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Indigenous landraces are heterogeneous and exhibit greater gene diversity, and are therefore an excellent source of variation and material for crop improvement. However, they are very prone to genetic erosion, therefore exploration of genetic variability in landraces is essential step for crop breeding. Discovery of the genetics of a character in rice, that cope adverse condition, is important for maintaining world-food supply. In this study, fifty rice genotypes were assessed for the phenotypic and genetic diversity and their relatedness using morpho-physiological traits of the genotypes. Further clustering and population structure analysis were performed using phenotypic and simple sequence repeat (SSR) markers data through unweighted pair group method with arithmetic mean (UPGMA) and STRUCTURE analysis. Significant variation among yield components were identified. Phenotypic and genotypic coefficients of variability were higher for filled grains, whereas heritability was highest for plant height. Panicle number and 100-grain weight displayed significant relationship with yield. Phylogenetic clustering of the agromorphological traits divided the genotypes into eight clusters, whereas SSR markers yielded ten clusters. SSR markers produced a total of 138 alleles varying from two to nine with 77.53% polymorphic allele having 3.69 alleles per locus (average). The polymorphic information content indices and observed number of alleles varied among markers with an average of 0.649, exhibiting RM336, RM316, and RM287 have the greatest potentiality in exploring genetic diversity among genotypes. Among the genotypes, Dolkochu, Jolduba, BRRI Dhan-32, and Mokbul displayed significant variability, suggesting their suitability as potential parents in hybridization programs. Population structure study demonstrated that the genotypes were structurally diverse that grouped the accessions into two subpopulations (K = 2). Therefore, this research aimed to identify potential genotypes and suitable traits of rice germplasms for breeding programs. [ABSTRACT FROM AUTHOR]

The CRISPR/Cas9 system represents a state-of-the-art technology for precise genome editing in plants. In this study, we performed in silico and evolutionary analyses, as well as designed guide RNA (gRNA) constructs for the precise modification of the thermosensitive genic male sterile (OsTMS5) gene using the CRISPR/Cas9 system in rice (Oryza sativa L.). The OsTMS5 promoter harbours a diverse array of cis-elements, which are linked to light responsiveness, hormonal regulation, and stress-related signaling. Further, expression pattern of OsTMS5 revealed that OsTMS5 exhibited responsiveness to hormones and was activated across diverse tissues and developmental stages in rice. In addition, we meticulously designed gRNA with a length of 20 base pairs. This design process was conducted using the CRISPR-P v2.0 online platform. The target of these gRNAs was the rice OsTMS5 gene. The selection of the top two gRNAs was made after conducting a thorough evaluation, which included assessing factors such as on-score value, minimum off-target score, GC content, potential off-target sites, and genomic location. Furthermore, two types of entry vectors were utilized, and the pMDC99 vector served as the destination vector for plant transformation. Following the annealing and ligation of the gRNAs through LR recombination, the resulting plasmid was named as "pMDC99-eSPCas9 + OsU6-OsTMS5-target1-gRNA + OsU6-OsTMS5-target2-gRNA". Subsequently, this plasmid obtained from the third LR recombination was introduced into Agrobacterium EHA105 for the purpose of conducting rice transformation. Therefore, these constructs have the potential for use not only in molecular genetic analyses and molecular breeding in rice but also in a wide range of other crop species. [ABSTRACT FROM AUTHOR]

Weed management through herbicide is costing economically and environmentally. Developing of improved weed-suppressive rice genotypes is one of the ultimate goals of rice breeders for sustainable cultivation. In the current investigation, we evaluated the weed-suppressive potential of different rice genotypes and the genetic behind transmitting this ability to their progeny. To achieve this goal, a half diallel mating system was designed and conducted to generate F1 hybrids from six genotypes. Among these genotypes a previously developed allelopathic-resistant pre-breeding advanced lines, the F1 crosses along with their parents were cultivated under weed stress and normal field condition during the 2022 summer growing season. Several vegetative, allelopathic, yield and physio-biochemical traits were studied. The results indicate that the crosses AL1/Sakha Super 300 and AL2/Sakha Super 300 have the highest yield under weed stress condition. AL1, AL2 and Sakha Super 300 have the highest general combining ability for yield and allelopathic characters under weed stress. Furthermore, the cross AL2/Sakha Super 300 ranked the highest based on the stress tolerance indices. High positive correlation was detected between grain yield and the most studied physio-biochemical characteristics. This investigation provides evidence of the potential of enhancing the allelopathic activity of rice crop through precise selection of parental genotypes. [ABSTRACT FROM AUTHOR]

Antioxidant complex enzymes have a significant role in cellular homeostasis control in plants, and they inhibit the toxic action of reactive oxygen species when they are in excess. There are many antioxidant enzymes executing this role; among these, superoxide dismutase, catalase, and ascorbate peroxidase are reported as the most studied in this process, as they prevent free radicals from becoming more reactive and toxic to cells. Thus, this research was conducted to evaluate antioxidant enzyme expression in response to hydric stress at the reproductive stage in upland rice genotypes. Three genotypes from the upland rice breeding program on agreement between UFLA, EPAMIG, and EMBRAPA, CMG2093, CMG2172, and BRSMG Relâmpago, were used as controls. Genotypes were grown under field conditions with supplementary irrigation during the whole crop cycle, and hydric stress was induced in the reproductive phase before panicle emission. Seedlings were used in enzyme analyses from the emergence test and IVE on substrate (soil + sand at a 2:1 rate) at 70% and 10% field capacity. Significant differences were observed among genotypes for vigor tests. In biochemical tests, the CMG2093 genotype had lower damage on hydric deficit, with the best performance under hydric restriction conditions, being considered tolerant for this stress type. [ABSTRACT FROM AUTHOR]

Summary Resistant starch (RS) is a special kind of starch with beneficial effects on obesity, type 2 diabetes and other chronic complications. Breeding high‐RS rice varieties is considered a valuable way to improve public health. However, most rice cultivars only contain an RS level lower than 2% in cooked rice, and cloning of RS genes is critical to improve RS levels in rice. The loss of function of Starch Synthases IIIa (SSIIIa) and SSIIIb, two amylopectin biosynthetic genes, could elevate RS levels up to 10%. Here, we performed a systematic genetic study of 14 amylopectin biosynthetic genes in the ssIIIa ssIIIb double mutant via genome editing, and investigated their effects on RS formation, the eating quality and grain yield. The results showed that deficiency in SSIIa, SSIVb or ISA2 under the ssIIIa ssIIIb background could each elevate RS content to above 14%, and the quadruple mutants of sbeI sbeIIb ssIIIa ssIIIb and sbeI ssIVb ssIIIa ssIIIb could further increase RS levels to over 18%. Furthermore, the eating quality of cooked rice and grain yield decreased along with the elevated RS contents, showing a trade‐off among these traits. In these mutants, ssIIIa ssIIIb showed the balanced performance of RS and grain yield. This study provides insights into RS biosynthesis with a series of RS genes in the amylopectin biosynthesis pathway and practical strategy to breed high‐RS rice varieties with balanced performance. [ABSTRACT FROM AUTHOR]

Background: Drought stress is a critical challenge to rice production, necessitating the development of drought-tolerant genotypes. This study aimed to evaluate the drought tolerance of rice genotypes, including traditional parental lines (Hashemi, Khazar, Fajr, and Tarom Mahalli) and their corresponding mutant lines, under normal and drought stress conditions. Methods: Agronomic traits such as plant height, spike number, spike length, seed fertility, and yield were analyzed under both conditions. The performance of these genotypes was further assessed using drought tolerance indices. Statistical methods including cluster analysis and principal component analysis (PCA) were applied to identify the most resilient genotypes. Results: Mutant lines demonstrated superior drought resilience compared to their parental counterparts. Specifically, genotypes like TM-230-VE-7-5-1, TM-B-2-1-E, and HM-250-7-6 exhibited higher yields and better stability of key traits under stress conditions. Cluster analysis and PCA emphasized the strong performance of TM-230-VE-7-5-1, which emerged as the most drought-tolerant genotype, excelling across various drought tolerance indices. Conclusions: The selected mutant lines, particularly TM-230-VE-7-5-1, showed significant potential for breeding programs aimed at improving drought tolerance in rice. These findings have substantial implications for enhancing rice production in drought-prone regions, contributing to sustainable agricultural practices. [ABSTRACT FROM AUTHOR]

The demand for rice varieties with lower amylose content (AC) is increasing in Southeast Asia, primarily due to their desirable texture and cooking qualities. This study presents the development of whole-grain rice lines with low to intermediate glycemic index (GI) and reduced AC. We selected six rice lines for in vivo GI assessment based on their starch properties. We successfully identified two lines with low AC that exhibited low and intermediate GI values, respectively. Our findings indicate that dietary fiber (DF) content may significantly influence rice GI. The selected whole-grain low-GI line showed a higher ratio of soluble dietary fiber (SDF) to insoluble dietary fiber (IDF) compared to control varieties, highlighting SDF's potential positive role in lowering whole-grain rice's GI. This study underscores the feasibility of developing rice varieties with desirable agronomic traits, nutritional traits, and culinary attributes, particularly for individuals managing their blood sugar levels. Additionally, we proposed the positive role of starch composition, especially DF content, in modulating the GI of rice. This study reinforces the importance of incorporating starch properties and DF content into rice breeding programs to produce more health-oriented and marketable rice varieties. [ABSTRACT FROM AUTHOR]

Introduction: Genetic improvement in rice increased yield potential and improved varieties for farmers over the last decades. However, the demand for rice is growing while its cultivation faces challenges posed by climate change. To address these challenges, rice breeding programs need to adopt efficient breeding strategies to provide a steady increase in the rate of genetic gain for major traits. The International Rice Research Institute (IRRI) breeding program has evolved over time to implement faster and more efficient breeding techniques such as rapid generation advance (RGA) and genomic selection (GS). Simulation experiments support data-driven optimization of the breeding program toward the desired rate of genetic gain for key traits. Methods: This study used stochastic simulations to compare breeding schemes with different cycle times. The objective was to assess the impact of different genomic selection strategies on medium- and long-term genetic gain. Four genomic selection schemes were simulated, representing the past approaches (5 years recycling), current schemes (3 years recycling), and two options for the future schemes (both with 2 years recycling). Results: The 2-Year within-cohort prediction scheme showed a significant increase in genetic gain in the medium-term horizon. Specifically, it resulted in a 22%, 24%, and 27% increase over the current scheme in the zero, intermediate, and high genotype-by-environment interaction (GEI) contexts, respectively. On the other hand, the 2-Year scheme based on between-cohort prediction was more efficient in the long term, but only in the absence of GEI. Consistent with our expectations, the shortest breeding schemes showed an increase in genetic gain and faster depletion of genetic variance compared to the current scheme. Discussion: These results suggest that higher rates of genetic gain are achievable in the breeding program by further reducing the cycle time and adjusting the target population of environments. However, more attention is needed regarding the crossing strategy to use genetic variance optimally. [ABSTRACT FROM AUTHOR]

SUMMARY Arsenic (As) is extremely toxic to plants, posing a serious concern for food safety. Identification of genes responsive to As is significative for figuring out this issue. Here, we identified a bHLH transcription factor OsbHLH6 that was involved in mediating the processes of As tolerance, uptake, and root‐to‐shoot translocation in rice. The expression of OsbHLH6 gene was strongly induced after 3 and 48 h of arsenite [As(III)] treatment. The OsbHLH6‐overexpressed transgenic rice (OE‐OsbHLH6) was sensitive to, while the knockout mutant of OsbHLH6 gene (Osbhlh6) was tolerant to As(III) stress by affecting the contents of reactive oxygen species (ROS) and non‐protein thiols (NPT), etc. Knockout of OsbHLH6 gene increased significantly the As concentration in roots, but decreased extensively As accumulation in shoots, compared to that in OE‐OsbHLH6 and WT plants. The transcripts of phytochelatins (PCs) synthetase encoding genes OsPCS1 and OsPCS2, as well as As(III) transporter encoding genes OsLsi1 and OsABCC1 were greatly abundant in Osbhlh6 mutants than in OE‐OsbHLH6 and WT plants under As(III) stress. In contrast, the expression of OsLsi2 gene was extensively suppressed by As(III) in Osbhlh6 mutants. OsbHLH6 acted as a transcriptional activator to bind directly to the promoter and regulate the expression of OsPrx2 gene that encodes a peroxidase precursor. Moreover, overexpression of OsbHLH6 gene resulted in significant change of expression of amounts of abiotic stress‐related genes, which might partially contribute to the As sensitivity of OE‐OsbHLH6 plants. These findings may broaden our understanding of the molecular mechanism of OsbHLH6‐mediated As response in rice and provide novel useful genes for rice As stress‐resistant breeding. [ABSTRACT FROM AUTHOR]

Rice breeding programs globally have worked to release increasingly productive and climate-smart cultivars, but the genetic gains have been limited for some reasons. One is the capacity for field phenotyping, which presents elevated costs and an unclear approach to defining the number and allocation of multi-environmental trials (MET). To address this challenge, we used soil information and ten years of historical weather data from the USA rice belt, which was translated into rice response based on the rice cardinal temperatures and crop stages. Next, we eliminated those highly correlated Environmental Covariates (ECs) (>0.95) and applied a supervised algorithm for feature selection using two years of data (2021-22) and 25 genotypes evaluated for grain yield in 18 representative locations in the Southern USA. To test the trials' optimization, we performed the joint analysis using prediction-based models in four different scenarios: i) considering trials as non-related, ii) including the environmental relationship matrix calculated from ECs, iii) within clusters; iv) sampling one location per cluster. Finally, we weigh the trial's allocation considering the counties' economic importance and the environmental group to which they belong. Our findings show that eight ECs explained 58% of grain yield variation across sites and 53% of the observed genotype-by-environment interaction. Moreover, it is possible to reduce 28% the number of locations without significant loss in accuracy. Furthermore, the US Rice belt comprises four clusters, with economic importance varying from 13 to 45%. These results will help us better allocate trials in advance and reduce costs without penalizing accuracy. [ABSTRACT FROM AUTHOR]

Saline-alkali soils limit rice growth and production. With an increasing global population, enhancing rice salt tolerance is crucial for improving yields in these areas. This study investigated the developmental characteristics of young panicles and pollen fertility in two rice varieties, 58M and 58L, under salt stress. Results showed that 58M had more substantial salt tolerance during panicle development. RNA sequencing of 18 samples from both varieties under high salt stress (0 h, 6 h, and 24 h) identified 469 common differentially expressed genes (DEGs) and 2,308 DEGs between the varieties. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment highlighted significant pathways such as phenylpropanoid biosynthesis, protein processing, and flavonoid biosynthesis. Six gene co-expression modules related to salt tolerance were identified, with six candidate genes (LOC_Os05g38530, LOC_Os04g07920, LOC_Os12g02105, LOC_Os01g06580, LOC_Os06g49250, and LOC_Os06g48300) potentially linked to salt tolerance. These findings provide insights into rice salt tolerance mechanisms and offer new genetic resources for breeding salt-tolerant rice. [ABSTRACT FROM AUTHOR]

The mechanized direct seeding of rice (Oryza sativa L.) is a major trend nowadays. The elongation of rice mesocotyl and coleoptile can facilitate the rapid emergence of seedlings under deep mechanized sowing. Currently, most of the cultivated rice accessions have short mesocotyls or coleoptiles, with only a few related genes cloned. However, understanding and enhancing the ability of rice seedlings to rapidly emerge from deep sowing depths is crucial. Herein, we assessed 745 core rice germplasm accessions sown under a soil cover depth of 10 cm and found few long mesocotyl and coleoptile germplasms. We conducted genome‐wide association study using six models to obtain three or more multi‐model co‐localization candidate regions and calculated Fst between the phenotypes of extreme samples to determine genetic differences. The candidate regions associated with mesocotyl and coleoptile lengths were identified by integrating Fst and multi‐model localization results. This multi‐model localization method may accelerate the mining of genes related to the mesocotyl and coleoptile, providing valuable targets for functional validation and marker‐assisted selection in rice breeding programs. Core Ideas: We utilized diverse GWAS models to co‐locate candidate loci for mesocotyl and coleoptile elongation.We calculated Fst in phenotypically divergent materials to refine candidate regions.This multi‐model localization method provides valuable targets for rice breeding and mechanized cultivation. Plain Language Summary: Rice requires longer mesocotyl and coleoptile for rapid seedling emergence in direct seeding. It is necessary to identify key genes that control mesocotyl and coleoptile traits to facilitate the breeding of new varieties. We analyzed the mesocotyl and coleoptile lengths of 745 rice samples and conducted genome‐wide association study using six different models to co‐locate candidate loci. Several valuable candidate regions were consistently detected using different models. These regions included previously reported genes related to mesocotyl/coleoptile elongation and other agronomic traits such as plant height, heading date, and yield. Our findings validated the accuracy of the multi‐model analysis and provided guidance on efficiently mining genes involved in mesocotyl/coleoptile elongation from those known genes controlling plant growth and development. This study may contribute to the breeding of new rice varieties suitable for direct‐seeding by synergistic selection of multi‐traits. [ABSTRACT FROM AUTHOR]

Plants are sensitive to photoperiods and are also equipped with systems to adjust their flowering time in response to various changes in the environment and developmental hormones. In the present study, previously generated rice OsWOX13 overexpression and newly generated OsWOX13 knockout lines constructed via CRISPR/Cas9 technology flowered 10 days earlier and 4-6 days later than the wild type, respectively. Quantitative real-time  polymerase chain reaction analyses revealed that OsWOX13 might be involved in drought escape responses through the b-ZIP TRANSCRIPTION FACTOR 23 signaling pathway during rice flowering via photoperiod signaling genes such as Grain number, plant height and heading date 7, Early heading date 1, RICE FLOWERING LOCUS T1, Heading date 3a , and MADS14. Future investigations of OsWOX13 may provide insight into how plants adjust their flowering under stress conditions and how OsWOX13 could be precisely controlled to achieve maximum productivity in rice breeding. [ABSTRACT FROM AUTHOR]

Summary: Germplasm resources serve as the foundations of advancements in breeding and are crucial for maintaining food security. Wild rice species of the genus Oryza include rich sources of genetic diversity and high adaptability, making them a substantial resource for rice breeding. The discovery of wild‐type cytoplasmic male sterility resources enabled the achievement of the 'three lines' goal in hybrid rice, significantly increasing rice yields. The application of resistance alleles from wild rice enables rice production to withstand losses caused by stress. Reduced genetic diversity due to rice breeding poses a significant limitation to further advances and can be alleviated through a systematic use of wild genetic resources that integrate geographic, climatic and environmental data of the original habitat, along with extensive germplasm collection and identification using advanced methods. Leveraging technological advancements in plant genomics, the understanding of genetic mechanisms and the application of artificial intelligence and gene editing can further enhance the efficiency and accuracy of this process. These advancements facilitate rapid isolation and functional studies of genes, and precise genome manipulation. This review systematically summarizes the utilization of superior genes and germplasm resources derived from wild rice sources, while also exploring the collection, conservation, identification and utilization of further wild rice germplasm resources. A focus on genome sequencing and biotechnology developments is leading to new breeding and biotechnology opportunities. These new opportunities will not only promote the development of rice varieties that exhibit high yields, superior stress resistance and high quality but also expand the genetic diversity among rice cultivars. [ABSTRACT FROM AUTHOR]

Summary: Soil salinity has negative impacts on food security and sustainable agriculture. Ion homeostasis, osmotic adjustment and reactive oxygen species scavenging are the main approaches utilized by rice to resist salt stress. Breeding rice cultivars with high salt tolerance (ST) and yield is a significant challenge due to the lack of elite alleles conferring ST. Here, we report that the elite allele LEA12OR, which encodes a late embryogenesis abundant (LEA) protein from the wild rice Oryza rufipogon Griff., improves osmotic adjustment and increases yield under salt stress. Mechanistically, LEA12OR, as the early regulator of the LEA12OR‐OsSAPK10‐OsbZIP86‐OsNCED3 functional module, maintains the kinase stability of OsSAPK10 under salt stress, thereby conferring ST by promoting abscisic acid biosynthesis and accumulation in rice. The superior allele LEA12OR provides a new avenue for improving ST and yield via the application of LEA12OR in current rice through molecular breeding and genome editing. [ABSTRACT FROM AUTHOR]

Strategies to enhance rice productivity in response to global demand have been the paramount focus of breeders worldwide. Multiple factors, including agronomical traits such as plant architecture and grain formation and physiological traits such as photosynthetic efficiency and NUE (nitrogen use efficiency), as well as factors such as phytohormone perception and homeostasis and transcriptional regulation, indirectly influence rice grain yield. Advances in genetic analysis methodologies and functional genomics, numerous genes, QTLs (Quantitative Trait Loci), and SNPs (Single-Nucleotide Polymorphisms), linked to yield traits, have been identified and analyzed in rice. Genome editing allows for the targeted modification of identified genes to create novel mutations in rice, avoiding the unintended mutations often caused by random mutagenesis. Genome editing technologies, notably the CRISPR/Cas9 system, present a promising tool to generate precise and rapid modifications in the plant genome. Advancements in CRISPR have further enabled researchers to modify a larger number of genes with higher efficiency. This paper reviews recent research on genome editing of yield-related genes in rice, discusses available gene editing tools, and highlights their potential to expedite rice breeding programs. [ABSTRACT FROM AUTHOR]

Flowering time of crops is critical for maximizing yield, quality and regional adaptability under target environments. In rice, Heading date 3a (Hd3a) and Rice Flowering Locus T 1 (RFT1) proteins are the key factors of flowering time regulation in the florigen activation complex. However, effects of hd3a and rft1 mutations on the flowering time under long-day conditions are not clear. In this study, we generated single and double mutants of Hd3a and RFT1 in japonica varieties Shen Nong 9816 (SN9816) background, termed hd3a-SNs, rft1-SNs and doub-SNs, by using CRISPR/Cas9 system. The flowering time of hd3a-SN mutants was similar to wild-type (WT); but mutations of RFT1 delayed flowering time by 11 to 14 days comparing to WT under nature long day (NLD) conditions. Double mutants of Hd3a and RFT1 (doub-SNs) exhibited an extremely late flowering phenotype, and they did not flower up to 365 days after regeneration under either NLD or short-day conditions. The leaf emergency rate of RFT1 mutants was similar to WT, suggesting that the late flowering phenotype of rft1-SNs was caused by delayed floral transition, but not by retarded growth. The expression of the key floral organ identity genes was significantly decreased in rft1-SN and doub-SN mutants, resulting in late flowering phenotypes. The expression profiles, evolution and haplotypes of Hd3a and RFT1 was also analyzed. Our studies provide insight into the potential utilization of Hd3a and RFT1 gene resources to improving growth period and regional adaptability in rice breeding. [ABSTRACT FROM AUTHOR]

The abounding variations in wild rice provided potential reservoirs of beneficial genes for rice breeding. Maintaining stable and high yields under environmental stresses is a long-standing goal of rice breeding but is challenging due to internal trade-off mechanisms. Here, we report wild rice GL12W improves grain length and salt tolerance in both indica and japonica genetic backgrounds. GL12W alters cell length by regulating grain size related genes including GS2, and positively regulates the salt tolerance related genes, such as NAC5, NCED3, under salt stresses. We find that a G/T variation in GL12 promoter determined its binding to coactivator GIF1 and transcription factor WRKY53. GIF1 promotes GL12W expression in young panicle and WRKY53 represses GL12W expression under salt stresses. The G/T variation also contributes to the divergence of indica and japonica subspecies. Our results provide useful resources for modern rice breeding and shed insights for understanding yield and salt tolerance trade-off mechanism. Maintaining yield under environmental stresses is a long-standing but challenging goal of rice breeding. Here, the authors report a MYB transcription factor encoding gene GL12 from wild rice can improve grain length and salt tolerance in cultivated rice and the identification of its upstream regulators GIF1 and WRKY53. [ABSTRACT FROM AUTHOR]

Background: Rice ECQ (eating and cooking quality) is an important determinant of rice consumption and market expansion. Therefore, improvement of ECQ is one of the primary goals in rice breeding. However, ECQ-related quantitative trait loci (QTL) have not yet been fully revealed. The present study aimed to identify a major effect QTL for rice taste, an important component of ECQ via genotyping-by-sequencing, to reveal the associated molecular mechanisms, and to predict key candidate genes. Results: A population of F9 recombinant inbred lines resulting from a cross between R668 (national standard of high-quality third class) and R838 (common edible rice) was used to construct a high-density genetic map (2,295.062 cM). The map comprises 639,504 markers distributed on 12 linkage elements with an average genetic distance of 0.004 cM. We detected a major taste-related QTL, qECQ8, which explained 41.4% of phenotypic variance and had LOD values of 4.42–7.73. Using a five-generation NIL population from the backcross of "Ganxiangzhan No. 1" carrying qECQ8 with the recurrent parent R838 (without qECQ8), we narrowed qECQ8 to a 187.5 kb interval between markers M33 and M37 on Chr8. Comparative transcriptomic analysis revealed that photosynthesis, glyoxylate and dicarboxylate metabolism, carbon fixation in photosynthetic organisms, and alpha-linolenic acid metabolism were induced in developing seeds of lines containing qECQ8. Furthermore, we identified two candidate genes in the qECQ8 region, including LOC_Os08g30550 (zinc knuckle family protein), a major candidate for genetic-assisted breeding of high-quality rice. Conclusion: Our findings provide important genetic resources for targeted improvement of rice taste quality and may facilitate the genetic breeding of rice ECQ. [ABSTRACT FROM AUTHOR]

ABSTRACT Grain size and grain weight are important determinants for grain yield. In this study, we identify a novel OsMAPK5–OsWRKY72 module that negatively regulates grain length and grain weight in rice. We found that loss‐of‐function of OsMAPK5 leads to larger cell size of the rice spikelet hulls and a significant increase in both grain length and grain weight in an indica variety Minghui 86 (MH86). OsMAPK5 interacts with OsMAPKK3/4/5 and OsWRKY72 and phosphorylates OsWRKY72 at T86 and S88. Similar to the osmapk5 MH86 mutants, the oswrky72 knockout MH86 mutants exhibited larger size of spikelet hull cells and increased grain length and grain weight, whereas the OsWRKY72‐overexpression MH86 plants showed opposite phenotypes. OsWRKY72 targets the W‐box motifs in the promoter of OsARF6, an auxin response factor involved in auxin signaling. Dual‐luciferase reporter assays demonstrated that OsWRKY72 activates OsARF6 expression. The activation effect of the phosphorylation‐mimicking OsWRKY72T86D/S88D on OsARF6 expression was significantly enhanced, whereas the effects of the OsWRKY72 phosphorylation‐null mutants were significantly reduced. In addition, auxin levels in young panicles of the osmapk5 and oswrky72 mutants were significantly higher than that in the wild‐type MH86. Collectively, our study uncovered novel connections of the OsMAPKK3/4/5‐OsMAPK5‐mediated MAPK signaling, OsWRKY72‐mediated transcription regulation, and OsARF6‐mediated auxin signaling pathways in regulating grain length and grain weight in an indica‐type rice, providing promising targets for molecular breeding of rice varieties with high yield and quality. [ABSTRACT FROM AUTHOR]

The brown planthopper (Nilaparvata lugens, BPH) is a serious insect pest responsible for causing immense economic losses to rice growers around the globe. The development of high-throughput sequencing technologies has significantly improved the research on this pest, and its genome structure, gene expression profiles, and host–plant interactions are being unveiled. The integration of genomic sequencing, transcriptomics, proteomics, and metabolomics has greatly increased our understanding of the biological characteristics of planthoppers, which will benefit the identification of resistant rice varieties and strategies for their control. Strategies like more optimal genome assembly and single-cell RNA-seq help to update our knowledge of gene control structure and cell type-specific usage, shedding light on how planthoppers adjust as well. However, to date, a comprehensive genome-wide investigation of the genetic interactions and population dynamics of BPHs has yet to be exhaustively performed using these next-generation omics technologies. This review summarizes the recent advances and new perspectives regarding the use of omics data for the BPH, with specific emphasis on the integration of both fields to help develop more sustainable pest management strategies. These findings, in combination with those of post-transcriptional and translational modifications involving non-coding RNAs as well as epigenetic variations, further detail intricate host–brown planthopper interaction dynamics, especially regarding resistant rice varieties. Finally, the symbiogenesis of the symbiotic microbial community in a planthopper can be characterized through metagenomic approaches, and its importance in enhancing virulence traits would offer novel opportunities for plant protection by manipulating host–microbe interactions. The concerted diverse omics approaches collectively identified the holistic and complex mechanisms of virulence variation in BPHs, which enables efficient deployment into rice resistance breeding as well as sustainable pest management. [ABSTRACT FROM AUTHOR]

SUMMARY: Mature embryos are the main explants of tissue culture used in rice transgenic technology. However, the mechanism of mature embryo callus formation remains unclear. In this study, a microRNA‐mediated gene regulatory network of rice calli was established using degradome sequencing. We identified a microRNA, OsmiR408, that regulates the formation of the callus derived from the mature rice embryo. OsUCLACYANIN 30 (OsUCL 30), a target gene of OsmiR408, was the most abundant cleavage mRNA in rice callus. OsUCL17 was verified as a target gene of OsmiR408 using RNA ligase‐mediated 5′‐RACE. In analysis of the OsmiR408 promoter reporter line and pri‐miR408 transcript level, the promoter activity and transcript level of MIR408 were increased dramatically during callus formation. In phenotypic observations, OsmiR408 knockout caused severe defects in mature embryo callus formation, whereas OsmiR408 overexpression promoted callus formation. Transcriptome analysis demonstrated that OsUCLs and certain genes related to the plant hormone signal transduction and phenylpropanoid‐flavonoid biosynthesis pathway had different differential expression patterns between OsmiR408 knockout and overexpression calli. Thus, OsmiR408 may regulate callus formation mainly by affecting plant hormone signal transduction and phenylpropanoid‐flavonoid biosynthesis pathway. Our findings provide insight into OsmiR408/UCLs module function in callus formation. Significance Statement: A novel function for the miR408 was determined, and its target genes OsUCL8, OsUCL17, and OsUCL30 were verified. miR408 regulates rice callus initiation through affecting plant hormone signal transduction and phenylpropanoid‐flavonoid biosynthesis pathway. This study expands our understanding of the function of OsmiR408 in the process of callus formation and will facilitate genetic manipulation based on callus explants in rice breeding. [ABSTRACT FROM AUTHOR]

ABSTRACT A crucial phenotypic attribute for breeding rice for direct seeded condition is rapid uniform germination and build‐up of biomass during the initial period of seedling establishment. Seed vigour constitutes such traits that have gained potential to meet the requirements of breeding for direct seeded rice. In the present study, a set of 295 markers, including 215 candidate gene‐derived markers covering all chromosome, was used to discover the casual alleles for eight rice seed vigour‐related traits. Using a mixed linear model, the study identified 99 significant associations for seed vigour traits. Many associated markers originated from diverse candidate genes in rice. Notably, alleles from genes like RSR1, OsSRS3 and OsSWEET15 exhibited pleiotropic effects, influencing multiple seed vigour traits. This discovery underscores the potential of certain genes to impact various facets of seed vigour simultaneously. The new candidate gene markers associated with seed vigour traits may be utilized to incorporate variable alleles for seed vigour traits through marker‐assisted breeding programmes. Markers identified to be closely associated with more than one trait have significant application in the simultaneous improvement of multiple traits. [ABSTRACT FROM AUTHOR]

Research indicates that, owing to the enhanced grain-filling rate of tetraploid rice, its yield has notably improved compared to previous levels. Studies conducted on diploid rice have revealed that optimal planting density and fertilization rates play crucial roles in regulating rice yield. In this study, we investigated the effects of different nitrogen application and planting density treatments on the growth, development, yield, and nitrogen utilization in tetraploid (represented by T7, an indica–japonica conventional allotetraploid rice) and diploid rice (Fengliangyou-4, represented by FLY4, a two-line super hybrid rice used as a reference variety for the approval of super rice with a good grain yield performance). The results indicated that the highest grain-filling rate of T7 could reach 77.8% under field experimental conditions due to advancements in tetraploid rice breeding. This is a significant improvement compared with the rate seen in previous research. Under the same conditions, T7 exhibited a significantly lower grain yield than FLY4, which could be attributed to its lower grain-filling rate, spikelets per panicle, panicle number m−2, and harvest index score. Nitrogen application and planting density displayed little effect on the grain yield of both genotypes. A higher planting density significantly enhanced the leaf area index and biomass accumulation, but decreased the harvest index score. Compared with T7, FLY4 exhibited a significantly higher nitrogen use efficiency (NUEg), which was mainly due to the higher nitrogen content in the straw. Increasing nitrogen application significantly decreased NUEg due to its minimal effect on grain yield combined with its significant enhancement of nitrogen uptake. Our results suggest that the yield and grain-filling rate of T7 have been improved compared with those of previously tested polyploid rice, but are still lower than those of FLY4, and the yield of tetraploid rice can be further improved by enhancing the grain-filling rate, panicle number m−2, and spikelets per panicle via genotype improvement. [ABSTRACT FROM AUTHOR]

Key message: The Agrobacterium-mediated transformation system of three elite indica rice varieties was explored and two varieties yielded positive transgenic plants. Fourteen elite indica rice varieties with different genotypes were selected for callus induction, and varieties NY49, KW and CL38 were chosen for the establishment of the Agrobacterium transformation system because of their excellent tissue culture characteristics. The callus induction frequency was the highest when the concentration of 2,4-Diphenoxyacetic acid (2,4-D) was respectively at 2.5 mg/L, 3.0 mg/L and 2.8 mg/L for NY49, KW and CL38 after optimizing the tissue culture conditions. Moreover, medium types of CIM1, CIM8 and CIM7 were most suitable for the varieties NY49, KW and CL38, respectively, with high callus induction frequency. The regeneration frequency of CL38 and NY49 was as high as 73.33% and 50.00%, respectively, in MS medium containing 2 mg/L 6-benzyladenine (BAP), 2 mg/L kinetin (KT) and 0.5 mg/L naphthylacetic acid (NAA). Finally, transgenic seedlings of CL38, NY49 and NIP were obtained with infection of Agrobacterium EHA105 carrying the pYLCRISPR/Cas9PUB-H vector. The successful editing frequency detecting by sequencing in CL38 and NIP were 62.50% and 77.78%, respectively. The establishment of the transformation system provides a useful tool for gene function study and gene editing breeding in indica rice cultivars. [ABSTRACT FROM AUTHOR]

Simple Summary: The adverse impact of cold temperatures on rice farming has resulted in a significant decrease in both the yield and quality of rice. Therefore, the identification of quantitative trait loci (QTLs) for cold tolerance (CT) holds immense theoretical and practical value for enhancing CT in rice breeding. In this study, we evaluated CT phenotypes at the seedling stage across 1992 rice germplasms and observed variations in CT among different subpopulations. We successfully identified high CT germplasms within both geng and xian subspecies. By conducting a genome-wide association study (GWAS), we dissected QTLs associated with CT and discovered favorable haplotypes linked to novel candidate genes at crucial QTLs. These findings offer valuable germplasms exhibiting high CT potential as well as favorable haplotypes that can be utilized for developing new varieties with enhanced CT through marker-assisted selection. Due to global climate change, cold temperatures have significantly impacted rice production, resulting in reduced yield and quality. In this study, we investigated two traits related to the cold tolerance (CT) of 1992 diverse rice accessions at the seedling stage. Geng accessions exhibited higher levels of CT compared to xian accessions, with the GJ-tmp subgroup displaying the strongest CT. However, extreme CT accessions were also identified within the xian subspecies. Through GWAS analysis based on the survival rate (SR) and leaf score of cold tolerance (SCT), a total of 29 QTLs associated with CT at the seedling stage were identified, among which four QTLs (qSR3.1a, qSR4.1a, qSR11.1x, and qSR12.1a) were found to be important. Furthermore, five candidate genes (LOC_Os03g44760, LOC_Os04g06900, LOC_Os04g07260, LOC_Os11g40610, and LOC_Os12g10710) along with their favorable haplotypes were identified through gene function annotation and haplotype analysis. Pyramiding multiple favorable haplotypes resulted in a significant improvement in CT performance. Subsequently, three selected accessions (CX534, B236, and IRIS_313-8565), carrying different superior alleles for CT, were selected and recommended for molecular breeding for CT using marker-assisted selection (MAS). The findings from this study provide valuable resources for enhancing rice's ability for CT while laying a foundation for the future cloning of novel genes involved in conferring CT. [ABSTRACT FROM AUTHOR]

Rice grain yield is a major focus of rice breeding, and with grain number per panicle being a major trait that largely determines overall grain yield. Despite its importance, the genetic architecture and underlying mechanisms governing grain number per panicle are not well understood. In this study, we adopted a whole-genome resequencing-based QTL-seq analysis to trace genomic regions related with grain number per panicle using a mapping population derived from a cross between CB12132 (High grain number) and IET28835 (Low grain number). This approach revealed five candidate genomic regions: qGNPP1.1 (10.40 Mb to 12.76 Mb), qGNPP1.2 (24.61 Mb to 25.33 Mb), qGNPP1.3 (26.57 Mb to 27.26 Mb), qGNPP4.1 (27.70 Mb to 31.34 Mb), and qGNPP5.1 (2.12 Mb to 5.50 Mb) on chromosomes 1, 4, and 5, respectively. Further, we searched for possible candidate genes using a comprehensive approach that included the analysis of gene sequences, functional annotation, and expression patterns. A total of 23 candidate genes, including most possible genes Os01g0292900 (SPL1), Os01g0622000 (OsCUGT1), Os01g0655300 (SDG705), Os04g0615000 (NAL1), Os04g0559800 (SMG2) and Os05g0155200 (ERS2), were identified across the five candidate genomic regions. Collectively, our study results shed light on the genetic mechanisms underlying grain number per panicle in rice and will be helpful for improving grain yield in future rice breeding programs. [ABSTRACT FROM AUTHOR]

In the present study, the aim was to predict and validate putative candidate genes underlying drought‐tolerant quantitative trait loci (QTLs) in rice crop using in silico approaches and real‐time polymerase chain reaction (RT‐PCR). The genes underlying major drought‐tolerant QTLs which have been reported by data mining, sequence variation, gene ontology analysis, quantitative traits gene finder and gene expression analysis were subjected to RiceVarmap software to design primers, and only a few variants gave the SNP/InDel primers; thus, finally, 15 primers were ultimately selected, which were used in identification of differentially expressed genes (DEGs) among contrasting rice genotypes IR 64 and N 22 for drought tolerance trait using quantitative RT‐PCR studies by providing drought stress treatment during panicle initiation stage. In this investigation, we predicted 11 genes as candidate genes underlying drought‐tolerant QTLs. Out of these, only four QTLs were found responsible for the major effect in drought tolerance regions such as QTL‐Qsn‐4b, QTL‐rn7a, QTL‐Qtgw‐2a and QTL‐phc4.1 and 11 prioritized candidates were identified that expressed in leaf tissues. Only four primers belong to two QTLs, primer vg0712623096 from QTL‐rn7a (LOC_Os07g22450) located on chromosome‐7 encoding NAC domain‐containing protein and the primers vg0431750843(LOC_Os04g53310) encoding soluble starch synthase 3‐ chloroplast precursor, vg0432626757 (LOC_Os04g54850) encoding pectin acetylesterase domain‐containing protein and vg0433031562 (LOC_Os04g55520) encoding AP2 domain‐containing protein, from QTL‐Qsn‐4b, located on chromosome‐4 found to have higher differential expression in N 22 in comparison with IR 64 during drought stress as per quantitative RT‐PCR 2–ΔΔCt values. Considering the overall study, these four primers/genes were identified as candidate genes underlying genomic regions governing drought tolerance. Therefore, these putative candidate genes could be focussed for further functional analysis to exploit in rice breeding. [ABSTRACT FROM AUTHOR]

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

Summary: Diurnal floret opening time (DFOT) is a pivotal trait for successful fertilization and hybrid breeding in rice. However, the molecular mechanism underlying this trait is poorly understood in rice.In this study, we combined the cytological, genetic and molecular studies to demonstrate that jasmonic acid (JA) regulates DFOT in rice through modulating the turgor and osmotic pressure of the lodicules.We show that lodicules undergo dramatic morphologic changes, accompanied by changes in water and sugar contents during the process of floret opening. Consistently, a large set of genes associated with cell osmolality and cell wall remodeling exhibits distinct expression profiles at different time points in our time‐course transcriptomes of lodicules. Notably, a group of JA biosynthesis and signaling genes is continuously upregulated, accompanied by a gradual increase in JA accumulation as floret opening approaching. Furthermore, we demonstrate that the JA biosynthesis gene OsAOS1 is required for endogenous JA biosynthesis in lodicules and promoting rice DFOT. Moreover, OsMYC2, a master regulator of JA signaling, regulates rice DFOT by directly activating OsAOS1, OsSWEET4, OsPIP2;2 and OsXTH9.Collectively, our findings establish a core regulatory network mediated by JA for modulating rice DFOT and provide effective gene targets for the genetic improvement of DFOT in rice. [ABSTRACT FROM AUTHOR]

Rice varieties with high anthocyanin content are often recognized for their vibrant colors and health benefits. The demand for rice with high anthocyanin is increasing domestically and internationally due to consumers becoming more health-conscious. However, the current increase in yield might not raise the anthocyanin content due to its location in the grain pericarp and seed coat, which are relative to the grain surface area. This study aims to develop rice lines to increase anthocyanin yield per production area by improving rice varieties with small, black, and three grains per spikelet. Accordingly, six rice recombinant inbred lines (RILs) were bred by crossing Niaw Dam Chaw Mai Pai 49 (NDCMP49) with Khao Nok (LLR059). The grain color, size, and number of grains per spikelet were selected from the F1 to the F4 population through the pedigree selection method. Six RILs and their parents were assigned in a randomized complete block design (RCBD) with three replications under field conditions during the rainy season of 2021 and 2022 in four locations. The results showed statistically significant differences in environmental conditions, affecting productivity and the yield components of rice lines. Consequently, the rice lines adapted to a specific environment, and there were significant differences in genotype. This study identified three RILs with higher yield performance (13-1 (3842 kg/ha), 374-1 (3699 kg/ha), and 903-3 (3550 kg/ha)) compared with the parent NDCMP49 (1996 kg/ha). However, the grain yields were unstable in the three top-yielding RILs due to varying environmental conditions, indicating that selective breeding requires a specific, narrow environment. Based on grain yield and grain size, the RILs performed better in the grain surface area than in the parent NDCMP49. Moreover, only two RILs (374-1 and 903-3) produced the highest anthocyanin content and yield, although this was lower than in the parent NDCMP49. However, the 374-1 and 903-3 RILs produced more grains, black grains, and three grains per spikelet with high yield and moderate anthocyanin content. They can, therefore, be backcrossed to the parent NDCMP49 to increase the accumulated anthocyanin content with a stable, high yield. This work provides a resource of small grains, black grains, and three grains per spikelet in the rice breeding line for breeding programs in the future. [ABSTRACT FROM AUTHOR]

Integrated rice–fish farming, an agricultural practice that combines cultivating rice and breeding fish in the same field, has attracted widespread attention. However, there is limited research on how the rice–carp coculture impacts the community structure of phytoplankton and microzooplankton in paddy water. This study employed eDNA metabarcoding sequencing to analyze the composition of phytoplankton and microzooplankton in a rice monoculture system (RM) and a rice–carp coculture system (RF). Following annotation, we identified 9 phyla, 89 families, 275 genera, and 249 species of phytoplankton, along with 20 phyla (or subphyla and classes), 85 families, 222 genera, and 179 species of microzooplankton. The alpha diversity indices revealed significantly higher richness, diversity, and evenness in the RF group compared to the RM group during grain-filling stage. Principal coordinates analysis (PCoA) demonstrated notable differences in the phytoplankton and microzooplankton compositions between the two groups across various rice growth stages. Composition analysis showed that rice–carp coculture increased the relative abundance of dominant phytoplankton phyla such as Bacillariophyta, Chrysophyta, and Euglenophyta while decreasing that of Cryptophyta. In microzooplankton, the coculture resulted in an increased abundance of Intramacronucleata (subphylum) and a decrease in Conoidasida (class). In conclusion, the rice–carp coculture enhances the diversity of plankton, particularly during the grain-filling stage, and simultaneously alters the composition and abundance of dominant plankton species in the paddy water. These findings enhance understanding of the broader impacts of integrated rice–carp farming on agricultural ecosystems, emphasizing alterations in the diversity and composition of aquatic microorganisms [ABSTRACT FROM AUTHOR]

Bacterial leaf blight (BLB), caused by Xanthomonas oryzae pv. oryzae (Xoo) is a significant disease attacking rice crops worldwide. This disease attacks at various stages of plant growth and causes significant yield loss. Breeding new varieties resistant to BLB is important to support sustainable agriculture in the future. This study aimed to identify new superior green super rice (GSR) lines resistant to BLB disease. The experiment evaluated the resistance of lowland rice lines obtained from anther culture using a factorial randomized complete block design. The 1st factor was genotype, consisting of 20 lines, 2 checks of commercial varieties (Inpari 42 Agritan GSR and Inpari 18), a resistant check (Conde), and a susceptible check (Taichung Native 1). The 2nd factor was BLB pathotypes (i.e., III, IV, and VIII). Quantitative data on disease severity and severity index were analyzed using analysis of variance and t-Dunnett test at 5% level. The results showed that the interaction between genotype and pathotype affected the disease severity and severity index in both growth phases. The tested lines exhibited varying resistance, from susceptible to resistant, to BLB. Four lines (SN 11, 13, 57, and 58) showed moderate to resistant criteria for BLB disease of 3 pathotypes in both growth phases. The selected lines can be used as a source of parents for breeders and candidates for new superior varieties with BLB resistance properties to support the reduction of synthetic chemical bactericide inputs and control BLB disease. However, further field evaluations are necessary to assess their performance.

The brown planthopper (BPH) is one of the most problematic pests affecting rice (Oryza sativa L.) yields in Asia. Breeding rice varieties containing resistance genes is the most economical and effective means of controlling BPH. In this study, the key factors in resistance to BPH were investigated between the high-resistance rice variety "R26" and the susceptible variety "TN1" using RNA-sequencing. We identified 9527 differentially expressed genes (DEGs) between the rice varieties under BPH-induced stress. Weighted time-course gene co-expression network analysis (WGCNA) indicated that the increased expression of genes is associated with plant hormones, MAPK signaling pathway and biosynthesis of other secondary metabolites, which were involved in disease resistance. A connection network identified a hub gene, OsREM4.1 (BGIOSGA024059), that may affect rice resistance to the BPH. Knocking out OsREM4.1 in rice can lead to a decrease in callose, making it less resistant to BPH. Overall, the expression of differentially expressed genes varies among rice varieties with different resistance in BPH invasion. Inaddition, R26 enhances resistance to BPH by upregulating genes and secondary metabolites related to stress resistance and plant immunity. In summary, our study provides valuable insights into the genome-wide expression profile of DEGs in rice under BPH invasion through high-throughput sequencing, and further suggests that R26 can be used to develop high resistance rice lines in BPH resistant breeding programs. [ABSTRACT FROM AUTHOR]

Background: Antioxidant properties of rice provide various health benefits due to its ability to inhibit cellular oxidation. Antioxidant content of rice is known to be linked with the pericarp pigmentation. The Rc gene of rice (Os07g0211500) codes for a basic helix-loop-helix (bHLH) protein, acting as a transcriptional factor in regulating proanthocyanidin biosynthesis. The current study was carried out to evaluate the variation of antioxidant properties in a selected panel of rice accessions and assess the possibility of using haplotypes defined based on the Rc gene to predict pericarp pigmentation and antioxidant content in rice. Results: Thirty-two rice accessions were evaluated for grain pericarp colour and antioxidant properties; total phenolic content (TPC), total flavonoids (TFC), proanthocyanidins (PAC) and radical scavenging activity (RSA). The parameters TPC, TFC and PAC showed significant positive correlation with RSA (r > 0.69; P < 0.01). The study panel showed a wide variation for antioxidant properties and rice accessions such as Sudu Heenati, Deweraddiri, Madathawalu, Masuran, Ld 368, At 311, Kalu Heenati, Bw 272-6B, Pokkali, At 362 and Wanni Dahanala exhibited profound potential with respect to antioxidant properties. Based on three-target sites previously reported as critical for the function of the coded bHLH protein (an A/C SNP at 1,353-bp, a 1-bp insertion/deletion at 1,388-bp, and a 14-bp insertion/deletion at 1,408-1,421-bp positioned in the mRNA corresponding to the exon 6 of rice Rc gene), three haplotypes were defined (H1-H3). Pigmentation of the rice pericarp could be successfully explained based on the defined haplotypes (H1 (C/G/+): red, and H2 (A/G/+) and H3 (C/G/-): white), and the H1 haplotype corresponded to a significantly (P < 0.05) higher TPC, TFC, PAC and RSA compared to the other haplotypes. Conclusions: The studied rice accessions showed a significant variation with respect to antioxidant properties. Haplotype H1 defined based on the three-target sites in the exon 6 of Rc gene can detect rice accessions with red pigmented pericarp and high antioxidant properties effectively. Hence, its use can be recommended as an alternative to biochemical assays for screening during rice breeding programs. [ABSTRACT FROM AUTHOR]

ABSTRACT Water and soil nutrients are the vital ingredients of crop production, and their efficient uptake is essentially dependent on root development, majorly regulated by auxin. For a water‐loving crop like rice, how water availability regulates nutrient acquisition, additionally, how ambient nutrient level modulates water uptake, and the role of auxin therein is not well studied. While investigating the cross‐talks among these components, we found water to be essential for auxin re‐distribution in roots and shaping the root architecture. We also found that supplementing rice seedlings with moderate concentrations of mineral nutrients facilitated faster water uptake and greater nutrient enrichment in leaves compared to adequate nutrient supplementation. Additionally, moderate nutrient availability favoured greater stomatal density, stomatal conductance, photosynthesis, transpiration rate and water use efficiency when water was not limiting. Further, auxin supplementation enhanced root formation in rice, while affecting their water uptake ability, photosynthesis and transpiration causing differential mineral‐specific uptake trends. The present study uncovers the existence of an intricate crosstalk among water, nutrients and auxin signalling the knowledge of which will enable optimizing the growth conditions for speed breeding of rice and harnessing the components of auxin signalling to improve water and nutrient use efficiency of rice. [ABSTRACT FROM AUTHOR]

Introduction: Hybrid rice demonstrated superior performance in enhancing yield and efficiency in rice production compared to inbred rice. Nevertheless, the underlying mechanism responsible for the increased yield and efficiency of hybrid rice in South China's double-cropping rice region remains understudied. Methods: Field experiments over two consecutive years were conducted. Firstly, yield variations among 20 inbred and 15 hybrid rice cultivars prevalent in South China's double-cropping rice system were examined. Secondly, selecting representative hybrid and inbred rice cultivars with significant yield disparities were carried out on further analyzing dry-matter production, source-sink relationships, and nutrient absorption and utilization in both rice types. Results: Hybrid rice displayed an average grain yield of 8.07 and 7.22 t hm-2 in the early and late seasons, respectively, which corresponds to a 12.29% and 13.75% increase over inbred rice with statistically significant differences. In comparison to inbred rice, hybrid rice exhibited enhanced nitrogen concentration in leaves at the heading stage (15.48-16.20%), post-heading dry matter accumulation (52.62-73.21%), post-heading dry matter conversion rate (29.23-34.12%), and harvest index (17.31-18.37%). Additionally, grain nitrogen and phosphorus uptake in hybrid rice increased by 11.88-22.50% and 16.38-19.90%. Hybrid rice mainly improved post-heading nitrogen and phosphorus uptake and transport, while not total nitrogen and phosphorus uptake. Internal nitrogen and phosphorus use efficiency enhanced by 9.83%-14.31% and 10.15%-13.66%, respectively. Postheading dry matter accumulation, harvest index, grain nitrogen and phosphorus uptake, and internal nitrogen and phosphorus use efficiency exhibited significant positive linear correlations with grain yield. Discussion: The period from heading to maturity is critical for enhancing hybrid rice yield and efficiency. Improving photosynthetic capacity during this period and promoting nutrient transport to grains serve as crucial pathways for increasing grain yield and efficiency. This study is of great significance for further improvement grain yield and breeding rice cultivars with high-yield and high nutrients use efficiency for South China's double-cropped rice system. [ABSTRACT FROM AUTHOR]

Jiangxi Province is a major province of rice breeding and planting in China. With the rapid improvement of rice breeding level, local varieties were constantly replaced by new varieties, resulted in the loss of a large number of excellent genes and the significant reduction of genetic diversity, and the genetic basis was increasingly narrow. The genetic diversity of 256 new rice varieties in Jiangxi Province was analyzed using the DUS test guide characteristics, aiming to understand the genetic diversity of new rice varieties in Jiangxi Province and provided some references for rice germplasm identification, breeding utilization and new variety testing in Jiangxi Province. The coefficient of variation of the 10 quantitative characteristics ranged from 8. 59% to 21. 83%, the Shannon-Wiener genetic diversity index of the 52 tested characteristics ranged from 0. 03 to 2. 10, with an average of 1. 05, and the cluster analysis showed that the material similarity coefficient ranged from 0. 77 to 0. 95. In recent years, the diversity of varieties selected and bred in Jiangxi Province was relatively narrow, and the development of special rice varieties was also insufficient, such as glutinous rice, colored rice and fragrant rice. [ABSTRACT FROM AUTHOR]

SUMMARY: 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. Significance Statement: OsMYC2 regulates diurnal flower‐opening time by directly regulating the transcription of JA biosynthesis genes and cell wall remodeling genes. This study not only elucidates the mechanism of JA regulating diurnal flower‐opening time but also helps reduce the cost of hybrid seed production and promote the development of indica and japonica rice hybrid breeding. [ABSTRACT FROM AUTHOR]

Heilongjiang, located in the cold region, is China's largest rice-producing and commercializing province. The variety selection of rice in cold regions (RCR) is indispensable in promoting the rice industry's development, and technological innovation in breeding theory plays a significant role in breeding breakthrough. Based primarily on long-term research, contemplation, and breeding practices, the 4S (selected topic, selected breeding, selected progenies, and selected promotion) phenotypic-design breeding technical system for RCR, which has revolutionized the theoretical basis and deepened the conceptual model, has been developed through systematic analyses and generalization. The system covers several key aspects such as scientific question formulation, breeding objective optimization, parental taxa hybridization, progeny population selection, and innovation dissemination, aiming to improve the foresight, precision, and efficiency of breeding. Furthermore, the system has demonstrated successful cases of rice variety breeding over the past 20 years, such as for Suijing 3, Suijing 4, Suijing 18, and a series of other rice varieties, providing theoretical and technical supports for cold-region rice breeding. [ABSTRACT FROM AUTHOR]

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

The nuclear factor Y (NF‐Y) has been shown to be involved in plant growth and development in response to various environmental signals. However, the integration of these mechanisms into breeding practices for new cultivars has not been extensively investigated. In this study, the Arabidopsis gene AtNF‐YB1 was introduced into rice, including inbred Kasalath and the hybrids Jinfeng × Chenghui 727 and Jinfeng × Chuanhui 907. The obtained transgenic rice showed early flowering under both natural long day (NLD) and natural short day (NSD) conditions. For the inbred Kasalath, the transgenic lines clearly showed a shorter plant height and lower grain yield, with a decrease in spike length and grain number but more productive panicles. However, the hybrids with AtNF‐YB1 had much smaller or even zero reduction in spike length and grain number and more productive panicles. Thus, maintained or even increased grain yields of the transgenic hybrids were recorded under the NLD conditions. Quantitative PCR analysis indicated that the rice flowering initiation pathways were early activated via the suppression of Ghd7 induction in the transgenic rice. RNA‐Seq further demonstrated that three pathways related to plant photosynthesis were markedly upregulated in both Jinfeng B and the hybrid Jinfeng × Chuanhui 907 with AtNF‐YB1 expression. Moreover, physiological experiments showed an upregulation of photosynthetic rates in the transgenic lines. Taken together, this study suggests that AtNF‐YB1 expression in rice not only induces early flowering but also benefits photosynthesis, which might be used to develop hybrid varieties with early ripening. [ABSTRACT FROM AUTHOR]

Rice cultivar ‘Saeodae1’ was generated by crossing ‘Saeodae’, which has good taste and a medium-short round grain, and ‘Unbong51’ which has a combined disease resistance and translucent grain. The aim of this was to develop an early maturing rice cultivar with medium-short round grain and high quality rice which adapts to the mid-northern inland plain, northern-middle highland, northern-east coastal region of Korea, and was undertaken by the rice breeding team of Cheolwon Substation, National Institute of Crop Science (NICS), RDA, in 2022. In the normal growing season in the mid-northern inland plain of Korea, the heading date of ‘Saeodae1’ was July 25 around the same time in ‘Odae’. ‘Saeodae1’ had a 75 cm culm length, 1 cm longer than that of ‘Odae’, and 75 spikelets per panicle, similar to that of ‘Odae’. The ripened grain ratio (84.7%) of ‘Saeodae1’ was higher than that (72.5%) of ‘Odae’. The head rice ratio (60.9%) of ‘Saeodae1’ was higher than that of ‘Odae’, which is advantageous in securing yield. 1,000 grain weight (25.9 g) was similar to that of ‘Odae’, but it has a smaller degree of white core rice, leading to an improved consumer preference. ‘Saeodae1’ exhibited resistance to blast and bacterial blight (K1, K2, K3 races), but was susceptible to the K3a race of bacterial blight, stripe virus, dwarf and black streak dwarf viruses, and plant-hoppers. The milled rice of this variety was translucent, with a medium-short grain shape. The cooked rice grains of ‘Saeodae1’ exhibited a good palatability index (0.13) and similar amylose content (18.2%) to that of ‘Odae’. Grain milling characteristics, including head rice milling recovery ratio and head rice ratio (82.0%) were better than those of ‘Odae’. Average milled rice productivity of ‘Saeodae1’ was 5.59 t/ha at six sites in the normal growing season (Registration No. 10182(2024.5.14.)). [ABSTRACT FROM AUTHOR]

Prime editing is a versatile CRISPR/Cas‐based precise genome‐editing technique for crop breeding. Four new types of prime editors (PEs) named PE6a–d were recently generated using evolved and engineered reverse transcriptase (RT) variants from three different sources. In this study, we tested the editing efficiencies of four PE6 variants and two additional PE6 constructs with double‐RT modules in transgenic rice (Oryza sativa) plants. PE6c, with an evolved and engineered RT variant from the yeast Tf1 retrotransposon, yielded the highest prime‐editing efficiency. The average fold change in the editing efficiency of PE6c compared with PEmax exceeded 3.5 across 18 agronomically important target sites from 15 genes. We also demonstrated the feasibility of using two RT modules to improve prime‐editing efficiency. Our results suggest that PE6c or its derivatives would be an excellent choice for prime editing in monocot plants. In addition, our findings have laid a foundation for prime‐editing‐based breeding of rice varieties with enhanced agronomically important traits. [ABSTRACT FROM AUTHOR]

Ratoon rice represents a viable means to enhance rice production efficiency in terms of both area and time. Nonetheless, the development of specific varieties tailored for ratoon rice has been hindered by the complexity of trait considerations required during breeding/screening processes. A pivotal step towards advancing ratoon rice breeding programs involves reducing the dimensionality of selection traits. In this study, we performed a comprehensive analysis exploring whether the yield of the main crop could serve as a predictor for ratoon crop yield, thereby simplifying the selection process. Our findings revealed significant variability in the rice yields of both main and ratoon crops, with the ratoon crop yield averaging 51% of the main crop. Importantly, the correlation between grain yields of the main and ratoon crops did not deviate from the identity line, substantiating the feasibility of predicting ratoon crop yield based on the main crop yield. The number of panicles in the ratoon crops was found to be closely linked to that of the main crop; however, the size values of the panicles in the ratoon crops exhibited less of a dependency on the main crop's panicle size. Additionally, a general decrease in grain weight was observed in the ratoon crops compared to the main crop. In summary, this study elucidates a pathway for the simplification of selection traits, thereby enhancing the efficiency of breeding high-yielding ratoon rice varieties, with the ultimate aim of fostering the sustainable development of ratoon rice. [ABSTRACT FROM AUTHOR]

Simple Summary: Rice breeding programs have included traditional varieties and wild rice species as sources of resistance to planthoppers and leafhoppers, which are major insect pests of rice in Asia. However, herbivores can adapt to resistance (known as virulence adaptation), sometimes in as little as 2 years. Virulence adaptation is a major obstacle for deploying resistant varieties. This review assesses knowledge of the rates, consequences, and mechanisms of virulence adaptation and on possible strategies to delay adaptation in rice landscapes. The review indicates that virulence is a complex of responses to minor and major resistance factors. Of particular interest are adaptations to major rice resistance genes that are likely governed by corresponding herbivore virulence genes. Evidence suggests that pre-adapted individuals (called forerunners) with these virulence genes occur in planthopper populations at relatively low frequencies but can rapidly build up numbers in response to planted resistant rice. However, gradual shifts in virulence may also occur due to intra- and intergenerational improvements in the herbivores' abilities to detoxify plant defense toxins, or to confound defense response networks. These may involve gradual changes in the expression of genes involved in successful herbivore attacks and may be associated with the herbivores or their endosymbionts. Several research gaps remain. In particular, there is a need for increased attention to practical, ecologically based deployment strategies that delay adaptation. In recent decades, research on developing and deploying resistant rice has accelerated due to the availability of modern molecular tools and, in particular, advances in marker-assisted selection. However, progress in understanding virulence adaptation has been relatively slow. This review tracks patterns in virulence adaptation to resistance genes (particularly Bph1, bph2, Bph3, and bph4) and examines the nature of virulence based on selection experiments, responses by virulent populations to differential rice varieties (i.e., varieties with different resistance genes), and breeding experiments that interpret the genetic mechanisms underlying adaptation. The review proposes that varietal resistance is best regarded as a combination of minor and major resistance traits against which planthoppers develop partial or complete virulence through heritable improvements that are reversable or through evolutionary adaptation, respectively. Agronomic practices, deployment patterns, and herbivore population pressures determine the rates of adaptation, and there is growing evidence that pesticide detoxification mechanisms can accelerate virulence adaptation. Research to delay adaptation has mainly focused on gene pyramiding (i.e., including ≥ two major genes in a variety) and multilines (i.e., including ≥ two resistant varieties in a field or landscape); however, these strategies have not been adequately tested and, if not managed properly, could inadvertently accelerate adaptation compared to sequential deployment. Several research gaps remain and considerable improvements in research methods are required to better understand and manage virulence adaptation. [ABSTRACT FROM AUTHOR]

Given the notable ecological and breeding disparities between southern and northern rice regions, delving into the genetic diversity and divergence between southern and northern japonica rice contributes to enhancing the genetic pool for japonica rice breeding. In this study, we analyzed 90 southern and 51 northern japonica rice varieties, focusing on nucleotide diversity (Pi), agronomic trait variations, population structure, genetic divergence, and a neutral test. For genetic diversity, the results demonstrated higher Pi in northern japonica rice varieties (NJRVs) on Chr2, Chr5, Chr6, Chr8, and Chr10, whereas in southern japonica rice varieties (SJRVs) on Chr7 and Chr9. In addition, SJRVs exhibited higher grain width and thickness, whereas NJRVs featured a higher grain aspect ratio, filled grain number, and grain number per panicle. Regarding genetic divergence, geographic differentiation existed between NJRVs and SJRVs, with Chr5 exhibiting numerous higher genetic differentiation windows, including cloned grain shape-controlling genes RGA1 and SFD5, stemming from intensified selection pressure on SJRVs. In summary, SJRVs and NJRVs exhibited diversity differences and genetic differentiation. Hence, it was suggested to conduct genetic introgression between NJRVs and SJRVs to broaden the genetic basis of the local japonica rice germplasm. By exploiting their heterotic advantage, new japonica rice cultivars with superior comprehensive traits could be developed. [ABSTRACT FROM AUTHOR]

Background: Soil salinization is one of the key factors restricting the production of cropland. Once rice is subjected to alkali stress at the bud burst stage, the yield will suffer irreparable serious loss. Compared with salt tolerance, studies on QTL mapping and candidate gene analysis of rice alkali tolerance are limited. Results: In this study, we used the F2:3 population derived from the alkali-tolerant cultivar LD21 and the alkali-sensitive cultivar WL138 to construct an alkali-tolerant DNA mixing pool, and the BSA (Bulked Segregation Analysis) method was used for re-sequencing. The main QTL qRSLB9 controlling the relative shoot length of rice under alkali stress was mapped by QTL-seq. The candidate interval was narrowed to 346.5 kb by regional linkage mapping, which containing 6 DEGs screened through transcriptome sequencing. The qRT-PCR and candidate gene sequencing showed that LOC_Os09g24260 was most likely to control relative shoot length (RSL) in rice as a major gene who encodes the WD domain, G-beta repeat domain-containing protein. Conclusions: Based on these results, LOC_Os09g24260 was the candidate gene of qRSLB9 conferring alkalinity tolerance to rice at the bud burst stage. Our study provides valuable genetic information and materials for breeding new rice varieties with alkalinity tolerance [ABSTRACT FROM AUTHOR]

Seed vigor is a complex trait encompassing seed germination, seedling emergence, growth, seed longevity, and stress tolerance, all are crucial for direct seeding in rice. Here, we report that the AP2/ERF transcription factor OsRAV1 (RELATED TO ABI3 AND VP1) positively regulates seed germination, vigor, and salt tolerance. Additionally, OsRAV1 was differently expressed in embryo and endosperm, with the OsRAV1 localized in the nucleus. Transcriptomic analysis revealed that OsRAV1 modulates seed vigor through plant hormone signal transduction and phenylpropanoid biosynthesis during germination. Haplotype analysis showed that rice varieties carrying Hap3 displayed enhanced salt tolerance during seed germination. These findings suggest that OsRAV1 is a potential target in breeding rice varieties with high seed vigor suitable for direct seeding cultivation. [ABSTRACT FROM AUTHOR]

Societal Impact Statement: Multiple cropping, the cultivation of several crops on the same land in a year, occupied an important part of Taiwan's agricultural research from 1950 to 1970. This research originated in the context of Taiwan's land reform and diversification programs and their connections to the government's political ambition to maximize food production. The study of how multiple cropping was politicized and depoliticized by different actors helps to expand the narratives of the Green Revolution in Asia, analyze their legacies, and highlight Taiwan's role in the international exchange of visions of agricultural development during the Cold War. Summary: Scholars have recently expanded the history of the Green Revolution to move beyond the narrative of North–South technological diffusion. This article enriches the scholarship with the case of multiple cropping in Taiwan and its connection to Cold War geopolitics.Rice productivity in postwar Taiwan was boosted through a land reform launched by the Sino‐American Joint Commission on Rural Reconstruction (JCRR) in the 1950s. Backed by American aid and staffed by scientists from the Republic of China (ROC) government, the JCRR envisioned to turn tenant farmers into landowners so as to encourage labor input and adoption of seeds and fertilizers.By 1960, the JCRR presented its reform as a "bloodless social revolution" and extended its focus to multiple cropping through a diversification program. The JCRR further created the Asian Vegetable Research and Development Center (AVRDC) in 1971 to spread Taiwan's breeding and cropping techniques. The ROC's diplomatic isolation in the 1970s, however, prompted the center to reinterpret Taiwan's success in multiple cropping from a political achievement to a technological triumph, thus reinforcing the technology‐driven narrative used by the International Rice Research Institute (IRRI).Through Taiwan's influences on IRRI's rice breeding and multiple cropping research, this paper illustrates that the history of the Green Revolution requires more complex narratives. In addition, with Taiwan's political and economic transition since the 1980s, farmers began to reclaim their voice and influence agricultural policies. The case thus highlights the need of democratic participation in agricultural research, a concern that remains relevant today. [ABSTRACT FROM AUTHOR]