Chalk5 encodes a vacuolar H+-translocating pyrophosphatase influencing grain chalkiness in rice

Effects of structural properties of glutelin on the formation of grain quality under elevated temperatures and additional nitrogen during the grain filling period

Glutelin, the key storage substance for determining rice quality, was sensitive to warming and nitrogen. However, the relationship between the structural properties of glutelin and rice quality needs to be further investigated under warming and nitrogen. The higher glutelin level was responsible for deteriorating quality under warming and additional nitrogen. The key amino acid components for glutelin were less affected by temperature and nitrogen, whereas glutelin subunit level was sensitive to nitrogen. A lower-ordered sequence for glutelin secondary structure may be involved in deteriorating rice quality for inferior spikelets. The higher level of disulfide bonds may not affect the texture properties of cooked rice. Overall, the results contributed to understanding rice quality formation under warming, as well as a theoretical basis for adjustment of protein extraction process to meet the needs of food processing industry in combination with cultivation measures in light of warming.

Mycotoxin concentrations in rice are affected by chalkiness, grain shape, processing type, and grain origin

Mycotoxins such as aflatoxins (AFs), fumonisins (FBs), zearalenone (ZEN), and deoxynivalenol (DON) pose a risk to public health due to their carcinogenic potency (AFs and FBs) and anti-nutritional effects. The hazards associated with mycotoxins are accentuated where food management practices, control, and regulatory systems from farm to plate are sub-optimal. Information on the frequency of these mycotoxins in rice commercialized in markets in sub-Sahara Africa (SSA) is limited. The current study examined AF concentrations in 527 rice samples collected from 54 markets in five SSA countries. Grain quality characteristics, processing methods, and origin of samples were contrasted with toxin levels. In total, 72% of the samples had detectable AFs levels (range = 3.0 to 89.8 µg/kg). Forty-seven percent (47%) of the samples had AFs above 4 µg/kg, the European Union maximum level (ML), and were evaluated for cooccurrence with FBs, ZEN, and DON. Total AFs and ZEN cooccurred in 40% of the samples, and 30% of the positive ZEN samples had concentrations above the ML of 75 µg/kg. Total AFs did not co-occur with FBs and DON. Multivariate analysis revealed that length-to-width ratio (p < 0.0001), mixed variety for width (p = 0.04), and chalkiness (p = 0.009) significantly influenced aflatoxin concentrations. Slender grains had higher AFs concentrations than bold and medium grains (p < 0.0001). Possible strategies to mitigate mycotoxin contamination in rice include improving grain quality traits and practicing proper drying and hermetic storage before and after milling. These findings provide valuable insights for both domestic and international actors in establishing and strengthening regulations and management systems to mitigate rice mycotoxin contamination.

Creeping Stem 1 regulates directional auxin transport for lodging resistance in soybean

Soybean, a staple crop on a global scale, frequently encounters challenges due to lodging under high planting densities, which results in significant yield losses. Despite extensive research, the fundamental genetic mechanisms governing lodging resistance in soybeans remain elusive. In this study, we identify and characterize the Creeping Stem 1 (CS1) gene, which plays a crucial role in conferring lodging resistance in soybeans. The CS1 gene encodes a HEAT-repeat protein that modulates hypocotyl gravitropism by regulating amyloplast sedimentation. Functional analysis reveals that the loss of CS1 activity disrupts polar auxin transport, vascular bundle development and the biosynthesis of cellulose and lignin, ultimately leading to premature lodging and aberrant root development. Conversely, increasing CS1 expression significantly enhances lodging resistance and improves yield under conditions of high planting density. Our findings shed light on the genetic mechanisms that underlie lodging resistance in soybeans and highlight the potential of CS1 as a valuable target for genetic engineering to improve crop lodging resistance and yield.

Molecular Mechanisms of Grain Chalkiness Variation in Rice Panicles

Grain chalkiness adversely affects rice quality, and the positional variation of grain chalkiness within a rice panicle presents a substantial obstacle to quality improvement in China. However, the molecular mechanism underlying this variation is unclear. This study conducted a genetic and physiological analysis of grains situated at distinct positions (upper, middle, and bottom primary branches of the rice panicle, denoted as Y1, Y2, and Y3) within a rice panicle using the Yangdao 6 variety. The results indicated that the percentage of chalky grains (PCG) in Y1 was the highest, i.e., 17.12% and 52.18% higher than that of Y2 and Y3, respectively. Y2 exhibited the highest degree of grain chalkiness (DGC), attributable to its greater area of endosperm chalkiness (AEC) than the others. Y3 demonstrated the lowest PCG and DGC. Additionally, Y1 and Y2 were characterized by lower amylose and protein contents, as well as looser starch granule morphology, in comparison to Y3. Compared with Y3, both the average and maximum filling rates of Y1 and Y2 increased markedly; however, the active filling duration was notably reduced by 7.10 d and 5.56 d, respectively. The analysis of genomic expression levels indicated an enrichment of starch and sucrose metabolism in Y1-vs.-Y2, Y2-vs.-Y3, and Y1-vs.-Y3, with 7 genes (5 up-regulated and 2 down-regulated), 53 genes (12 up-regulated and 41 down-regulated), and 12 genes (2 up-regulated and 10 down-regulated) in the Y1-vs.-Y2, Y2-vs.-Y3, and Y1-vs.-Y3. The majority of these genes were down-regulated, linking metabolic activity to grain filling and contributing to the occurrence of grain chalkiness in rice panicles. In conclusion, the metabolic processes associated with sucrose and starch play a crucial role in regulating grain filling and the formation of chalkiness in rice.

Multi-omics analyses reveal mechanism for high resistant starch formation in an indica rice SSIIIa mutant

Soluble starch synthase IIIa (SSIIIa) is a key enzyme involved in amylopectin biosynthesis in rice, and deficiency of SSIIIa results in high content of resistant starch, which is benefit to human health. However, little is known about metabolic differences and carbon re-allocation in the seeds of the indica rice ss3a mutant. We found that SSIIIa deficiency impaired the storage of starch, but increased the soluble sugars, free amino acids and lipids. By multi-omic analyses, we found inactivation of SSIIIa triggered carbon repartitioning by downregulating sucrose synthase, grain incomplete filling 1, fructokinase and hexokinase (HK), and promoted the accumulation of soluble sugars. Meanwhile, the downregulation of HK and upregulation of plastidic phosphoglucomutase reduced the carbon flow through glycolysis and promoted glycogenesis. The downregulation of OsbZIP58 and the deleterious effect on ribosome formation might result in the reduction of storage protein synthesis and increased free amino acids content in ss3a. The higher levels of amylose and lipids could form more amylose-lipid complexes (starch phospholipids), resulting in a higher resistant starch content. Taken together, our study unraveled a functional cross talk between starch, protein and lipids in rice endosperm during seed development of ss3a, providing new insights for formation of high resistant starch in rice.

The LCG1-OsBP5/OsEBP89-Wx module regulates the grain chalkiness and taste quality in rice

It is well known that the overall quality of japonica/geng rice is superior to that of indica/xian rice varieties. However, the molecular mechanisms underlying the quality disparities between these two subspecies of rice are still largely unknown. In this study, we have pinpointed a gene homologous to SLR1, termed LCG1, exhibiting significant expression during early caryopsis development and playing a specific role in regulating rice chalkiness and taste by affecting the accumulation of grain storage components, starch granule structure and chain length distribution of amylopectin. LCG1 physically interacts with OsBP5 and indirectly influences the expression of the amylose synthesis gene Waxy (Wx) by hindering the transcriptional activity of the OsBP5/OsEBP89 complex. Notably, sequence variations in the promoter region of LCG1 result in enhanced transcription in japonica rice accessions. This leads to elevated LCG1 expression in CSSL-LCG1Nip, thereby enhancing rice quality. Our research elucidates the molecular mechanism underlying the impact of the LCG1-OsBP5/OsEBP89-Wx regulatory pathway on rice chalkiness and taste quality, offering new genetic resources for improving the indica rice quality.

Phenotypic evolution of appearance quality and cooking and taste quality of hybrid rice over the past 40 years in China

Since the inception of hybrid rice technology 50 years ago, it has not only substantially increased rice yield per unit area but also expedited the development of high-quality rice varieties. However, the evolutionary characteristics of hybrid rice quality remain unclear. To address this gap, it is imperative to leverage more representative and comprehensive hybrid rice resources to analyze phenotypic variation diversity and its primary genetic basis, thereby offering more efficient guidance for molecular breeding. In this study, we selected 2,618 hybrid rice varieties that have been nationally or provincially approved in China over the past 40 years. We analyzed the ecological and chronological evolution characteristics of eight rice quality-related traits: grain length, grain width, grain length-width ratio, chalky grain ratio, chalkiness degree, alkali spreading value, gel consistency, and amylose content (AC). Additionally, we utilized the 'Rice-Navi' system to evaluate the primary molecular basis underlying this evolution. The results revealed that among the eight traits, the coefficient of variation for chalkiness degree was the highest at 0.88, whereas the lowest value of 0.07 was observed for grain width. Significant correlations were found among these traits. The phenotypic evolution results for six major ecological types-Early-season cultivation of indica in South China, Late-season cultivation of indica in South China, Mid-season cultivation of indica in the upper reaches of the Yangtze River, Early-season cultivation of indica in the middle and lower reaches of the Yangtze River, Mid-season cultivation of indica in the middle and lower reaches of the Yangtze River, and Late-season cultivation of indica in the middle and lower reaches of the Yangtze River-indicated that, except for E4, the quality of rice in the other five major ecological types exhibited a significant chronological improvement trend. This trend was highly correlated with the utilization of major superior alleles. Concurrently, the primary genetic background of hybrid rice quality displayed certain ecological diversity characteristics. Overall, this study elucidated the evolutionary characteristics of appearance quality and cooking and taste quality of hybrid rice in southern China from both ecological and chronological perspectives, providing valuable data support for the efficient molecular improvement of rice quality.

Engineering rice genomes towards green super rice

Rice, cultivated for millennia across diverse geographical regions, has witnessed tremendous advancements in recent decades, epitomized by the emergence of Green Super Rice. These efforts aim to address challenges such as climate change, pest and disease threats, and sustainable agriculture. Driven by the advent of multiomics big data, breakthroughs in genomic tools and resources, hybrid rice breeding techniques, and the extensive utilization of green genes, rice genomes are undergoing delicate modifications to produce varieties with high yield, superior quality, enhanced nutrient efficiency, and resilience to pests and environmental stresses, leading to the development of green agriculture in China. Additionally, the utilization of wild relatives and the promotion of genomic breeding approaches have further enriched our understanding of rice improvement. In the future, international efforts to develop next-generation green rice varieties remain both challenging and imperative for the whole community.

Manipulating hormones to mitigate trade-offs in crops

Addressing trait coupling due to gene pleiotropy presents challenges in conventional breeding system. However, targeted hormonal manipulation and precise genetic engineering designs hold promise to alleviate trade‐offs and unlock the potential of crops for multiple desirable traits.

Beat the heat: Breeding, genomics, and gene editing for high nighttime temperature tolerance in rice

High nighttime temperature (HNT) is a major obstacle in rice production worldwide. It severely impacts spikelet fertility and induces grain chalk, the two undesirable factors leading to yield and quality decline in rice. Recently, major efforts have been undertaken to understand the genetic mechanisms underlying HNT tolerance. Here, we highlight phenotypic diversity and recent studies on breeding, genomics, and gene editing targeting this trait. These studies point to the challenges in the process as HNT tolerance has so far been found only in non-adapted varieties, and no known modern cultivar bred in the United States is able to withstand exposure to HNT during the reproductive stage. At the same time, identification of the tolerant genotypes enabled genomics, opened up tortuous but promising approaches for breeding, and showed a path for gene editing towards HNT tolerance. The recent advances have set a strong foundation for addressing this current and looming threat.

An Integrative Analysis of the Transcriptome and Proteome of Rice Grain Chalkiness Formation Under High Temperature

Exposure to high temperatures can impair the grain-filling process in rice (Oryza sativa L.), potentially leading to the formation of chalky endosperm, but the molecular regulation mechanism remains largely elusive. Here, we reported that high-temperature (HT) stress (day/night, 35 °C/30 °C) reduces both the grain-filling rate and grain weight of Ningjing 1 variety compared to normal temperatures (NT, day/night, 28 °C/23 °C). Grains under HT stress exhibited an opaque, milky-white appearance, alongside significant alterations in starch physicochemical properties. An integrated transcriptomic analysis of grains under HT revealed up-regulation of genes related to defense mechanisms and oxidoreductase activity, while genes involved in sucrose and starch synthesis were down-regulated, and α-amylase genes were up-regulated. Proteomic analysis of grains under HT echoed this pattern. These results demonstrate that high temperature during the grain-filling stage significantly increases rice chalkiness by down-regulating genes related to sucrose and starch synthesis, while up-regulating those involved in starch degradation.

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.

Breaking the yield-quality tradeoff: OsNLP3 in rice

A recent study by Sun et al. OsNLP3 enhances grain weight and reduces grain chalkiness in rice sheds new insight on the crucial role of OsNLP3 in regulating grain weight and chalkiness through its interaction with OsCEP6.1 and OsNF-YA8 and suppress their expression. The research reveals a promising pathway for developing strategies to reduce chalkiness while enhancing grain yield, paving the way for improved rice crop productivity.

Natural variation of WBR7 confers rice high yield and quality by modulating sucrose supply in sink organs

Grain chalkiness is an undesirable trait that negatively regulates grain yield and quality in rice. However, the regulatory mechanism underlying chalkiness is complex and remains unclear. We identified a positive regulator of white-belly rate (WBR). The WBR7 gene encodes sucrose synthase 3 (SUS3). A weak functional allele of WBR7 is beneficial in increasing grain yield and quality. During the domestication of indica rice, a functional G/A variation in the coding region of WBR7 resulted in an E541K amino acid substitution in the GT-4 glycosyltransferase domain, leading to a significant decrease in decomposition activity of WBR7A (allele in cultivar Jin23B) compared with WBR7G (allele in cultivar Beilu130). The NIL(J23B) and knockout line NIL(BL130)KO exhibited lower WBR7 decomposition activity than that of NIL(BL130) and NIL(J23B)COM, resulting in less sucrose decomposition and metabolism in the conducting organs. This caused more sucrose transportation to the endosperm, enhancing the synthesis of storage components in the endosperm and leading to decreased WBR. More sucrose was also transported to the anthers, providing sufficient substrate and energy supply for pollen maturation and germination, ultimately leading to an increase rate of seed setting and increased grain yield. Our findings elucidate a mechanism for enhancing rice yield and quality by modulating sucrose metabolism and allocation, and provides a valuable allele for improved rice quality.

OsNLP3 enhances grain weight and reduces grain chalkiness in rice

Grain weight, a key determinant of yield in rice (Oryza sativa L.), is governed primarily by genetic factors, whereas grain chalkiness, a detriment to grain quality, is intertwined with environmental factors such as mineral nutrients. Nitrogen (N) is recognized for its effect on grain chalkiness, but the underlying molecular mechanisms remain to be clarified. This study revealed the pivotal role of rice NODULE INCEPTION-LIKE PROTEIN 3 (OsNLP3) in simultaneously regulating grain weight and grain chalkiness. Our investigation showed that loss of OsNLP3 leads to a reduction in both grain weight and dimension, in contrast to the enhancement observed with OsNLP3 overexpression. OsNLP3 directly suppresses the expression of OsCEP6.1 and OsNF-YA8, which were identified as negative regulators associated with grain weight. Consequently, two novel regulatory modules, OsNLP3-OsCEP6.1 and OsNLP3-OsNF-YA8, were identified as key players in grain weight regulation. Notably, the OsNLP3-OsNF-YA8 module not only increases grain weight but also mitigates grain chalkiness in response to N. This research clarifies the molecular mechanisms that orchestrate grain weight through the OsNLP3-OsCEP6.1 and OsNLP3-OsNF-YA8 modules, highlighting the pivotal role of the OsNLP3-OsNF-YA8 module in alleviating grain chalkiness. These findings reveal potential targets for simultaneous enhancement of rice yield and quality.

The OsGAPC3 mutation significantly affects grain quality traits and improves the nutritional quality of rice

The glycolytic enzyme cytoplasmic glyceraldehyde-3-phosphate dehydrogenase (GAPC3) is involved in multiple biological processes in plants, including transcriptional regulation, and material metabolism. However, the relationship between OsGAPC3 and the quality traits of rice is poorly understood. Here we identify OsGAPC3 mutations that enhance the protein content and grain nutritional quality of rice by regulating the OsAAP6 gene expression. The number and volume of type-II protein bodies in the endosperm of the OsGAPC3 mutants, and GPC increase significantly. We report significant increases in chalkiness area and degree, and decreases for starch content, gel consistency, and taste value. Results of proteomic detection and analysis reveal that OsGAPC3 affects the major storage substances (proteins and starch) metabolism in rice, and the accumulation of proteins and starch in the endosperm. Additionally, the OsGAPC3 mutation significantly decreases the rice-seedling salt tolerance. Therefore, OsGAPC3 affects multiple quality traits of rice, participates in regulating rice-seedling salt-stress response. These data can be used to design better-quality and stronger salt-resistant rice varieties.

Knocking out isopropylmalate synthase simultaneously improves grain appearance and nutritional quality in rice

Grain appearance and nutritional quality are critical traits for rice marketing. However, how to simultaneously improve grain appearance (slender grain and low chalkiness) and nutritional quality (improved protein and amino acid contents) in rice remains a major challenge. Here, we show that knocking out rice isopropylmalate synthase genes OsIPMS1 and OsIPMS2 can improve both grain appearance and nutritional quality. We find that OsIPMS1 directly interacts with OsIPMS2 to form heterodimers. Meanwhile, we observe that OsIPMS1 and OsIPMS2 influence the expression of genes previously reported to be involved in the determination of grain size and nutritional quality in the developing panicles and grains. Furthermore, we show that Osipms1/2 double mutants exhibit significantly improved grain appearance and nutritional quality in polished rice in both the japonica (Wuyungeng 23) and indica (Huanghuazhan) varieties. Our findings indicate that OsIPMS is a useful target gene for breeding of rice varieties appealing for marketing and with health-benefiting properties.

Application of CRISPR/Cas9 system to knock out GluB gene for developing low glutelin rice mutant

The nutritional quality improvement is among the most integral objective for any rice molecular breeding programs. The seed storage proteins (SSPs) have greater role to determine the nutritional quality of any cereal grains. Rice contains relatively balanced amino acid composition and the SSPs are fractioned into albumins (ALB), globulins (GLO), prolamins (PRO) and glutelins (GLU) according to differences in solubility. GLUs are further divided into subfamilies: GluA, GluB, GluC, and GluD depending on resemblance in amino acid. The GLU protein accounts for 60-80% of total protein contents, encoded by 15 genes located on different chromosomes of rice genome. The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system was employed to knockout Glu-B (LOC-Os02g15070) gene in non-basmati rice PK386 cultivar. The mutant displayed two base pair and three base pair mutation in the targeted regions. The homozygous mutant plant displayed reduction for both in total protein contents and GLU contents whereas, elevation in GLO, ALB and PRO. Moreover, the mutant plant also displayed reduction in physio-chemical properties e.g., total starch, amylose and gel consistency. The agronomic characteristics of both mutant and wild type displayed non-significant differences along with increase in higher percentage of chalkiness in mutant plants. The results obtained from scanning electron microscopy showed the loosely packed starch granules compared to wild type. The gene expression analysis displayed the lower expression of gene at 5 days after flowering (DAF), 10 DAF, 15 DAF and 20 DAF compared to wild type. GUS sub-cellular localization showed the staining in seed which further validated the results obtained from gene expression. Based on these findings it can be concluded Glu-B gene have significant role in controlling GLU contents and can be utilized in breeding programs to enhance the nutritional quality of rice, and may serve as healthy diet for patient allergic with high GLU contents.

Profiling and Improvement of Grain Quality Traits for Consumer Preferable Basmati Rice in the United States

Basmati rice is a premium aromatic rice that consumers choose primarily because of its distinct aroma and excellent grain quality. The grain quality of Basmati rice (GQBR) reflects the perspectives of producers, processors, sellers, and consumers related to the production, processing, marketing, and consumption of Basmati rice. Consumers, an invaluable part of the production demand and value chain of the Basmati rice industry, have the freedom to choose from different types of aromatic rice. Consumers expect their preferred Basmati rice to possess all superior rice grain qualities, including the physical, biochemical, and physiological properties. Gene functional analysis explained that a 10-base pair deletion in the promoter region of the OsSPL16 gene causes the slender grains in Basmati rice, whereas an 8-base-pair deletion in exon 7 of the OsBadh2 gene (located in the fgr region on rice chromosome 8) results in the distinct aroma. Furthermore, a combination of the genetic characteristics of the gw8 and gs3 genes has led to the creation of a long-grain Basmati-type rice cultivar. It has also been demonstrated that agricultural, genetic, and environmental conditions significantly influence GQBR. Hence, research on improving GQBR requires a multidimensional approach and sophisticated elements due to the complexity of its nature and preference diversity. This review covers the basic definitions of grain quality traits, consumer preference criteria, influencing factors, and strategies for producing superior-quality Basmati rice in the United States. This knowledge will be useful in improving the grain quality of Basmati and Basmati-type rice, as well as developing appropriate breeding programs that will meet the preferences of different countries and cultures.

Generation of Two-Line Restorer Line with Low Chalkiness Using Knockout of Chalk5 through CRISPR/Cas9 Editing

Chalkiness is an important grain quality trait in rice. Chalk5, encoding a vacuolar H+-translocating pyrophosphatase, is a major gene affecting both the percentage of grains with chalkiness (PGWC) and chalkiness degree (DEC) in rice. Reducing its expression can decrease both PGEC and DEC. In this study, the first exon of Chalk5 was edited in the elite restorer line 9311 using the CRISPR/Cas9 system and two knockout mutants were obtained, one of which did not contain the exogenous Cas9 cassette. PGWC and DEC were both significantly reduced in both mutants, while the seed setting ratio (SSR) was also significantly decreased. Staggered sowing experiments showed that the chalkiness of the mutants was insensitive to temperature during the grain-filling stage, and the head milled rice rate (HMRR) could be improved even under high-temperature conditions. Finally, in the hybrid background, the mutants showed significantly reduced PGWC and DEC without changes in other agronomic traits. The results provide important germplasm and allele resources for breeding high-yield rice varieties with superior quality, especially for high-yield indica hybrid rice varieties with superior quality in high-temperature conditions.

Comparative Proteomic Analysis Provides New Insights into Improved Grain-filling in Ratoon Season Rice

Grain-filling of rice spikelets (particularly for the later flowering inferior spikelets) is an important characteristic that affects both quality and yield. Rice ratooning technology is used to cultivate a second crop from dormant buds that sprout from stubble left after the first harvest. This study used two rice varieties, the conventional indica rice 'Jinhui 809' and the hybrid indica-japonica rice 'Yongyou 1540', to assess the impact of rice ratooning on grain-filling. The results indicated that the grain-filling process in inferior spikelets of ratoon season rice (ISR) showed significant improvement compared to inferior spikelets of main crop (late season) rice (ISL). This improvement was evident in the earlier onset of rapid grain-filling, higher seed-setting percentage, and improved grain quality. A label-free quantitative proteomic analysis using mass spectrometry identified 1724 proteins with significant abundance changes, shedding light on the molecular mechanisms behind the improved grain-filling in ISR. The functional analysis of these proteins indicated that ratooning stimulated the metabolic processes of sucrose-starch, trehalose, and hormones in rice inferior spikelets, leading to enhanced enzyme activities related to starch synthesis, elevated concentrations of trehalose-6-phosphate (T6P), indole-3-acetic acid (IAA) and zeatin riboside (ZR) during the active grain-filling phase. This research highlighted the importance of the GF14f protein as a key regulator in the grain-filling process of ISR. It revealed that GF14f transcriptional and protein levels declined more rapidly in ISR compared to ISL during grain-filling. Additionally, the GF14f-RNAi plants specific to the endosperm exhibited improved quality in inferior spikelets. These findings suggest that the enhancement of starch synthesis, increased levels of IAA, ZR, and T6P, along with the rapid decrease in GF14f protein, play a role in enhancing grain-filling in ratoon season rice.

Improving Rice Grain Quality Through Ecotype Breeding for Enhancing Food and Nutritional Security in Asia-Pacific Region

Rice grain is widely consumed as a staple food, providing essential nutrition for households, particularly marginalized families. It plays a crucial role in ensuring food security, promoting human nutrition, supporting good health, and contributing to global food and nutritional security. Addressing the diverse quality demands of emerging diverse and climate-risked population dietary needs requires the development of a single variety of rice grain that can meet the various dietary and nutritional requirements. However, there is a lack of concrete definition for rice grain quality, making it challenging to cater to the different demands. The lack of sufficient genetic study and development in improving rice grain quality has resulted in widespread malnutrition, hidden hunger, and micronutrient deficiencies affecting a significant portion of the global population. Therefore, it is crucial to identify genetically evolved varieties with marked qualities that can help address these issues. Various factors account for the declining quality of rice grain and requires further study to improve their quality for healthier diets. We characterized rice grain quality using Lancastrians descriptor and a multitude of intrinsic and extrinsic quality traits. Next, we examined various components of rice grain quality favored in the Asia-Pacific region. This includes preferences by different communities, rice industry stakeholders, and value chain actors. We also explored the biological aspects of rice grain quality in the region, as well as specific genetic improvements that have been made in these traits. Additionally, we evaluated the factors that can influence rice grain quality and discussed the future directions for ensuring food and nutritional security and meeting consumer demands for grain quality. We explored the diverse consumer bases and their varied preferences in Asian-Pacific countries including India, China, Nepal, Bhutan, Vietnam, Sri Lanka, Pakistan, Thailand, Cambodia, Philippines, Bangladesh, Indonesia, Korea, Myanmar and Japan. The quality preferences encompassed a range of factors, including rice head recovery, grain shape, uniform size before cooking, gelatinization, chalkiness, texture, amylose content, aroma, red-coloration of grain, soft and shine when cooked, unbroken when cooked, gelatinization, less water required for cooking, gelatinization temperature (less cooking time), aged rice, firm and dry when cooked (gel consistency), extreme white, soft when chewed, easy-to-cook rice (parboiled rice), vitamins, and minerals. These preferences were evaluated across high, low, and medium categories. A comprehensive analysis is provided on the enhancement of grain quality traits, including brown rice recovery, recovery rate of milled rice, head rice recovery, as well as morphological traits such as grain length, grain width, grain length-width ratio, and grain chalkiness. We also explored the characteristics of amylose, gel consistency, gelatinization temperature, viscosity, as well as the nutritional qualities of rice grains such as starch, protein, lipids, vitamins, minerals, phytochemicals, and bio-fortification potential. The various factors that impact the quality of rice grains, including pre-harvest, post-harvest, and genotype considerations were explored. Additionally, we discussed the future direction and genetic strategies to effectively tackle these challenges. These qualitative characteristics represent the fundamental focus of regional and national breeding strategies employed by different countries to meet consumer preference. Given the significance of rice as a staple food in Asia-Pacific countries, it is primarily consumed domestically, with only a small portion being exported internationally. All the important attributes must be clearly defined within specific parameters. It is crucial for geneticists and breeders to develop a rice variety that can meet the diverse demands of consumers worldwide by incorporating multiple desirable traits. Thus, the goal of addressing global food and nutritional security, and human healthy can be achieved.

OsG6PGH1 affects various grain quality traits and participates in the salt stress response of rice

Cytoplasmic 6-phosphogluconate dehydrogenase (G6PGH) is a key enzyme in the pentose phosphate pathway that is involved in regulating various biological processes such as material metabolism, and growth and development in plants. However, it was unclear if OsG6PGH1 affected rice grain quality traits. We perform yeast one-hybrid experiments and reveal that OsG6PGH1 may interact with OsAAP6. Subsequently, yeast in vivo point-to-point experiments and local surface plasmon resonance experiments verified that OsG6PGH1 can bind to OsAAP6. OsG6PGH1 in rice is a constitutive expressed gene that may be localized in the cytoplasm. OsAAP6 and protein-synthesis metabolism-related genes are significantly upregulated in OsG6PGH1 overexpressing transgenic positive endosperm, corresponding to a significant increase in the number of protein bodies II, promoting accumulation of related storage proteins, a significant increase in grain protein content (GPC), and improved rice nutritional quality. OsG6PGH1 positively regulates amylose content, negatively regulates chalkiness rate and taste value, significantly affects grain quality traits such as appearance, cooking, and eating qualities of rice, and is involved in regulating the expression of salt stress related genes, thereby enhancing the salt-stress tolerance of rice. Therefore, OsG6PGH1 represents an important genetic resource to assist in the design of high-quality and multi-resistant rice varieties.

Genome-wide association mapping of quantitative trait loci for chalkiness-related traits in rice (Oryza sativa L.)

Grain chalkiness directly affects the commercial value of rice. Genes related to chalkiness reported thus far have been discovered in mutants, but it has not been identified whether these genes can be used to improve rice quality by breeding. Therefore, discovering more quantitative trait loci (QTLs) or genes related to chalkiness in the rice germplasm is necessary. This study entails a genome-wide association study on the degree of endosperm chalkiness (DEC) and percentage of grains with chalkiness (PGWC) by combining 1.2 million single-nucleotide polymorphisms (SNPs) with the phenotypic data of 173 rice accessions. Thirteen QTLs for DEC and nine for PGWC were identified, of which four were detected simultaneously for both DEC and PGWC; further, qDEC11/qPGWC11 was identified as the major QTL. By combining linkage disequilibrium analysis and SNP information, LOC_Os11g10170 was identified as the candidate gene for DEC. There were significant differences among the haplotypes of LOC_Os11g10170, and the Hap 1 of LOC_Os11g10170 was observed to reduce the DEC by 6.19%. The qRT-PCR results showed that the gene expression levels in accessions with high DEC values were significantly higher than those in accessions with low DEC values during days 21-42 after flowering, with a maximum at 28 days. These results provide molecular markers and germplasm resources for genetic improvement of the chalkiness-related traits in rice.

Rapid improvement of grain appearance in three-line hybrid rice via CRISPR/Cas9 editing of grain size genes

KEY MESSAGE

Genetic editing of grain size genes quickly improves three-line hybrid rice parents to increase the appearance quality and yield of hybrid rice. Grain size affects rice yield and quality. In this study, we used CRISPR/Cas9 to edit the grain size gene GW8 in the maintainer line WaitaiB (WTB) and restorer line Guanghui998 (GH998). The new slender sterile line WTEA (gw8) was obtained in the BC2F1 generation by transferring the grain mutation of the maintainer plant to the corresponding sterile line WantaiA (WTA, GW8) in the T1 generation. Two slender restorer lines, GH998E1 (gw8(II)) and GH998E2 (gw8(I)), were obtained in T1 generation. In the early stage, new sterile and restorer lines in grain mutations were created by targeted editing of GS3, TGW3, and GW8 genes. These parental lines were mated to detect the impact of grain-type mutations on hybrid rice yield and quality. Mutations in gs3, gw8, and tgw3 had a minimal impact on agronomic traits except the grain size and thousand-grain weight. The decrease in grain width in the combination mainly came from gw8/gw8, gs3/gs3 increased the grain length, gs3/gs3-gw8/gw8 had a more significant effect on the grain length, and gs3/gs3-gw8/gw8(I) contributed more to grain length than gs3/gs3-gw8/gw8(II). The heterozygous TGW3/tgw3 may not significantly increase grain length. Electron microscopy revealed that the low-chalky slender-grain variety had a cylindrical grain shape, a uniform distribution of endosperm cells, and tightly arranged starch grains. Quantitative fluorescence analysis of endospermdevelopment-related genes showed that the combination of slender grain hybrid rice caused by gs3 and gw8 mutations promoted endosperm development and improved appearance quality. An appropriate grain size mutation resulted in hybrid rice varieties with high yield and quality.

Genetic Effects of Grain Quality Enhancement in Indica Hybrid Rice: Insights for Molecular Design Breeding

Improving rice quality remains a crucial breeding objective, second only to enhancing yield, yet progress in quality improvement lags behind yield. The high temperature and ripening conditions in Southern China often result in poor rice quality, impacting hybrid rice production and utilization. Therefore, to address this challenge, analyzing the molecular basis of high-quality traits is essential for molecular design breeding of high-quality hybrid rice varieties. In this study, we investigated the molecular basis of grain shape, amylose content, gel consistency, gelatinization temperature, and aroma, which influence rice quality. We discovered that quality related alleles gs3, GW7TFA, gw8, chalk5, Wxb, ALKTT, and fgr can enhance rice quality when applied in breeding programs. Polymerization of gs3, GW7TFA, gw8, and chalk5 genes improves rice appearance quality. The gs3 and GW7TFA allele polymerization increasing the grain's length-width ratio, adding the aggregation of gw8 allele can further reducing grain width. The chalk5 gene regulates low chalkiness, but low correlation to chalkiness was exhibited with grain widths below 2.0 mm, with minimal differences between Chalk5 and chalk5 alleles. Enhancing rice cooking and eating quality is achieved through Wxb and ALKTT gene polymerization, while introducing the fgr(E7) gene significantly improved rice aroma. Using molecular marker-assisted technology, we aggregated these genes to develop a batch of indica hybrid rice parents with improved rice quality are obtained. Cross-combining these enhanced parents can generate new, high-quality hybrid rice varieties suitable for cultivation in Southern China. Therefore, our findings contribute to a molecular breeding model for grain quality improvement in high-quality indica hybrid rice. This study, along with others, highlights the potential of molecular design breeding for enhancing complex traits, particularly rice grain quality.

Enhancing grain shape, thermotolerance, and alkaline tolerance via Gγ protein manipulation in rice

KEY MESSAGE

Our findings highlight a valuable breeding resource, demonstrating the potential to concurrently enhance grain shape, thermotolerance, and alkaline tolerance by manipulating Gγ protein in rice. Temperate Geng/Japonica (GJ) rice yields have improved significantly, bolstering global food security. However, GJ rice breeding faces challenges, including enhancing grain quality, ensuring stable yields at warmer temperatures, and utilizing alkaline land. In this study, we employed CRISPR/Cas9 gene-editing technology to knock out the GS3 locus in seven elite GJ varieties with superior yield performance. Yield component measurements revealed that GS3 knockout mutants consistently enhanced grain length and reduced plant height in diverse genetic backgrounds. The impact of GS3 on the grain number per panicle and setting rate depended on the genetic background. GS3 knockout did not affect milling quality and minimally altered protein and amylose content but notably influenced chalkiness-related traits. GS3 knockout indiscriminately improved heat and alkali stress tolerance in the GJ varieties studied. Transcriptome analysis indicated differential gene expression between the GS3 mutants and their wild-type counterparts, enriched in biological processes related to photosynthesis, photosystem II stabilization, and pathways associated with photosynthesis and cutin, suberine, and wax biosynthesis. Our findings highlight GS3 as a breeding resource for concurrently improving grain shape, thermotolerance, and alkaline tolerance through Gγ protein manipulation in rice.

Integration of molecular breeding and multi-resistance screening for developing a promising restorer line Guihui5501 with heavy grain, good grain quality, and endurance to biotic and abiotic stresses

Rice, a critical staple on a global scale, faces escalating challenges in yield preservation due to the rising prevalence of abiotic and biotic stressors, exacerbated by frequent climatic fluctuations in recent years. Moreover, the scorching climate prevalent in the rice-growing regions of South China poses obstacles to the cultivation of good-quality, heavy-grain varieties. Addressing this dilemma requires the development of resilient varieties capable of withstanding multiple stress factors. To achieve this objective, our study employed the broad-spectrum blast-resistant line Digu, the brown planthopper (BPH)-resistant line ASD7, and the heavy-grain backbone restorer lines Fuhui838 (FH838) and Shuhui527 (SH527) as parental materials for hybridization and multiple crossings. The incorporation of molecular markers facilitated the rapid pyramiding of six target genes (Pi5, Pita, Pid2, Pid3, Bph2, and Wxb ). Through a comprehensive evaluation encompassing blast resistance, BPH resistance, cold tolerance, grain appearance, and quality, alongside agronomic trait selection, a promising restorer line, Guihui5501 (GH5501), was successfully developed. It demonstrated broad-spectrum resistance to blast, exhibiting a resistance frequency of 77.33% against 75 artificially inoculated isolates, moderate resistance to BPH (3.78 grade), strong cold tolerance during the seedling stage (1.80 grade), and characteristics of heavy grains (1,000-grain weight reaching 35.64 g) with good grain quality. The primary rice quality parameters for GH5501, with the exception of alkali spreading value, either met or exceeded the second-grade national standard for premium edible rice varieties, signifying a significant advancement in the production of good-quality heavy-grain varieties in the southern rice-growing regions. Utilizing GH5501, a hybrid combination named Nayou5501, characterized by high yield, good quality, and resistance to multiple stresses, was bred and received approval as a rice variety in Guangxi in 2021. Furthermore, genomic analysis with gene chips revealed that GH5501 possessed an additional 20 exceptional alleles, such as NRT1.1B for efficient nitrogen utilization, SKC1 for salt tolerance, and STV11 for resistance to rice stripe virus. Consequently, the restorer line GH5501 could serve as a valuable resource for the subsequent breeding of high-yielding, good-quality, and stress-tolerant hybrid rice varieties.

The elite eating quality alleles Wxb and ALKb are regulated by OsDOF18 and coordinately improve head rice yield

Head rice yield (HRY) measures rice milling quality and determines final grain yield and commercial value. Here, we report that two major quantitative trait loci for milling quality in rice, qMq-1 and qMq-2, represent allelic variants of Waxylv/Waxyb (hereafter Wx) encoding Granule-Bound Starch Synthase I (GBSSI) and Alkali Spreading Value ALKc/ALKb encoding Soluble Starch Synthase IIa (SSIIa), respectively. Complementation and overexpression transgenic lines in indica and japonica backgrounds confirmed that Wx and ALK coordinately regulate HRY by affecting amylose content, the number of amylopectin branches, amyloplast size, and thus grain filling and hardness. The transcription factor OsDOF18 acts upstream of Wx and ALK by activating their transcription. Furthermore, rice accessions with Wxb and ALKb alleles showed improved HRY over those with Wxlv and ALKc. Our study not only reveals the novel molecular mechanism underlying the formation of HRY but also provides a strategy for breeding rice cultivars with improved HRY.

The GW5-WRKY53-SGW5 module regulates grain size variation in rice

Grain size is a crucial agronomic trait that affects stable yield, appearance, milling quality, and domestication in rice. However, the molecular and genetic relationships among QTL genes (QTGs) underlying natural variation for grain size remain elusive. Here, we identified a novel QTG SGW5 (suppressor of gw5) by map-based cloning using an F2 segregation population by fixing same genotype of the master QTG GW5. SGW5 positively regulates grain width by influencing cell division and cell size in spikelet hulls. Two nearly isogenic lines exhibited a significant differential expression of SGW5 and a 12.2% increase in grain yield. Introducing the higher expression allele into the genetic background containing the lower expression allele resulted in increased grain width, while its knockout resulted in shorter grain hulls and dwarf plants. Moreover, a cis-element variation in the SGW5 promoter influenced its differential binding affinity for the WRKY53 transcription factor, causing the differential SGW5 expression, which ultimately leads to grain size variation. GW5 physically and genetically interacts with WRKY53 to suppress the expression of SGW5. These findings elucidated a new pathway for grain size regulation by the GW5-WRKY53-SGW5 module and provided a novel case for generally uncovering QTG interactions underlying the genetic diversity of an important trait in crops.

Pleiotropic Effects of miR5504 Underlying Plant Height, Grain Yield and Quality in Rice

MicroRNAs (miRNAs) are known to play critical roles in regulating rice agronomic traits through mRNA cleavage or translational repression. Our previous study indicated that miR5504 regulates plant height by affecting cell proliferation and expansion. Here, the two independent homozygous mir5504 mutants (CR1 and CR2) and overexpression lines (OE1 and OE2) were further used to investigate the functions of miR5504. The panicle length, 1000-grain weight and grain yield per plant of miR5504-OE lines were identical to those of Nipponbare (NIP), but the 1000-grain weight of mir5504 mutants was reduced by about 10% and 9%, respectively. Meanwhile, the grain width and thickness of mir5504 mutants decreased significantly by approximately 10% and 11%, respectively. Moreover, the cytological results revealed a significant decrease in cell number along grain width direction and cell width in spikelet in mir5504, compared with those in NIP. In addition, several major storage substances of the rice seeds were measured. Compared to NIP, the amylose content of the mir5504 seeds was noticeably decreased, leading to an increase of nearly 10 mm in gel consistency (GC) in mir5504 lines. Further investigation confirmed that LOC_Os08g16914 was the genuine target of miR5504: LOC_Os08g16914 over-expression plants phenocopied the mir5504 mutants. This study provides insights into the role of miR5504 in rice seed development.

Identifying the Quantitative Trait Locus and Candidate Genes of Traits Related to Milling Quality in Rice via a Genome-Wide Association Study

Milling quality directly affects production efficiency in rice, which is closely related to the brown rice recovery (BRR), the milled rice recovery (MRR) and the head milled rice recovery (HMRR). The present study investigated these three traits in 173 germplasms in two environments, finding abundant phenotypic variation. Three QTLs for BRR, two for MRR, and three for HMRR were identified in a genome-wide association study, five of these were identified in previously reported QTLs and three were newly identified. By combining the linkage disequilibrium (LD) analyses, the candidate gene LOC_Os05g08350 was identified. It had two haplotypes with significant differences and Hap 2 increased the BRR by 4.40%. The results of the qRT-PCR showed that the expression of LOC_Os05g08350 in small-BRR accessions was significantly higher than that in large-BRR accessions at Stages 4-5 of young panicle development, reaching the maximum value at Stage 5. The increase in thickness of the spikelet hulls of the accession carrying LOC_Os05g08350TT occurred due to an increase in the cell width and the cell numbers in cross-sections of spikelet hulls. These results help to further clarify the molecular genetic mechanism of milling-quality-related traits and provide genetic germplasm materials for high-quality breeding in rice.

OsAAP8 mutation leads to significant improvement in the nutritional quality and appearance of rice grains

Members of the permease gene family are responsible for important biological functions in the growth and development of rice. Here, we show that OsAAP8 is a constitutive expression gene, and its translated protein is localized on the cell membrane. Mutation of the OsAAP8 can promote the expression of genes related to protein and amylopectin synthesis, and also promote the enlargement of protein bodies in its endosperm, leading to an increase in the protein, amylopectin, and total amino acid content of grains in OsAAP8 mutants. Seeds produced by the OsAAP8 mutant were larger, and the chalkiness traits of the OsAAP8 mutants were significantly reduced, thereby improving the nutritional quality and appearance of rice grains. The OsAAP8 protein is involved in the transport of various amino acids; OsAAP8 mutation significantly enhanced the root absorption of a range of amino acids and might affect the distribution of various amino acids. Therefore, OsAAP8 is an important quality trait gene with multiple biological functions, which provides important clues for the molecular design of breeding strategies for developing new high-quality varieties of rice.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-024-01473-w.

QTL Analysis for Rice Quality-Related Traits and Fine Mapping of qWCR3

The quality of rice, evaluated using multiple quality-related traits, is the main determinant of its market competitiveness. In this study, two japonica rice varieties with significant differences in quality-related traits were used as parents to construct two populations, BC3F2 and BC3F2:3, with Kongyu131 (KY131) as the recurrent parent. A genetic linkage map was constructed using the BC3F2 population based on 151 pairs of SSR/InDel polymorphic markers selected between the parents. Grain-shape-related traits (grain length GL, grain width GW, and length-to-width ratio LWR), chalkiness-related traits (white-core rate WCR, white-belly rate WBR, white-back rate BR, and chalkiness rate CR), and amylose content (AC) were investigated in the two populations in 2017 and 2018. Except for BR and CR, the traits showed similar characteristics with a normal distribution in both populations. Genetic linkage analysis was conducted for these quality-related traits, and a total of 37 QTLs were detected in the two populations. Further validation was performed on the newly identified QTLs with larger effects, and three grain shape QTLs and four chalkiness QTLs were successfully validated in different environments. One repeatedly validated QTL, qWCR3, was selected for fine mapping and was successfully narrowed down to a 100 kb region in which only two genes, LOC_0s03g45210 and LOC_0s03g45320, exhibited sequence variations between the parents. Furthermore, the variation of LOC_Os03g45210 leads to a frameshift mutation and premature protein termination. The results of this study provide a theoretical basis for positional cloning of the qWCR3 gene, thus offering new genetic resources for rice quality improvement.

Moderate Salinity Stress Affects Rice Quality by Influencing Expression of Amylose- and Protein-Content-Associated Genes

Salinity is an environmental stress that severely impacts rice grain yield and quality. However, limited information is available on the molecular mechanism by which salinity reduces grain quality. In this study, we investigated the milling, appearance, eating and cooking, and nutritional quality among three japonica rice cultivars grown either under moderate salinity with an electrical conductivity of 4 dS/m or under non-saline conditions in a paddy field in Dongying, Shandong, China. Moderate salinity affected rice appearance quality predominantly by increasing chalkiness rate and chalkiness degree and affected rice eating and cooking and nutritional quality predominantly by decreasing amylose content and increasing protein content. We compared the expression levels of genes determining grain chalkiness, amylose content, and protein content in developing seeds (0, 5, 10, 15, and 20 days after flowering) of plants grown under saline or non-saline conditions. The chalkiness-related gene Chalk5 was up-regulated and WHITE-CORE RATE 1 was repressed. The genes Nuclear factor Y and Wx, which determine amylose content, were downregulated, while protein-content-associated genes OsAAP6 and OsGluA2 were upregulated by salinity in the developing seeds. These findings suggest some target genes that may be utilized to improve the grain quality under salinity stress conditions via gene-pyramiding breeding approaches.

Enhancing rice panicle branching and grain yield through tissue-specific brassinosteroid inhibition

Crop yield potential is constrained by the inherent trade-offs among traits such as between grain size and number. Brassinosteroids (BRs) promote grain size, yet their role in regulating grain number is unclear. By deciphering the clustered-spikelet rice germplasm, we show that activation of the BR catabolic gene BRASSINOSTEROID-DEFICIENT DWARF3 (BRD3) markedly increases grain number. We establish a molecular pathway in which the BR signaling inhibitor GSK3/SHAGGY-LIKE KINASE2 phosphorylates and stabilizes OsMADS1 transcriptional factor, which targets TERMINAL FLOWER1-like gene RICE CENTRORADIALIS2. The tissue-specific activation of BRD3 in the secondary branch meristems enhances panicle branching, minimizing negative effects on grain size, and improves grain yield. Our study showcases the power of tissue-specific hormonal manipulation in dismantling the trade-offs among various traits and thus unleashing crop yield potential in rice.

Multi-model genome-wide association studies for appearance quality in rice

Improving the quality of the appearance of rice is critical to meet market acceptance. Mining putative quality-related genes has been geared towards the development of effective breeding approaches for rice. In the present study, two SL-GWAS (CMLM and MLM) and three ML-GWAS (FASTmrEMMA, mrMLM, and FASTmrMLM) genome-wide association studies were conducted in a subset of 3K-RGP consisting of 198 rice accessions with 553,831 SNP markers. A total of 594 SNP markers were identified using the mixed linear model method for grain quality traits. Additionally, 70 quantitative trait nucleotides (QTNs) detected by the ML-GWAS models were strongly associated with grain aroma (AR), head rice recovery (HRR, %), and percentage of grains with chalkiness (PGC, %). Finally, 39 QTNs were identified using single- and multi-locus GWAS methods. Among the 39 reliable QTNs, 20 novel QTNs were identified for the above-mentioned three quality-related traits. Based on annotation and previous studies, four functional candidate genes (LOC_Os01g66110, LOC_Os01g66140, LOC_Os07g44910, and LOC_Os02g14120) were found to influence AR, HRR (%), and PGC (%), which could be utilized in rice breeding to improve grain quality traits.

Pyramiding of Low Chalkiness QTLs Is an Effective Way to Reduce Rice Chalkiness

Rice chalkiness is a key limiting factor of high-quality rice. The breeding of low chalkiness varieties has always been a challenging task due to the complexity of chalkiness and its susceptibility to environmental factors. In previous studies, we identified six QTLs for the percentage of grain chalkiness (PGC), named qPGC5, qPGC6, qPGC8.1, qPGC8.2, qPGC9 and qPGC11, using single-segment substitution lines (SSSLs) with genetic background of Huajingxian 74 (HJX74). In this study, we utilized the six low chalkiness QTLs to develop 17 pyramiding lines with 2-4 QTLs. The results showed that the PGC decreased with the increase of QTLs in the pyramiding lines. The pyramiding lines with 4 QTLs significantly reduced the chalkiness of rice and reached the best quality level. Among the six QTLs, qPGC5 and qPGC6 showed greater additive effects and were classified as Group A, while the other four QTLs showed smaller additive effects and were classified as Group B. In pyramiding lines, although the presence of epistasis, additivity remained the main component of QTL effects. qPGC5 and qPGC6 showed stronger ability to reduce rice chalkiness, particularly in the environment of high temperature (HT) in the first cropping season (FCS). Our research demonstrates that by pyramiding low chalkiness QTLs, it is feasible to develop the high-quality rice varieties with low chalkiness at the best quality level even in the HT environment of FCS.

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.

Lipid transfer protein, OsLTPL18, is essential for grain weight and seed germination in rice

Nonspecific lipid transfer proteins (nsLTPs) promote the intermembrane transportation of phospholipids, fatty acids, and steroids, and play diverse roles in various biological processes. However, the potential roles of the rice nsLTPs have not been well elucidated yet. Here, the functions of OsLTPL18 were analyzed using CRISPR/Cas9 strategy and cytological analysis. The osltpl18 (osltpl18-1, osltpl18-2, and osltpl18-3) seeds were thinner, and 1000-grain weight and grain thickness of osltpl18 plants were decreased obviously, compared to the ZH11. Meanwhile, the results of germination assay and 1 % TTC staining showed that vigor of osltpl18 seeds decreased significantly. Furthermore, the results of scanning electron microscopy (SEM) revealed that the cell width of spikelet hull in osltpl18 lines was significantly reduced than that in WT, as well as cell number in grain-width direction. Finally, we found that co-expressed genes were enriched in glucan biosynthesis, protein transporter activity, serine-type endopeptidase inhibitor activity, and nutrient reservoir activity. In this study, we discussed that OsLTPL18 might have coordinating functions in regulation of grain weight and germination in rice.

Negative regulators of grain yield and mineral contents in rice: potential targets for CRISPR-Cas9-mediated genome editing

Rice is a major global staple food crop, and improving its grain yield and nutritional quality has been a major thrust research area since last decades. Yield and nutritional quality are complex traits which are controlled by multiple signaling pathways. Sincere efforts during past decades of research have identified several key genetic and molecular regulators that governed these complex traits. The advent of clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9)-mediated gene knockout approaches has accelerated the development of improved varieties; however, finding out target gene with negative regulatory function in particular trait without giving any pleiotropic effect remains a challenge. Here, we have reviewed past and recent literature and identified important negative regulators of grain yield and mineral contents which could be potential targets for CRISPR-Cas9-mediated gene knockout. Additionally, we have also compiled a list of microRNAs (miRNAs), which target positive regulators of grain yield, plant stress tolerance, and grain mineral contents. Knocking out these miRNAs could help to increase expression of such positive regulators and thus improve the plant trait. The knowledge presented in this review would help to further accelerate the CRISPR-Cas9-mediated trait improvement in rice.

Gene editing of non-coding regulatory DNA and its application in crop improvement

The development of the clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas) system has provided precise and efficient strategies to edit target genes and generate transgene-free crops. Significant progress has been made in the editing of protein-coding genes; however, studies on the editing of non-coding DNA with regulatory roles lags far behind. Non-coding regulatory DNAs, including those which can be transcribed into long non-coding RNAs (lncRNAs), and miRNAs, together with cis-regulatory elements (CREs), play crucial roles in regulating plant growth and development. Therefore, the combination of CRISPR/Cas technology and non-coding regulatory DNA has great potential to generate novel alleles that affect various agronomic traits of crops, thus providing valuable genetic resources for crop breeding. Herein, we review recent advances in the roles of non-coding regulatory DNA, attempts to edit non-coding regulatory DNA for crop improvement, and potential application of novel editing tools in modulating non-coding regulatory DNA. Finally, the existing problems, possible solutions, and future applications of gene editing of non-coding regulatory DNA in modern crop breeding practice are also discussed.

Starch Properties and Morphology of Eight Floury Endosperm Mutants in Rice

Besides increasing grain yield, improving rice (Oryza sativa L.) quality has been paid more and more attention recently. Cooking and eating quality (CEQ) is an important indicator of rice quality. Since CEQs are quantitative traits and challenging for measurement, efforts have mainly focused on two major genes, Wx and SSIIa. Chalkiness and floury endosperm significantly affect the eating quality of rice, leading to noticeable changes in CEQ. Due to the easily observable phenotype of floury endosperm, cloning single gene mutations that cause floury endosperm and evaluating changes in CEQs indirectly facilitate the exploration of the minor genes controlling CEQ. In this study, eight mutants with different degrees of floury endosperm, generated through ethylmethane sulfonate (EMS) mutagenesis, were analyzed. These mutants exhibited wide variation in starch morphology and CEQs. Particularly, the z2 mutant showed spherical starch granules significantly increased rapid visco analyzer (RVA) indexes and urea swelling, while the z4 mutant displayed extremely sharp starch granules and significantly decreased RVA indexes and urea swelling compared to the wild type. Additionally, these mutants still maintained correlations with certain RVA profiles, suggesting that the genes PUL, which affect these indexes, may not undergo mutation. Cloning these mutated genes in the future, especially in z2 and z4, will enhance the genetic network of rice eating quality and hold significant importance for molecular marker-assisted breeding to improve rice quality.

Integrated genome-wide differentiation and association analyses identify causal genes underlying breeding-selected grain quality traits in japonica rice

Improving grain quality is a primary objective in contemporary rice breeding. Japanese modern rice breeding has developed two different types of rice, eating and sake-brewing rice, with different grain characteristics, indicating the selection of variant gene alleles during the breeding process. Given the critical importance of promptly and efficiently identifying genes selected in past breeding for future molecular breeding, we conducted genome scans for divergence, genome-wide association studies, and map-based cloning. Consequently, we successfully identified two genes, OsMnS and OsWOX9D, both contributing to rice grain traits. OsMnS encodes a mannan synthase that increases the white core frequency in the endosperm, a desirable trait for sake brewing but decreases the grain appearance quality. OsWOX9D encodes a grass-specific homeobox-containing transcription factor, which enhances grain width for better sake brewing. Furthermore, haplotype analysis revealed that their defective alleles were selected in East Asia, but not Europe, during modern improvement. In addition, our analyses indicate that a reduction in grain mannan content during African rice domestication may also be caused a defective OsMnS allele due to breeding selection. This study not only reveals the delicate balance between grain appearance quality and nutrition in rice but also provides a new strategy for isolating causal genes underlying complex traits, based on the concept of "breeding-assisted genomics" in plants.

Fine mapping of qAHPS07 and functional studies of AhRUVBL2 controlling pod size in peanut (Arachis hypogaea L.)

Cultivated peanut (Arachis hypogaea L.) is an important oil and cash crop. Pod size is one of the major traits determining yield and commodity characteristic of peanut. Fine mapping of quantitative trait locus (QTL) and identification of candidate genes associated with pod size are essential for genetic improvement and molecular breeding of peanut varieties. In this study, a major QTL related to pod size, qAHPS07, was fine mapped to a 36.46 kb interval on chromosome A07 using F2 , recombinant inbred line (RIL) and secondary F2 populations. qAHPS07 explained 38.6%, 23.35%, 37.48%, 25.94% of the phenotypic variation for single pod weight (SPW), pod length (PL), pod width (PW) and pod shell thickness (PST), respectively. Whole genome resequencing and gene expression analysis revealed that a RuvB-like 2 protein coding gene AhRUVBL2 was the most likely candidate for qAHPS07. Overexpression of AhRUVBL2 in Arabidopsis led to larger seeds and plants than the wild type. AhRUVBL2-silenced peanut seedlings represented small leaves and shorter main stems. Three haplotypes were identified according to three SNPs in the promoter of AhRUVBL2 among 119 peanut accessions. Among them, SPW, PW and PST of accessions carrying Hap_ATT represent 17.6%, 11.2% and 26.3% higher than those carrying Hap_GAC，respectively. In addition, a functional marker of AhRUVBL2 was developed. Taken together, our study identified a key functional gene of peanut pod size, which provides new insights into peanut pod size regulation mechanism and offers practicable markers for the genetic improvement of pod size-related traits in peanut breeding.

Targeted mutagenesis of the vacuolar H+ translocating pyrophosphatase gene reduces grain chalkiness in rice

Grain chalkiness is a major concern in rice production because it impacts milling yield and cooking quality, eventually reducing market value of the rice. A gene encoding vacuolar H+ translocating pyrophosphatase (V-PPase) is a major quantitative trait locus in indica rice, controlling grain chalkiness. Higher transcriptional activity of this gene is associated with increased chalk content. However, whether the suppression of V-PPase could reduce chalkiness is not clear. Furthermore, natural variation in the chalkiness of japonica rice has not been linked with V-PPase. Here, we describe promoter targeting of the japonica V-PPase allele that led to reduced grain chalkiness and the development of more translucent grains. Disruption of a putative GATA element by clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 suppressed V-PPase activity, reduced grain chalkiness and impacted post-germination growth that could be rescued by the exogenous supply of sucrose. The mature grains of the targeted lines showed a much lower percentage of large or medium chalk. Interestingly, the targeted lines developed a significantly lower chalk under heat stress, a major inducer of grain chalk. Metabolomic analysis showed that pathways related to starch and sugar metabolism were affected in the developing grains of the targeted lines that correlated with higher inorganic pyrophosphate and starch contents and upregulation of starch biosynthesis genes. In summary, we show a biotechnology approach of reducing grain chalkiness in rice by downregulating the transcriptional activity of V-PPase that presumably leads to altered metabolic rates, including starch biosynthesis, resulting in more compact packing of starch granules and formation of translucent rice grains.

Comparative Proteome-wide Characterization of Three Different Tissues of High-Protein Mutant and Wild Type Unravels Protein Accumulation Mechanisms in Rice Seeds

Improving the proteins and amino acid contents of rice seeds is one of the prime objectives of plant breeders. We recently developed an EMS mutant/high-protein mutant (HPM) of rice that exhibits 14.8% of the total protein content as compared to its parent Dharial (wild-type), which shows only 9.3% protein content in their mature seeds. However, the mechanisms underlying the higher protein accumulation in these HPM seeds remain largely elusive. Here, we utilized high-throughput proteomics to examine the differences in the proteome profiles of the embryo, endosperm, and bran tissues of Dharial and HPM seeds. Utilizing a label-free quantitative proteomic and subsequent functional analyses of the identified proteins revealed that nitrogen compound biosynthesis, intracellular transport, protein/amino acid synthesis, and photosynthesis-related proteins were specifically enriched in the endosperm and bran of the high-protein mutant seed. Our data have uncovered proteome-wide changes highlighting various functions of metabolic pathways associated with protein accumulation in rice seeds.

Regulation of Grain Chalkiness and Starch Metabolism by FLO2 Interaction Factor 3, a bHLH Transcription Factor in Oryza sativa

Chalkiness is a key determinant that directly affects the appearance and cooking quality of rice grains. Previously, Floury endosperm 2 (FLO2) was reported to be involved in the formation of rice chalkiness; however, its regulation mechanism is still unclear. Here, FLO2 interaction factor 3 (OsFIF3), a bHLH transcription factor, was identified and analyzed in Oryza sativa. A significant increase in chalkiness was observed in OsFIF3-overexpressed grains, coupled with a round, hollow filling of starch granules and reduced grain weight. OsFIF3 is evolutionarily conserved in monocotyledons, but variable in dicotyledons. Subcellular localization revealed the predominant localization of OsFIF3 in the nucleus. The DAP-seq (DNA affinity purification sequencing) results showed that OsFIF3 could affect the transcriptional accumulation of β-amylase 1, α-amylase isozyme 2A-like, pectinesterase 11, β-glucosidase 28 like, pectinesterase, sucrose transport protein 1 (SUT1), and FLO2 through the binding of the CACGTG motif on their promoters. Moreover, FLO2 and SUT1 with abundant OsFIF3 binding signals showed significant expression reduction in OsFIF3 overexpression lines, further confirming OsFIF3's role in starch metabolism regulation and energy material allocation. Taken together, these findings show that the overexpression of OsFIF3 inhibits the expression of FLO2 and SUT1, thereby increasing grain chalkiness and affecting grain weight.

Joint analysis of phenotype-effect-generation identifies loci associated with grain quality traits in rice hybrids

Genetic improvement of grain quality is more challenging in hybrid rice than in inbred rice due to additional nonadditive effects such as dominance. Here, we describe a pipeline developed for joint analysis of phenotypes, effects, and generations (JPEG). As a demonstration, we analyze 12 grain quality traits of 113 inbred lines (male parents), five tester lines (female parents), and 565 (113×5) of their hybrids. We sequence the parents for single nucleotide polymorphisms calling and infer the genotypes of the hybrids. Genome-wide association studies with JPEG identify 128 loci associated with at least one of the 12 traits, including 44, 97, and 13 loci with additive effects, dominant effects, and both additive and dominant effects, respectively. These loci together explain more than 30% of the genetic variation in hybrid performance for each of the traits. The JEPG statistical pipeline can help to identify superior crosses for breeding rice hybrids with improved grain quality.

Mapping of qChalk1 controlling grain chalkiness in japonica rice

BACKGROUND

Rice grain chalkiness is an undesirable characteristic that affects grain quality. The aim of this study was to map QTLs controlling grain chalkiness in japonica rice.

METHODS AND RESULTS

In this study, two japonica rice cultivars with similar grain shapes but different grain chalkiness rates were crossed and the F₂ and BC₁F₂ populations were subjected to QTL-seq analysis to map the QTLs controlling the grain chalkiness rate. QTL-seq analysis revealed SNP index differences on chromosome 1 in both of the segregating populations. Using polymorphic markers between the two parents, QTL mapping was conducted on 213 individual plants in the BC₁F₂ population. QTL mapping confined a QTL controlling grain chalkiness, qChalk1, to a 1.1 Mb genomic region on chromosome 1. qChalk1 explained 19.7% of the phenotypic variation.

CONCLUSION

A QTL controlling grain chalkiness qChalk1 was detected in both F₂ and BC₁F₂ segregating populations by QTL-Seq and QTL mapping methods. This result would be helpful for further cloning of the genes controlling grain chalkiness in japonica rice.