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Summary: 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. [ABSTRACT FROM AUTHOR]

The FZP gene plays a critical role in the formation of lateral branches and spikelets in rice panicle architecture. This study investigates the qSBN7 allele, a hypomorphic variant of FZP, and its influence on panicle architectures in different genetic backgrounds. We evaluated two backcross inbred lines (BILs), BC5_TCS10sbn and BC3_TCS10sbn, each possessing the homozygous qSBN7 allele but demonstrating differing degrees of spikelet degeneration. Our analysis revealed that BC5_TCS10sbn had markedly low FZP expression, which corresponded with an increase in axillary branches and severe spikelet degeneration. Conversely, BC3_TCS10sbn exhibited significantly elevated FZP expression, leading to fewer secondary and tertiary branches, and consequently decreased spikelet degeneration. Compared to BC5_TCS10sbn, BC3_TCS10sbn carries three additional chromosomal substitution segments from its donor parent, IR65598-112-2. All three segments significantly enhance the expression of FZP and reduce the occurrence of tertiary branch and spikelet degeneration. These findings enhance our understanding of the mechanisms regulating FZP and aid rice breeding efforts. [ABSTRACT FROM AUTHOR]

Grain size is a quantitative trait with a complex genetic mechanism, characterized by the combination of grain length (GL), grain width (GW), length to width ration (LWR), and grain thickness (GT). In this study, we conducted quantitative trait loci (QTL) analysis to investigate the genetic basis of grain size using BC1F2 and BC1F2:3 populations derived from two indica lines, Guangzhan 63-4S (GZ63-4S) and TGMS29 (core germplasm number W240). A total of twenty-four QTLs for grain size were identified, among which, three QTLs (qGW1, qGW7, and qGW12) controlling GL and two QTLs (qGW5 and qGL9) controlling GW were validated and subsequently fine mapped to regions ranging from 128 kb to 624 kb. Scanning electron microscopic (SEM) analysis and expression analysis revealed that qGW7 influences cell expansion, while qGL9 affects cell division. Conversely, qGW1, qGW5, and qGW12 promoted both cell division and expansion. Furthermore, negative correlations were observed between grain yield and quality for both qGW7 and qGW12. Nevertheless, qGW5 exhibited the potential to enhance quality without compromising yield. Importantly, we identified two promising QTLs, qGW1 and qGL9, which simultaneously improved both grain yield and quality. In summary, our results laid the foundation for cloning these five QTLs and provided valuable resources for breeding rice varieties with high yield and superior quality. [ABSTRACT FROM AUTHOR]

Preharvest sprouting (PHS) is an undesirable trait that decreases yield and quality in rice production. Understanding the genes and regulatory mechanisms underlying PHS is of great significance for breeding PHS-resistant rice. In this study, we identified a mutant, preharvest sprouting 39 (phs39), that exhibited an obvious PHS phenotype in the field. MutMap+ analysis and transgenic experiments demonstrated that OsAAH, which encodes allantoate amidohydrolase, is the causal gene of phs39 and is essential for PHS resistance. OsAAH was highly expressed in roots and leaves at the heading stage and gradually increased and then weakly declined in the seed developmental stage. OsAAH protein was localized to the endoplasmic reticulum, with a function of hydrolyzing allantoate in vitro. Disruption of OsAAH increased the levels of ureides (allantoate and allantoin) and activated the tricarboxylic acid (TCA) cycle, and thus increased energy levels in developing seeds. Additionally, the disruption of OsAAH significantly increased asparagine, arginine, and lysine levels, decreased tryptophan levels, and decreased levels of indole-3-acetic acid (IAA) and abscisic acid (ABA). Our findings revealed that the OsAAH of ureide catabolism is involved in the regulation of rice PHS via energy and hormone metabolisms, which will help to facilitate the breeding of rice PHS-resistant varieties. [ABSTRACT FROM AUTHOR]

The quality of rice (Oryza sativa L) is determined by a combination of appearance, flavor, aroma, texture, storage characteristics, and nutritional composition. Rice quality directly influences acceptance by consumers and commercial value. The genetic mechanism underlying rice quality is highly complex, and is influenced by genotype, environment, and chemical factors such as starch type, protein content, and amino acid composition. Minor variations in these chemical components may lead to substantial differences in rice quality. Among these components, starch is the most crucial and influential factor in determining rice quality. In this study, quantitative trait loci (QTLs) associated with eight physicochemical properties related to the rapid viscosity analysis (RVA) profile were identified using a high-density sequence map constructed using recombinant inbred lines (RILs). Fifty-nine QTLs were identified across three environments, among which qGT6.4 was a novel locus co-located across all three environments. By integrating RNA-seq data, we identified the differentially expressed candidate gene OsCRLK2 within the qGT6.4 interval. osclrk2 mutants exhibited decreased gelatinization temperature (GT), apparent amylose content (AAC) and viscosity, and increased chalkiness. Furthermore, osclrk2 mutants exhibited downregulated expression of the majority of starch biosynthesis-related genes compared to wild type (WT) plants. In summary, OsCRLK2, which encodes a receptor-like protein kinase, appears to consistently influence rice quality across different environments. This discovery provides a new genetic resource for use in the molecular breeding of rice cultivars with improved quality. [ABSTRACT FROM AUTHOR]

The development of germplasm resources and advances in breeding methods have led to steady increases in yield and quality of rice (Oryza sativa L.). Three milestones in the recent history of rice breeding have contributed to these increases: dwarf rice breeding, hybrid rice breeding, and super rice breeding. On the 50th anniversary of the success of three‐line hybrid rice, we highlight important scientific discoveries in rice breeding that were made by Chinese scientists and summarize the broader history of the field. We discuss the strategies that could be used in the future to optimize rice breeding further in the hope that China will continue to play a leading role in international rice breeding. [ABSTRACT FROM AUTHOR]

Heading date is a critical agronomic trait that significantly affects grain yield and quality in rice. As early heading is typically associated with reduced yield due to shorter growth duration, it is essential to harness optimum heading date genes and their allelic combinations to promote heading while minimizing yield penalties. In this study, we identified quantitative trait loci (QTLs) for heading date and other major agronomic traits in a recombinant inbred line (RIL) population derived from a cross between Koshihikari and Baegilmi. Analyses on 3 major QTLs for heading date and their underlying genes (Hd1 , Hd16 , and Ghd7) revealed their pleiotropic effects on culm length, panicle length, and head rice percentage. Additionally, Ghd7 exhibited pleiotropic effects on panicle number and grain size. Among 8 different types of allelic combinations of the 3 heading date genes, RILs carrying a single nonfunctional hd16 or ghd7 under the functional background of the other 2 genes (Hd1hd16Ghd7 and Hd1Hd16ghd7) showed potential for maintaining yield and quality-related traits while accelerating heading. These results provide valuable insights for fine-tuning heading dates in rice breeding programs. [ABSTRACT FROM AUTHOR]

Radiation mutagenesis, which typically involves gamma rays, is important for generating new rice germplasm resources. Determining the appropriate radiation dose range is critical for the success of radiation mutagenesis. Clarifying the sensitivity and tolerance of genotypically diverse rice varieties to gamma irradiation as well as the radiation-induced changes to reactive oxygen species (ROS) generation and antioxidant enzyme activities is crucial for increasing the utility of radiation mutagenesis in rice breeding programs. The seeds of the following four rice varieties with different genotypes were used as test materials: indica Zhe 1613, glutinous indica Zhe 1708, japonica Zhejing 100, and glutinous japonica Zhenuo 65. Additionally,60Co was used as the source of gamma rays. The rice seeds were irradiated with 14 doses (0, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, and 750 Gy). Non-irradiated seeds were used as the control. The seedling survival rate for each variety was recorded at 3, 7, 14, and 28 days after sowing. Moreover, the median lethal dose (LD50) and critical dose (LD40) were calculated according to the seedling survival rates at 28 days after sowing. The seedling superoxide anion (O2•−), hydrogen peroxide (H2O2), and malondialdehyde (MDA) contents and the superoxide dismutase (SOD), catalase (CAT), peroxidase (POD), and ascorbate peroxidase (APX) activities were analyzed at 7 days after sowing. As the radiation dose increased, the seedling survival rate decreased. The seedling survival rate also decreased significantly as the number of days after sowing increased. Among the rice genotypes, the rank-order of the radiation tolerance was as follows: indica Zhe 1613 > glutinous indica Zhe 1708 > japonica Zhejing 100 > glutinous japonica Zhenuo 65. The LD50 values were 426.7 Gy for Zhe 1613, 329.2 Gy for Zhe 1708, 318.3 Gy for Zhejing 100, and 316.6 Gy for Zhenuo 65. Increases in the radiation dose resulted in significant increases in the seedling O2•− and H2O2 contents, but only up to a certain point. Further increases in the radiation dose caused the seedling O2•− and H2O2 contents to decrease. The H2O2 content for each variety peaked when the radiation dose was very close to the LD50. We propose that the radiation dose associated with the highest H2O2 content (±50 Gy) should be used as the recommended dose for the gamma irradiation of rice. The radiation dose that resulted in peak seedling O2•− contents in the analyzed rice varieties was very close to the LD40. In all rice varieties, the MDA content increased as the radiation dose increased. The SOD, CAT, POD, and APX activities increased as the radiation dose increased within a certain range (less than 600 Gy for Zhe 1613 and 400 Gy for the other varieties), but there were slight differences among the rice varieties. Genotypically diverse rice varieties vary regarding their sensitivity to gamma irradiation. Our findings suggest that ROS generation and antioxidant enzyme activities are important factors associated with the radiation mutagenesis of rice. The close relationship between the activities of key antioxidant enzymes, such as SOD, POD, APX, and CAT, and the LD50 and LD40 may be exploited to enhance radiation mutagenesis through the use of plant growth regulators. [ABSTRACT FROM AUTHOR]

The presented study sought to phenotype the rice cultivars procured from the Unique Scientific Installation (USI) - Collection of Federal Scientific Rice Centre, Krasnodar, Russian Federation, as sources of valuable grain quality traits, as well as BC2 populations with the selection of the best genotypes for quality traits in developing the red grain rice cultivars with high nutritional properties. The studied rice plant material, grown in the artificial climate chambers of FSBSI - Federal Scientific Rice Centre, had the following conditions: temperature - 28-30 °C during the day (12 h) and 24 °C at night (12 h); illumination - 30,000 lux, and humidity = 70%. Rice determination and phenotyping for grain quality traits commenced on high-tech certified equipment per GOSTs. The experiment results had the parental genotypes used in the backcrossing program assigned to the group of medium-grain cultivars, except for the long-grain cultivars, i.e., Svetlana and Gagat. The 1000-grain weight ranged from 23.0 to 27.4 g, filminess (17.8% to 19.9%), and total milling yield (65.0% to 70.4%). Low fracturing appeared in rice cultivars, viz., Rubin, Alliance, Kurazh, Gagat, and VNIIR10163, while a high vitreosity emerged in rice cultivars Veles, Svetlana, VNIIR10163, and Khaw-sri-nin. BC2 plant populations' evaluation depended on the technological quality traits. The effective heterosis was evident for most grain quality traits. Rice genotypes selected based on lower fracturing and higher grain size will undergo further breeding work to develop the high-yielding rice genotypes with desirable grain quality traits. [ABSTRACT FROM AUTHOR]

SUMMARY: Optimal grain‐appearance quality is largely determined by grain size. To date, dozens of grain size‐related genes have been identified. However, the regulatory mechanism of slender grain formation is not fully clear. We identified the OsSG34 gene by map‐based cloning. A 9‐bp deletion on 5'‐untranslated region of OsSG34, which resulted in the expression difference between the wild‐type and sg34 mutant, led to the slender grains and good transparency in sg34 mutant. OsSG34 as an α/β fold triacylglycerol lipase affected the triglyceride content directly, and the components of cell wall indirectly, especially the lignin between the inner and outer lemmas in rice grains, which could affect the change in grain size by altering cell proliferation and expansion, while the change in starch content and starch granule arrangement in endosperm could affect the grain‐appearance quality. Moreover, the OsERF71 was identified to directly bind to cis‐element on the mutant site, thereby regulating the OsSG34 expression. Knockout of three OsSG34 homologous genes resulted in slender grains as well. The study demonstrated OsSG34, involved in lipid metabolism, affected grain size and quality. Our findings suggest that the OsSG34 gene could be used in rice breeding for high yield and good grain‐appearance quality via marker‐assisted selection and gene‐editing approaches. Significance Statement: The gene OsSG34, its three homologous genes, involved in lipid metabolism network, could play an important role in grain‐appearance quality by altering cell proliferation and expansion. The OsERF71 directly bound to cis‐element on the mutant site and upregulated OsSG34 expression. [ABSTRACT FROM AUTHOR]

Improving quality is an essential goal of rice breeding and production. However, rice quality is not solely determined by genotype, but is also influenced by the environment. Phenotype plasticity refers to the ability of a given genotype to produce different phenotypes under different environmental conditions, which can be a representation of the stability of traits. Seven quality traits of 141 hybrid combinations, deriving from the test-crossing of 7 thermosensitive genic male sterile (TGMS) and 25 restorer lines, were evaluated at 5 trial sites with intermittent sowing of three to five in Southern China. In the Yangtze River Basin, it was observed that delaying the sowing time of hybrid rice combinations leads to an improvement in their overall quality. Twelve parents were identified to have lower plasticity general combing ability (GCA) values with increased ability to produce hybrids with a more stable quality. The parents with superior quality tend to exhibit lower GCA values for plasticity. The genome-wide association study (GWAS) identified 13 and 15 quantitative trait loci (QTLs) associated with phenotype plasticity and BLUP measurement, respectively. Notably, seven QTLs simultaneously affected both phenotype plasticity and BLUP measurement. Two cloned rice quality genes, ALK and GL7, may be involved in controlling the plasticity of quality traits in hybrid rice. The direction of the genetic effect of the QTL6 (ALK) on alkali spreading value (ASV) plasticity varies in different cropping environments. This study provides novel insights into the dynamic genetic basis of quality traits in response to different cropping regions, cultivation practices, and changing climates. These findings establish a foundation for precise breeding and production of stable and high-quality rice. [ABSTRACT FROM AUTHOR]

This article succinctly outlines the requirements for rice quality in Guangdong Province and the role of government regulatory policies in advancing high-quality rice breeding. By collecting the regional trial data of 1 101 rice varieties approved by Guangdong Province from 2004 to 2022, the number of varieties meeting the national or ministerial standards approved in each year were counted, and the progress of high-quality rice breeding in Guangdong was evaluated from the perspectives of quality index, resistance and yield. From 2004 to 2022, 106 varieties (combinations) meeting the quality of national standard (ministerial standard) (9.63% of all approved varieties) level I and 320 varieties (combinations) reaching the quality of national standard (ministerial standard) (29.06%) level II were approved by Guangdong. Notably, early season varieties exhibited lower quality rates compared with late season varieties. For rice quality traits, early-season trial varieties displayed lower compliance rates in the quality of national standard (ministerial standard) level II, with chalkiness and chalky grain rate of 41.8% and 43.5%, respectively; the amylose content compliance rate in early-season trial varieties was only 37.32%, indicating that key improvements should be conducted in these three areas for new variety breeding. The average yield of rice varieties with quality meeting national standard level II or above has consistently risen, indicating synergistic improvements in yield and rice quality during the high-quality rice breeding in Guangdong. Varieties meeting the national standard (ministerial standard) level II or above also showed promising resistance rates against rice blast disease (85% at medium resistance or above) and bacterial blight disease (22.2% at medium resistance or above). Generally, while the percentage of hybrid rice varieties meeting high-quality standards is increasing, there is still a notable gap compared to conventional rice breeding. The proportion of highquality rice varieties in Guangdong has been steadily growing, with a positive trend in “excellent, abundant and resistant” varieties. However, further optimization is possible. To cultivate high-quality rice varieties with double resistances, efforts should be put to enhance resistance to bacterial wilt disease. The evaluation and utilization of specific germplasm resources like local varieties should be increased to diversify the genetic background. This approach helps avoid variety homogenization, improves disease and stress resistance and strengthens the synergy between traditional and molecular breeding, enhancing overall breeding efficiency. [ABSTRACT FROM AUTHOR]

Improving rice yield is one of the most important food issues internationally. It is an undeniable goal of rice breeding, and the effective panicle number (EPN) is a key factor determining rice yield. Increasing the EPN in rice is a major way to increase rice yield. Currently, the main quantitative trait locus (QTL) for EPN in rice is limited, and there is also limited research on the gene for EPN in rice. Therefore, the excavation and analysis of major genes related to EPN in rice is of great significance for molecular breeding and yield improvement. This study used japonica rice varieties Dongfu 114 and Longyang 11 to construct an F5 population consisting of 309 individual plants. Two extreme phenotypic pools were constructed by identifying the EPN of the population, and QTL-seq analysis was performed to obtain three main effective QTL intervals for EPN. This analysis also helped to screen out 34 candidate genes. Then, EPN time expression pattern analysis was performed on these 34 genes to screen out six candidate genes with higher expression levels. Using a 3K database to perform haplotype analysis on these six genes, we selected haplotypes with significant differences in EPN. Finally, five candidate genes related to EPN were obtained. [ABSTRACT FROM AUTHOR]

Rice is sensitive to high-temperature stress during almost all stages of growth and development. High-temperature stress has become one of the main factors restricting high yield and superior quality of rice. In this study, recombinant inbred lines (RILs) derived from an indica rice cross between two restorer lines were planted in two years. One sowing date was applied in 2019, and four sowing dates were set in 2020 according to the period of local high temperatures in recent years. Two traits closely related to high-temperature tolerance, heading date (HD), and spikelet fertility (SF) were measured. In each trial, the HD showed a bimodal distribution, whereas SF had a continuous and left-skewed distribution. QTL analysis was performed using a high-density bin map. For HD, a total of six QTL were detected. All of them correspond in position to the cloned genes, among which qHD8 in the DTH8/Ghd8 region showed the largest genetic effect. For SF, a total of eight QTL were detected. Five of them, qSF1, qSF2, qSF3.1, qSF3.2, and qSF8, showed high-temperature tolerance and had an important potential in rice breeding. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

High yield and superior quality are the main objectives of rice breeding and research. While innovations in rice breeding have increased production to meet growing demand, the universal issue of balancing high yield and susperior quality has led to a lack of focus on improving rice quality. With rising living standards, improving rice quality has become increasingly important. Rice grain quality is a complex trait influenced by both genetic and environmental factors, with four primary aspects: milling quality, appearance quality, eating and cooking quality, and nutritional quality. While different populations have varying demands for rice quality, the core traits that contribute to rice quality include grain shape and chalkiness in terms of appearance, as well as endosperm composition that influences cooking and sensory evaluation. Researchers have made substantial advancements in discovering genes/QTLs associated with critical traits including appearance, aroma, texture, and nutritional properties. Markers derived from these genetic discoveries have provided an efficient tool for marker-assisted selection to improve rice quality. Thus, this review focuses on elite genes and their applications in breeding practices to quickly develop superior quality rice varieties that meet various market demands. [ABSTRACT FROM AUTHOR]

The source strength and sink demand as well as their interaction have been demonstrated to co-regulate the synthesis of starch and determine the grain quality, but the knowledge of the underlying physiological mechanisms is limiting. An indica variety, Yangdao 6, and a japonica variety, Jinxiangyu 1, were planted with three treatments, including normal growth plant (CK), leaf-cutting (LC) and spikelet-thinning (ST). The transcript levels of starch metabolic genes, physicochemical characteristics of starch and appearance, milling, cooking and tasting qualities of rice under different treatments were determined. The ST treatment increased the relative expression of genes related to the synthesis of short branch-chains of amylopectin (SSI, BEI, BEIIb) and amylose (GBSSI) and reduced the relative expression of medium-long to long branch-chains of amylopectin synthesis genes (SSIIa, SSIIIa, SSIIIb, ISA1). When comparing ST with the CK treatment, starch granules became smoother with higher contents of short branch-chains and lower ratios of medium-long and long branch-chains of amylopectin; the crystallinity and the value of 1045/1022 cm−1 was decreased; for pasting properties, the setback and pasting temperature were decreased; the peak viscosity, hot viscosity, breakdown and final viscosity were significantly increased. Meanwhile, the ST treatment improved the appearance, milling and cooking and tasting qualities. The opposite results were observed under the LC treatment. These results indicated that source strength and sink size would regulate expression levels of starch metabolic genes, which is pivotal for the contents of amylose and short/long branch chains ratio of amylopectin, thus changing the structure and physicochemical properties of starch and grain quality. Here, we speculated that the improved source strength in terms of higher leaf/canopy photosynthesis and small sink size, such as small panicle size, would be preferred traits in high grain quality rice breeding. [ABSTRACT FROM AUTHOR]

Rice quality is one of the main targets of rice breeding and is a complex trait that involves grain appearance, milling, cooking, eating and nutritional quality. For many years, rice breeding has contended with imbalances in rice yield, quality, and disease and lodging resistance. Here, the milling and appearance quality, cooking quality, starch rapid viscosity analyzer (RVA) profile, and nutritional quality of grains of Yuenongsimiao (YNSM), an indica rice variety with high yield, high quality and disease resistance, were determined. YNSM had excellent appearance and quality, with low amylose contents and high gel consistency, and these characteristics exhibited significant correlations with the RVA profile such as hot paste viscosity, cool paste viscosity, setback viscosity, and consistency. Moreover, 5 genes related to length-to-width ratio (LWR) as well as the Wx gene were used to detect the main quality genotype of YNSM. The results showed that YNSM is a semilong-grain rice with a relatively high brown rice rate, milled rice rate and head rice yield and low chalkiness. The results indicated that the LWR and food quality of YNSM might be related to gs3, gw7 and Wxb. This study also reports the quality characteristics of hybrid rice developed using YNSM as a restorer line. The quality characteristics and the genotype for grain quality determined through gene analysis in YNSM may facilitate the breeding of new rice varieties that achieve a balance of grain yield, resistance and quality. [ABSTRACT FROM AUTHOR]

High salinity is a major stress factor affecting the quality and productivity of rice (Oryza sativa L.). Although numerous salt tolerance-related genes have been identified in rice, their molecular mechanisms remain unknown. Here, we report that OsJRL40, a jacalin-related lectin gene, confers remarkable salt tolerance in rice. The loss of function of OsJRL40 increased sensitivity to salt stress in rice, whereas its overexpression enhanced salt tolerance at the seedling stage and during reproductive growth. β-glucuronidase (GUS) reporter assays indicated that OsJRL40 is expressed to higher levels in roots and internodes than in other tissues, and subcellular localization analysis revealed that the OsJRL40 protein localizes to the cytoplasm. Further molecular analyses showed that OsJRL40 enhances antioxidant enzyme activities and regulates Na+-K+ homeostasis under salt stress. RNA-seq analysis revealed that OsJRL40 regulates salt tolerance in rice by controlling the expression of genes encoding Na+/K+ transporters, salt-responsive transcription factors, and other salt response-related proteins. Overall, this study provides a scientific basis for an in-depth investigation of the salt tolerance mechanism in rice and could guide the breeding of salt-tolerant rice cultivars. [ABSTRACT FROM AUTHOR]

Direct seeding has been widely adopted as an economical and labor-saving technique in rice production, though problems such as low seedling emergence rate, emergence irregularity and poor lodging resistance are existing. These problems are currently partially overcome by increasing seeding rate, however it is not acceptable for hybrid rice due to the high seed cost. Improving direct seeding by breeding is seen as the ultimate solution to these problems. For hybrid breeding, identifying superior hybrids among a massive number of hybrids from crossings between male and female parental populations by phenotypic evaluation is tedious and costly. Contrastingly, genomic selection/prediction (GS/GP) could efficiently detect the superior hybrids capitalizing on genomic data, which holds a great potential in plant hybrids breeding. In this study, we utilized 402 rice inbred varieties and 401 hybrids to investigate the effectiveness of GS on rice mesocotyl length, a representative indicative trait of direct seeding suitability. Several GP methods and training set designs were studied to seek the optimal scenario of hybrid prediction. It was shown that using half-sib hybrids as training set with the phenotypes of all parental lines being fitted as a covariate could optimally predict mesocotyl length. Partitioning the molecular markers into trait-associated and -unassociated groups based on genome-wide association study using all parental lines and hybrids could further improve the prediction accuracy. This study indicates that GS could be an effective and efficient method for hybrid breeding for rice direct seeding. [ABSTRACT FROM AUTHOR]

As rice is a staple food for nearly half of the world's population, rice varieties with excellent agronomic traits as well as high flavor and nutritional quality such as fragrant rice and purple rice are naturally favored by the market. In the current study, we adopt a fast breeding strategy to improve the aroma and anthocyanin content in the excellent rice inbred line, F25. The strategy skillfully used the advantages of obtaining editing pure lines in T0 generation of CRISPR/Cas9 editing system and easy observation of purple character and grain shape, integrated the subsequent screening of non-transgenic lines, and the elimination of undesirable edited variants from gene-editing and cross-breeding at the same time as the separation of the progeny from the purple cross, thus expediting the breeding process. Compared with conventional breeding strategies, this strategy saves about 6–8 generations and reduces breeding costs. Firstly, we edited the OsBADH2 gene associated with rice flavor using an Agrobacterium-mediated CRISPR/Cas9 system to improve the aroma of F25. In the T0 generation, a homozygous OsBADH2-edited F25 line (F25B) containing more of the scented substance 2-AP was obtained. Then, we crossed F25B (♀) with a purple rice inbred line, P351 (♂), with high anthocyanin enrichment to improve the anthocyanin content of F25. After nearly 2.5 years of screening and identification over five generations, the undesirable variation characteristics caused by gene-editing and hybridization and the transgenic components were screened out. Finally, the improved F25 line with highly stable aroma component, 2-AP, increased anthocyanin content and no exogenous transgenic components were obtained. This study not only provides high-quality aromatic anthocyanin rice lines that meet the market demand, but also offers a reference for the comprehensive use of CRISPR/Cas9 editing technology, hybridization, and marker-assisted selection to accelerate multi-trait improvement and breeding process. [ABSTRACT FROM AUTHOR]

BACKGROUND: Storage affects rice quality significantly. The aim of this study was to investigate the changes in the chemical composition and in the physiological and cooking quality characteristics of three rice types after 1 year storage at 25 °C. RESULTS: Two japonica, two indica, and two indica–japonica hybrid rice varieties were selected. After storage, the total starch content decreased. The amylose content of japonica, indica, and indica–japonica hybrid rice increased by 9.63%–11.65%, 2.99%–4.67%, and 8.07%–8.97%, respectively, and the fat content decreased by 60.00%–65.00%, 37.21%–46.51%, and 41.67%–42.42%, respectively. The abscisic acid (ABA) and raffinose content decreased after 1 year's storage; the former decreased gradually during the storage and the latter increased by 19.35%–45.45%, 7.02%–10.77%, and 16.13%–28.13%, respectively, after 4 months' storage and then decreased to the lowest level after 1 year's storage. The activity of antioxidant enzymes deceased, which resulted in the increases in fatty acid value and malondialdehyde (MDA). The changes in chemical composition after 1 year storage led to the deterioration of rice cooking quality, which was reflected in the decrease in viscosity and increases in gelatinization temperature and cooked rice hardness. CONCLUSION: After 1 year's storage, the rice chemical composition changed and physiological and cooking quality characteristics decreased. Compared with japonica and indica–japonica hybrid rice, indica rice was more stable during 1 year storage. This may be due to the higher content of ABA and raffinose in fresh rice. Our findings will provide information for the identification and breeding of storable rice cultivars. © 2022 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

The indica rice variety XYXZ carries elite traits including appearance and eating quality. Here, we report the de novo assembly of XYXZ using Illumine paired-end whole-genome shotgun sequencing and Nanopore sequencing. We annotated 39,722 protein-coding genes in the 395.04 Mb assembly. In comparison to other cultivars, XYXZ showed a larger gene size including the transcripts and introns, and more exons per gene. And hundreds of ultra-long genes were also detected. A total of 4362 complete LTRs were annotated, and among them, many were located next to or in protein-coding genes including several genes related to rice quality. We observed the different distributions of LTRs in these genes among XYXZ, Nipponbare, and R498, implying these LTRs might potentially affect expressions of the proximal genes and rice quality. Overall, This chromosome-length genome assembly of XYXZ provides a valuable resource for gene discovery, genetic variation and evolution, and the breeding of high-quality rice. [ABSTRACT FROM AUTHOR]

BACKGROUND: Improving rice quality is one of the main goals of global rice breeding programs, and rice protein content is one of the most important factors affecting rice eating quality. The protein content of rice is mainly determined by genetic factors and also affected by environmental factors. However, the differences and regional distribution of protein content during the evolution of different rice varieties are still unclear. RESULTS: The purpose of this study was to understand the differences in grain protein content of 706 rice accessions in different regions and different rice subtypes. The influencing factors of grain protein content differences were analyzed from the perspectives of genetic characteristics, environment, rice subtypes, and breeding process. The results showed that the grain protein content of indica rice in most countries and regions was higher than that of japonica rice. From the perspective of the rice breeding process, the protein content of modern varieties in japonica was lower than that of landrace varieties. In most countries, modern varieties of indica rice had higher protein content than landrace varieties did. CONCLUSION: The environment and genetic characteristics caused the change in the protein content of rice. This study has improved our understanding of the differences in protein content of rice from different rice varieties. [ABSTRACT FROM AUTHOR]

Rice noodles are a popular food widely consumed in South Asia. Up to now the breeding progress in the development of rice varieties used for rice noodle-making by conventional breeding methods is very limited, owing to the complex nature of grain quality traits. Fortunately, two functional genes, i.e., Wxg2 (showing high amylose and hard gel consistency) and ALKGC (associated with intermediate high gelatinization temperature), have been identified to have desired starch quality phenotypes for rice noodle-making. This research was carried out to transfer the two major dominant genes from two rice donors HJX74 (carrying Wxg2) and ZX14 (carrying ALKGC) into new rice lines through marker-assisted breeding. Based on the functional mutations of Wxg2 and ALKGC, two sets of allele-specific PCR markers were developed. An intercross was made between HJX74 and ZX14 to develop a F2 population in which marker-assisted selection was applied to select individuals possessing both Wxg2 and ALKGC in homozygous condition. According to the marker genotypes, five homozygous lines were finally selected from 60 F2 progenies. The two-gene pyramided lines were selfed to generate F3 generation. Several promising F3 lines with fine agro-morphological traits were identified and then advanced to F4 generation for further evaluation of grain quality traits. All F4 selected lines exhibited desired starch properties required for rice noodles, demonstrating that marker-assisted pyramiding of Wxg2 and ALKGC is an essential approach to develop the rice lines suitable for rice noodle-making. [ABSTRACT FROM AUTHOR]

For the purpose of breeding documentation, researchers and breeders kept handwritten records of the breeding history, including parental information and breeding methods. The cultivars were used again as parents for further breeding, and modern cultivars of rice have a wide range of alleles from many generations of parents and ancestors. To understand such a breeding history, it is necessary to ask around for relevant information, which is then usually documented in Excel or Word by multiple breeders or breeding institutes. Here, we constructed RicePedigree, which contains the breeding history of rice based on the documents provided by the Rural Development Administration (RDA) in Korea. We devised a simple method for collecting a breeding history and storing it in a database. RicePedigree is a web-based application on the database that facilitates researchers' and breeders' utilization of the breeding history of rice. Based on the query cultivar name, it will return a hierarchical tree of breeding histories and a list of cultivars and breeding lines that contain query cultivars in their breeding histories. This app would be a good way to review and keep track of information about current and future cultivars. [ABSTRACT FROM AUTHOR]

The super hybrid rice breeding program in China has raised genetic yield ceilings through morphological improvements and inter-subspecific heterosis. Despite this, little information on the physiological basis underlying this yield transformation exists, and less so on the genotype x environment x management conditions enabling consistent yield gains. Here, we assess grain yield, photosynthetic physiology, and leaf carbon and nitrogen (N) metabolic properties of super rice (Y-liangyou900) under four management practices (i.e., zero-fertilizer control, CK; farmers' practice, FP; high-yield and high-efficiency management, OPT1; and super-high-yield management, OPT2) using a field experiment conducted over five years. Grain yield and agronomic N use efficiency (AEN) of OPT2 were 15% and 10% higher than OPT1, and 30% and 78% higher than FP, respectively. The superior yields of OPT2 were attributed to higher source production capacity, that is, higher leaf photosynthetic rate, carbon metabolic enzyme activity (i.e., AGP and SPS), nitrogen metabolic enzyme activity (i.e., NR, GS, and GOGAT), soluble protein and sugar content, and delayed leaf senescence (the latter due to elevated activity of protective enzyme systems) during grain filling. The higher AEN of OPT2 was associated with higher activity of leaf carbon metabolic enzyme (i.e., AGP and SPS), nitrogen metabolic enzyme (i.e., NR, GS, GDH, and GOGAT) and protective enzyme (POD) after heading, and lower C/N ratio in grains. We conclude that optimized management (optimized water and fertilizer management with appropriate dense planting) improved grain yield and N use efficiency simultaneously by enhancing post-heading leaf carbon and N metabolism and delayed leaf senescence. [ABSTRACT FROM AUTHOR]

Rice's yield, cooking, and sensory quality are primary considerations in selecting new breeding rice varieties, which are determined by the rice eating quality such as processing and flavor characteristics. Thus, in this study, to advance the breed of new superior japonica rice varieties, the differences in the rice quality, processing characteristics, and flavor characteristics between 12 newly‐bred varieties (H2‐36, H2‐42, H2‐53, H2‐59, H2‐63, H2‐73, H2‐74, H2‐79, H2‐81, H2‐82, H2‐89, and H2‐91) and 1 commercial variety (Kenyu38) were analyzed. The results indicated that H2‐42 has a reasonable length‐to‐width ratio (1.51), high rice yield, good color, reasonable amylose, protein content, excellent water existence index, accessible storage, and the highest taste value. Electronic nose results showed significant differences in aldehydes, ketones, and alcohols among 13 rice varieties. Aroma analysis results showed that H2‐42 had the highest n‐hexanal (14.63 µg/kg), (E,E)‐2,4‐nonadienal (37.24 µg/kg), nonanal (19.93 µg/kg), and decanal (4.81 µg/kg); those were important aroma components in cooked rice. The Pearson correlation analysis showed that hardness, springiness, cohesiveness, trough viscosity, peak time, and pasting temperature were the crucial factors that affected rice quality. According to partial least squares regression analysis, total color change, final viscosity, setback, (E)‐2‐heptenal, and 2‐methyl‐undecanol were the most important factors that distinguished the rice quality. In conclusion, H2‐42 rice was better apparent quality, processing characteristics, and aroma compounds. Therefore, H2‐42 has the potential for identification and promotion. Practical Application: The results from this study will provide data support for the cultivation, application, and quality improvement of high‐quality rice varieties. In addition, it gives new ideas and methods for studying rice eating quality. [ABSTRACT FROM AUTHOR]

This study was performed to determine the optimum transplanting dates of ‘Bbareumi’ in the Chungnam Plain area. ‘Bbareumi’ was transplanted into a rice research field of Chungnam Agricultural Research and Extension Services at intervals of approximately 15 days from April 17th to August 1st in 2019 and 2020. The heading dates of ‘Bbareumi’ were June 23rd to September 2nd depending on transplanting dates. The highest milled-rice yield was 5.61 MT/ha on May 1st and the lowest was 3.65 MT/ha on August 1st. As the transplanting date was delayed, protein content increased; however, the number of days from transplanting to heading decreased. Protein content and the number of days from transplanting to heading showed a highly significant correlation (R² = 0.802**). Therefore, it was found that early transplanting was beneficial to produce lower protein content because head rice percentage was 84-87% for early (April 17th to May 16th), 74-80% normal (June 1st to June 16th), and 86-95% for the late transplanting date (July 1st to August 1st). The mean temperature during the ripening stage differed according to the transplanting dates, and early transplanting showed a lower temperature than the normal one (May 16th to June 15th) and a higher head rice percentage. Therefore, extremely early maturing rice cultivars should be transplanted between late April and early May to obtain lower protein content and higher head rice percentage. These results will be useful for rice breeding programs, as it is generally recognized that early transplanting results in poor rice quality; however, this study revealed contrasting results. [ABSTRACT FROM AUTHOR]

Panicle length (PL) is an important trait that determines panicle architecture and strongly affects grain yield and quality in rice. However, this trait has not been well characterized genetically, and its contribution to yield improvement is not well understood. Characterization of novel genes related to PL is of great significance for breeding high-yielding rice varieties. In our previous research, we identified qPL5, a quantitative trait locus for PL. In this study, we aimed to determine the exact position of qPL5 in the rice genome and identify the candidate gene. Through substitution mapping, we mapped qPL5 to a region of 21.86 kb flanked by the molecular marker loci STS5-99 and STS5-106 in which two candidate genes were predicted. By sequence analysis and relative expression analysis, LOC-Os05g41230, which putatively encodes a BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1 precursor, was considered to be the most likely candidate gene for qPL5. In addition, we successfully developed a pair of near-isogenic lines (NILs) for qPL5 in different genetic backgrounds to evaluate the genetic effects of qPL5. Agronomic trait analysis of the NILs indicated that qPL5 positively contributes to plant height, grain number per panicle, panicle length, grain yield per plant, and flag leaf length, but it had no influence on heading date and grain-size-related traits. Therefore, qPL5 and the markers tightly linked to it should be available for molecular breeding of high-yielding varieties. [ABSTRACT FROM AUTHOR]

The japonica rice (Oryza sativa L.) cultivar Koshihikari is considered an important breeding material with good eating quality (EQ). To effectively utilize Koshihikari in molecular breeding programs, determining its whole genome sequence including cultivar-specific segment is crucial. Here, the Koshihikari genome was sequenced using Nanopore and Illumina platforms, and de novo assembly was performed. A highly contiguous Koshihikari genome sequence was compared with Nipponbare, the reference genome of japonica. Genome-wide synteny was observed, as expected, without large structural variations. However, several gaps in alignment were detected on chromosomes 3, 4, 9, and 11. It was notable that previously identified EQ-related QTLs were found in these gaps. Moreover, sequence variations were identified in chromosome 11 at a region flanking the P5 marker, one of the significant markers of good EQ. The Koshihikari-specific P5 region was found to be transmitted through the lineage. High EQ cultivars derived from Koshihikari possessed P5 sequences; on the other hand, Koshihikari-derived low EQ cultivars didn't contain the P5 region, which implies that the P5 genomic region affects the EQ of Koshihikari progenies. The EQ of near-isogenic lines (NILs) of Samnam (a low EQ cultivar) genetic background harboring the P5 segment was improved compared to that of Samnam in Toyo taste value. The structure of the Koshihikari-specific P5 genomic region associated with good EQ was analyzed, which is expected to facilitate the molecular breeding of rice cultivars with superior EQ. [ABSTRACT FROM AUTHOR]

Rice grain damage due to dark spots was noted more than 10 years ago in Russia. However, this phenomenon has long existed in other rice-growing countries. The factor limiting high rice yields are insect pests and pathogenic microorganisms, the vital activity of which leads to the occurrence of dark spots on the grain shells. This study hopes to assess the effects of dark spots on rice grains of six rice cultivars bred in Russia, i.e., Rapan, Khazar, Romans, Favorit, Trio, and Prestige. The study was carried out in 2020-2021 at the Federal State Budgetary Scientific Institution, Federal Scientific Rice Centre, Krasnodar, Russia. With an increase in the content of damaged grains from 5% to 10% and 20%, the mass of 1000 absolutely dry grains, vitreosity, and head rice content decrease, the filminess increased, and the content of damaged grains negatively affecting the quality traits of rice grains. If the content of damaged grains is up to 5%, grain quality decreases giving no impact of the parameter. The need to predict rice grain yield and quality based on grain damage intensity caused by dark spots ensures the profitability of growing various cultivars in rice production. [ABSTRACT FROM AUTHOR]

Key message: The cloning and characterization of a novel C2H2 zinc finger protein that affects rice eating and cooking quality by regulating amylose content and amylopectin chain-length distribution in rice. One of the major objectives in rice breeding aims to increase simultaneously yield and grain quality especially eating and cooking quality (ECQ). Controlling amylose content (AC) and amylopectin chain-length distribution (ACLD) in rice is a major strategy for improving rice ECQ. Previous studies show that some starch synthesis-related genes (SSRGs) are required for normal AC and ACLD, but its underlying regulating network is still unclear. Here, we report the cloning and characterization of a novel C2H2 zinc finger protein TL1 (Translucent endosperm 1) that positively regulates amylose synthesis in rice grains. Loss of TL1 function reduced apparent amylose content (AAC), total starch, gel consistency, and gelatinisation temperature, whereas increased viscosity, total lipid, and ratio of amylopectin A chains with degree of polymerization (DP) 6–12 to B1 chains with DP 13–24, resulting in an enhanced grain ECQ. The improved ECQ was accompanied by altered expression patterns of several tested SSRGs in tl1 mutant grains. Furthermore, knockout of TL1 in the high-yielding rice variety JiaHua NO.1 reduced AAC without obvious side effects on major agronomic traits. These findings expand our understanding of the regulating networks of grain starch metabolism and provide new insights into how rice ECQ quality can be improved via genetic approach. [ABSTRACT FROM AUTHOR]

The type of soft rice with low amylose content (AC) is more and more favored by consumers for its better eating and cooking quality, as people's quality of life continuously improves in China. The Wx gene regulates the AC of rice grains, thus affecting the degree of softness of the rice. Mei Meng B (MMB), Tian Kang B (TKB), and DR462 are three indica rice maintained lines with good morphological characters, but also with undesirably high AC. Therefore, CRISPR/Cas9 technology was used to edit the Wx gene of these lines to create a batch of soft rice breeding materials. New gene-edited lines MMB-10-2, TKB-21-12, and DR462-9-9, derived from the above parental lines, respectively, were selected in the T2 generations, with an AC of 17.2%, 16.8%, and 17.8%, and gel consistency (GC) of 78.6 mm, 77.4 mm, and 79.6 mm, respectively. The rapid viscosity analysis (RVA) spectrum showed that the three edited lines had a better eating quality as compared to the corresponding wild type, and showing new characteristics, different from the high-quality soft rice popular in the market. There was no significant difference in the main agronomic traits in the three edited lines compared to the corresponding wild types. Moreover, the chalkiness of DR462-9-9 was reduced, resulting in an improved appearance of its polished rice. The present study created soft rice germplasms for breeding improved quality hybrid rice, without changing the excellent traits of their corresponding wild type varieties. [ABSTRACT FROM AUTHOR]

Grain weight is a key trait that determines rice quality and yield, and it is primarily controlled by quantitative trait loci (QTL). Recently, attention has been paid to minor QTLs. A minor effect QTL qTGW7 that controls grain weight was previously identified in a set of chromosomal fragment substitution lines (CSSLs) derived from Nipponbare (NPB)/93-11. Compared to NPB, the single segment substitution line (SSSL) N83 carrying the qTGW7 introgression exhibited an increase in grain length and width and a 4.5% increase in grain weight. Meanwhile, N83 was backcrossed to NPB to create a separating population, qTGW7b, a QTL distinct from qTGW7, which was detected between markers G31 and G32. Twelve near-isogenic lines (NILs) from the BC9F3 population and progeny of five NILs from the BC9F3:4 population were genotyped and phenotyped, resulting in the fine mapping of the minor effect QTL qTGW7b to the approximately 86.2-kb region between markers G72 and G32. Further sequence comparisons and expression analysis confirmed that five genes, including Os07g39370, Os07g39430, Os07g39440, Os07g39450, and Os07g39480, were considered as the candidate genes underlying qTGW7b. These results provide a crucial foundation for further cloning of qTGW7b and molecular breeding design in rice. [ABSTRACT FROM AUTHOR]

【Objective】The present paper aimed to clarify the relationship between rice flavor quality and nitrogen nutrient absorption and utilization, the genotypes of high nitrogen efficient and good taste value rice were selected.【Method】The excellent japonica rice varieties（strains） cultivated along the yellow area were used as the test materials, and the influence of nitrogen on different rice genotype rice quality and nitrogen absorption and utilization was studied by setting different nitrogen fertilizer levels. 【Result】The taste value of different genotypes rice showed high difference, which decreased with nitrogen application increasing. The taste value of no nitrogen fertilizer was the highest and up to 83.9. Protein and straight starches increased with nitrogen application increasing. The linear analysis showed a significant open downward parabolic relationship and was performed with the nitrogen application quantity and the taste value(r=0.998**). The milled rice rate and the whole head rice rate increased with the nitrogen amount increasing, and the chalky grain rate and the chalkiness decreased with the nitrogen amount increasing. The nitrogen use efficiency, nitrogen grain production efficiency and nitrogen harvest index differed greatly between genotypes. The excellent and high-efficient nitrogen rice genotypes represented by by xindao 89 and xinkedao 31 were generally manifested with good appearance quality and relative high nitrogen grain production efficiency, up to 56.44 kg/kg. The related analysis showed that the nitrogen grain production efficiency was significantly positively with the rice taste value and significantly negatively with the protein content. The nitrogen use efficiency was significantly negatively with the taste value, negatively with the chalky grain rice rate and chalkiness, and positively with the milled rice rate and the whole head rice rate. It showed that the taste quality of rice improved and the appearance quality decreased under the level of no or less nitrogen fertilizer.【Conclusion】The nitrogen grain production efficiency can be used as an important evaluation index of excellent quality and high nitrogen efficient rice breeding. Improving the nitrogen use efficiency may be more conducive to improving rice processing, appearance quality and rice yield level. Good quality with high nitrogen efficiency（high nitrogen grain production efficiency） and high yield with high nitrogen efficiency（high nitrogen use efficiency） can be used as important evaluation standards for excellent food taste rice breeding and high yield rice breeding, respectively. [ABSTRACT FROM AUTHOR]

Aroma is one of the primary rice grain quality traits that play a vital role in consumer preferences. In Malaysia, consumers have shown a marked preference for high-quality rice. Therefore, it is essential to identify rice landraces with considerable aroma for promotion as potential donors for the development of high-quality rice in future breeding programs to meet consumer demand and reduce dependency on imported high-quality rice types. Thirty-three rice genotypes comprising thirty Malaysian rice landraces and three modern rice cultivars were evaluated for aroma using sensory tests and molecular markers. The presence of aroma in cooked rice was determined through nose sensory evaluation by five panellists. Molecular analysis was performed using two aroma-specific SSR primers i.e., FMbadh2-E7 and Badex7-5. The sensory test revealed that only five rice landraces had a strong aroma; whereas eleven had a slight aroma. FMbadh2-E7 was found to have most of the alleles with a major allele frequency of 0.53. Whereas, Badex7-5, has a major allele frequency of 0.51, with five alleles at the locus. The dendrogram was generated by UPGMA cluster analysis using two aroma-specific primers, which characterized the rice genotypes into two distinct clusters; Cluster 1 consisted of fifteen rice landraces with non-aroma standards, while Cluster 2 consisted of fifteen rice landraces with aroma standards. Based on the sensory test and molecular approach, the identified rice landraces with aroma were i.e., Kenawit, Gertok, Pandan, Nangka, Tiga Bulan, Lumpur, Grik, Sanguo Pandan, Kurau, Bidor, and Wangi, which can be further promoted as potential donors through breeding. [ABSTRACT FROM AUTHOR]

• For the first time, we apply the principle of three-line hybrid rice breeding to the field of feature fusion. • We propose a feature fusion method that can automatically learn and dynamically update the weights. • Solve the problems of nonlinearity and high data dimensionality in the field of software defect prediction. Software defect prediction (SDP) plays a crucial role in ensuring the security and quality of software systems. However, it faces challenges posed by high-dimensional features present in software defect datasets and the limited effectiveness of traditional nonlinear dimensionality reduction methods in extracting essential feature information. To address these issues, we propose a novel approach called learnable three-line hybrid feature fusion (LTHFFA), which incorporates the principle of three-line hybrid breeding into feature fusion for the first time. In this method, three distinct dimensionality reduction techniques are initially employed to obtain three separate sets of features. Subsequently, a learnable weight factor feature fusion method is proposed to facilitate automatically learn and dynamically update of feature weights. By integrating the three feature sets based on the principle of three-line hybrid breeding, we derive learnable three-line hybrid fusion features. These features are then utilized in the context of software defect prediction. Experimental results demonstrate the superior performance of LTHFFA compared to nine other dimensionality reduction methods across seventeen publicly available software defect datasets. LTHFFA exhibits the ability to effectively integrate multiple feature sets, reduce feature redundancy, and enhance predictive accuracy. Moreover, statistical analysis using Friedman ranking and Holm's post-hoc test confirms the significant advantage of LTHFFA over alternative dimensionality reduction methods. [ABSTRACT FROM AUTHOR]

Background: There is great productivity of rice(Oryza sativa L. spp. japonica) straw in China, which is a potential source of biomass for biofuel and forage. However, the high levels of lignins in rice straw limited its usage and induced the formation of agricultural waste. In order to modify the lignins contents to improve biofuel production and forage digestibility, we selected Soybean hull peroxidase (SHP) and Glyoxal oxidase (GLOX) as candidate genes to improve quality of rice straw. SHP, a class III plant peroxidase, is derived from multiple sources. It has several advantages, such as high resistance to heat, high stability under acidic and alkaline conditions, and a broad substrate range. SHP is speculated to be useful for lignin degradation. Glyoxal oxidase (GLOX) is an extracellular oxidase that can oxidize glyoxal and methylglyoxal in the extracellular medium to generate H2O2. Results: In the present study, the SHP and GLOX genes in pCAMBIA3301-glycine-rich protein (GRP)-SHP-GLOX, designated the K167 vector, were optimized and introduced into rice embryos using Agrobacterium-mediated transformation. Positive transgenic rice embryos were examined using molecular, physiological, biochemical and fermentation tests. The outcomes suggested that SHP degraded lignin effectively. Conclusions: This research has created a rice breeding material with normal growth and yield but stalks that are more amenable to degradation in the later stage for use in breeding rice varieties whose stalks are easily used for energy. Our results will improve the industrial and commercial applications of rice straw. [ABSTRACT FROM AUTHOR]

Improvement of eating and cooking quality is one of the main objectives in rice breeding programs in Iran. In this study various rice genotypes, including upland, aerobic rice, Iranian improved varieties and landraces known for grain quality, were studied for eating, cooking, physicochemical characteristics as well as molecular evaluation with SSR molecular marker and three genes based markers (GBSSI (Wx), GW8/OsSPL1 and AGPase-S), at the University of Guilan, Rasht, Iran across two years: 2015 and 2017. According to the results, the best quality and aromatic varieties showed moderate values for amylose content (AC) and gelatinization temperature (GT) 21.06 and 4.27%, respectively and also moderate trough viscosity (TV) 149.06, final viscosity (FV) 276.77 and setback viscosity (SBV) 67.05. Association analysis revealed that SSR marker, RM589 was associated significantly with AC, peak viscosity (PV), SBV and consistency viscosity (COV). SSR marker, RM190 was also found as the common SSR marker associated with peak viscosity (PV), TV, and FV and RM3498 was correlated with GT, SBV and COV in both the years. On the other hand, haplotype analysis with reference to Domsiah as a famous aromatic variety revealed the best quality Iranian rice varieties such as Hashemi, Hasansaraei and Sadri had the Domsiah alleles for RM276, RM190, and RM3498 markers. The results suggest that the identified informative markers have a strong association with rice grain quality and could be utilized in subsequent studies and marker-assisted breeding aiming to improve grain quality. [ABSTRACT FROM AUTHOR]

Quality-related traits are some of the most important traits in rice, and screening and breeding rice lines with excellent quality are common ways for breeders to improve the quality of rice. In this study, we used 151 recombinant inbred lines (RILs) obtained by crossing the northern cultivated japonica rice variety ShenNong265 (SN265) with the southern indica rice variety LuHui99 (LH99) and simplified 18 common rice quality-related traits into 8 independent principal components (PCs) by principal component analysis (PCA). These PCs included peak and hot paste viscosity, chalky grain percentage and chalkiness degree, brown and milled rice recovery, width length rate, cooked taste score, head rice recovery, milled rice width, and cooked comprehensive score factors. Based on the weight ratio of each PC score, the RILs were classified into five types from excellent to poor, and five excellent lines were identified. Compared with SN265, these 5 lines showed better performance regarding the chalky grain percentage and chalkiness degree factor. Moreover, we performed QTL localization on the RIL population and identified 94 QTLs for quality-related traits that formed 6 QTL clusters. In future research, by combining these QTL mapping results, we will be using backcrossing to aggregate excellent traits and achieve quality improvement of SN265. [ABSTRACT FROM AUTHOR]

With the improvement of people's living standards and rice trade worldwide, the demand for high-quality rice is increasing. Therefore, breeding high quality rice is critical to meet the market demand. However, progress in improving rice grain quality lags far behind that of rice yield. This might be because of the complexity of rice grain quality research, and the lack of consensus definition and evaluation standards for high quality rice. In general, the main components of rice grain quality are milling quality (MQ), appearance quality (AQ), eating and cooking quality (ECQ), and nutritional quality (NQ). Importantly, all these quality traits are determined directly or indirectly by the structure and composition of the rice seeds. Structurally, rice seeds mainly comprise the spikelet hull, seed coat, aleurone layer, embryo, and endosperm. Among them, the size of spikelet hull is the key determinant of rice grain size, which usually affects rice AQ, MQ, and ECQ. The endosperm, mainly composed of starch and protein, is the major edible part of the rice seed. Therefore, the content, constitution, and physicochemical properties of starch and protein are crucial for multiple rice grain quality traits. Moreover, the other substances, such as lipids, minerals, vitamins, and phytochemicals, included in different parts of the rice seed, also contribute significantly to rice grain quality, especially the NQ. Rice seed growth and development are precisely controlled by many genes; therefore, cloning and dissecting these quality-related genes will enhance our knowledge of rice grain quality and will assist with the breeding of high quality rice. This review focuses on summarizing the recent progress on cloning key genes and their functions in regulating rice seed structure and composition, and their corresponding contributions to rice grain quality. This information will facilitate and advance future high quality rice breeding programs. [ABSTRACT FROM AUTHOR]

Grain quality has become one of the foci in rice breeding worldwide since it is crucial for farmers, millers and consumers. Previous studies have revealed that rice gain quality is mainly determined with several major characteristics including milling, physical appearance, eating and cooking, sensory and nutritional value. In genetics, rice grain quality is a complex trait controlled by polygene/QTL. Better understanding the mechanism underlying the grain quality is fundamental for developing new breeding strategies. Therefore, abundant studies had been conducted to discover the factors that control the quality traits, and led to dozens of QTL identified and several major genes cloned. This has enabled development of the functional markers to facilitate selection of the complex traits. But breeding for rice varieties with desired grain quality needs to pyramid multiple and beneficial loci or alleles, some of which are still untapped. In this chapter, we first summarize the literatures on rice grain quality traits and the relevant phenotyping approaches, and then review the progress in genetic dissection of these traits. This review also presented the breeding attempts using marker-assisted selection, genomics-assisted breeding approaches, as well as genome editing technologies, and finally provided innovative insights into the future of rice grain quality breeding by using the modern technology with integration of machine learning and genomic selection. [ABSTRACT FROM AUTHOR]

This study was carried out using 22 promising restorer lines of rice and their parental lines to study genetic variability and genetic advance for yield and yield-associated grain quality traits and floral traits. These genotypes are evaluated in a replicated trial using Randomized Complete Block Design (RCBD) with three replications at the Experimental Farm of Sakha Agricultural Research Station, Sakha, Kafr El-Sheikh, Egypt, during the seasons from 2012 to 2020. Analysis of variance revealed that highly significant variations were observed among the genotypes for all the studied characters. Both GCV% and PCV% were high for the number of spikelets per panicle, the number of filled grains per panicle, and panicle weight. The genetic advance in the percentage of mean was high for days to plant height, panicle length, number of spikelets per panicle, number of filled grains per panicle, panicle weight, grain yield per plant, anther length, anther breadth, duration of floret opening, and head rice percentage. Mean performance of the rice genotypes indicated that the genotypes NRL 59, NRL 55, NRL 62, NRL 63, NRL 66, and NRL 54-2 were promising for grain yield and associated desirable traits. Thus, some of these promising lines can be promoted as a new rice variety and could be used as a source for developing new hybrid combinations in hybrid rice breeding programs. The percentage of advantage over better parent and Giza 178 as the commercial variety was significant and there were highly significant desirable values among the genotypes for all the studied traits in the two years, indicating that the selection is effective in the genetic improvements for these traits. [ABSTRACT FROM AUTHOR]

Significant achievements have been made in breeding programs for the heavy‐panicle‐type (HPT) rice (Oryza sativa) in Southwest China. The HPT varieties now exhibit excellent lodging resistance, allowing them to overcome the greater pressures caused by heavy panicles. However, the genetic mechanism of this lodging resistance remains elusive. Here, we isolated a major quantitative trait locus, Panicle Neck Diameter 1 (PND1), and identified the causal gene as GRAIN NUMBER 1A/CYTOKININ OXIDASE 2 (Gn1A/OsCKX2). The null gn1a allele from rice line R498 (gn1aR498) improved lodging resistance through increasing the culm diameter and promoting crown root development. Loss‐of‐function of Gn1a/OsCKX2 led to cytokinin accumulation in the crown root tip and accelerated the development of adventitious roots. Gene pyramiding between the null gn1aR498 allele with two gain‐of‐function alleles, STRONG CULM 2 (SCM2) and SCM3, further improved lodging resistance. Moreover, Gn1a/OsCKX2 had minimal influence on overall rice quality. Our research thus highlights the distinct genetic components of lodging resistance of HPT varieties and provides a strategy for tailor‐made crop improvement of both yield and lodging resistance in rice. [ABSTRACT FROM AUTHOR]

The determination of rice grain quality (RGQ) parameters is important because it is the benchmark of rice breeding success to meet up the consumers' demand. RGQ includes milling, storage, cooking, eating, nutrition, and market quality of rice grain. Furthermore, demand for high-quality rice has increased globally and is expected to continue to rise due to consumer preferences. However, global consumer demand, culture, and demographic variances determine acceptable RGQ attributes. For example, European consumers prefer long-grain, nonaromatic rice, whereas Middle Eastern consumers prefer long-grain, well-milled rice with a strong aroma. To improve the rice quality, RGQ analysis is the best way; besides we need to understand the genetic mechanism of the several grain quality quantitative trait loci (QTLs) actions. A better understanding of these QTLs can be tremendously useful in the development of novel RGQ varieties. This review is intended to study major RGQ parameters and their assessment tools. This study is focusing on the limitations and prospects of QTLs to improve RGQ. [ABSTRACT FROM AUTHOR]

Rice is the most staple food consuming in China. During the past six decades, a large number of indica inbred rice cultivars have been developed. However, seldom studies have focused on evaluating the dynamic changes of grain quality improvement among the major cultivars. Our study evaluated the genetic improvement of 12 quality traits in indica inbred rice cultivars developed in rice breeding programs in South China during 1956–2020. The results indicated that significant improvement had been gained for the appearance quality, cooking and eating quality in the breeding program since the 1990s, while slight genetic improvement was attained before 1990. Among all the 12 traits, MGL (Milled Grain Length), LWR (Length Rate Ratio), GC (Gel Consistency), and ASV (Alkali Spreading Value) were significantly increased among these different cultivars; MGW (Milled Grain Width), CGR (Chalky Grain Rate), CA (Chalkiness Area), and AC (Amylase Content) showed a tremendously decreased trend from last thirty years. However, the other four traits, such as BRR (Brown Rice Rate), MRR (Milled Rice Rate), HMRR (Head Milled Rice Rate), and PC (Protein Content) showed little improvement during the breeding processes in these cultivars. The results also suggested that selecting a slender grain shape would be beneficial for breeding high quality indica rice. We also discussed that improving milling quality, especially HMRR of the high-quality cultivars and nutrition quality for special consumer groups as an meaningful direction for rice breeding. [ABSTRACT FROM AUTHOR]

Higher-yield and superior-quality rice are the major goals in rice breeding and nitrogen management. Genetic modification combined with optimal nitrogen (N) fertilization is expected to realize it. Modification in transaldolase (TAL) expression alters both the number and pattern of vascular bundles in rice plants, but its interactions with N rate remains unknown. We employed three representative lines with different expression levels of TAL in the same genetic background (Wuyunjing 7, WT), and analyzed their responses in dry matter accumulation (DMA), carbohydrate transport, grain filling, yield, yield components, and grain quality under a wide range of N rate. Increased expression of TAL (OE) promoted rice yield by producing more spikelets per panicle and higher 1000-grain weight, while decreased expression of TAL lowered the seed setting rate and grain weight significantly. Under a fixed N rate, when TAL expression was altered, the direct path coefficients of the seed setting rate and 1000-grain weight to the yield were higher than other yield components, especially at a high N rate. Decreased expression of TAL (RNAi) significantly reduced the starch and non-structural carbohydrates (NSC) contents in the stems, but enhanced the soluble sugar retention, whereas increased expression of TAL enhanced the translocation of NSC. The grain weight at maturity and mean grain-filling rate (mg d−1) increased significantly along with the TAL expression, but their differences among RNAi, WT and OE narrowed at higher N rate. Decreased expression of TAL enhanced the apparent amylose content (ACC) and protein (PC), reduced the starch granule size, and caused a loose starch arrangement and elevated chalkiness, as a consequence, significantly reduced the peak viscosity, hot viscosity, final viscosity, and taste value in a N rate dependent manner. The taste values of OE and WT were similar and the highest value was attained under a moderate N rate. TAL expression plays an important role in the regulation of assimilate supply, grain filling, yield formation, and grain quality. Increased expression of TAL alleviates competition effect among the yield components and enhances the yield potential, especially under moderate to high N rate. Higher TAL expression combined with a moderate N rate improves ECQ. TAL expression and N rate interacts to regulate yield components and quality. This finding provides meaningful knowledge to administering N rate and genetically modifying TAL expression in a rice variety. • Altered TAL gene expression impacts seed setting and grain weight dependent on N-rate. • High TAL level improves grain filling and final weight via more assimilate supply. • Higher TAL under mild N rate improves taste value by amylose and protein contents. [ABSTRACT FROM AUTHOR]

Summary: The source–sink relationship determines the overall agronomic performance of rice. Cloning and characterizing key genes involved in the regulation of source and sink dynamics is imperative for improving rice yield. However, few source genes with potential application in rice have been identified. Glucan, Water‐Dikinase 1 (GWD1) is an essential enzyme that plays a pivotal role in the first step of transitory starch degradation in source tissues. In the present study, we successfully generated gwd1 weak mutants by promoter editing using CRISPR/Cas9 system, and also leaf‐dominant overexpression lines of GWD1 driven by Osl2 promoter. Analysis of the gwd1 plants indicated that promoter editing mediated down‐regulation of GWD1 caused no observable effects on rice growth and development, but only mildly modified its grain transparency and seed germination. However, the transgenic pOsl2::GWD1 overexpression lines showed improvements in multiple key traits, including rice yield, grain shape, rice quality, seed germination and stress tolerance. Therefore, our study shows that GWD1 is not only involved in transitory starch degradation in source tissues, but also plays key roles in the seeds, which is a sink tissue. In conclusion, we find that GWD1 is an ideal biotechnological target with promising potential for the breeding of elite rice cultivars via genetic engineering. [ABSTRACT FROM AUTHOR]