Exploration of the pearl millet phospholipase gene family to identify potential candidates for grain quality traits.

BACKGROUND: Phospholipases constitute a diverse category of enzymes responsible for the breakdown of phospholipids. Their involvement in signal transduction with a pivotal role in plant development and stress responses is well documented. RESULTS: In the present investigation, a thorough genome-wide analysis revealed that the pearl millet genome contains at least 44 phospholipase genes distributed across its 7 chromosomes, with chromosome one harbouring the highest number of these genes. The synteny analysis suggested a close genetic relationship of pearl millet phospholipases with that of foxtail millet and sorghum. All identified genes were examined to unravel their gene structures, protein attributes, cis-regulatory elements, and expression patterns in two pearl millet genotypes contrasting for rancidity. All the phospholipases have a high alpha-helix content and distorted regions within the predicted secondary structures. Moreover, many of these enzymes possess binding sites for both metal and non-metal ligands. Additionally, the putative promoter regions associated with these genes exhibit multiple copies of cis-elements specifically responsive to biotic and abiotic stress factors and signaling molecules. The transcriptional profiling of 44 phospholipase genes in two genotypes contrasting for rancidity across six key tissues during pearl millet growth revealed a predominant expression in grains, followed by seed coat and endosperm. Specifically, the genes PgPLD-alpha1-1, PgPLD-alpha1-5, PgPLD-delta1-7a, PgPLA1-II-1a, and PgPLD-delta1-2a exhibited notable expression in grains of both the genotypes while showing negligible expression in the other five tissues. The sequence alignment of putative promoters revealed several variations including SNPs and InDels. These variations resulted in modifications to the corresponding cis-acting elements, forming distinct transcription factor binding sites suggesting the transcriptional-level regulation for these five genes in pearl millet. CONCLUSIONS: The current study utilized a genome-wide computational analysis to characterize the phospholipase gene family in pearl millet. A comprehensive expression profile of 44 phospholipases led to the identification of five grain-specific candidates. This underscores a potential role for at least these five genes in grain quality traits including the regulation of rancidity in pearl millet. Therefore, this study marks the first exploration highlighting the possible impact of phospholipases towards enhancing agronomic traits in pearl millet.

Comparative transcriptome analysis of vegetable soybean grain discloses genes essential for grain quality.

BACKGROUND: Vegetable soybean is an important vegetable crop in world. Seed size and soluble sugar content are considered crucial indicators of quality in vegetable soybean, and there is a lack of clarity on the molecular basis of grain quality in vegetable soybean. RESULTS: In this context, we performed a comprehensive comparative transcriptome analysis of seeds between a high-sucrose content and large-grain variety (Zhenong 6, ZN6) and a low-sucrose content and small-grain variety (Williams 82, W82) at three developmental stages, i.e. stage R5 (Beginning Seed), stage R6 (Full Seed), and stage R7 (Beginning Maturity). The transcriptome analysis showed that 17,107 and 13,571 differentially expressed genes (DEGs) were identified in ZN6 at R6 (vs. R5) and R7 (vs. R6), respectively, whereas 16,203 and 16,032 were detected in W82. Gene expression pattern and DEGs functional enrichment proposed genotype-specific biological processes during seed development. The genes participating in soluble sugar biosynthesis such as FKGP were overexpressed in ZN6, whereas those responsible for lipid and protein metabolism such as ALDH3 were more enhanced in W82, exhibiting different dry material accumulation between two genotypes. Furthermore, hormone-associated transcriptional factors involved in seed size regulation such as BEH4 were overrepresented in ZN6, exhibiting different seed size regulation processes between two genotypes. CONCLUSIONS: Herein, we not only discovered the differential expression of genes encoding metabolic enzymes involved in seed composition, but also identified a type of hormone-associated transcriptional factors overexpressed in ZN6, which may regulate seed size and soluble content. This study provides new insights into the underlying causes of differences in the soybean metabolites and appearance, and suggests that genetic data can be used to improve its appearance and textural quality.

Molecular basis of genetic improvement for key rice quality traits in Southern China.

Grain qualities including milling quality, appearance quality, eating and cooking quality, and nutritional quality are important indicators in rice breeding. Significant achievements in genetic improvement of rice quality have been made. In this study, we analyzed the variation patterns of 16 traits in 1570 rice varieties and found significant improvements in appearance quality and eating and cooking quality, particularly in hybrid rice. Through genome-wide association study and allelic functional nucleotide polymorphisms analysis of quality trait genes, we found that ALK, FGR1, FLO7, GL7/GW7, GLW7, GS2, GS3, ONAC129, OsGRF8, POW1, WCR1, and Wx were associated with the genetic improvement of rice quality traits in Southern China. Allelic functional nucleotide polymorphisms analysis of 13 important rice quality genes, including fragrance gene fgr, were performed using the polymerase chain reaction amplification refractory mutation system technology. The results showed that Gui516, Gui569, Gui721, Ryousi, Rsimiao, Rbasi, and Yuehui9802 possessed multiple superior alleles. This study elucidates the phenotypic changes and molecular basis of key quality traits of varieties in Southern China. The findings will provide guidance for genetic improvement of rice quality and the development of new varieties.

Biological Roles of Lipids in Rice.

Lipids are organic nonpolar molecules with essential biological and economic importance. While the genetic pathways and regulatory networks of lipid biosynthesis and metabolism have been extensively studied and thoroughly reviewed in oil crops such as soybeans, less attention has been paid to the biological roles of lipids in rice, a staple food for the global population and a model species for plant molecular biology research, leaving a considerable knowledge gap in the biological roles of lipids. In this review, we endeavor to furnish a current overview of the advancements in understanding the genetic foundations and physiological functions of lipids, including triacylglycerol, fatty acids, and very-long-chain fatty acids. We aim to summarize the key genes in lipid biosynthesis, metabolism, and transcriptional regulation underpinning rice's developmental and growth processes, biotic stress responses, abiotic stress responses, fertility, seed longevity, and recent efforts in rice oil genetic improvement.

Response of rice yield, grain quality to chilling at grain filling stages.

BACKGROUND: This study aims to quantify the impacts of chilling at the grain filling stage on rice yield and grain quality. A factorial experiment with four levels of temperature and duration of chilling treatments at the early and late grain filling stages was conducted in 2017, 2018 and 2019. RESULTS: Per 10 °C·day increase in the accumulated cooling degree day at the early and late grain filling stages, the rice emergence-maturity duration was delayed by 0.8% (0.6%) and rice yield decreased by 2.2% (1.7%). Chilling at the early grain filling stage decreased the rice heading rate, while chilling at the late grain filling stage increased rice amylose but decreased protein content. For chilling treatment at the early grain filling stage, rice yield and grain quality were mainly correlated with seed-setting rate, whereas for chilling treatment at the late grain filling stage the rice yield and grain quality were mainly correlated with 1000-grain weight. CONCLUSION: This study improved the understanding of how chilling at the grain filling stages affects rice phenology, yield and grain quality, providing a theoretical basis for maintaining rice yield while ensuring grain quality. The results could be used to guide the rice-growing community in combating chilling at grain filling stages. © 2024 Society of Chemical Industry.

Delayed sowing and its ramifications: biophysical, yield and quality analysis of wheat cultivars in the northwest Indo-Gangetic plains.

BACKGROUND: The continuous cultivation of rice-wheat in the same field is a key element of double-cropping systems in the Indo-Gangetic plains. Yields of such cropping systems are increasingly challenged as climate change drives increases in temperature, terminal stress and uneven rainfall, delaying rice harvesting and subsequently delaying sowing of wheat. In this paper, we evaluate the optimum sowing dates to achieve high grain yield and quality of wheat cultivars in northwest India. Three cultivars of wheat, HD-2967, HD-3086 and PBW-723, were sown on three different dates at the research farm of ICAR-IARI, New Delhi, to generate different weather conditions at different phenological stages. Different biophysical attributes, photosynthetic rate, stomatal conductance and transpiration rate, were measured at different phenological stages. Yield and grain quality parameters such as protein, starch, amylopectin, amylose and gluten were measured in different cultivars sown on different dates. RESULTS: Biophysical parameters were found to be higher in timely sown crops followed by late-sown and very late-sown crops. Further, the different sowing dates had a significant (P < 0.05) impact on the grain quality parameters such as protein, starch, amylopectin, amylose and gluten content. Percentage increases in the value of starch and amylose content under timely sown were ~7% and 11.6%, ~5% and 8.4%, compared to the very late-sown treatment. In contrast, protein and amylopectin contents were found to increase by ~9.7% and 7.5%, ~13.8% and 16.6% under very late-sown treatment. CONCLUSION: High-temperature stress during the grain-filling periods significantly decreased the grain yield. Reduction in the grain yield was associated with a reduction in starch and amylose content in the grains. The protein content in the grains is less affected by terminal heat stress. Cultivar HD-3086 had higher growth, yield as well as quality parameters, compared to HD-2967 and PBW-723 in all treatments, hence could be adopted by farmers in northwest India. © 2024 Society of Chemical Industry.

Individual and combined effects of high-temperature stress at booting and flowering stages on rice grain quality.

BACKGROUND: High temperature stress (HTS) has become a serious threat to rice grain quality and few studies have examined the effects of HTS across multiple stages on rice grain quality. In the present study, we conducted 2 years of HTS treatments under three temperature regimes (32/22 °C, 40/30 °C and 44/34 °C) and HTS durations of 2 days and 4 days at three critical stages: booting, flowering, and a combination of booting and flowering. We employed the heat degree days (HDD) metric, which accounts for both the level and duration of HTS, to quantify the relationships between grain quality traits and HTS. RESULTS: The results revealed the diverse effects of HTS on rice grain quality at different stages, durations and temperature levels. HTS significantly (P < 0.05) reduced grain quality, with the highest sensitivities (reduction per 1 °C day-1 increase in HDD) observed at the flowering stage, followed by the combined and booting stages treatments under mild HTS treatment (40/30 °C). However, under extreme HTS treatments (44/34 °C) for 4 days, rice grains subjected to combined HTS treatment experienced complete mortality. CONCLUSION: Pre-exposed to HTS at the booting stage within a certain intensity can alleviate the adverse effects of post-flowering HTS on grain quality. This provides valuable insights for assessing the potential impact of multiple HTS events on the grain quality under future climate warming. © 2024 Society of Chemical Industry.

Grain quality traits within the wheat (Triticum spp.) genepool: prospects for improved nutrition through de novo domestication.

BACKGROUND: Wild relatives of wheat (Triticum spp.) harbor beneficial alleles for potential improvement and de novo domestication of selected genotypes with advantageous traits. We analyzed the nutrient composition in wild diploid and tetraploid wheats and their domesticated diploid, tetraploid and hexaploid relatives under field conditions in Germany and compared them with modern Triticum aestivum and Triticum durum cultivars. Grain iron (Fe) and zinc (Zn) concentrations, phytate:mineral molar ratios, grain protein content (GPC) and antioxidant activity were analyzed across 125 genotypes. RESULTS: Grain Fe and Zn concentrations in wild wheats were 72 mg kg-1 and 59 mg kg-1, respectively, with improved bioavailability indicated by Phytate:Fe and Phytate:Zn molar ratios (11.7 and 16.9, respectively) and GPC (231 g kg-1). By comparison, grain Fe and Zn concentrations in landrace taxa were 54 mg kg-1 and 55 mg kg-1, respectively, with lower Phytate:Fe and Phytate:Zn molar ratios (15.1 and 17.5, respectively) and GPC (178 g kg-1). Average grain Fe accumulation in Triticum araraticum was 73 mg kg-1, reaching 116 mg kg-1, with high Fe bioavailability (Phyt:Fe: 11.7; minimum: 7.2). Wild wheats, landraces and modern cultivars showed no differences in antioxidant activity. Triticum zhukovskyi stood out with high grain micronutrient concentrations and favorable molar ratios. It was also the only taxon with elevated antioxidant activity. CONCLUSION: Our results indicate alteration of grain quality during domestication. T. araraticum has promising genotypes with advantageous grain quality characteristics that could be selected for de novo domestication. Favorable nutritional traits in the GGAA wheat lineage (T. araraticum and T. zhukovskyi) hold promise for improving grain quality traits. © 2024 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

The potentiality of biostimulant (Lawsonia inermis L.) on some morpho-physiological, biochemical traits, productivity and grain quality of Triticum aestivum L.

BACKGROUND: In conformity with the international trend to substitute the artificial agro-chemicals by natural products to improve growth and productivity of crops, there is a necessity to focus on the environment sustainable and eco-friendly resources to increase crops productivity per unit area. One of these resources is the use of biostimulants. The aim of this study is to allow the vertical expansion of wheat crop by improving its growth and productivity per unit area as well as enhancing its grain quality using henna leaf extract as a biostimulant. RESULTS: Field study was conducted to evaluate the potentiality of different doses of henna leaf extract (HLE) for improving the performance of wheat plants (Triticum aestivum L.) at three development stages. Results revealed that the response was dose dependent hence both 0.5 and 1.0 g/L doses significantly enhanced the growth of shoot and root systems, biochemical traits, yield and yield related components with being 1.0 g/L the most effective one. Furthermore, 1.0 g/L HLE markedly enhanced the quality of the yielded grains as revealed by increasing the content of soluble sugars (23%), starch (19%), gluten (50%), soluble proteins (37%), amylase activity (27%), total phenolics, flavonoids and tannins (67, 87 and 23%, respectively) as well as some elements including Ca (184%), Na and Fe (10%). Also, HPLC analysis of grains revealed that 1.0 g/L dose significantly increased the level of different phytohormones, soluble sugars and flavonoids (quercetin, resveratrol and catechin). CONCLUSION: Application of Henna (Lawsonia inermis) leaf extract at 1.0 g/L dose as a combination of seed priming and foliar spray can be recommended as a nonpolluting, inexpensive promising biostimulant, it can effectively enhance wheat growth, biochemical traits and productivity as well as improving the quality of the yielded grains.

The OsNAC24-OsNAP protein complex activates OsGBSSI and OsSBEI expression to fine-tune starch biosynthesis in rice endosperm.

Starch accounts for up to 90% of the dry weight of rice endosperm and is a key determinant of grain quality. Although starch biosynthesis enzymes have been comprehensively studied, transcriptional regulation of starch-synthesis enzyme-coding genes (SECGs) is largely unknown. In this study, we explored the role of a NAC transcription factor, OsNAC24, in regulating starch biosynthesis in rice. OsNAC24 is highly expressed in developing endosperm. The endosperm of osnac24 mutants is normal in appearance as is starch granule morphology, while total starch content, amylose content, chain length distribution of amylopectin and the physicochemical properties of the starch are changed. In addition, the expression of several SECGs was altered in osnac24 mutant plants. OsNAC24 is a transcriptional activator that targets the promoters of six SECGs; OsGBSSI, OsSBEI, OsAGPS2, OsSSI, OsSSIIIa and OsSSIVb. Since both the mRNA and protein abundances of OsGBSSI and OsSBEI were decreased in the mutants, OsNAC24 functions to regulate starch synthesis mainly through OsGBSSI and OsSBEI. Furthermore, OsNAC24 binds to the newly identified motifs TTGACAA, AGAAGA and ACAAGA as well as the core NAC-binding motif CACG. Another NAC family member, OsNAP, interacts with OsNAC24 and coactivates target gene expression. Loss-of-function of OsNAP led to altered expression in all tested SECGs and reduced the starch content. These results demonstrate that the OsNAC24-OsNAP complex plays key roles in fine-tuning starch synthesis in rice endosperm and further suggest that manipulating the OsNAC24-OsNAP complex regulatory network could be a potential strategy for breeding rice cultivars with improved cooking and eating quality.

Dynamic monitoring of TGW6 by selective autophagy during grain development in rice.

Crop yield must increase to achieve food security in the face of a growing population and environmental deterioration. Grain size is a prime breeding target for improving grain yield and quality in crop. Here, we report that autophagy emerges as an important regulatory pathway contributing to grain size and quality in rice. Mutations of rice Autophagy-related 9b (OsATG9b) or OsATG13a causes smaller grains and increase of chalkiness, whereas overexpression of either promotes grain size and quality. We also demonstrate that THOUSAND-GRAIN WEIGHT 6 (TGW6), a superior allele that regulates grain size and quality in the rice variety Kasalath, interacts with OsATG8 via the canonical Atg8-interacting motif (AIM), and then is recruited to the autophagosome for selective degradation. In consistent, alteration of either OsATG9b or OsATG13a expression results in reciprocal modulation of TGW6 abundance during grain growth. Genetic analyses confirmed that knockout of TGW6 in either osatg9b or osatg13a mutants can partially rescue their grain size defects, indicating that TGW6 is one of the substrates for autophagy to regulate grain development. We therefore propose a potential framework for autophagy in contributing to grain size and quality in crops.

The hot science in rice research: How rice plants cope with heat stress.

Global climate change has great impacts on plant growth and development, reducing crop productivity worldwide. Rice (Oryza sativa L.), one of the world's most important food crops, is susceptible to high-temperature stress from seedling stage to reproductive stage. In this review, we summarize recent advances in understanding the molecular mechanisms underlying heat stress responses in rice, including heat sensing and signalling, transcriptional regulation, transcript processing, protein translation, and post-translational regulation. We also highlight the irreversible effects of high temperature on reproduction and grain quality in rice. Finally, we discuss challenges and opportunities for future research on heat stress responses in rice.

Rice FERONIA-LIKE RECEPTOR 3 and 14 affect grain quality by regulating redox homeostasis during endosperm development.

Chalky endosperm negatively affects the appearance, milling, and eating qualities of rice (Oryza sativa L.) grains. Here, we report the role of two receptor-like kinases, FERONIA-LIKE RECEPTOR 3 (FLR3) and FERONIA-LIKE RECEPTOR 14 (FLR14), in grain chalkiness and quality. Knockouts of FLR3 and/or FLR14 increased the number of white-core grains caused by aberrant accumulation of storage substances, resulting in poor grain quality. Conversely, the overexpression of FLR3 or FLR14 reduced grain chalkiness and improved grain quality. Transcriptome and metabolome analyses showed that genes and metabolites involved in the oxidative stress response were significantly up-regulated in flr3 and flr14 grains. The content of reactive oxygen species was significantly increased in flr3 and flr14 mutant endosperm but decreased in overexpression lines. This strong oxidative stress response induced the expression of programmed cell death (PCD)-related genes and caspase activity in endosperm, which further accelerated PCD, resulting in grain chalkiness. We also demonstrated that FLR3 and FLR14 reduced grain chalkiness by alleviating heat-induced oxidative stress in rice endosperm. Therefore, we report two positive regulators of grain quality that maintain redox homeostasis in the endosperm, with potential applications in breeding rice for optimal grain quality.

Prediction of near-term climate change impacts on UK wheat quality and the potential for adaptation through plant breeding.

Wheat is a major crop worldwide, mainly cultivated for human consumption and animal feed. Grain quality is paramount in determining its value and downstream use. While we know that climate change threatens global crop yields, a better understanding of impacts on wheat end-use quality is also critical. Combining quantitative genetics with climate model outputs, we investigated UK-wide trends in genotypic adaptation for wheat quality traits. In our approach, we augmented genomic prediction models with environmental characterisation of field trials to predict trait values and climate effects in historical field trial data between 2001 and 2020. Addition of environmental covariates, such as temperature and rainfall, successfully enabled prediction of genotype by environment interactions (G × E), and increased prediction accuracy of most traits for new genotypes in new year cross validation. We then extended predictions from these models to much larger numbers of simulated environments using climate scenarios projected under Representative Concentration Pathways 8.5 for 2050-2069. We found geographically varying climate change impacts on wheat quality due to contrasting associations between specific weather covariables and quality traits across the UK. Notably, negative impacts on quality traits were predicted in the East of the UK due to increased summer temperatures while the climate in the North and South-west may become more favourable with increased summer temperatures. Furthermore, by projecting 167,040 simulated future genotype-environment combinations, we found only limited potential for breeding to exploit predictable G × E to mitigate year-to-year environmental variability for most traits except Hagberg falling number. This suggests low adaptability of current UK wheat germplasm across future UK climates. More generally, approaches demonstrated here will be critical to enable adaptation of global crops to near-term climate change.

The genetic basis of grain protein content in rice by genome-wide association analysis.

The grain protein content (GPC) of rice is an important factor that determines its nutritional, cooking, and eating qualities. To date, although a number of genes affecting GPC have been identified in rice, most of them have been cloned using mutants, and only a few genes have been cloned in the natural population. In this study, 135 significant loci were detected in a genome-wide association study (GWAS), many of which could be repeatedly detected across different years and populations. Four minor quantitative trait loci affecting rice GPC at four significant association loci, qPC2.1, qPC7.1, qPC7.2, and qPC1.1, were further identified and validated in near-isogenic line F2 populations (NIL-F2), explaining 9.82, 43.4, 29.2, and 13.6% of the phenotypic variation, respectively. The role of the associated flo5 was evaluated with knockdown mutants, which exhibited both increased grain chalkiness rate and GPC. Three candidate genes in a significant association locus region were analyzed using haplotype and expression profiles. The findings of this study will help elucidate the genetic regulatory network of protein synthesis and accumulation in rice through cloning of GPC genes and provide new insights on dominant alleles for marker-assisted selection in the genetic improvement of rice grain quality. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-022-01347-z.

Genome-wide association analysis of kernel nutritional quality in two natural maize populations.

As one of the three staple crops, nutritional traits in maize are important for human and animal nutrition. Grain quality-related traits are closely related to grain commercial value. Understanding the genetic basis of quality-related traits in maize would be helpful for breeding high-quality maize varieties. In this study, two association panels (AM122 and AM180) were subjected to genome-wide association analysis of grain quality-related traits, including protein content, oil content, starch content, and fiber content. In total, 98 SNPs (P < 1 × 10-4) were identified to be significantly associated with these four grain quality-related traits. By integrating two sets of public transcriptome data, 31 genes located in 200 kb regions flanking the associated SNP showed high expression during kernel development and were differentially expressed in two maize inbred lines, KA225 and KB035, with significantly different quality. These genes might regulate maize grain quality by participating in plant hormone processes, autophagy processes, and others. All these results could provide important reference information for breeding high­quality maize varieties. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-023-01360-w.

QTL detection for rice grain storage protein content and genetic effect verifications.

Rice grain quality is a multifarious attribute mainly governed by multiple nutritional factors. Grain protein is the central component of rice grain nutrition dominantly affecting eating-cooking qualities. Grain protein content is quantitatively influenced by its protein fractions. Genetic quantification of five protein fractions-albumins, globulins, prolamins, glutelin, and grain protein content-were evaluated by exploiting two BC3F2 mapping populations, derived from Kongyu131/TKM9 (population-I) and Kongyu131/Bg94-1 (population-II), which were grown in a single environment. Correlation studies among protein fractions and grain protein content were thoroughly investigated. A genetic linkage map was developed by using 146 single sequence repeat (SSR) markers in population-I and 167 markers in population-II. In total, 40 QTLs were delineated for five traits in both populations. Approximately 22 QTLs were dissected in population-I, derived from Kongyu131/TKM9, seven QTLs for albumin content, four QTLs for globulin content, three QTLs for prolamin content, four QTLs for glutelin content, and four QTLs for grain protein content. In total, 18 QTLs were detected in population-II, derived from Kongyu131/Bg94-1, five QTLs for albumin content, three QTLs for globulin content, four QTLs for prolamin content, two QTLs for glutelin content, and four QTLs for grain protein content. Three QTLs, qAlb7.1, Alb7.2, and qGPC7.2, derived from population-II (Kongyu131/Bg94-1) for albumin and grain protein content were successfully validated in the near isogenic line (NIL) populations. The localized chromosomal locus of the validated QTLs could be helpful for fine mapping via map-based cloning to discover underlying candidate genes. The functional insights of the underlying candidate gene would furnish novel perceptivity for the foundation of rice grain protein content and trigger the development of nutritionally important rice cultivars by combining marker-assisted selection (MAS) breeding. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-023-01436-7.

Knocking Out OsAAP11 to Improve Rice Grain Quality Using CRISPR/Cas9 System.

The demand for rice grain quality, particularly in terms of eating and cooking quality, is increasingly concerning at present. However, the limited availability of rice-quality-related gene resources and time-consuming and inefficient traditional breeding methods have severely hindered the pace of rice grain quality improvement. Exploring novel methods for improving rice grain quality and creating new germplasms is an urgent problem that needs to be addressed. In this study, an amino-acid-transporter-encoding gene OsAAP11 (Os11g0195600) mainly expressed in endosperm was selected as the target for gene editing using the CRISPR/Cas9 system in three japonica genetic backgrounds (Wuyungeng30, Nangeng9108, and Yanggeng158, hereafter referred to as WYG30, NG9108, and YG158). We successfully obtained homozygous osaap11 mutants without transgenic insertion. Subsequently, we conducted comprehensive investigations on the agronomic traits, rice grain quality traits, and transcriptomic analysis of these mutants. The results demonstrate that loss of OsAAP11 function led to a reduced amino acid content and total protein content in grains without affecting the agronomic traits of the plants; meanwhile, it significantly increased the peak viscosity, holding viscosity, and final viscosity values during the cooking process, thereby enhancing the eating and cooking quality. This study not only provides valuable genetic resources and fundamental materials for improving rice grain quality but also provides novel technical support for the rapid enhancement of rice grain quality.

OsMADS1 Regulates Grain Quality, Gene Expressions, and Regulatory Networks of Starch and Storage Protein Metabolisms in Rice.

OsMADS1 plays a vital role in regulating floret development and grain shape, but whether it regulates rice grain quality still remains largely unknown. Therefore, we used comprehensive molecular genetics, plant biotechnology, and functional omics approaches, including phenotyping, mapping-by-sequencing, target gene seed-specific RNAi, transgenic experiments, and transcriptomic profiling to answer this biological and molecular question. Here, we report the characterization of the 'Oat-like rice' mutant, with poor grain quality, including chalky endosperms, abnormal morphology and loose arrangement of starch granules, and lower starch content but higher protein content in grains. The poor grain quality of Oat-like rice was found to be caused by the mutated OsMADS1Olr allele through mapping-by-sequencing analysis and transgenic experiments. OsMADS1 protein is highly expressed in florets and developing seeds. Both OsMADS1-eGFP and OsMADS1Olr-eGFP fusion proteins are localized in the nucleus. Moreover, seed-specific RNAi of OsMADS1 also caused decreased grain quality in transgenic lines, such as the Oat-like rice. Further transcriptomic profiling between Oat-like rice and Nipponbare grains revealed that OsMADS1 regulates gene expressions and regulatory networks of starch and storage protein metabolisms in rice grains, hereafter regulating rice quality. In conclusion, our results not only reveal the crucial role and preliminary mechanism of OsMADS1 in regulating rice grain quality but also highlight the application potentials of OsMADS1 and the target gene seed-specific RNAi system in improving rice grain quality by molecular breeding.

High Daytime Temperature Responsive MicroRNA Profiles in Developing Grains of Rice Varieties with Contrasting Chalkiness.

High temperature impairs starch biosynthesis in developing rice grains and thereby increases chalkiness, affecting the grain quality. Genome encoded microRNAs (miRNAs) fine-tune target transcript abundances in a spatio-temporal specific manner, and this mode of gene regulation is critical for a myriad of developmental processes as well as stress responses. However, the role of miRNAs in maintaining rice grain quality/chalkiness during high daytime temperature (HDT) stress is relatively unknown. To uncover the role of miRNAs in this process, we used five contrasting rice genotypes (low chalky lines Cyp, Ben, and KB and high chalky lines LaGrue and NB) and compared the miRNA profiles in the R6 stage caryopsis samples from plants subjected to prolonged HDT (from the onset of fertilization through R6 stage of caryopsis development). Our small RNA analysis has identified approximately 744 miRNAs that can be grouped into 291 families. Of these, 186 miRNAs belonging to 103 families are differentially regulated under HDT. Only two miRNAs, Osa-miR444f and Osa-miR1866-5p, were upregulated in all genotypes, implying that the regulations greatly varied between the genotypes. Furthermore, not even a single miRNA was commonly up/down regulated specifically in the three tolerant genotypes. However, three miRNAs (Osa-miR1866-3p, Osa-miR5150-3p and canH-miR9774a,b-3p) were commonly upregulated and onemiRNA (Osa-miR393b-5p) was commonly downregulated specifically in the sensitive genotypes (LaGrue and NB). These observations suggest that few similarities exist within the low chalky or high chalky genotypes, possibly due to high genetic variation. Among the five genotypes used, Cypress and LaGrue are genetically closely related, but exhibit contrasting chalkiness under HDT, and thus, a comparison between them is most relevant. This comparison revealed a general tendency for Cypress to display miRNA regulations that could decrease chalkiness under HDT compared with LaGrue. This study suggests that miRNAs could play an important role in maintaining grain quality in HDT-stressed rice.