 technology. We found that OsPHYB knockout increased rice grain size and chalkiness, and increased the contents of amylose, free fatty acids and soluble sugar, while the gel consistency and contents of proteins were reduced in mutant grains. Furthermore, OsPHYB is involved in the regulation of grain size and chalk formation by controlling cell division and complex starch grain morphology. Transcriptomic analysis revealed that loss of OsPHYB function affects multiple metabolic pathways, especially enhancement of glycolysis, fatty acid, oxidative phosphorylation, and antioxidant pathways, as well as differential expression of starch and phytohormone pathways. An analysis of grain metabolites showed an increase in the free fatty acids and lysophosphatidylcholine, whereas the amounts of sugars, alcohols, amino acids and derivatives, organic acids, phenolic acids, alkaloids, nucleotides and derivatives, and flavonoids decreased, which were significantly associated with grain size and chalk formation.

CONCLUSIONS

Our study reveals that, OsPHYB plays an important regulatory role in the growth and development of rice grains, especially grain size and chalkiness. Furthermore, OsPHYB regulates grain size and chalkiness formation by affecting gene metabolism interaction network. Thus, this study not only revealed that OsPHYB plays a vital role in regulating grain size and chalkiness of rice but reveal new functions and highlighted the importance and value of OsPHYB in rice grain development and provide a new strategy for yield and quality improvement in rice breeding.

Starch molecular structural differences between chalky and translucent parts of chalky rice grains

Chalky rice has an undesirable appearance and reduced commercial value. To understand the relationship between starch structural characteristics and chalkiness, a comprehensive investigation was conducted of molecular structural differences between starch in chalky and translucent parts of the same chalky grains (three Japonica and two Indica rices), this strategy being such as to minimize genetic and environmental effects. Compared to translucent parts, chalky parts had a larger ratio of large to small branched molecules and more short amylopectin chains (degree of polymerization < 35), but fewer longer chains, which affect higher-level starch structures, such as crystallinity. No significant differences in amylose structure were observed. White-belly and white-core chalky grains showed distinguishable starch characteristics, suggesting studying different chalkiness types separately. These findings extend understanding of chalkiness from the perspective of starch structure, and control of this structure can in the future help breeders to develop strategies against the formation of chalkiness.

iTRAQ-Based Proteomic Analysis of Rice Grains

Cereal proteins have formed the basis of human diet worldwide, and their level of consumption is expected to increase. The knowledge of the protein composition and variation of the cereal grains is helpful for characterizing cereal varieties and to identify biomarkers for tolerance mechanisms. Grains produce a wide array of proteins, differing under conditions. Quantitative proteomics is a powerful approach allowing the identification of proteins expressed under defined conditions that may contribute understanding the complex biological systems of grains. Isobaric tags for relative and absolute quantitation (iTRAQ) is a mass spectrometry-based quantitative approach allowing, simultaneously, for protein identification and quantification from multiple samples with high coverage. One of the challenges in identifying grains proteins is their relatively high content (~90-95%) of carbohydrate (starch) and low protein (~4-10%) and lipid (~1%) fractions. In this chapter, we present a robust workflow to carry out iTRAQ quantification of the starchy rice grains.

Grain Quality of Panicle Portions in Chalky and Low-Chalky Rice Cultivars

Carbohydrate stress reduces grain size and head rice percentage and increases the chalkiness in rice. This study aims to compare low and high-quality cultivars for their milled rice and chalky grain percentages, as well as grain size, in the top, middle, and bottom panicle portions. Low-chalky and chalky long-grain rice cultivars were grown at Beaumont in 2019 and 2022. Panicles were harvested, partitioned into top, middle, and bottom portions, and phenotyped for grain size, head rice percentage, and chalkiness. Grain area reduction percentage from top to middle panicle portions is higher in the low-chalky cultivars, Presidio and Kaybonnet. This could relieve the carbohydrate stress that leads to chalkiness. The rice cultivars were also genotyped for Chalk5 and OsPPDK. The low-chalky cultivars had the same allele as the low-chalk Lemont for Chalk5. Presidio had a different allele for OsPPDK compared with the cultivars tested. Consistent with the genotyping result for Chalk5, Presidio and Kaybonnet had lower chalkiness than LaGrue and Leah. There was a positive correlation between the number of primary panicle branches and head rice percentage. The improvement in breeding efficiency for high grain quality requires phenotypic screening for a high number of primary panicle branches and for low chalky and partially chalky grain percentages.

Fine mapping of the grain chalkiness quantitative trait locus qCGP6 reveals the involvement of Wx in grain chalkiness formation

Grain chalkiness is an important index of rice appearance quality and is negatively associated with rice processing and eating qualities. However, the genetic mechanism underlying chalkiness formation is largely unknown. To identify the genetic basis of chalkiness, 410 recombinant inbred lines (RILs) derived from two representative indica rice varieties, Shuhui498 (R498) and Yihui3551 (R3551), were used to discover quantitative trait loci (QTL). The two parental lines and RILs were grown in three locations in China under three controlled fertilizer application level. Analyses indicated that chalkiness was significantly affected by genotype, the environment, and the interaction between the two, and that heritability was high. Several QTLs were isolated, including the two stable QTLs, i.e., qCGP6 and qCGP8. Fine mapping and candidate gene verification of qCGP6 showed that Wx may play a key role in chalkiness formation. Chromosomal segment substitution lines (CSSLs) and near-isogenic lines (NILs) carrying the Wxa or Wxin allele produced more chalky grain than the R498 parent. A similar result was also observed in the 3611 background. Notably, the effect of the Wx genotype on rice chalkiness was shown to be dependent on environmental conditions and Wx alleles exhibited different sensitivities to shading treatment. Using CRISPR/Cas9, the Wxa promoter region was successfully edited, down-regulating Wx alleviates chalkiness formation in NILR498-Wxa. This study developed a new strategy for synergistic improvement of eating and appearance qualities in rice, and created a novel Wx allele with great potential in breeding applications.

Appearance, components, pasting, and thermal characteristics of chalky grains of rice varieties with varying protein content

This study investigated two rice varieties, GuichaoII and Jiazao311, with distinct protein content to determine the variation in appearance, components, pasting, and thermal properties of rice with different chalkiness degrees. Grain length, width, head rice weight, and whiteness of both varieties markedly increased as chalkiness increased from 0% to 50%. However, the variation in components, pasting, and thermal characteristics of chalky grain substantially differed between the rice varieties. The protein content of GuichaoII (low protein content) significantly increased with the chalkiness degree, along with a significant increase in onset, peak, and conclusion temperatures and gelatinization enthalpy. In Jiazao311 (high protein content), the chalkiness degree increased with the protein content but decreased with the starch content, along with increased trough, final, setback, and consistency viscosities. Compared to amylose content, protein content had a greater influence on the thermal properties and pasting characteristics of chalky grains of GuichaoII and Jiazao311, respectively.

OsCHR728 encodes a chromatin remodeling factor involved in seed size and grain chalkiness in rice

The Imitation Switch (ISWI)ATP-dependent chromatin remodeling factor proteins regulate various developmental processes, spanning from flowering to stress response. However, researches on the roles of ISWI subfamily genes in rice have been limited. This study investigated the expression profile of the rice chromatin remodeler OsCHR728, encoding an ISWI protein, across various tissues and developing stages. Our findings reveal that OsCHR728 is highly accumulated during early stage of the panicle development. We generated OsCHR728 knockout (KO) lines in rice using CRISPR/Cas9 technology. These mutant lines displayed smaller grain size compared to the wild type (Zhonghua 11, ZH11). Expression analysis revealed a significant downregulation of the transcript levels of five genes associated with cell cycle regulation in KO grains compared to the wild type, consistent with the reduced cell number in the mutant grains. Additionally, total free amino acid levels were higher in the KO mutant compared to the wild type, consequently enhancing the nutritional quality of the KO mutant grains. The mature endosperm of the KO mutant exhibited a reduced percentage of chalky grains and less chalkiness, suggesting an improvement in the appearance quality of the KO mutant. These results suggest that chromatin remodeling factor OsCHR728 plays a role in grain development, potentially providing a new avenue to enhance both the appearance and nutritional quality of rice cultivars.