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Selenium is an essential trace element in the human body. However, its intake is generally low. Therefore, the production and utilisation of selenium-enriched foods is currently a research hotspot. In this study, the effects of low (0.2 mg·kg−1), medium (1.0 mg·kg−1), and high (5.0 mg·kg−1) concentrations of selenium on the physiological and biochemical characteristics of rice were investigated to develop selenium-enriched rice. High concentrations of selenium have been found to inhibit the growth, physiology, and biochemistry of rice, while low concentrations of selenium promote its growth. The height of mature rice plants exposed to high concentrations of selenium was reduced by 7.20% compared with the height of control rice. Selenium decreased the proline content of rice during the growth period except in mature rice treated with medium and high concentrations of selenium. Excluding high concentrations, selenium treatment increased the soluble sugar content of rice from the tillering to the mature stages. The peroxidase activity of rice at the heading stage treated with medium levels of selenium was significantly higher than that of the control rice, while the superoxide dismutase activity of rice exposed to selenium was significantly enhanced at the mature stage. The malondialdehyde levels of mature rice treated with medium and high levels of selenium were significantly lower than those of the control rice. The selenium content of each plant part was significantly correlated with the soil selenium level. An increase in the soil selenium level facilitated the production of selenium-enriched rice. [ABSTRACT FROM AUTHOR]

Rice blast caused by the pathogenic fungus Magnaporthe oryzae poses a significant threat to rice cultivation. The identification of robust resistance germplasm is crucial for breeding resistant varieties. In this study, we employed functional molecular markers for 10 rice blast resistance genes, namely Pi1, Pi2, Pi5, Pi9, Pia, Pid2, Pid3, Pigm, Pikh, and Pita, to assess blast resistance across 91 indica rice backbone varieties in South China. The results showed a spectrum of resistance levels ranging from highly resistant (HR) to highly susceptible (HS), with corresponding frequencies of 0, 19, 40, 27, 5, and 0, respectively. Yearly correlations in blast resistance genes among the 91 key indica rice progenitors revealed Pid2 (60.44%), Pia (50.55%), Pita (45.05%), Pi2 (32.97%), Pikh (4.4%), Pigm (2.2%), Pi9 (2.2%), and Pi1 (1.1%). Significant variations were observed in the distribution frequencies of these 10 resistance genes among these progenitors across different provinces. Furthermore, as the number of aggregated resistance genes increased, parental resistance levels correspondingly improved, though the efficacy of different gene combinations varied significantly. This study provides the initial steps toward strategically distributing varieties of resistant indica rice genotypes across South China. [ABSTRACT FROM AUTHOR]

Panicle-type structure is an important factor affecting rice yield, and an excellent panicle type has become a key indicator in rice breeding. In this study, the indica rice variety R766, which has an open panicle type, was obtained through natural mutation and hybrid selection. Through analyzing differences in panicle structure, panicle yield, and chemical composition between open panicle rice R766 and conventional panicle rice R2928, we found that the angles of the middle and lower branches in R766 were 186.99% and 135.93% greater than those in R2928, respectively. By comparing the grain-filling characteristics of different panicle positions in the two rice varieties, we found that the grain filling at the middle and lower panicle positions of R2928 was significantly lower, accompanied by an increase in the percentage of empty spikelets. However, in R766, the grain-filling rates in the middle and lower panicle positions were consistent with those in the upper panicle position, with significantly higher rates of grain filling and grain plumpness in the middle and lower panicle positions than in R2928. The empty grain rate at the lower panicle position of R766 was 15.25% lower than that of R2928, and the grain filling was 24.75% higher than that of R2928. Additionally, the variation in the 1000-grain weight of grains at different panicle positions in R766 was relatively small, with decreases of 1.55% and 0.38% in the middle and lower panicle positions, respectively, compared with the upper position, whereas R2928 showed decreases of 5.99% and 7.12% in the 1000-grain weight of grains at the middle and lower panicle positions, respectively, compared with the upper position. The cellulose content in the stems of R766 was 7.51% higher than that of R2928, with no significant difference in the cellulose content in the panicle axis and primary branches compared to R2928. The lignin content of the panicle axis in R766 was 8.03% higher than that in R2928, whereas there was no significant difference between the lignin content of the stems and primary branches. This preliminary study revealed the open panicle characteristics of R766 and the reasons for its high basal grain setting rate. This study provides a reference for promoting this open panicle-type indica rice variety to improve yield and disease resistance in environments with high humidity and low sunlight levels. [ABSTRACT FROM AUTHOR]

The latest CRISPR-Cas9-mediated genome editing technology is expected to bring about revolution in rice yield and quality improvement, and thus validation of rice transformation protocols using CRISPR-Cas9-gRNA constructs is the need of the hour. Moreover, regeneration of more number of transgenic rice plants is prerequisite for developing genome-edited rice lines, as recalcitrant rice varieties were shown to have lower editing efficiencies which necessities screening of large number of transgenic plants to find the suitable edits. In the present study, we have simplified the Agrobacterium-mediated rice transformation protocol for both Indica and Japonica rice cultivars using CRISPR/Cas9 empty vector construct, and the protocols have been suitably optimized for getting large numbers of the regenerated plantlets within the shortest possible time. The Japonica transgenic lines were obtained within 65 days and for the Indica cultivars, it took about 76–78 days. We also obtained about 90% regeneration efficiency for both Japonica and Indica cultivars. The transformation efficiency was about 97% in the case of Japonica and 69–83% in the case of Indica rice cultivars. Furthermore, we screened the OsWRKY24 gene editing efficiency by transforming rice cultivars with CRISPR/Cas9 construct harbouring sgRNA against OsWRKY24 gene and found about 90% editing efficiency in Japonica rice cultivars, while 30% of the transformed Indica cultivars were found to be edited. This implicated the presence of a robust repair mechanism in the Indica rice cultivars. [ABSTRACT FROM AUTHOR]

Backgrounds and Objectives: Fermented rice cake is a common traditional fermented food in China with a crystal clear color, unique flavor, dense honeycomb structure, and soft and delicate texture. As its raw materials are not uniform, different batches often have poor product quality stability and different volatile flavor components. Therefore, this study investigates the effects of different indica rice flours on processing adaptability and their impacts on the flavor characteristics. Findings: The results show that the seven indica rice flours have significantly different basic compositions and physicochemical properties (p <.05). Specifically, the fermented rice cake prepared with TG2 showed a large specific volume, good elasticity, bright color, high volatile flavor compound contents, and the maximum comprehensive sensory evaluation score. Additionally, partial least squares discriminant analysis was conducted, and three volatile compounds were identified with variable importance for the projection >1 and odor activity value >1 as the criteria, namely, ethanol, styrene, and phenethyl alcohol, which played major roles in forming the overall aroma of fermented rice cakes. Conclusions: The texture, color, and sensory score of fermented rice cakes are closely related to the basic components of the indica rice flour, and the most popular fermented rice cakes have a specific volume of no less than 2 mL/g, an L* of above 78, and a TPA‐tested elasticity of about 3 mm. Significance and Novelty: This study may help improve the processing of fermented rice cakes and provide a theoretical basis for their production and flavor control. [ABSTRACT FROM AUTHOR]

Rice is a staple food for nearly two-thirds of China's population. As socio-economic development continues, there is a growing demand for high-quality rice. This study collected grain quality traits for 17,785 rice varieties approved throughout China, and categorized them into the following five types: indica inbred (II), indica hybrid (IH), japonica inbred (JI), japonica hybrid (JH), and indica-japonica hybrid (IJ). Comprehensive analyses were conducted to assess the differences and trends in rice quality across these varieties. We found that JI and JH excel in processing and cooking qualities, featuring higher brown rice and head milled rice rates, coupling with longer gel consistency. Inbred varieties display lower chalky rice rates than hybrids. Over several decades, head milled rice rates have notably increased across all types except for IJ. Transparency grade has decreased in nearly all types except for IJ, with similar declines observed in chalky rice rates and chalkiness degree, suggesting an overall progress in appearance quality. In terms of cooking and taste attributes, amylose content has decreased in most varieties except for IJ, and gel consistency has improved in indica varieties. Generally, the rice quality of varieties approved in China has shown a clear trend of improvement over the past 40 years. This study provides significant data support and theoretical backing for ongoing rice breeding efforts. [ABSTRACT FROM AUTHOR]

Simple Summary: Photoperiod sensitivity is important for rice breeders to enable crop adaptation to changing climatic conditions. This study aims to pinpoint candidate insertion/deletion (INDEL) markers linked to photoperiod sensitivity in indica rice cultivars. The INDEL marker can be utilized to explore the gene function in rice flowering, potentially facilitating gene editing using CRISPR/Cas9 technology. Applying this INDEL marker in breeding programs can enhance the genetic gain and economic efficiency of a targeted breeding strategy. The current study aims to identify candidate insertion/deletion (INDEL) markers associated with photoperiod sensitivity (PS) in rice landraces from the Vietnamese Mekong Delta. The whole-genome sequencing of 20 accessions was conducted to analyze INDEL variations between two photoperiod-sensitivity groups. A total of 2240 INDELs were identified between the two photoperiod-sensitivity groups. The selection criteria included INDELs with insertions or deletions of at least 20 base pairs within the improved rice group. Six INDELs were discovered on chromosomes 01 (5 INDELs) and 6 (1 INDEL), and two genes were identified: LOC_Os01g23780 and LOC_Os01g36500. The gene LOC_Os01g23780, which may be involved in rice flowering, was identified in a 20 bp deletion on chromosome 01 from the improved rice accession group. A marker was devised for this gene, indicating a polymorphism rate of 20%. Remarkably, 20% of the materials comprised improved rice accessions. This INDEL marker could explain 100% of the observed distinctions. Further analysis of the mapping population demonstrated that an INDEL marker associated with the MADS-box gene on chromosome 01 was linked to photoperiod sensitivity. The F1 population displayed two bands across all hybrid individuals. The marker demonstrates efficacy in distinguishing improved rice accessions within the indica accessions. This study underscores the potential applicability of the INDEL marker in breeding strategies. [ABSTRACT FROM AUTHOR]

The rapid increase in soil acidity coupled with the deleterious effects of cadmium (Cd) toxicity had led to a decline in worldwide agricultural production. Rice absorbs and accumulates Cd(II) from polluted paddy soils, increasing human health risks throughout the food chain. A 35-day hydroponic experiment with four japonica and four indica (two each of them tolerant and sensitive cultivars) was conducted in this study to investigate the adsorption and absorption of Cd(II) by rice roots as related with surface chemical properties of the roots. The results showed that the three chemical forms of exchangeable, complexed, and precipitated Cd(II) increased with the increase in Cd(II) concentration for all rice cultivars. The roots of indica rice cultivars carried more negative charges and had greater functional groups and thus adsorbed more exchangeable and complexed Cd(II) than those of japonica rice cultivars. This led to more absorption of Cd(II) by the roots and greater toxicity of Cd(II) to the roots of indica rice cultivars and more inhibition of Cd(II) stress on the growth of the roots and whole plants of indica rice cultivars compared with japonica rice cultivars, which was one of the main reasons for more declines in the biomass and length of indica rice roots and shoots than japonica rice cultivars. Cd(II) stress showed more toxicity to the sensitive rice cultivars and thus greater inhibition on the growth of the cultivars due to more exchangeable and complexed Cd(II) adsorbed by their roots induced by more negative charges and functional groups on the roots compared with tolerant rice cultivar for both indica and japonica, which resulted in greater decreases in the biomass and length of roots and shoots as well as chlorophyll contents of the sensitive cultivars than the tolerant cultivars. The roots of sensitive rice cultivars also absorbed more Cd(II) than tolerant rice cultivars due to the same reasons as above. These findings will provide useful references for the safe utilization and health risk prevention of Cd-contaminated paddy fields. [ABSTRACT FROM AUTHOR]

To reveal differences in arsenic (As) accumulation among indica rice cultivars and assess the human health risks arising from inorganic arsenic (iAs) intake via rice consumption, a total of 320 field indica rice samples and corresponding soil samples were collected from Fujian Province in China. The results showed that available soil As (0.03 to 3.83 mg/kg) showed a statistically significant positive correlation with total soil As (0.10 to 19.45 mg/kg). The inorganic As content in brown rice was between 0.001 and 0.316 mg/kg. Among the cultivars, ten brown rice samples (3.13%) exceeded the maximum contaminant level (MCL) of iAs in food of 0.2 mg/kg in China. The estimated daily intake (EDI) and calculated individual incremental lifetime cancer risk (ILCR) ranged from 0.337 µg/day to 106.60 µg/day and from 8.18 × 10–6 to 2.59 × 10–3, respectively. Surprisingly, the average EDI and the EDIs of 258 (80.63%) brown rice samples were higher than the maximum daily intake (MDI) of 10 µg/day in drinking water as set by the National Research Council. The mean ILCR associated with iAs was 54.3 per 100,000, which exceeds the acceptable upper limit (AUL) of 10 per 100,000 set by the USEPA. Notably, the cultivars Y-Liang-You 1 and Shi-Ji 137 exhibited significantly higher mean ILCRs compared to the AUL and other cultivars, indicating that they pose more serious cancer risks to the local population. Finally, this study demonstrated that the cultivars Yi-Xiang 2292 and Quan-Zhen 10 were the optimal cultivars to mitigate risks associated with iAs to human health from rice consumption. [ABSTRACT FROM AUTHOR]

To obtain immediate homozygosity by androgenesis, the doubled haploid method is often used. As a result, a mapping population was created utilizing rice (Oryza sativa L.) cvs. Mahulata and IR 20 as parents in order to find QTLs/genes for drought tolerance at the vegetative stage. The effectiveness of the doubled haploids (DHs) approach, on the other hand, is largely dependent on the ability to distinguish haploids from diploids among the green regenerants. Although flow cytometry and cytological screening for pollen sterility can be used to identify haploids, these methods are expensive, time-consuming, and need a sophisticated laboratory with highly trained workers. Plant height and other spikelet features have also been used to differentiate haploids from doubled haploids. However, no systematic analysis of several morphological features for distinguishing haploids in doubled haploids has been published to date. As a result, a cost-effective approach for distinguishing haploids from true DHs obtained from anther culture is required. The goal of this work was to identify haploids using morphological features and simple microscopic examinations without the use of chemicals or complex laboratory facilities. The cross between the IR20 and Mahulata yielded a total of 198 anther culture (AC) derived plants. A group of 41 plantlets was chosen as putative haploids based on their shorter height and Cq values using qPCR-based genotyping and finally validated that, in addition to plant height, other morphological traits such as total number of leaves/plant, total number of tillers/plant, and floral characters can be used to successfully identify haploids. We report a variety of morphological signs as indicators of haploid plants, including smaller plants, higher tiller density, narrower and shorter leaf length, and partial exertion of panicle from the flag leaf sheath. Other morphological markers for identifying haploids from DHs include smaller florets and anthers, and small desiccated microspores.

Based on the analysis of rice quality characteristics of indica rice varieties from regional trials in recent 10 years, we hope to provide references for quality improvement of indica rice varieties in the next stage. We analyzed 2 701 samples of early season, medium season and late season indica rice samples in 17 provinces (autonomous regions and municipalities directly under the central government) from 2011 to 2020, and divided them into 8 groups according to maturity and regional trials group. Based on the agricultural industry standard “Cooking rice variety quality” NY/T 593, we analyzed the development trend of qualified rate and rice quality index of indica rice varieties in recent 10 years. The results showed that the quality of indica rice varieties in China presented a steady upward trend in recent 10 years, especially for late season indica rice, which improved the most significantly after 2017. The rice quality of mid-late ripe of late season indica rice and sensitive late season indica rice in south China was better than early ripe of late season indica rice; rice quality of medium season indica rice in the middle was better than that of medium season indica rice in the upper Yangtze River; the rice quality of early season indica rice in south China was better than that of other two early season indica rice varieties and has been improved steadily in recent years. Chalkiness degree, alkali spreading value and amylose content of quality indexes have been increasing steadily, gel consistency and brown rice rate keep high standard rate in recent 10 years, the variation of qualified rate in head rice rate and translucency above one level changed greatly from year to year, and there was no obvious trend of improvement. For rice quality index, in addition to keeping on reducing the amylose content and chalkiness degree of indica rice, it is also needed o strengthen the study on inter annual stability of head rice rate and transparency of indica rice. And the improvement of rice quality of medium season indica rice is the key direction for the improvement of indica rice quality in the future.

Selenium is an essential trace element in the human body. However, its intake is generally low. Therefore, the production and utilisation of selenium-enriched foods is currently a research hotspot. In this study, the effects of low (0.2 mg·kg−1), medium (1.0 mg·kg−1), and high (5.0 mg·kg−1) concentrations of selenium on the physiological and biochemical characteristics of rice were investigated to develop selenium-enriched rice. High concentrations of selenium have been found to inhibit the growth, physiology, and biochemistry of rice, while low concentrations of selenium promote its growth. The height of mature rice plants exposed to high concentrations of selenium was reduced by 7.20% compared with the height of control rice. Selenium decreased the proline content of rice during the growth period except in mature rice treated with medium and high concentrations of selenium. Excluding high concentrations, selenium treatment increased the soluble sugar content of rice from the tillering to the mature stages. The peroxidase activity of rice at the heading stage treated with medium levels of selenium was significantly higher than that of the control rice, while the superoxide dismutase activity of rice exposed to selenium was significantly enhanced at the mature stage. The malondialdehyde levels of mature rice treated with medium and high levels of selenium were significantly lower than those of the control rice. The selenium content of each plant part was significantly correlated with the soil selenium level. An increase in the soil selenium level facilitated the production of selenium-enriched rice.

Rice blast caused by the pathogenic fungus Magnaporthe oryzae poses a significant threat to rice cultivation. The identification of robust resistance germplasm is crucial for breeding resistant varieties. In this study, we employed functional molecular markers for 10 rice blast resistance genes, namely Pi1, Pi2, Pi5, Pi9, Pia, Pid2, Pid3, Pigm, Pikh, and Pita, to assess blast resistance across 91 indica rice backbone varieties in South China. The results showed a spectrum of resistance levels ranging from highly resistant (HR) to highly susceptible (HS), with corresponding frequencies of 0, 19, 40, 27, 5, and 0, respectively. Yearly correlations in blast resistance genes among the 91 key indica rice progenitors revealed Pid2 (60.44%), Pia (50.55%), Pita (45.05%), Pi2 (32.97%), Pikh (4.4%), Pigm (2.2%), Pi9 (2.2%), and Pi1 (1.1%). Significant variations were observed in the distribution frequencies of these 10 resistance genes among these progenitors across different provinces. Furthermore, as the number of aggregated resistance genes increased, parental resistance levels correspondingly improved, though the efficacy of different gene combinations varied significantly. This study provides the initial steps toward strategically distributing varieties of resistant indica rice genotypes across South China.

Due to global climate change resulting in extreme temperature fluctuations, it becomes increasingly necessary to explore the natural genetic variation in model crops such as rice to facilitate the breeding of climate-resilient cultivars. To uncover genomic regions in rice involved in managing cold stress tolerance responses and to identify associated cold tolerance genes, two inbred line populations developed from crosses between cold-tolerant and cold-sensitive parents were used for quantitative trait locus (QTL) mapping of two traits: degree of membrane damage after 1 week of cold exposure quantified as percent electrolyte leakage (EL) and percent low-temperature seedling survivability (LTSS) after 1 week of recovery growth. This revealed four EL QTL and 12 LTSS QTL, all overlapping with larger QTL regions previously uncovered by genomewide association study (GWAS) mapping approaches. Within the QTL regions, 25 cold-tolerant candidate genes were identified based on genomic differences between the cold-tolerant and cold-sensitive parents. Of those genes, 20% coded for receptor-like kinases potentially involved in signal transduction of cold tolerance responses; 16% coded for transcription factors or factors potentially involved in regulating cold tolerance response effector genes; and 64% coded for protein chaperons or enzymes potentially serving as cold tolerance effector proteins. Most of the 25 genes were cold temperature regulated and had deleterious nucleotide variants in the cold-sensitive parent, which might contribute to its cold-sensitive phenotype. [ABSTRACT FROM AUTHOR]

An efficient multiple shoot induction, plant regeneration, and subsequent genetic transformation system for two locally adapted recalcitrant indica rice cultivars ASD16 and ADT43 using shoot apex explants were established. Three different plant growth regulators (PGRs) were tested for their efficacy in forming multiple shoots from shoot apices. Thidiazuron (TDZ) (5.0 mg/L) induced the highest frequencies of multiple shoot induction compared to Benzyl Amino Purine (BAP) and Kinetin (Kin). Shoot apices cultured on MS basal medium devoid of plant growth regulators formed single shoots. All tested PGRs produced multiple shoots at concentrations higher than 3.0 mg/L. Indole-3-Acetic Acid (IAA) and Indole-3-Butyric Acid (IBA) were supplemented to media containing TDZ (5.0 mg/L) for assessing the root induction efficiencies and it was found that media devoid of growth hormones were sufficient to produce better-rooting frequencies comparatively. Among the two tested cultivars, ASD16 responded with better shooting frequencies than ADT43. Further, genetic transformation experiments were carried out with the shoot apex explants of both cultivars. The putative transgenic plants were screened and confirmed by transient GUS expression, PCR, and Southern hybridization in both T0 and T1 generations, respectively. This rapid and efficient regeneration system amenable to Agrobacterium-mediated genetic transformation from shoot apices may be used for genetic manipulation of recalcitrant indica varieties for varietal crop improvement strategies. [ABSTRACT FROM AUTHOR]

In the context of growing environmental challenges and the push for sustainable agriculture, this study delves into the eco-efficiency of three-season indica rice across 16 key provinces in China from 2004 to 2021. Utilizing the super-efficiency Slacks-Based Measure (SBM) model coupled with the Malmquist index, our approach uniquely incorporates undesirable outputs, focusing on carbon emissions from chemical and plastic inputs. Findings indicate that while the overall efficiency hinged around a modest mean, periods like 2005–2006 and 2017–2018 spotlighted the pivotal role of technological advancements and judicious resource use. The Malmquist Index revealed an intricate interplay between technological change and efficiency, notably when accounting for environmental impact. Diverse provincial efficiencies spotlighted the need for bespoke strategies harmonizing efficiency objectives with ecological sustainability. This study emphasizes the indispensable role of technological innovation in advancing eco-efficiency and fostering sustainable agricultural practices, urging for policy changes that prioritize both technology adoption and ecological awareness. [ABSTRACT FROM AUTHOR]

Low-glutelin-content rice, a type of functional rice with glutelin levels below 4%, is an essential dietary supplement for chronic kidney disease (CKD) patients. Developing low-glutelin-content rice varieties is crucial to catering to the growing CKD population. In this study, we aimed to create a new low-glutelin indica rice variety with excellent agronomic traits. To achieve this, we employed a combination of molecular-marker-assisted selection and traditional breeding techniques. The cultivars W3660, Wushansimiao (WSSM), and Nantaixiangzhan (NTXZ) were crossbred, incorporating the Lgc-1, Pi-2, Xa23, and fgr alleles into a single line. The result of this breeding effort was "Yishenxiangsimiao", a new indica rice variety that inherits the desirable characteristics of its parent lines. Yishenxiangsimiao (YSXSM) possesses not only a low glutelin content but also dual resistance to blast and bacterial blight (BB). It exhibits high-quality grains with a fragrant aroma. This new low-glutelin indica cultivar not only ensures a stable food supply for CKD patients but also serves as a healthy dietary option for the general public. We also performed RNA-seq of these rice varieties to investigate their internal gene expression differences. The YSXSM exhibited a higher biotic-resistance gene expression in comparison to NTXZ. In summary, we successfully developed a novel low-glutelin indica rice variety, "Yishenxiangsimiao", with superior agronomic traits. This rice variety addresses the dietary needs of CKD patients and offers a nutritious choice for all consumers. [ABSTRACT FROM AUTHOR]

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Panicle-type structure is an important factor affecting rice yield, and an excellent panicle type has become a key indicator in rice breeding. In this study, the indica rice variety R766, which has an open panicle type, was obtained through natural mutation and hybrid selection. Through analyzing differences in panicle structure, panicle yield, and chemical composition between open panicle rice R766 and conventional panicle rice R2928, we found that the angles of the middle and lower branches in R766 were 186.99% and 135.93% greater than those in R2928, respectively. By comparing the grain-filling characteristics of different panicle positions in the two rice varieties, we found that the grain filling at the middle and lower panicle positions of R2928 was significantly lower, accompanied by an increase in the percentage of empty spikelets. However, in R766, the grain-filling rates in the middle and lower panicle positions were consistent with those in the upper panicle position, with significantly higher rates of grain filling and grain plumpness in the middle and lower panicle positions than in R2928. The empty grain rate at the lower panicle position of R766 was 15.25% lower than that of R2928, and the grain filling was 24.75% higher than that of R2928. Additionally, the variation in the 1000-grain weight of grains at different panicle positions in R766 was relatively small, with decreases of 1.55% and 0.38% in the middle and lower panicle positions, respectively, compared with the upper position, whereas R2928 showed decreases of 5.99% and 7.12% in the 1000-grain weight of grains at the middle and lower panicle positions, respectively, compared with the upper position. The cellulose content in the stems of R766 was 7.51% higher than that of R2928, with no significant difference in the cellulose content in the panicle axis and primary branches compared to R2928. The lignin content of the panicle axis in R766 was 8.03% higher than that in R2928, whereas there was no significant difference between the lignin content of the stems and primary branches. This preliminary study revealed the open panicle characteristics of R766 and the reasons for its high basal grain setting rate. This study provides a reference for promoting this open panicle-type indica rice variety to improve yield and disease resistance in environments with high humidity and low sunlight levels.

Rice is a staple food for nearly two-thirds of China’s population. As socio-economic development continues, there is a growing demand for high-quality rice. This study collected grain quality traits for 17,785 rice varieties approved throughout China, and categorized them into the following five types: indica inbred (II), indica hybrid (IH), japonica inbred (JI), japonica hybrid (JH), and indica-japonica hybrid (IJ). Comprehensive analyses were conducted to assess the differences and trends in rice quality across these varieties. We found that JI and JH excel in processing and cooking qualities, featuring higher brown rice and head milled rice rates, coupling with longer gel consistency. Inbred varieties display lower chalky rice rates than hybrids. Over several decades, head milled rice rates have notably increased across all types except for IJ. Transparency grade has decreased in nearly all types except for IJ, with similar declines observed in chalky rice rates and chalkiness degree, suggesting an overall progress in appearance quality. In terms of cooking and taste attributes, amylose content has decreased in most varieties except for IJ, and gel consistency has improved in indica varieties. Generally, the rice quality of varieties approved in China has shown a clear trend of improvement over the past 40 years. This study provides significant data support and theoretical backing for ongoing rice breeding efforts.

The current study aims to identify candidate insertion/deletion (INDEL) markers associated with photoperiod sensitivity (PS) in rice landraces from the Vietnamese Mekong Delta. The whole-genome sequencing of 20 accessions was conducted to analyze INDEL variations between two photoperiod-sensitivity groups. A total of 2240 INDELs were identified between the two photoperiod-sensitivity groups. The selection criteria included INDELs with insertions or deletions of at least 20 base pairs within the improved rice group. Six INDELs were discovered on chromosomes 01 (5 INDELs) and 6 (1 INDEL), and two genes were identified: LOC_Os01g23780 and LOC_Os01g36500. The gene LOC_Os01g23780, which may be involved in rice flowering, was identified in a 20 bp deletion on chromosome 01 from the improved rice accession group. A marker was devised for this gene, indicating a polymorphism rate of 20%. Remarkably, 20% of the materials comprised improved rice accessions. This INDEL marker could explain 100% of the observed distinctions. Further analysis of the mapping population demonstrated that an INDEL marker associated with the MADS-box gene on chromosome 01 was linked to photoperiod sensitivity. The F1 population displayed two bands across all hybrid individuals. The marker demonstrates efficacy in distinguishing improved rice accessions within the indica accessions. This study underscores the potential applicability of the INDEL marker in breeding strategies.

Due to global climate change resulting in extreme temperature fluctuations, it becomes increasingly necessary to explore the natural genetic variation in model crops such as rice to facilitate the breeding of climate-resilient cultivars. To uncover genomic regions in rice involved in managing cold stress tolerance responses and to identify associated cold tolerance genes, two inbred line populations developed from crosses between cold-tolerant and cold-sensitive parents were used for quantitative trait locus (QTL) mapping of two traits: degree of membrane damage after 1 week of cold exposure quantified as percent electrolyte leakage (EL) and percent low-temperature seedling survivability (LTSS) after 1 week of recovery growth. This revealed four EL QTL and 12 LTSS QTL, all overlapping with larger QTL regions previously uncovered by genome-wide association study (GWAS) mapping approaches. Within the QTL regions, 25 cold-tolerant candidate genes were identified based on genomic differences between the cold-tolerant and cold-sensitive parents. Of those genes, 20% coded for receptor-like kinases potentially involved in signal transduction of cold tolerance responses; 16% coded for transcription factors or factors potentially involved in regulating cold tolerance response effector genes; and 64% coded for protein chaperons or enzymes potentially serving as cold tolerance effector proteins. Most of the 25 genes were cold temperature regulated and had deleterious nucleotide variants in the cold-sensitive parent, which might contribute to its cold-sensitive phenotype.

Introduction: Nitrogen (N) fertilizer management, especially postponing N topdressing can affect rice eating quality by regulating starch quality of superior and inferior grains, but the details are unclear. This study aimed to evaluate the effects of N topdressing on starch structure and properties of superior and inferior grains in hybrid indica rice with different tastes and to clarify the relationship between starch structure, properties, and taste quality. Methods: Two hybrid indica rice varieties, namely the low-taste Fyou 498 and high-taste Shuangyou 573, were used as experimental materials. Based on 150 kg·N hm-2, three N fertilizer treatments were established: zero N (N0), local farmer practice (basal fertilizer: tillering fertilizer: panicle fertilizer=7:3:0) (N1), postponing N topdressing (basal fertilizer: tillering fertilizer: panicle fertilizer=3:1:6) (N2). Results: The starch granules of superior grains were more complete, and the decrease in small granules content and the stability of starch crystals were a certain extent less than those of inferior grains. Compared with N1, under N2, low-taste and high-taste varieties large starch granules content were significantly reduced by 6.89%, 0.74% in superior grains and 4.26%, 2.71% in inferior grains, the (B2 + B3) chains was significantly reduced by 1.61%, 0.98% in superior grains, and 1.18%, 0.97% in inferior grains, both reduced the relative crystallinity and 1045/1022 cm-1, thereby decreasing the stability of the starch crystalline region and the orderliness of starch granules. N2 treatment reduced the ΔHgel of two varieties. These changes ultimately contributed to the enhancement of the taste values in superior and inferior grains in both varieties, especially the inferior grains. Correlation analysis showed that the average starch volume diameter (D[4,3]) and relative crystallinity were significantly positively correlated with the taste value of superior and inferior sgrains, suggesting their potential use as an evaluation index for the simultaneous enhancement of the taste value of rice with superior and inferior grains. Discussion: Based on 150 kg·N hm-2, postponing N topdressing (basal fertilizer: tillering fertilizer: panicle fertilizer=3:1:6) promotes the enhancement of the overall taste value and provides theoretical information for the production of rice with high quality. [ABSTRACT FROM AUTHOR]

It is important to clarify the effects of starch fine structure and protein components on the eating quality of indica rice. In this study, seven indica rice varieties with similar apparent amylose content (AAC) and protein content (PC) but different sensory taste values were selected and compared systematically. It was found that except for AAC and PC, these varieties showed significant differences in starch molecular structure and protein components. Compared with rice varieties with a low sensory taste value, varieties with a higher sensory taste value showed significantly lower amylose and higher amylopectin short chains (degree of polymerization 6–12) content; the protein component showed that the varieties with good taste value had higher albumin and lower globulin and glutelin content (p < 0.05). Rice varieties with lower AC, globulin, and glutelin content, as well as a higher content of albumin and amylopectin short chains, resulted in a higher swelling factor, peak viscosity, breakdown value, and ratio of hardness to stickiness, in which condition cooked rice showed a higher sensory taste value. Moreover, this study indicated that rice varieties with a higher content of albumin and amylopectin short chains were conducive to the good appearance of cooked rice. This study lays the foundation for the taste evaluation of good-tasting indica rice. [ABSTRACT FROM AUTHOR]

Summary: Aphelenchoides besseyi is among the most devastating plant-parasitic nematodes and causes severe loss, mainly on japonica rice in China. Recently the nematode has been found to be present in the seeds of indica rice and the hybrid rice cultivars also show symptoms of the nematode damage. To understand the variations in different rice cultivars against A. besseyi , the dynamics of nematode population, the incidence of symptoms and the effects on plant yield were investigated in field experiments during 2017-2018 by inoculation of mixed stages of A. besseyi onto the seeds and seedlings of different types of rice cultivars. The results showed few nematodes could be recovered from the plants at the seedling and the end of tillering stages in all the cultivars. After flowering, the number of nematodes per panicle increased and the highest number was found in 'Zheyou 18' in 2017 (1050.2) and 2018 (732.1). The average incidence of the inoculated plants showing white-tip symptoms ranged from 0.5 to 10.3% and from 0.0 to 75.7% at the tillering stage in 2017 and 2018, respectively. The incidences of white-tip symptoms in the indica cultivars, including '9311', 'Minghui 63' and 'Nei 5 you 39', were significantly lower than in 'Xingxiang', a japonica cultivar and 'Zheyou 18', a hybrid rice cultivar, both at the flowering stage in 2017 and at the end of the tillering stage in 2018. A strong interaction of the treatments and cultivars on the 1000-grain weight and panicle length was evident. [ABSTRACT FROM AUTHOR]

Haploid plants are of significant interest to crop breeders due to their ability to expedite the development of inbred lines. Chromosome-doubling of haploids, produced by either in vitro or in vivo methods, results in fully homozygous doubled haploids. For nearly five decades, in vitro methods of anther and microspore culture have been attempted in many crops. In rice, in vitro methods are used with some success in japonica cultivars, although indica types have remained recalcitrant to a large extent. This review aims to explore the reasons for the lack of success of in vitro methods in indica rice and discuss new advancements in in vivo haploid induction protocols in other cereals and their relevance to rice. In particular, the current level of understanding of in vivo haploid inducer systems that utilize MTL and CENH3 mutants is analyzed in detail. One notable advantage of in vivo haploid induction systems is that they do not require tissue culture competence. This makes these methods more accessible and potentially transformative for research, offering a pragmatic approach to improving indica rice cultivars. By embracing these in vivo methods and harnessing the power of gene editing technologies like CRISPR/Cas9 systems, breeders can reshape their approach to indica rice improvement. [ABSTRACT FROM AUTHOR]

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SUMMARY: Heterosis has been widely used in multiple crops. However, the molecular mechanism and prediction of heterosis remains elusive. We generated five F1 hybrids [four showing better‐parent heterosis (BPH) and one showing mid‐parent heterosis], and performed the transcriptomic and methylomic analyses to identify the candidate genes for BPH and explore the molecular mechanism of heterosis and the potential predictors for heterosis. Transcriptomic results showed that most of the differentially expressed genes shared in the four better‐parent hybrids were significantly enriched into the terms of molecular function, and the additive and dominant effects played crucial roles for BPH. DNA methylation level, especially in CG context, significantly and positively correlated with grain yield per plant. The ratios of differentially methylated regions in CG context in exons to transcription start sites between the parents exhibited significantly negative correlation with the heterosis levels of their hybrids, as was further confirmed in 24 pairwise comparisons of other rice lines, implying that this ratio could be a feasible predictor for heterosis level, and this ratio of less than 5 between parents in early growth stages might be a critical index for judging that their F1 hybrids would show BPH. Additionally, we identified some important genes showing differential expression and methylation, such as OsDCL2, Pi5, DTH2, DTH8, Hd1 and GLW7 in the four better‐parent hybrids as the candidate genes for BPH. Our findings helped shed more light on the molecular mechanism and heterosis prediction. Significance Statement: It is still difficult to effectively predict the level of heterosis between varieties or lines in crop breeding. Our finding indicates that the methylation level, especially in CG context, significantly positively correlates with grain yield per plant, and the ratio of the number of differential methylation in CG context in exons to that in transcription start sites (TSSs) between parental lines is a potential indicator to predict the magnitude of heterosis of their hybrids. [ABSTRACT FROM AUTHOR]

Drought is a major abiotic constraint on rice (Oryza sativa L.) production in Malaysia. Malaysian Agricultural Research and Development Institute (MARDI) has released more than 50 indica rice genotypes so far. However, little has been studied about their drought tolerance. The study aimed to evaluate the germination and early seedling growth performances of 15 rice genotypes under polyethylene glycol (PEG) 6000-induced drought stresses. Four osmotic potentials of PEG 6000 (0, -0.3, -0.6, -0.9 MPa) were used in the study denoted as control, low, moderate and severe stresses respectively. Data on seed germination percentage, germination index, germination energy, germination rate, seedling height, seedling vigor I and II, fresh and dry weight of seedlings were measured. Studied parameters varied greatly among genotypes with different osmotic stresses. The findings suggested most of the rice genotypes showed an apparent reduction in germination and growth traits, while MR211 showed less reduction under all of the stresses. The Multivariate clustering grouped genotypes into five different clusters, where cluster V (MR220, MR269, MR253, MR297, MR303 and MR284) incorporated six genotypes showed better germination and growth under different osmotic potentials, followed by cluster IV (MR211 and MR307). Cluster II incorporated one genotype MARDI WARNA98 which had minimal germination and growth attributes. Principal component analysis (PCA) was performed to identify the maximum contributing variables for diversity, revealed maximum variation by first two components (81.8% and 7.7%) respectively. Therefore, PEG 6000 can be used as an efficient tool for discrimination and identification of drought tolerance in rice. [ABSTRACT FROM AUTHOR]

Bacterial leaf blight (BLB) is a devastating disease caused by Xanthomonas oryzae pv. oryzae (Xoo), which poses a significant threat to global rice production. In this study, a genome-wide association study (GWAS) was conducted using the genotyping-by-sequencing (GBS) approach to identify candidate single nucleotide polymorphisms (SNPs) associated with BLB resistance genes. The study utilized 200 indica rice accessions inoculated with seven distinct Xoo isolates and filtered highly significant SNPs using a minor allele frequency (MAF) of >5% and a call rate of 75%. Four statistical models were used to explore potential SNPs associated with BLB resistance, resulting in the identification of 32 significant SNPs on chromosomes 1–8 and 12 in the rice genome. Additionally, 179 genes were located within ±100 kb of the SNP region, of which 49 were selected as candidate genes based on their known functions in plant defense mechanisms. Several candidate genes were identified, including two genes in the same linkage disequilibrium (LD) decay as the well-known BLB resistance gene (Xa1). These findings represent a valuable resource for conducting further functional studies and developing novel breeding strategies to enhance the crop's resistance to this disease. [ABSTRACT FROM AUTHOR]

Abstract Background The Qinba region is the transition region between Indica and Japonica varieties in China. It has a long history of Indica rice planting of more than 7000 years and is also a planting area for fine-quality Indica rice. The aims of this study are to explore different genetic markers applied to the analysis population structure, genetic diversity, selection and optimization of molecular markers of Indica rice, thus providing more information for the protection and utilization on germplasm resources of Indica rice. Methods Fifteen phenotypic traits, a core set of 48 SSR markers which originated protocol for identification of rice varieties-SSR marker method in agricultural industry standard of the People's Republic of China (Ministry of Agriculture of the PRC, NY/T1433-2014, Protocol for identification of rice varieties-SSR marker method, 2014), and SNPs data obtained by genotyping-by-sequencing (GBS, NlaIII and MseI digestion, referred to as SNPs-NlaIII and SNPs-MseI, respectively) for this panel of 93 samples using the Illumina HiSeq2000 sequencing platform, were employed to explore the genetic diversity and population structure of 93 samples. Results The average of coefficient of variation (CV) and diversity index (He) were 29.72% and 1.83 ranging from 3.07% to 137.43%, and from 1.45 to 2.03, respectively. The correlation coefficient between 15 phenotypic traits ranged from 0.984 to -0.604. The first four PCs accounted for 70.693% phenotypic variation based on phenotypic analysis. A total of 379 alleles were obtained using SSR markers, encompassing an average of 8.0 alleles per primer. Polymorphic bands (PPB) and polymorphism information content (PIC) was 88.65% and 0.77, respectively. The Mantel test showed that the correlation between the genetic distance matrix based on SNPs-NlaIII and SNPs-MseI was the largest (R2=0.88), and that based on 15 phenotypic traits and SSR was the smallest (R2=0.09). The 93 samples could be clustered into two subgroups by 3 types of genetic markers. Molecular variance analysis revealed that the genetic variation was 2% among populations and 98% within populations (the Nm was 0.16), Tajima’s D value was 1.66, the FST between the two populations was 0.61 based on 72,824 SNPs. Conclusions The population genetic variation explained by SNPs was larger than that explained by SSRs. The gene flow of 93 samples used in this study was larger than that of naturally self-pollinated crops, which may be caused by long-term breeding selection of Indica rice in the Qinba region. The genetic structure of the 93 samples was simple and lacked rare alleles.

Seed vigor is the key performance parameter of good quality seed. A panel was prepared by shortlisting genotypes from all the phenotypic groups representing seedling growth parameters from a total of 278 germplasm lines. A wide variation was observed for the traits in the population. The panel was classified into four genetic structure groups. Fixation indices indicated the existence of linkage disequilibrium in the population. A moderate to high level of diversity parameters was assessed using 143 SSR markers. Principal component, coordinate, neighbor-joining tree and cluster analyses showed subpopulations with a fair degree of correspondence with the growth parameters. Marker–trait association analysis detected eight novel QTLs, namely qAGR4.1, qAGR6.1, qAGR6.2 and qAGR8.1 for absolute growth rate (AGR); qRSG6.1, qRSG7.1 and qRSG8.1 for relative shoot growth (RSG); and qRGR11.1 for relative growth rate (RGR), as analyzed by GLM and MLM. The reported QTL for germination rate (GR), qGR4-1, was validated in this population. Additionally, QTLs present on chromosome 6 controlling RSG and AGR at 221 cM and RSG and AGR on chromosome 8 at 27 cM were detected as genetic hotspots for the parameters. The QTLs identified in the study will be useful for improvement of the seed vigor trait in rice. [ABSTRACT FROM AUTHOR]

The eating quality evaluation of rice is raising further concerns among researchers and consumers. This research is aimed to apply lipidomics in determining the distinction between different grades of indica rice and establishing effective models for rice quality evaluation. Herein, a high-throughput ultrahigh-performance liquid chromatography coupled with quadrupole time-of-flight (UPLC-QTOF/MS) method for comprehensive lipidomics profiling of rice was developed. Then, a total of 42 significantly different lipids among 3 sensory levels were identified and quantified for indica rice. The orthogonal partial least-squares discriminant analysis (OPLS-DA) models with the two sets of differential lipids showed clear distinction among three grades of indica rice. A correlation coefficient of 0.917 was obtained between the practical and model-predicted tasting scores of indica rice. Random forest (RF) results further verified the OPLS-DA model, and the accuracy of this method for grade prediction was 90.20%. Thus, this established approach was an efficient method for the eating grade prediction of indica rice. [ABSTRACT FROM AUTHOR]

There is a need to comprehensively evaluate the rice quality of different rice varieties under different nitrogen treatments. Therefore, in this study, we used twenty-one hybrid indica rice varieties and twenty-three inbred japonica rice varieties with three nitrogen fertilizer levels to investigate differences in rice qualities. As compared with hybrid indica rice, inbred japonica rice had lower coefficient of variation values for grain shape, mild rice percentage, and head rice percentage, but relatively higher coefficient of variation values for chalkiness traits, appearance, and taste value of cooked rice. A principal component analysis and membership function method were used to comprehensively evaluate the qualities of rice. The overall eating quality value by sensory evaluation and head rice percentage explained 61.3% and 67.9% of the variations in comprehensive quality of hybrid indica rice and inbred japonica rice across different nitrogen levels, respectively. We also found that rice comprehensive quality was better under low nitrogen levels for hybrid indica rice, while for inbred japonica rice, properly increasing nitrogen application could improve the comprehensive quality. [ABSTRACT FROM AUTHOR]

The HAK (High-affinity K+) family members mediate K+ transport that confers normal plant growth and resistance against unfavourable environmental conditions. Rice (Oryza sativa L.) HAK transporters have been extensively investigated for phylogenetic analyses with other plants species with very few of them functionally characterised. But very little information is known about their evolutionary aspects, overall structural, functional characterisation, and global expression pattern of the complete HAK family members in response to salt stress. In this study, 27 rice transporters were phylogenetically clustered with different dicot and monocot family members. Subsequently, the exon–intron structural patterns, conserved motif analyses, evolutionary divergence based different substitution matrix, orthologous-paralogous relationships were studied elaborately. Structural characterisations included a comparative study of secondary and tertiary structure, post-translational modifications, correspondence analyses, normal mode analyses, K+/Na+ binding affinities of each of the OsHAK gene members. Global expression profile under salt stress showed clade-specific expression pattern of the proteins. Additionally, five OsHAK genes were chosen for further expression analyses in root and shoot tissues of two rice varieties during short-term salinity in the presence and absence of exogenous spermidine. All the information can be used as first-hand data for dissecting the administrative role of rice HAK transporters under various abiotic stresses. The HAK (High-affinity K+) family members mediate K+ transport that confers normal plant growth and resistance against unfavourable environmental conditions. The phylogenetic, structural, functional characterisations of 27 rice (Oryza sativa L.) HAK transporters were performed and the effect of exogenous spermidine on five OsHAK genes under salt stress was studied. All these studies will pave the way to scrutinise the specific role of oshak transporter genes in improving crop resistance towards environmental stress conditions. [ABSTRACT FROM AUTHOR]

Low-glutelin-content rice, a type of functional rice with glutelin levels below 4%, is an essential dietary supplement for chronic kidney disease (CKD) patients. Developing low-glutelin-content rice varieties is crucial to catering to the growing CKD population. In this study, we aimed to create a new low-glutelin indica rice variety with excellent agronomic traits. To achieve this, we employed a combination of molecular-marker-assisted selection and traditional breeding techniques. The cultivars W3660, Wushansimiao (WSSM), and Nantaixiangzhan (NTXZ) were crossbred, incorporating the Lgc-1, Pi-2, Xa23, and fgr alleles into a single line. The result of this breeding effort was “Yishenxiangsimiao”, a new indica rice variety that inherits the desirable characteristics of its parent lines. Yishenxiangsimiao (YSXSM) possesses not only a low glutelin content but also dual resistance to blast and bacterial blight (BB). It exhibits high-quality grains with a fragrant aroma. This new low-glutelin indica cultivar not only ensures a stable food supply for CKD patients but also serves as a healthy dietary option for the general public. We also performed RNA-seq of these rice varieties to investigate their internal gene expression differences. The YSXSM exhibited a higher biotic-resistance gene expression in comparison to NTXZ. In summary, we successfully developed a novel low-glutelin indica rice variety, “Yishenxiangsimiao”, with superior agronomic traits. This rice variety addresses the dietary needs of CKD patients and offers a nutritious choice for all consumers.

Abstract Background In this study, indica rice (Oryza sativa L.) was bioconversioned using Lactobacillus plantarum ATCC14917 and Lactobacillus rhamnosus GG KCTC5033. Results Compared to the control treatment (RE), rice extract fermented with Lactobacillus plantarum ATCC14917 (LP-RE) and Lactobacillus rhamnosus GG KCTC5033 (LR-RE) inhibited the growth of pathogenic bacteria significantly except for E. coli O157:H7 (p

To obtain immediate homozygosity by androgenesis, the doubled haploid method is often used. As a result, a mapping population was created utilizing rice (Oryza sativa L.) cvs. Mahulata and IR 20 as parents in order to find QTLs/genes for drought tolerance at the vegetative stage. The effectiveness of the doubled haploids (DHs) approach, on the other hand, is largely dependent on the ability to distinguish haploids from diploids among the green regenerants. Although flow cytometry and cytological screening for pollen sterility can be used to identify haploids, these methods are expensive, time-consuming, and need a sophisticated laboratory with highly trained workers. Plant height and other spikelet features have also been used to differentiate haploids from doubled haploids. However, no systematic analysis of several morphological features for distinguishing haploids in doubled haploids has been published to date. As a result, a cost-effective approach for distinguishing haploids from true DHs obtained from anther culture is required. The goal of this work was to identify haploids using morphological features and simple microscopic examinations without the use of chemicals or complex laboratory facilities. The cross between the IR20 and Mahulata yielded a total of 198 anther culture (AC) derived plants. A group of 41 plantlets was chosen as putative haploids based on their shorter height and Cq values using qPCR-based genotyping and finally validated that, in addition to plant height, other morphological traits such as total number of leaves/plant, total number of tillers/plant, and floral characters can be used to successfully identify haploids. We report a variety of morphological signs as indicators of haploid plants, including smaller plants, higher tiller density, narrower and shorter leaf length, and partial exertion of panicle from the flag leaf sheath. Other morphological markers for identifying haploids from DHs include smaller florets and anthers, and small desiccated microspores. [ABSTRACT FROM AUTHOR]

Mature and efficient tissue culture systems are already available for most japonica rice varieties (Oryza sativa ssp. geng). However, it remains challenging to regenerate the majority of indica rice varieties (Oryza sativa ssp. xian). In this study, quantitative trait loci (QTLs) associated with rice callus regeneration ability were identified based on the plant regeneration rate (PRR) and total green plant rate (TGPR) of the 93-11 × Nip recombinant inbred line population. Significant positive correlations were found between PRR and TGPR. A total of three QTLs (one for PRR and two for TGPR) were identified. qPRR3 (located on chromosome 3) was detected for both traits, which could explain 13.40% and 17.07% of the phenotypic variations of PRR and TGPR, respectively. Subsequently, the effect of qPRR3 on callus regeneration ability was validated by cryptographically tagged near-isogenic lines (NILs), and the QTL was narrowed to an interval of approximately 160 kb. The anatomical structure observation of the regenerated callus of the NILs revealed that qPRR3 can improve the callus regeneration ability by promoting the regeneration of shoots. [ABSTRACT FROM AUTHOR]

Sucrose is the primary form of mobile photoassimilates, and its level is regulated by sucrose-phosphate synthase (SPS) in plants. Increasing in the SPS activity was accompanied by an increase in sucrose accumulation. This study was designed to examine the effect of the overexpression sugarcane SoSPS1 gene on sucrose metabolizing enzymes, growth, and grain yield of indica rice. The SoSPS1 gene was constructed in a binary vector under the control of a rice ubiquitin promoter and transformed into indica rice using an Agrobacterium vector. Five lines of transgenic rice were selected to develop homozygous transgenic lines and used for analysis. The overexpression of the SoSPS1 gene significantly increased the transcript and protein levels, followed by increasing in SPS activity and sucrose content in the leaves of the transgenic rice lines. Moreover, the activity of soluble acid invertase (SAI) was elevated rather than sucrose synthase (SuSy) in the transgenic lines. The increase in the sucrose-degrading enzymes leads to an increase in plant growth and development. The plant height and number of tillers were significantly higher in the transgenic line compared to non-transgenic (NT) rice. In addition, the amylose content, the number of seeds per panicle, and the weight of 1000 grains of seed, including dry biomass weight, were increased in the transgenic lines. The results indicated that enhancement of SPS activity, as well as sucrose content, provides a higher carbon partitioning for higher growth and productivity of the transgenic rice lines. [ABSTRACT FROM AUTHOR]

Because of the higher nitrogen (N) recovery efficiency (NRE) of panicle-stage fertilization compared with basal and tillering fertilization, increasing the proportion of N topdressing at the booting stage (panicle-N) is recommended and commonly practiced in parts of China. To investigate the effects of increasing panicle-N on grain yield and N use efficiency (NUE) and the relationships of the increase and the rice cultivar and soil fertility status, we increased the percentage of panicle-N from 20% to 40% by correspondingly reducing the N amount applied only at the tillering stage in both high- and low-fertility blue clayey paddy fields in 2018 and 2019. Four indica cultivars with diverse panicle types were used, and their grain yield, dry matter accumulation, and NUE were compared. In high-fertility soil, increasing topdressing panicle-N from 20% to 40% reduced tillering ability and reduced the effective panicle numbers of the multi- and medium-panicle cultivars Huanghuazhan (HHZ), C Liangyouhuazhan (CHZ), and Tianyouhuazhan (THZ). These cultivars gave the greatest yield when 30% of N was supplied as panicle fertilizer, whereas the yield, NRE, N agronomic efficiency (NAE), and nitrogen physiological efficiency (NPE) of the heavy-panicle inbred cultivar Yangdao 6 (YD6) continued to increase, resulting in improved dry matter accumulation and grain filling in the late growth stage. The yield, NAE, NRE, and NPE of YD6 peaked when the panicle-N constituted 40%. While in low-fertility soil, the multipanicle cultivar HHZ showed the greatest yield when 30% of fertilizer-N was applied once at the panicle initiation (PI) stage, while the medium-panicle cultivar CHZ showed the greatest yield when the panicle-N percentage was 40%. Our results suggest that the percentage of panicle-N fertilizer should not exceed 30% for multipanicle cultivars, while can be appropriately increased to 40% for heavy-panicle indica cultivars. The effect of increasing topdressing panicle-N on the yield of medium-panicle cultivars was related to soil fertility. The optimum panicle-N percentage was 30% in the high-fertility soil and 40% in the low-fertility soil. [ABSTRACT FROM AUTHOR]

Rice plants display a unique root ecosystem comprising oxic-anoxic zones, harboring a plethora of metabolic interactions mediated by its root microbiome. Since agricultural land is limited, an increase in rice production will rely on novel methods of yield enhancement. The nascent concept of tailoring plant phenotype through the intervention of synthetic microbial communities (SynComs) is inspired by the genetics and ecology of core rhizobiome. In this direction, we have studied structural and functional variations in the root microbiome of 10 indica rice varieties. The studies on α and β-diversity indices of rhizospheric root microbiome with the host genotypes revealed variations in the structuring of root microbiome as well as a strong association with the host genotypes. Biomarker discovery, using machine learning, highlighted members of class Anaerolineae, α-Proteobacteria, and bacterial genera like Desulfobacteria, Ca. Entotheonella, Algoriphagus, etc. as the most important features of indica rice microbiota having a role in improving the plant’s fitness. Metabolically, rice rhizobiomes showed an abundance of genes related to sulfur oxidation and reduction, biofilm production, nitrogen fixation, denitrification, and phosphorus metabolism. This comparative study of rhizobiomes has outlined the taxonomic composition and functional diversification of rice rhizobiome, laying the foundation for the development of next-generation microbiome-based technologies for yield enhancement in rice and other crops. [ABSTRACT FROM AUTHOR]

Much attention has shifted to the effects of temperature and solar radiation on rice production and grain quality due to global climate change. Meanwhile, lodging is a major cause of rice yield and quality losses. However, responses of the lodging resistance of rice to temperature and solar radiation are still unclear. To decipher the mechanisms through which the lodging resistance might be affected by temperature and solar radiation, 32 rice cultivars with different lodging resistance were grown at two eco-sites on three sowing dates over a period of three years. Based on the field observation, 12 indica rice cultivars which did not lodge were selected for analysis. Significant differences were found in the lodging resistance of the indica rice cultivars at different temperature and solar radiation treatments. The results showed that temperature was the main factor that affected the lodging resistance of indica rice cultivars under the conditions of this study. With the increased average daily temperature, the lodging resistance decreased rapidly, primarily due to the significant reduction in physical strength of the culm, which was attributed to the longer and thinner basal second internode. Among the 12 indica rice cultivars, the lodging-moderate cultivar Chuanxiang 29B was most sensitive to temperature, and the lodging-resistant cultivar Jiangan was least responsive to temperature. These results suggested that rice breeders could set the shorter and thicker basal internode as the main selection criteria to cultivate lodging-resistant indica cultivars to ensure a high yield at a higher ambient temperature. [ABSTRACT FROM AUTHOR]

Abstract Rice endosperm accumulates large amounts of photosynthetic products as insoluble starch within amyloplasts by properly arranging structured, highly branched, large amylopectin molecules, thus avoiding osmotic imbalance. The amount and characteristics of starch directly influence the yield and quality of rice grains, which in turn influence their application and market value. Therefore, understanding how various allelic combinations of starch biosynthetic genes, with different expression levels, affect starch properties is important for the identification of targets for breeding new rice cultivars. Research over the past few decades has revealed the spatiotemporal expression patterns and allelic variants of starch biosynthetic genes, and enhanced our understanding of the specific roles and compensatory functions of individual isozymes of starch biosynthetic enzymes through biochemical analyses of purified enzymes and characterization of japonica rice mutants lacking these enzymes. Furthermore, it has been shown that starch biosynthetic enzymes can mutually and synergistically increase their activities by forming protein complexes. This review focuses on the more recent discoveries made in the last several years. Generation of single and double mutants and/or high-level expression of specific starch synthases (SSs) allowed us to better understand how the starch granule morphology is determined; how the complete absence of SSIIa affects starch structure; why the rice endosperm stores insoluble starch rather than soluble phytoglycogen; how to elevate amylose and resistant starch (RS) content to improve health benefits; and how SS isozymes mutually complement their activities. The introduction of active-type SSIIa and/or high-expression type GBSSI into ss3a ss4b, isa1, be2b, and ss3a be2b japonica rice mutants, with unique starch properties, and analyses of their starch properties are summarized in this review. High-level accumulation of RS is often accompanied by a reduction in grain yield as a trade-off. Backcrossing rice mutants with a high-yielding elite rice cultivar enabled the improvement of agricultural traits, while maintaining high RS levels. Designing starch structures for additional values, breeding and cultivating to increase yield will enable the development of a new type of rice starch that can be used in a wide variety of applications, and that can contribute to food and agricultural industries in the near future.

The effects of soil pH variations induced by submergence/drainage and biochar application on soil cadmium (Cd) availability to different rice (Oryza sativa L.) varieties are not well understood. This study aims to investigate the possible reasons for available Cd(II) reduction in paddy soil as influenced by biochar and to determine Cd(II) absorption and translocation rates in different parts of various rice varieties. A pot experiment in a greenhouse using four japonica and four indica rice varieties was conducted in Cd(II) contaminated paddy soil with peanut straw biochar. The results indicated that the submerging led to an increase in soil pH due to the consumption of protons (H+) by the reduction reactions of iron/manganese (Fe/Mn) oxides and sulfate (SO 4 2−) and thus the decrease in soil available Cd(II) contents. However, the drainage decreased soil pH due to the release of protons during the oxidation of Fe2+, Mn2+, and S2− and thus the increase in soil available Cd(II) contents. Application of the biochar increased soil pH during soil submerging and inhibited the decline in soil pH during soil drainage, and thus decreased soil available Cd(II) contents under both submerging and drainage conditions. The indica rice varieties absorbed more Cd(II) in their roots and accumulated higher amounts of Cd(II) in their shoots and grains than the japonica rice varieties. The Cd(II) sensitive varieties exhibited a greater absorption and translocation rate of Cd(II) compared to the tolerant varieties of both indica and japonica rice. Biochar inhibited the absorption and accumulation of Cd(II) in the rice varieties, which ultimately lowered the Cd(II) contents in rice grains below the national food safety limit (0.2 mg kg−1). Overall, planting japonica rice varieties in Cd(II) polluted paddy soils combined with the use of biochar can effectively reduce Cd(II) content in rice grains which protects human health against Cd(II) toxicity. [Display omitted] • Redox reactions were responsible for soil pH change in submergence/drainage alteration. • Biochar inhibited soil pH decline and reduced available soil Cd(II) during drainage. • Indica rice varieties absorbed more Cd(II) from soils than japonica rice varieties. • Cd(II)-sensitive rice varieties absorbed more Cd(II) than tolerant rice varieties. • Biochar decreased Cd(II) contents in the roots, shoots and grains of rice varieties. [ABSTRACT FROM AUTHOR]

In the context of growing environmental challenges and the push for sustainable agriculture, this study delves into the eco-efficiency of three-season indica rice across 16 key provinces in China from 2004 to 2021. Utilizing the super-efficiency Slacks-Based Measure (SBM) model coupled with the Malmquist index, our approach uniquely incorporates undesirable outputs, focusing on carbon emissions from chemical and plastic inputs. Findings indicate that while the overall efficiency hinged around a modest mean, periods like 2005–2006 and 2017–2018 spotlighted the pivotal role of technological advancements and judicious resource use. The Malmquist Index revealed an intricate interplay between technological change and efficiency, notably when accounting for environmental impact. Diverse provincial efficiencies spotlighted the need for bespoke strategies harmonizing efficiency objectives with ecological sustainability. This study emphasizes the indispensable role of technological innovation in advancing eco-efficiency and fostering sustainable agricultural practices, urging for policy changes that prioritize both technology adoption and ecological awareness.

It is important to clarify the effects of starch fine structure and protein components on the eating quality of indica rice. In this study, seven indica rice varieties with similar apparent amylose content (AAC) and protein content (PC) but different sensory taste values were selected and compared systematically. It was found that except for AAC and PC, these varieties showed significant differences in starch molecular structure and protein components. Compared with rice varieties with a low sensory taste value, varieties with a higher sensory taste value showed significantly lower amylose and higher amylopectin short chains (degree of polymerization 6–12) content; the protein component showed that the varieties with good taste value had higher albumin and lower globulin and glutelin content (p < 0.05). Rice varieties with lower AC, globulin, and glutelin content, as well as a higher content of albumin and amylopectin short chains, resulted in a higher swelling factor, peak viscosity, breakdown value, and ratio of hardness to stickiness, in which condition cooked rice showed a higher sensory taste value. Moreover, this study indicated that rice varieties with a higher content of albumin and amylopectin short chains were conducive to the good appearance of cooked rice. This study lays the foundation for the taste evaluation of good-tasting indica rice.

Haploid plants are of significant interest to crop breeders due to their ability to expedite the development of inbred lines. Chromosome-doubling of haploids, produced by either in vitro or in vivo methods, results in fully homozygous doubled haploids. For nearly five decades, in vitro methods of anther and microspore culture have been attempted in many crops. In rice, in vitro methods are used with some success in japonica cultivars, although indica types have remained recalcitrant to a large extent. This review aims to explore the reasons for the lack of success of in vitro methods in indica rice and discuss new advancements in in vivo haploid induction protocols in other cereals and their relevance to rice. In particular, the current level of understanding of in vivo haploid inducer systems that utilize MTL and CENH3 mutants is analyzed in detail. One notable advantage of in vivo haploid induction systems is that they do not require tissue culture competence. This makes these methods more accessible and potentially transformative for research, offering a pragmatic approach to improving indica rice cultivars. By embracing these in vivo methods and harnessing the power of gene editing technologies like CRISPR/Cas9 systems, breeders can reshape their approach to indica rice improvement.