Indica Rice Varieties Research Articles

Pollution assessment, ecological risk and source identification of heavy metals in paddy soils and rice grains from Salem, South India

The present study investigated concentrations of metals (Cu, Zn, Fe, Mn, Ni, Pb, and Cd) in paddy soils and rice tissues of nine different widely used indica rice varieties in Salem district, India. The order of DTPA soil available metal contents (mg kg-1) were Fe (33.50) > Mn (8.86) > Cu (2.58) > Pb (1.99) > Zn (1.67) > Ni (1.48) > Cd (0.13). Pollution load index (PLI) levels for Cd (1.28) were ‘moderately polluted’, contamination factor (CF) and enrichment factor (EF) values for all metals showed ‘medium contamination’ and ‘less enrichment’ except for Cu and Pb. Ecological risk factor (ERF) and potential ecological risk index (PRI) values of Cd (31.94 and 287.50) showed ‘moderate risk’ and ‘strong ecological risk’. Bio-accumulation factor (BAF) levels of Cd (48.12) and Pb (27.89) are classified as ‘high concentrators’. Translocation factor (TF) values of Pb (2.9), Cd (2.5) and Ni (1.7) were greater than one for roots to plants. Children had higher target hazard quotient (THQ) and hazard index (HI) values for Cd, Pb and Ni than adults. Principal component analysis (PCA) revealed with all parameters that they fell within the two primary factors 1 and 2, with an eigenvalue of 4.69 (33.52% variation) and 3.73 (26.66% variation), respectively. However, cluster analysis (CA) revealed three distinct groups between the metals studied. Although the soil metal contents were within the permissible levels, the grain Cd (6.07 mg kg-1), Pb (56.20 mg kg-1), and Fe (116.11 mg kg-1) contents in all the rice varieties exceeded the prescribed limits of 0.4, 0.2, and 15 mg kg-1, respectively. Our findings will provide important data for metal enrichment in soils to implement more effective measures to reduce the contamination of metals in paddy fields.

Genetic Loci Mining and Candidate Gene Analysis for Determining Fatty Acid Composition in Rice

Fatty acid composition and its proportions are critical to the nutritional value and storage quality of rice (Oryza sativa L.) as the third major nutrient component in this staple food. This study involved crossing an indica rice variety, Huazhan (HZ), as the male parent, with a japonica variety, Nekken2, as the female parent, to produce the F1 generation. Subsequently, a population of 120 recombinant inbred lines (RILs) was developed through multiple generations of self-breeding. By utilizing a high-density molecular genetic linkage map and phenotypic data of four fatty acid components, we identified a total of 14 quantitative trait loci (QTLs) related to fatty acid composition across chromosomes 1, 3, 4, 6, 8, and 9. These included two QTLs for C14 content, three for C16:0 content, six for C18:1 content, and three for C18:2 content. Notably, the QTL qCOPT4.2 exhibited a high LOD score of 5.22. Within QTL intervals, genes such as OsACX3 and SLG affecting grain length were identified. The expression of candidate genes within these intervals was assessed and further analyzed by using quantitative real-time PCR. Genes such as LOC_Os01g15000, LOC_Os04g47120, LOC_Os04g49194, LOC_Os06g22080, LOC_Os06g23870, LOC_Os06g24704, LOC_Os06g30780, LOC_Os08g44840, and LOC_Os09g36860 were found to regulate fatty acid synthesis or metabolic pathways, potentially enhancing fatty acid content in rice. These QTLs are indispensable for breeding rice varieties with improved fatty acid profiles, offering new genetic resources for enhancing the nutritional and storage qualities of rice.

OsPDIL1-5: dual role in promoting growth and development while modulating drought stress tolerance in rice (Oryza sativa L.).

Drought tolerance and plant growth are critical factors affecting rice yield, and identifying genes that can enhance these traits is essential for improving crop resilience and productivity. Using a growth-depressed and drought-tolerant (gddt) mutant of the indica rice variety Huanghuazhan (HHZ) generated by radiation mutagenesis, we discovered a novel gene, GDDT, which plays a dual role in plant biology: it acts as a positive regulator of growth and development, but as a negative regulator of drought resistance. The gddt mutant displayed a marked reduction in plant growth and seed setting rate, yet exhibited an unexpected advantage in terms of drought tolerance. Our research revealed that the enhanced drought tolerance of the gddt mutant is primarily due to a decrease in stomatal size, density, and aperture, which reduces water loss, and an activation of the reactive oxygen species (ROS) scavenging system, which helps protect the plant from oxidative stress. These physiological changes are observed both under drought conditions and in normal growth conditions. This discovery highlights the importance of GDDT as a pleiotropic gene with significant implications for both plant growth and drought resistance. Through map-based cloning, we determined that the protein disulfide isomerase-like (PDIL) gene OsPDIL1-5 is the GDDT gene. The protein encoded by this gene was localized to the endoplasmic reticulum, consistent with its predicted function. Our findings provide new insights into the role of PDIL genes in rice and suggest that further study of GDDT could lead to a better understanding of how these genes contribute to the complex interplay between plant growth, development, and stress responses. This knowledge could pave the way for the development of rice varieties that are more resilient to drought, thereby increasing crop yields and ensuring food security in water-limited environments.

Involvement of plasma membrane H+-ATPase in the nitrate-nutrition uptake and utilization in indica rice

Utilization of nitrogen by crops is essential for sustainable agriculture. The transport of nitrate (NO3−) across the plasma membrane is a critical gateway for N uptake and subsequent utilization. This process requires proton (H+) coupled cotransport, which is driven by proton motive force, provided by plasma membrane (PM) H+-ATPase. In this report, two indica rice varieties [Meixiangzhan 2 (MXZ) and Jifengyou 1002 (JFY)] in South China were selected and cultivated in hydroponic solution with 0.5 mM or 2.0 mM NO3− as the N source. The JFY exhibited stronger growth with higher biomass than MXZ under both 0.5 mM and 2.0 mM NO3−. PM H+-ATPase activity of JFY roots was significantly higher than that of MXZ. The higher PM H+-ATPase activity in JFY was consistent with a higher abundance of PM H+-ATPase protein and higher transcription levels of OSAs, such as OSA2, OSA7 and OSA8 in roots, OSA3, OSA7 and OSA8 in leaves. The expression of nitrate transporters (OsNRT1;1b, OsNRT2.1, OsNRT2.2, and OsNAR2.1) were also higher in roots or shoots of JFY than those in MXZ. Under 0.5 mM and 2.0 mM NO3−, the NO3− absorption and translocation rate, nitrate content, as well as nitrate reductase (NR) activity were all significantly higher in JFY, as compared to those in MXZ. Taken together, in JFY and MXZ, a higher level of PM H+-ATPase protein and higher activity coupled with greater efficiency in nitrate uptake, translocation and assimilation, suggesting the existence of a close correlation between PM H+-ATPase and nitrate utilization in indica rice. PM H+-ATPase may one of the elite genes that can contribute to nitrate use efficiency in rice.

Proline Priming Enhances Seed Vigour and Biochemical Attributes of Rice (Oryza sativa L.) during Germination.

Seed vigour is a desirable trait especially for direct seeded rice (DSR) cultivation. Seeds with high vigour could improve seed germination, support seedlings in competing with weeds for water and nutrients, and improving seedling establishment throughout the early stages of crop growth. The success of DSR system which account for more 25% of world cultivation areas is highly dependent on the seed vigour and seedling establishment. Seed priming is a promising technique to improve seed vigour. Proline is an amino acid that has been well studied for its roles in plants under different environmental stress conditions. Nevertheless, the effect of proline as a seed priming agent in improving seed vigour in rice remain elusive. In this research, the effect of 24 h of proline priming at various concentrations (0 mM, 1 mM, 2 mM, 10 mM and 20 mM) on rice seed vigour, amylase activity, and total soluble sugar (TSS) content of a Malaysia indica rice variety, MR269 was investigated. Results showed that seeds primed with lower concentration of proline (0 mM, 1 mM and 2 mM) had better germination responses while priming at high concentrations (10 mM and 20 mM) reduced seed germination. Among the concentration tested, priming with 1 mM proline enhanced seed vigour with significantly higher germination percentage (GP), germination rate index (GRI) and seedling vigour index (SVI). In addition, proline primed seeds also exhibited increased amylase activity and TSS content as compared to unprimed seeds. However, priming seed with 20 mM proline was detrimental to the seed vigour and seedling growth whereby lower GP, GRI and SVI and higher mean germination time (MGT) were observed. In short, this study shows that proline could be a potential seed priming agent to improve seed vigour in rice.

Molecular Evolution of Rice Blast Resistance Gene bsr-d1

Rice blast, caused by the fungus Magnaporthe oryzae, reduces rice yields by 10% to 35%. Incorporating plant blast resistance genes into breeding programs is an effective strategy to combat this disease. Understanding the genetic variants that confer resistance is crucial to this strategy. The gene Bsr-d1 encodes a C2H2-like transcription factor, and its recessive allele confers broad-spectrum resistance against infections by various strains of M. oryzae. In this study, we investigated the molecular evolution of the rice blast resistance gene bsr-d1 in a representative population consisting of 827 cultivated and wild rice varieties. Our results revealed that wild rice exhibited significantly higher nucleotide diversity, with polymorphic regions primarily concentrated in the promoter region, in contrast to indica and japonica rice varieties. The Bsr-d1 gene displayed significant differentiation between indica and japonica, with the bsr-d1 resistance allele being unique to indica. Haplotype network and phylogenetic analyses suggested that the bsr-d1 resistance allele most likely originated from Oryza nivara in the region adjacent to the Indian Peninsula and the Indochina Peninsula. Moreover, we explored the utilization of bsr-d1 resistance alleles in China and designed a pair of DNA primers based on the polymorphic sites for the detection of the bsr-d1 resistance gene. In summary, our study uncovering the origin and evolution of bsr-d1 will enhance our comprehension of resistance gene variation and expedite the resistance breeding process.

Genomic and transcriptomic analyses of the elite rice variety Huizhan provide insight into disease resistance and heat tolerance

The indica rice variety Huizhan shows elite traits of disease resistance and heat tolerance. However, the underlying genetic basis of these traits is not fully understood due to limited genomic resources. Here, we used Nanopore long-read and next-generation sequencing technologies to generate a chromosome-scale genome assembly of Huizhan. Comparative genomics analysis uncovered a large chromosomal inversion and expanded gene families that are associated with plant growth, development and stress responses. Functional rice blast resistance genes, including Pi2, Pib and Ptr, and bacterial blight resistance gene Xa27, contribute to disease resistance of Huizhan. Furthermore, integrated genomics and transcriptomics analyses showed that OsHIRP1, OsbZIP60, the SOD gene family, and various transcription factors are involved in heat tolerance of Huizhan. The high-quality genome assembly and comparative genomics results presented in this study facilitate the use of Huizhan as an elite parental line in developing rice varieties adapted to disease pressure and climate challenges.

Detection and Evaluation of Blast Resistance Genes in Backbone Indica Rice Varieties from South China.

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.

Application of Open Panicle Traits in Improving the Filling Characteristics at the Base of Indica Rice Panicles.

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.

Retraction Note: Dissecting the biochemical and molecular-genetic regulation of diverse metabolic pathways governing aroma formation in indigenous aromatic indica rice varieties.

Retraction Note: Dissecting the biochemical and molecular-genetic regulation of diverse metabolic pathways governing aroma formation in indigenous aromatic indica rice varieties.

Transcription factor OsbZIP10 modulates rice grain quality by regulating OsGIF1.

Understanding and optimizing the process of grain filling helps the quest to maximize rice (Oryza sativa L.) seed yield and quality, yet the intricate mechanisms at play remain fragmented. Transcription factors (TFs) are major players in the gene networks underlying the grain filling process. Here, we employed grain incomplete filling (OsGIF1)/cell wall invertase 2, a key gene involved in grain filling, to explore its upstream TFs and identified a bZIP family TF, OsbZIP10, to be a transcriptional activator of OsGIF1. Rice grains of the knockouts of OsbZIP10 showed increased white-core rates but lower amylose content (AC), leading to better eating and cooking qualities in all genetic backgrounds investigated, though the impact of mutations in OsbZIP10 on grain weight depended on genetic background. Multi-omics analyses suggested that, in addition to OsGIF1, multiple genes involved in different biological processes contributing to grain filling were targeted by OsbZIP10, including OsAGPS1, a gene encoding the ADP-Glc pyrophosphorylase (AGPase) small subunit, and genes contributing to homeostasis of reactive oxygen species. Distinct genetic make-up was observed in OsbZIP10 between japonica and indica rice varieties, with the majority varieties of each subspecies belonging to two different haplotypes that were closely associated with AC. Overexpressing the haplotype linked to high-AC in the low-AC genetic background increased AC. Overall, this study sheds crucial light on the significance of the OsbZIP10-OsGIF1 module in the determination of rice grain quality, offering a potential avenue for genetic engineering of rice to produce seeds with tailored attributes.

Investigating cold tolerance mechanisms in rice seedlings: Alternative splicing, promoter analysis, and their applications for marker development

Cold stress harms rice seedlings, causing yield reduction. Enhancing cold tolerance at the seedling stage is crucial for rice breeding. OsFH10, OsFER1, ONAC045, and OsProT were selected to study gene expression including alternative splicing and promoter sequence analysis in rice seedlings. Under cold stress, the four genes exhibited alternative splicing showing intron retention isoforms, and displayed a consistent pattern of upregulation in a group of cold-tolerant varieties, while no isoforms were presented in a group of sensitive varieties. These intron retention isoforms might play a role in facilitating improved cold adaptation in rice seedlings. Promoter sequence analysis revealed polymorphisms of Single nucleotide polymorphisms (SNPs) or Insertions and Deletions (InDels) in ONAC045 and OsProT that distinguished cold-tolerant from cold-sensitive varieties. ONAC045 SNP and OsProT InDel markers were developed and validated using 159 rice lines. These markers were associated with cold tolerance (P < 0.05) and practical to use with general agarose gel. The ONAC045 marker showed high efficacy in predicting tolerance in rice germplasm seedlings, achieving an accuracy of 43.8%. Furthermore, the OsProT marker exhibited greater sensitivity towards cold-tolerant indica seedlings. Both markers have a wide distribution in all rice subspecies. Our findings elucidate the cold response mechanisms and provide insights into potential application in developing cold-tolerant indica rice varieties.

The OsMYC2-JA feedback loop regulates diurnal flower-opening time via cell wall loosening in rice.

Diurnal flower-opening time (DFOT), the time of spikelet opening during the day, is an important trait for hybrid rice (Oryza sativa L.) seed production. Hybrids between indica and japonica rice varieties have strong heterosis, but the parental lines usually have different, nonoverlapping DFOTs. This reduces the success of hybrid seed production in crosses between indica and japonica subspecies, thus hindering the utilization of indica and japonica inter-subspecies heterosis. However, little is known about the molecular mechanisms regulating DFOT in rice. Here, we obtained japonica rice lines with a DFOT 1.5 h earlier than the wild type by overexpressing OsMYC2, a gene encoding a key transcription factor in the jasmonate (JA) signaling pathway. OsMYC2 is activated by JA signaling and directly regulates the transcription of genes related to JA biosynthesis and cell wall metabolism. Overexpressing OsMYC2 led to significantly increased JA contents and decreased cellulose and hemicellulose contents in lodicule cells, as well as the softening of lodicule cell walls. This may facilitate the swelling of lodicules, resulting in early diurnal flower-opening. These results suggest that the OsMYC2-JA feedback loop regulates DFOT in rice via cell wall remodeling. These findings shed light on the understanding of regulatory mechanism of the DFOT of plants, which should promote the development of indica and japonica varieties suitable for hybrid rice breeding.

Multiple cytokinin elevates indirect regeneration potential of indica rice mature embryo

The concept of producing high quality mature seed derived callus competent to genetic transformation followed by efficient full plant regeneration is not unique in rice. But the process is lacking in terms of regeneration efficiency, genotype dependency especially in indica rice. Further, most of the research has only been focused on elite indica cultivars and popular local varieties are neglected. Our extensive literature study also revealed that among all the factors responsible for higher rice regeneration efficiency, the combination, concentration, and type plant growth regulators (PGRs) are mostly responsible for indica rice genotypes. Hence, the present study is focused on standardization of popular local indica rice cultivars for callus induction and regeneration by tweaking the PGRs in culture media, according to their amenability. The plant regeneration potential was assessed on both traditional organogenesis frequency and morphology-based scoring matrix. This revealed the best suitable PGR concentration-combination for efficient organogenesis and the genotype Khitish to be most responsive for indirect regeneration (78.68 ± 1.50 %). The highly polymorphic SSR marker based clonal fidelity test also validated the absence of somaclonal variation among the regenerated plants. This study would be helpful in improving the regeneration potential in local indica rice varieties and genetic transformation studies.

Pooled Mapping of QTLs Associated With Salt Tolerance Traits at Seedling Stage in Rice

Salt stress has been identified as a vital limiting factor affecting rice output across the world. In rice, the salt tolerance nature is complicated, since it is dependent on different components and is lowly heritable. Consequently, it is a key method to breed salt-tolerant varieties for improving rice output upon salt stress. To investigate the genetic foundation for salt stress tolerance of rice seedlings (Oryza sativa L.), bulked segregant analysis coupled with whole-genome sequencing (BSA-seq) was performed in QTL mapping on the huge F2 population including totally 2,500 plants obtained through crossing the indica rice variety 1892S with the japonica rice variety Huaidao 5 (HD5). In BSA-seq, only extremely-sensitive (ES) and extremely-tolerant (ET) seedlings were utilized, making it not difficult for identification with no requirement of quantitative analysis. Therefore, the seedling survival state was an appropriate indicator trait in BSA-seq. HD5 in seedling stage exhibited enhanced tolerance to extended salt stress when compared with 1892S. The DNA pools prepared based on 235 ES together with 165 ET seedlings of F2 population through block regression mapping (BRM) were analyzed, and a QTL was mapped onto chromosome 3 and termed QTL qSLST3.1. There were numerous rice salt tolerance-associated QTLs on chromosome 3 in seedling stage, but just one was situated in the confidence interval of qSLST3.1. These QTLs did not have identical positions. So qSLST3.1 should be the new QTL. Moreover, our results can shed more lights on marker-assisted salt-resistant variety breeding and positional cloning of rice salt tolerance trait-related genes. Bangladesh J. Bot. 53(2): 405-410, 2024 (June)

Alteration of soil pH induced by submerging/drainage and application of peanut straw biochar and its impact on Cd(II) availability in an acidic soil to indica-japonica rice varieties

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 (SO42−) 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.

Effects of urea topdressing time on yield, nitrogen utilization, and quality of mechanical direct-seeding hybrid indica rice under slow-mixed fertilizer base application.

The use of controlled-release nitrogen (N) fertilizers has been shown to improve yield and N-use efficiency (NUE) in mechanical transplanted rice. However, the fertilizer requirements for mechanical direct-seeding rice differ from those for mechanical transplanted rice. The effects of controlled-release fertilizers on yield, NUE, and quality in mechanical direct-seeding rice are still unknown. Hybrid indica rice varieties Yixiangyou 2115 and Fyou 498 were used as test materials, and slow-mixed N fertilizer (120kg hm-2) as a base (N1), N1+urea-N (30kg hm-2) once as a base (N2), N1+urea-N (30kg hm-2) topdressing at the tillering stage (N3), N1+urea-N (30kg hm-2) topdressing at the booting stage (N4) four N fertilizer management to study their impact on the yield, NUE and quality of mechanical direct-seeding rice. Compared with Yixiangyou 2115, Fyou 498 significantly increased photosynthetic potential, population growth rate, root vigor, and N transport rate by 3.34-23.88%. This increase further resulted in a significant improvement in the yield and NUE of urea-N topdressing by 1.73-5.95 kg kg-1. However, Fyou 498 showed a significant decrease in the head rice rate and taste value by 3.34-7.67%. All varieties were treated with N4 that significantly increase photosynthetic potential and population growth rate by 15.41-62.72%, reduce the decay rate of root vigor by 5.01-21.39%, promote the N transport amount in stem-sheaths (leaves) by 13.54-59.96%, and then significantly increase the yields by 4.45-20.98% and NUE of urea-N topdressing by 5.20-45.56 kg kg-1. Moreover, the rice processing and taste values were optimized using this model. Correlation analysis revealed to achieve synergistic enhancement of high-yield, high-quality, and high-NUE in rice, it is crucial to focus on increasing photosynthetic potential, population growth rate, and promoting leaf N transport. Specifically, increasing the contribution rate of N transport in stem-sheaths is the most important. These findings offer an effective N management strategy for 4R nutrient stewardship (right source, right method, right rate and right timing) of mechanical direct-seeding hybrid indica rice.

SMS2, a Novel Allele of OsINV3, Regulates Grain Size in Rice.

Grain size has an important effect on rice yield. Although several key genes that regulate seed size have been reported in rice, their molecular mechanisms remain unclear. In this study, a rice small grain size 2 (sms2) mutant was identified, and MutMap resequencing analysis results showed that a 2 bp insertion in the second exon of the LOC_Os02g01590 gene resulted in a grain length and width lower than those of the wild-type Teqing (TQ). We found that SMS2 encoded vacuolar acid invertase, a novel allele of OsINV3, which regulates grain size. GO and KEGG enrichment analyses showed that SMS2 was involved in endoplasmic reticulum protein synthesis, cysteine and methionine metabolism, and propionic acid metabolism, thereby regulating grain size. An analysis of sugar content in young panicles showed that SMS2 reduced sucrose, fructose, and starch contents, thus regulating grain size. A haplotype analysis showed that Hap2 of SMS2 had a longer grain and was widely present in indica rice varieties. Our results provide a new theoretical basis for the molecular and physiological mechanisms by which SMS2 regulates grain size.

Effect of Cd(II) adsorption onto rice roots on its uptake by different indica and japonica rice varieties and toxicity effect of Cd(II) under acidic conditions.

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.

Analysis of Erect-Panicle Japonica Rice in Northern China: Yield, Quality Status, and Quality Improvement Directions.

China is the only country that extensively cultivates the indica and japonica rice varieties, with the largest japonica rice production area being in northeast China. A study of the relationship between the yield and quality of japonica rice and the effect of nitrogen fertilizer application on this relationship is important. In this paper, we aimed to assess the current yield and quality of japonica rice in northeast China. We selected erect-panicle varieties as the test materials. Field experiments were conducted using different nitrogen fertilizer levels for two consecutive years to analyze the rice varieties' yield, quality, interrelationship, and nitrogen fertilizer response. The average yield following high- and low-nitrogen treatments exceeded 10,000.00 kg/hm2, with a maximum of 12,285.63 kg/hm2. The high-yield-high-nitrogen treatment group had more panicles, a higher seed-setting rate, and a higher 1000-grain weight than the other groups. The high-yield-low-nitrogen group had a higher number of panicles and seed-setting rate than the other groups. The low-yield-high-nitrogen group had a lower number of whole grains, grain length-to-width ratio, and taste value than the other groups. The low-yield-low-nitrogen group had fewer primary branches than the other groups; excluding the primary branch-setting rate and 1000-grain weight, the values of the other panicle traits of the group were significantly higher than those of the other groups. The high-nitrogen-high-flavor group had lower panicle and spikelet numbers and higher spikelet fertility rates than the other groups. The low-nitrogen-high-flavor group had higher spikelet fertility rates and 1000-grain weight than the other groups. Compared to the other groups, the low-nitrogen-high-flavor group had a higher head rice yield, and the high-nitrogen-high-flavor group had a lower chalkiness rate. The main goal of the breeding and cultivation of high-yield and high-quality erect-panicle japonica rice in northern China is to achieve "dual high, dual low, and one high and one low" conditions, signifying a high yield with high or low nitrogen levels, low protein and amylose contents, high head rice rates, and low chalkiness. This study provides a new technique for enhancing the taste of northern erect-panicle japonica rice to promote the sustainable, high-yield, and high-quality development of japonica rice in northern China.