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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 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. [ABSTRACT FROM AUTHOR]

Summary: Modern cultivated rice (Oryza sativa) typically experiences limited growth benefits from arbuscular mycorrhizal (AM) symbiosis. This could be due to the long‐term domestication of rice under favorable phosphorus conditions. However, there is limited understanding of whether and how the rice domestication has modified AM properties.This study compared AM properties between a collection of wild (Oryza rufipogon) and domesticated rice genotypes and investigated the mechanisms underlying their differences by analyzing physiological, genomic, transcriptomic, and metabolomic traits critical for AM symbiosis.The results revealed significantly lower mycorrhizal growth responses and colonization intensity in domesticated rice compared to wild rice, and this change of AM properties may be associated with the domestication modifications of plant phosphorus utilization efficiency at physiological and genomic levels. Domestication also resulted in a decrease in the activity of the mycorrhizal phosphorus acquisition pathway, which may be attributed to reduced mycorrhizal compatibility of rice roots by enhancing defense responses like root lignification and reducing carbon supply to AM fungi.In conclusion, rice domestication may have changed its AM properties by modifying P nutrition‐related traits and reducing symbiotic compatibility. This study offers new insights for improving AM properties in future rice breeding programs to enhance sustainable agricultural production. [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]

Introduction: Breeding rice with drought tolerance for harsh environments is crucial for agricultural sustainability. Understanding the genetic underpinnings of drought tolerance is vital for developing resilient rice varieties. Genome-wide association studies (GWAS) have emerged as pivotal tools in unravelling the complex genetic architecture of traits like drought tolerance, capitalizing on the natural genetic diversity within rice germplasm collections. Methods: In this study, a comprehensive panel of 210 rice varieties was phenotyped over ten days in controlled conditions, subjected to simulated drought stress using 20% PEG 6000 in petri dishes. Throughout the stress period, crucial traits such as germination percentage (GP), germination rate index (GRI), mean germination time (MGT), and seedling percentage (SP) were meticulously monitored. Results: The GWAS analysis uncovered a total of 38 QTLs associated with drought tolerance traits, including novel loci like qMGT-5.2, qSP-3, qSP7.2, and qGP-5.2. Additionally, RNA-seq analysis identified ten genes with significant expression differences under drought stress conditions. Notably, haplotype analysis pinpointed elite haplotypes in specific genes linked to heightened drought tolerance. Discussion: Overall, this study underscores the importance of GWAS in validating known genes while unearthing novel loci to enrich the genetic resources for enhancing drought tolerance in rice breeding programs. [ABSTRACT FROM AUTHOR]

Strong early growth vigor is an essential target in both direct seeded rice breeding and high-yielding rice breeding for rice varieties with relatively short growth duration in the double-cropping region. Shoot dry weight (SDW) is one of the important traits associated with early growth vigor, and breeders have been working to improve this trait. Finding stable QTLs or functional genes for SDW is crucial for improving the early growth vigor by implementing molecular breeding in rice. Here, a genome-wide association analysis revealed that the QTL for SDW, qSDW-5, was stably detected in the three cultivation methods commonly used in production practice. Through gene-based haplotype analysis of the annotated genes within the putative region of qSDW-5, and validated by gene expression and knockout transgenic experiments, LOC_Os05g09520, which is identical to the reported GW5/GSE5 controlling grain width (GW) and thousand grain weight (TGW) was identified as the causal gene for qSDW-5. Five main haplotypes of LOC_Os05g09520 were identified in the diverse international rice collection used in this study and their effects on SDW, GW and TGW were analyzed. Phenotypic comparisons of the major haplotypes of LOC_Os05g09520 in the three subpopulations (indica, japonica and aus) revealed the same patterns of wider GW and higher TGW along with higher SDW. Furtherly, the haplotype analysis of 138 rice varieties/lines widely used in southern China showed that 97.8% of the cultivars/lines carry Hap2LOC_Os05g09520. These results not only provide a promising gene source for the molecular breeding of rice varieties with strong early growth vigor, but also elucidate the effect of the LOC_Os05g09520 haplotypes on SDW, GW, and TGW in rice. Importantly, this study provides direct genetic evidence that these three traits are significantly correlated, and suggests a breeding strategy for developing high-yielding and slender grain-shaped indica cultivars with strong early growth vigor. [ABSTRACT FROM AUTHOR]

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

Summary: Inter‐subspecific indica–japonica hybrid rice (Oryza sativa) has the potential for increased yields over traditional indica intra‐subspecies hybrid rice, but limited yield of F1 hybrid seed production (FHSP) hinders the development of indica–japonica hybrid rice breeding. Diurnal flower‐opening time (DFOT) divergence between indica and japonica rice has been a major contributing factor to this issue, but few DFOT genes have been cloned. Here, we found that manipulating the expression of jasmonate (JA) pathway genes can effectively modulate DFOT to improve the yield of FHSP in rice. Treating japonica cultivar Zhonghua 11 (ZH11) with methyl jasmonate (MeJA) substantially advanced DFOT. Furthermore, overexpressing the JA biosynthesis gene OPDA REDUCTASE 7 (OsOPR7) and knocking out the JA inactivation gene CHILLING TOLERANCE 1 (OsHAN1) in ZH11 advanced DFOT by 1‐ and 2‐h respectively; and knockout of the JA signal suppressor genes JASMONATE ZIM‐DOMAIN PROTEIN 7 (OsJAZ7) and OsJAZ9 resulted in 50‐min and 1.5‐h earlier DFOT respectively. The yields of FHSP using japonica male‐sterile lines GAZS with manipulated JA pathway genes were significantly higher than that of GAZS wildtype. Transcriptome analysis, cytological observations, measurements of elastic modulus and determination of cell wall components indicated that the JA pathway could affect the loosening of the lodicule cell walls by regulating their composition through controlling sugar metabolism, which in turn influences DFOT. This research has vital implications for breeding japonica rice cultivars with early DFOT to facilitate indica–japonica hybrid rice breeding. [ABSTRACT FROM AUTHOR]

Summary: Salinity, as one of the most challenging environmental factors restraining crop growth and yield, poses a severe threat to global food security. To address the rising food demand, it is urgent to develop crop varieties with enhanced yield and greater salt tolerance by delving into genes associated with salt tolerance and high‐yield traits. MiR396b/GRF6 module has previously been demonstrated to increase rice yield by shaping the inflorescence architecture. In this study, we revealed that miR396b/GRF6 module can significantly improve salt tolerance of rice. In comparison with the wild type, the survival rate of MIM396 and OE‐GRF6 transgenic lines increased by 48.0% and 74.4%, respectively. Concurrent with the increased salt tolerance, the transgenic plants exhibited reduced H2O2 accumulation and elevated activities of ROS‐scavenging enzymes (CAT, SOD and POD). Furthermore, we identified ZNF9, a negative regulator of rice salt tolerance, as directly binding to the promoter of miR396b to modulate the expression of miR396b/GRF6. Combined transcriptome and ChIP‐seq analysis showed that MYB3R serves as the downstream target of miR396b/GRF6 in response to salt tolerance, and overexpression of MYB3R significantly enhanced salt tolerance. In conclusion, this study elucidated the potential mechanism underlying the response of the miR396b/GRF6 network to salt stress in rice. These findings offer a valuable genetic resource for the molecular breeding of high‐yield rice varieties endowed with stronger salt tolerance. [ABSTRACT FROM AUTHOR]

Callus induction (CI) is a critical trait for transforming desirable genes in plants. A genome-wide association study (GWAS) analysis was conducted on the rice germplasms of 110 Indica rice accessions, in which three tissue culture media, B5, MS, and N6, were used for the CI of those rice panels' mature seeds. Seven quantitative trait loci (QTLs) on rice chromosomes 2, 6, 7, and 11 affected the CI percentage in the three media. For the B5 medium, one QTL (qCI–B5–Chr6) was identified on rice chromosome 6; for the MS medium, two QTLs were identified on rice chromosomes 2 and 6 (qCI–MS–Chr2 and qCI–MS–Chr6, respectively); for the N6 medium, four QTLs were identified on rice chromosomes 6, 7, and 11 (qCI–N6–Chr6.1 and qCI–N6–Chr6.2, qCI–N6–Chr7, and qCI–N6–Chr11, respectively). Fifty-five genes were identified within the haplotype blocks corresponding to these QTLs, thirty-one of which showed haplotypes associated with different CI percentages in those media. qCI–B5–Chr6 was located in the same region as qCI–N6–Chr6.2, and the Caleosin-related family protein was also identified in this region. Analysis of the gene-based haplotype revealed the association of this gene with different CI percentages in both B5 and N6 media, suggesting that the gene may play a critical role in the CI mechanism. Moreover, several genes, including those that encode the beta-tubulin protein, zinc finger protein, RNP–1 domain-containing protein, and lysophosphatidic acid acyltransferase, were associated with different CI percentages in the N6 medium. The results of this study provide insights into the potential QTLs and candidate genes for callus induction in rice that contribute to our understanding of the physiological and biochemical processes involved in callus formation, which is an essential tool in the molecular breeding of rice. [ABSTRACT FROM AUTHOR]

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

Background: Improving the rate of genetic gain of cereal crop will rely on the accelerated crop breeding pipelines to allow rapid delivery of improved crop varieties. The laborious, time-consuming traditional breeding cycle, and the seasonal variations are the key factor restricting the breeder to develop new varieties. To address these issues, a revolutionized cost-effective speed breeding protocol for large-scale rice germplasm advancement is presented in the present study. The protocol emphasises on optimizing potting material, balancing the double-edged sword of limited nutritional dose, mode and stage of application, plant density, temperature, humidity, light spectrum, intensity, photoperiod, and hormonal regulation to accelerate rice growth and development. Results: The plant density of 700 plants/m2, cost-effective halogen tubes (B:G:R:FR-7.0:27.6:65.4:89.2) with an intensity of ∼ 750–800 µmol/m2/s and photoperiod of 13 h light and 11 h dark during seedling and vegetative stage and 8 h light and 16 h dark during reproductive stage had a significant effect (P < 0.05) on reducing the mean plant height, tillering, and inducing early flowering. Our results confirmed that one generation can be achieved within 68–75 days using the cost-effective SpeedyPaddy protocol resulting in 4–5 generations per year across different duration of rice varieties. The other applications include hybridization, trait-based phenotyping, and mapping of QTL/genes. The estimated cost to run one breeding cycle with plant capacity of 15,680 plants in SpeedyPaddy was $2941 including one-time miscellaneous cost which is much lower than the advanced controlled environment speed breeding facilities. Conclusion: The protocol offers a promising cost-effective solution with average saving of 2.0 to 2.6 months per breeding cycle with an integration of genomics-assisted selection, trait-based phenotyping, mapping of QTL/genes, marker development may accelerate the varietal development and release. This outstanding cost-effective break-through marks a significant leap in rice breeding addressing climate change and food security. [ABSTRACT FROM AUTHOR]

Background: Rice is one of the major staples that feeds about one half of the global populations, and it is important to identify the genetic loci for the traits related to yield improvement. Lodging will cause severe yield loss when it happens, and stem diameter has been characterized as an important trait for lodging resistance. However, most QTLs for stem diameter have not been finely dissected due to their sensitivity to environmental fluctuation. Result: In this study, we performed QTL analysis for stem diameter using populations derived from Nipponbare (NIP) and strong culm variety YYP1, and confirmed the single and combined effect of three major QTLs by recombinant inbred lines (RILs). Based on the QTL location, we found that qWS5 is a novel QTL not well characterized before. To finely dissect the novel locus, several recombinant heterogeneous inbred families (HIFs) were selected from the RILs for linkage analysis and their derived nearly isogenic lines (NILs) were subjected to detailed trait investigation throughout different years. The HIF-NILs strategy confined the QTL to about 380 kb region supported by repeated genotype and phenotype data, and it lays the foundation for QTL cloning in the future. In addition, introgression of the QTL to an elite japonica variety SD785 was performed by successive backcrossing, and it confirmed the value of qWS5 in increasing stem diameter and other agronomic traits during rice breeding. Conclusions: We prove that qWS5 is a novel QTL with relatively stable effect for stem diameter and the QTL can be finely mapped to small region by the HIF-NILs strategy. The result will facilitate the improvement of rice lodging resistance by molecular marker assisted selection breeding. [ABSTRACT FROM AUTHOR]

This study aimed to evaluate the impacts of wild and breeding juvenile rice field eel under conditions of ammonia and heat stress. The growth performance (FBW, WGR, SGR, and FCR) of 360 wild (24.22 ± 0.30 g) and 360 breeding (24.16 ± 0.27 g) strains was significantly hindered by ammonia and heat stress. The inhibitory effects were more obvious when the two stresses were combined. The growth performance and survival rates of the breeding strains outperformed that of the wild strains under identical stress conditions, this was explained by the expression of the growth-related gene (gh). They have increased the enzyme activity (CAT and GSH-Px) and expression of immune-related genes (cat, gpx3, and hsp90a) in response to oxidative stress. However, the results of certain indicator enzymes indicate the presence of oxidative damage in their tissues. The presence of an inflammatory response in the tissues was suggested by the up-regulation of genes associated with pro-inflammatory cytokines (il-1b and il-8) and the downregulation of genes related to anti-inflammatory cytokines (il-10). Additionally, the presence of tissue damage was shown by the up-regulation of genes connected to apoptosis (cas2, cas8, and cas9) and the down-regulation of genes connected to tight junctions (zo-1). Nevertheless, it is noteworthy that breeding strains exhibited superior adaptability to ammonia and heat stress in comparison to wild strains. [ABSTRACT FROM AUTHOR]

Plants must accurately integrate external environmental signals with their own development to initiate flowering at the appropriate time for reproductive success. Photoperiod and temperature are key external signals that determine flowering time; both are cyclical and periodic, and they are closely related. In this review, we describe photoperiod-sensitive genes that simultaneously respond to temperature signals in rice (Oryza sativa). We introduce the mechanisms by which photoperiod and temperature synergistically regulate heading date and regional adaptation in rice. We also discuss the prospects for designing different combinations of heading date genes and other cold tolerance or thermo-tolerance genes to help rice better adapt to changes in light and temperature via molecular breeding to enhance yield in the future. [ABSTRACT FROM AUTHOR]

ABSTRACT 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]

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. [ABSTRACT FROM AUTHOR]

A low-input-based farming system can reduce the adverse effects of modern agriculture through proper utilization of natural resources. Modern varieties often need to improve in low-input settings since they are not adapted to these systems. In addition, rice is one of the most widely cultivated crops worldwide. Enhancing rice performance under a low input system will significantly reduce the environmental concerns related to rice cultivation. Traits that help rice to maintain yield performance under minimum inputs like seedling vigor, appropriate root architecture for nutrient use efficiency should be incorporated into varieties for low input systems through integrated breeding approaches. Genes or QTLs controlling nutrient uptake, nutrient assimilation, nutrient remobilization, and root morphology need to be properly incorporated into the rice breeding pipeline. Also, genes/QTLs controlling suitable rice cultivars for sustainable farming. Since several variables influence performance under low input conditions, conventional breeding techniques make it challenging to work on many traits. However, recent advances in omics technologies have created enormous opportunities for rapidly improving multiple characteristics. This review highlights current research on features pertinent to low-input agriculture and provides an overview of alternative genomics-based breeding strategies for enhancing genetic gain in rice suitable for low-input farming practices. [ABSTRACT FROM AUTHOR]

Leaf angle (LA) is a major agronomic trait of rice plant architecture, which is determined by the development of the leaf lamina joint (LJ) and closely related to plant yield. The LJ is formed by the leaf collar belt (ligule band), leaf tongue (ligule) and leaf ear (auricle). Parenchyma cells (PCs), sclerenchyma cells (SCs), vascular bundles (VBs), and arenchyma tissue (Ac) are present in the cross sections of LJ. The genetic and molecular regulation of rice leaf angle and LJ development has been well investigated in recent years. However, the underlying complex regulatory network still requires further elucidation and comprehensive discussion. In this review, we briefly describe the cellular characteristics of four typical stages of LJ development, and systematically summarize the genes regulating rice leaf inclination based on their roles in PC proliferation and elongation, as well as SC proliferation and differentiation. We also introduce the emerging regulatory pathways of phytohormones and transcription factors (TFs), environmental cues that are involved in rice LJ development, discussing the relevant intricate signal network that is relevant to provide further insights into the genetic improvement of leaf angle traits in rice breeding. [ABSTRACT FROM AUTHOR]

Bakanae disease is mainly caused by Fusarium fujikuroi and is a significant fungal disease with a number of disastrous consequences. It causes great losses in rice production. However, few studies have focused on the details of bakanae disease resistance in rice. Here, we summarize and discuss the progress of bakanae disease resistance in rice. Besides rice germplasm screening and resistance-related gene/quantitative trait locus (QTL) exploration, the route of pathogen invasion in rice plants was determined. We further discussed the regulation of phytohormone-related genes and changes in endogenous phytohormones in rice plants that are induced by the pathogen. To achieve better control of bakanae disease, the use of natural fungicides was assessed in this review. During rice—F. fujikuroi interactions, the infection processes and spatial distribution of F. fujikuroi in infected seedlings and adult plants exhibit different trends. Fungal growth normally occurs both in resistant and susceptible cultivars, with less abundance in the former. Generally, bakanae disease is seed-borne, and seed disinfection using effective fungicides should always be the first and main option to better control the disease. Besides the friendly and effective measure of using natural fungicides, breeding and utilization of resistant rice cultivars is also an effective control method. To some extent, rice cultivars with low grain quality, indica subspecies, and some dwarf or semi-dwarf rice germplasms are more resistant to bakanae disease. Although no highly resistant germplasms were obtained, 37 QTLs were located, with almost half of the QTLs being located on chromosome 1. Using omics methods, WRKYs and MAPKs were usually found to be regulated during rice—F. fujikuroi interactions. The regulation of certain phytohormone-related genes and changes in some endogenous phytohormones induced by the pathogen were clear, i.e., it downregulated gibberellin-related genes and repressed endogenous gibberellins in resistant genotypes, but the opposite results were noted in susceptible rice genotypes. Overall, exploring resistant germplasms or resistance-related genes/QTLs for the breeding of rice with bakanae disease resistance, expanding research on the complex mechanism of rice—F. fujikuroi interactions, and using cost-effective and eco-friendly innovative control methods against the disease are necessary for present and future bakanae disease management. [ABSTRACT FROM AUTHOR]

The rice blight poses a significant threat to the rice industry, and the discovery of disease-resistant genes is a crucial strategy for its control. By exploring the rich genetic resources of Yuanjiang common wild rice (Oryza rufipogon) and analyzing their expression patterns, genetic resources can be provided for molecular rice breeding. The target genes' expression patterns, subcellular localization, and interaction networks were analyzed based on the annotated disease-resistant genes on the 9th and 10th chromosomes in the rice genome database using fluorescent quantitative PCR technology and bioinformatics tools. Thirty-three disease-resistant genes were identified from the database, including 20 on the 9th and 13 on the 10th. These genes were categorized into seven subfamilies of the NLR family, such as CNL and the G subfamily of the ABC family. Four genes were not expressed under the induction of the pathogen Y8, two genes were significantly down-regulated, and the majority were up-regulated. Notably, the expression levels of nine genes belonging to the ABCG, CN, and CNL classes were significantly up-regulated, yet the expression levels varied among roots, stems, and leaves; one was significantly expressed in the roots, one in the stems, and the remaining seven were primarily highly expressed in the leaves. Two interaction network diagrams were predicted based on the seven highly expressed genes in the leaves: complex networks regulated by CNL proteins and specific networks controlled by ABCG proteins. The disease-resistant genes on the 9th chromosome are actively expressed in response to the induction of rice blight, forming a critical gene pool for the resistance of Yuanjiang common wild rice (O. rufipogon) to rice blight. Meanwhile, the disease-resistant genes on the 10th chromosome not only participate in resisting the rice blight pathogen but may also be involved in the defense against other stem diseases. [ABSTRACT FROM AUTHOR]

The performance of novel genetic combinations under untested environmental scenarios and management practices can be virtually examined using process‐based crop models. Indeed, there has been a long‐standing interest in the crop modeling community to expand the utility of process‐based models to broader germplasm panels (e.g., breeding lines or diversity panels). Yet, there is often a misalignment between data needed to parameterize process‐based crop models and data routinely collected by breeding programs. To address this gap, we leverage a dataset from a long‐term trial on advanced experimental lines and released varieties from the Louisiana rice breeding program to calibrate and evaluate the decision support for agrotechnology transfer (DSSAT) CSM‐CERES‐Rice model. Next, we use data collected by the same program on a large collection of breeding lines to generate numerous in silico genotypes and evaluate their performance across different management practices (different planting dates) and three climatic conditions (current climate and two future scenarios based on CMIP6‐SSP5‐8.5 climate projections). Our simulations indicate that shifting the current planting date (i.e., March) back by 1–2 months (to January) under moderate warming conditions (+1.3°C warmer and 41% higher CO2 level), and 2–3 months (to December) under extreme warming conditions (+4.1°C warmer and 133% higher CO2 level) could potentially offset the negative impacts of the increased future temperature. Given earlier planting, shorter duration varieties (i.e., those with shorter growing degree day requirements during the vegetative and grain filling periods) are found to be more favorable for supporting high yields. Such varieties with a shorter thermal time to anthesis are found to remain just outside of the current pool of variation for this trait. Opportunities and challenges for leveraging breeding data in process‐based modeling to derive insights into adaptation strategies for future climates are further discussed. Core Ideas: There has been a long‐standing interest in the crop modeling community to extend the utility of process‐based models to breeding.Data required for models are often misaligned with data routinely collected from applied breeding programs.Parameterization of the CERES‐Rice model was informed using historical and recent data collected from the Louisiana rice breeding program.The impact of future climate, planting dates, and novel genetic combinations on the yield and phenology was tested.The range of genetic variability for phenology in the current breeding program to adapt varieties to future conditions was assessed. [ABSTRACT FROM AUTHOR]

Rice (Oryza sativa L.) is a common staple food widely cultivated and consumed globally. The increase in world population and slow genetic gain in rice production in the face of a rapidly evolving climate could cause food scarcity and decreased crop productivity. It is crucial to expedite the development and release of climate-resilient crop varieties through selective breeding and improvement to mitigate the impact of climate change. Speed breeding has emerged as a promising tool for rice breeding, offering the potential to accelerate the generation time. By streamlining the breeding process and reducing the time taken for each generation, speed breeding empowers breeders to screen for desired traits rapidly and efficiently, enhancing the selection and development of improved rice varieties to meet the growing global demand for food. This review focuses on the applications of speed breeding technology to accelerate rice breeding and further highlights the critical factors for speed breeding development in rice production, such as temperature, humidity, light, and genetic diversity. Understanding and optimizing these factors is vital in successfully implementing speed breeding technology in developing robust, high-yielding, and climate-resilient rice varieties for feeding the future. [ABSTRACT FROM AUTHOR]

Grain yield is determined mainly by grain number and grain weight. In this study, we identified and characterized MORE GRAINS1 (MOG1), a gene associated with grain number and grain weight in rice (Oryza sativa L.), through map‐based cloning. Overexpression of MOG1 increased grain yield by 18.6%–22.3% under field conditions. We determined that MOG1, a bHLH transcription factor, interacts with OsbHLH107 and directly activates the expression of LONELY GUY (LOG), which encodes a cytokinin‐activating enzyme and the cell expansion gene EXPANSIN‐LIKE1 (EXPLA1), positively regulating grain number per panicle and grain weight. Natural variations in the promoter and coding regions of MOG1 between Hap‐LNW and Hap‐HNW alleles resulted in changes in MOG1 expression level and transcriptional activation, leading to functional differences. Haplotype analysis revealed that Hap‐HNW, which results in a greater number and heavier grains, has undergone strong selection but has been poorly utilized in modern lowland rice breeding. In summary, the MOG1–OsbHLH107 complex activates LOG and EXPLA1 expression to promote cell expansion and division of young panicles through the cytokinin pathway, thereby increasing grain number and grain weight. These findings suggest that Hap‐HNW could be used in strategies to breed high‐yielding temperate japonica lowland rice. [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]

Societal Impact Statement: Rice wild relatives (RWR) provide valuable genetic resources for modern rice breeding, yet knowledge gaps constrain their conservation and further utilization. To address these gaps, the potential distributions of 22 RWR taxa were modeled, and their conservation statuses were assessed. Most taxa were identified as medium priority for further conservation. Further ex‐situ collecting hotspots are in Southeast and South Asia, Northern Australia, West Africa, and tropical Americas, while habitat protection lies in Southeast and South Asia, Northern Australia, and West Africa. Climate change may shift equatorial habitats to higher latitudes and mountain habitats to higher altitudes. Summary: Rice wild relatives (RWR) provide valuable genetic resources for modern rice breeding. However, knowledge gaps on their geographic distributions and conservation status constrain their conservation and further utilization.To fill these critical gaps, we modeled the potential distributions of 22 RWR taxa under current climate scenarios, assessed their conservation status, both ex situ (in genebanks or botanical gardens) and in situ (in protected areas), and examined changes in taxa richness of RWR in predicted areas under future climate scenarios.The RWR were primarily distributed in tropical Asia to tropical Australia, tropical Africa, and South and Central America. We identified 4 out of 22 taxa as high priority (HP) for further conservation action and 18 taxa as medium priority (MP).Hotspots requiring further collecting for ex situ conservation are concentrated in Southeast and South Asia, Northern Australia, West Africa, and tropical Americas. Meanwhile, habitat protection should be enhanced in Southeast and South Asia, Northern Australia, and West Africa. Under future climate change, suitable habitats near the equator are expected to shift toward higher latitudes and some in lower‐latitude basins may become unsuitable due to excessive heat, resulting in decreased taxa richness in these areas. Additionally, suitable habitats in high mountain areas may shift to higher altitudes, potentially augmenting taxa richness in the highlands. Our findings provide vital insights to guide future rescue conservation efforts for RWR. [ABSTRACT FROM AUTHOR]

Low temperature severely affects rice development and yield. Ethylene signal is essential for plant development and stress response. Here, we reported that the OsEIN2‐OsEIL1/2 pathway reduced OsICE1‐dependent chilling tolerance in rice. The overexpressing plants of OsEIN2, OsEIL1 and OsEIL2 exhibited severe stress symptoms with excessive reactive oxygen species (ROS) accumulation under chilling, while the mutants (osein2 and oseil1) and OsEIL2‐RNA interference plants (OsEIL2‐Ri) showed the enhanced chilling tolerance. We validated that OsEIL1 and OsEIL2 could form a heterxodimer and synergistically repressed OsICE1 expression by binding to its promoter. The expression of OsICE1 target genes, ROS scavenging‐ and photosynthesis‐related genes were downregulated by OsEIN2 and OsEIL1/2, which were activated by OsICE1, suggesting that OsEIN2‐OsEIL1/2 pathway might mediate ROS accumulation and photosynthetic capacity under chilling by attenuating OsICE1 function. Moreover, the association analysis of the seedling chilling tolerance with the haplotype showed that the lower expression of OsEIL1 and OsEIL2 caused by natural variation might confer chilling tolerance on rice seedlings. Finally, we generated OsEIL2‐edited rice with an enhanced chilling tolerance. Taken together, our findings reveal a possible mechanism integrating OsEIN2‐OsEIL1/2 pathway with OsICE1‐dependent cascade in regulating chilling tolerance, providing a practical strategy for breeding chilling‐tolerant rice. Summary Statement: The OsEIN2‐OsEIL1/2 ethylene pathway has negative effect on rice tolerance to low temperature stress through transcriptionally repressing OsICE1‐mediated chilling response. [ABSTRACT FROM AUTHOR]

There is a need to exploit the genetic variability in rice to improve the Fe deficiency tolerance, particularly under aerobic conditions, and to improve the Fe uptake and accumulation in the grain to facilitate biofortification. The present research was conducted to ascertain the regulators and determinants of Fe-deficiency tolerance in rice. Fifty-seven diverse genotypes were investigated under Fe-deficient (1 µM, FDS, -Fe) and Fe-sufficient (100 µM, FSS, +Fe) nutrient solution cultures for growth and physiological attributes, Fe uptake and accumulation and root release of phytosiderophores (PS), etc., and Fe-deficiency tolerance index (FeDTI). A strong positive correlation was observed between root traits and the PS release. Further, a higher release of PS was evidenced as a major determinant of shoot Fe and grain Fe in rice particularly under Fe deficiency. Based on FeDTI, a total of ten rice genotypes were identified, and their Fe deficiency response was further validated on Fe deficient (∼2.1 ppm Fe, FeDS) and Fe-sufficient soils (∼10 ppm Fe, FeSS) in pot culture. Maintenance of high active Fe content and consequently a higher leaf chlorophyll content throughout the plant growth were extremely important determinants of grain yield and grain Fe fortification in rice under Fe deficiency than under the Fe sufficient condition. Based on the FeDTI, this study further identifies the Fe-deficiency tolerant rice genotypes which can be exploited through conventional and molecular breeding approaches to improve the Fe uptake efficiency and grain Fe content of the high-yielding rice genotypes. [ABSTRACT FROM AUTHOR]

Long-term storage of crop seeds is critical for the conservation of germplasm resources, ensuring food supply, and supporting sustainable production. Rice, as a major food staple, has a substantial stock for consumption and production worldwide. However, its food value and seed viability tend to decline during storage. Understanding the physiological responses and molecular mechanisms of aging tolerance forms the basis for enhancing seed storability in rice. This review outlines the latest progress in influential factors, evaluation methods, and identification indices of seed storability. It also discusses the physiological consequences, molecular mechanisms, and strategies for breeding aging-tolerant rice in detail. Finally, it highlights challenges in seed storability research that require future attention. This review offers a theoretical foundation and research direction for uncovering the mechanisms behind seed storability and breeding aging-tolerant rice. [ABSTRACT FROM AUTHOR]

The yield potential of rice is seriously affected by heat stress due to climate change. Since rice is a staple food globally, it is imperative to develop heat-resistant rice varieties. Thus, a thorough understanding of the complex molecular mechanisms underlying heat tolerance and the impact of high temperatures on various critical stages of the crop is needed. Adoption of both conventional and innovative breeding strategies offers a long-term advantage over other methods, such as agronomic practices, to counter heat stress. In this review, we summarize the effects of heat stress, regulatory pathways for heat tolerance, phenotyping strategies, and various breeding methods available for developing heat-tolerant rice. We offer perspectives and knowledge to guide future research endeavors aimed at enhancing the ability of rice to withstand heat stress and ultimately benefit humanity. [ABSTRACT FROM AUTHOR]

As one of the most important food crops in the world, rice yield is directly related to national food security. Lodging is one of the most important factors restricting rice production, and the cultivation of rice varieties with lodging resistance is of great significance in rice breeding. The lodging resistance of rice is directly related to the mechanical strength of the stalks. In this paper, we reviewed the cell wall structure, its components, and its genetic regulatory mechanism, which improved the regulatory network of rice stalk mechanical strength. Meanwhile, we analyzed the new progress in genetic breeding and put forward some scientific problems that need to be solved in this field in order to provide theoretical support for the improvement and application of rice breeding. [ABSTRACT FROM AUTHOR]

The number of grains per sea rice panicle is an important parameter directly related to rice yield, and it is also a very important agronomic trait in research related to sea rice breeding. However, the grain number per sea rice panicle still mainly relies on manual calculation, which has the disadvantages of being time-consuming, error-prone, and labor-intensive. In this study, a novel method was developed for the automatic calculation of the grain number per rice panicle based on a deep convolutional neural network. Firstly, some sea rice panicle images were collected in complex field environment and annotated to establish the sea rice panicle image data set. Then, a sea grain detection model was developed using the Faster R-CNN embedded with a feature pyramid network (FPN) for grain identification and location. Also, ROI Align was used to replace ROI pooling to solve the problem of relatively large deviations in the prediction frame when the model detected small grains. Finally, the mAP (mean Average Precision) and accuracy of the sea grain detection model were 90.1% and 94.9%, demonstrating that the proposed method had high accuracy in identifying and locating sea grains. The sea rice grain detection model can quickly and accurately predict the number of grains per panicle, providing an effective, convenient, and low-cost tool for yield evaluation, crop breeding, and genetic research. It also has great potential in assisting phenotypic research. [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]

Polyploid is considered an advantage that has evolved to be more environmentally adaptable than its diploid. To understand if doubled chromosome of diploid rice can improve drought tolerance, we evaluated the diploid (2X) and autotetraploid (4X) plants of three indica and three japonica varieties. Drought stress in the plastic bucket of four-leaf stage revealed that the drought tolerance of 4X plants was lower than that of its diploid donor plants. The assay of photosynthetic rate of all varieties showed that all 4X varieties had lower rates than their diploid donors. The capacity for reactive oxygen species production and scavenging varied among different 2X and 4X varieties. Further, transcriptomic analysis of 2X and 4X plants of four varieties under normal and drought condition showed that the wide variation of gene expression was caused by difference of varieties, not by chromosome ploidy. However, weighted gene co-expression network analysis (WGCNA) revealed that the severe interference of photosynthesis-related genes in tetraploid plants under drought stress is the primary reason for the decrease of drought tolerance in autotetraploid lines. Consistently, new transcripts analysis in autotetraploid revealed that the gene transcription related with mitochondrion and plastid of cell component was influenced most significantly. The results indicated that chromosome doubling of diploid rice weakened their drought tolerance, primarily due to disorder of photosynthesis-related genes in tetraploid plants under drought stress. Maintain tetraploid drought tolerance through chromosome doubling breeding in rice needs to start with the selection of parental varieties and more efforts. [ABSTRACT FROM AUTHOR]

SUMMARY: Rice (Oryza sativa L.) is a short‐day plant whose heading date is largely determined by photoperiod sensitivity (PS). Many parental lines used in hybrid rice breeding have weak PS, but their F1 progenies have strong PS and exhibit an undesirable transgressive late‐maturing phenotype. However, the genetic basis for this phenomenon is unclear. Therefore, effective methods are needed for selecting parents to create F1 hybrid varieties with the desired PS. In this study, we used bulked segregant analysis with F1 Ningyou 1179 (strong PS) and its F2 population, and through analyzing both parental haplotypes and PS data for 918 hybrid rice varieties, to identify the genetic basis of transgressive late maturation which is dependent on dominance complementation effects of Hd1, Ghd7, DTH8, and PRR37 from both parents rather than from a single parental genotype. We designed a molecular marker‐assisted selection system to identify the genotypes of Hd1, Ghd7, DTH8, and PRR37 in parental lines to predict PS in F1 plants prior to crossing. Furthermore, we used CRISPR/Cas9 technique to knock out Hd1 in Ning A (sterile line) and Ning B (maintainer line) and obtained an hd1‐NY material with weak PS while retaining the elite agronomic traits of NY. Our findings clarified the genetic basis of transgressive late maturation in hybrid rice and developed effective methods for parental selection and gene editing to facilitate the breeding of hybrid varieties with the desired PS for improving their adaptability. Significance Statement: We identified the genetic basis of transgressive late maturation in hybrid rice, which is dependent on dominance complementation effects of Hd1, Ghd7, DTH8, and PRR37 from both parents and developed effective methods for parental selection and gene editing to facilitate the breeding of hybrid varieties with the desired photoperiod sensitivity. Our study lays an important foundation for improving the breeding efficiency and latitude adaptability of hybrid rice. [ABSTRACT FROM AUTHOR]

Grain-related traits are pivotal in rice cultivation, influencing yield and consumer preference. The complex inheritance of these traits, involving multiple alleles contributing to their expression, poses challenges in breeding. To address these challenges, a multi-locus genome-wide association study (ML-GWAS) utilizing 35,286 high-quality single-nucleotide polymorphisms (SNPs) was conducted. Our study utilized an association panel comprising 483 rice genotypes sourced from a northeast core set and a landraces set collected from various regions in India. Forty quantitative trait nucleotides (QTNs) were identified, associated with four grain-related traits: grain length (GL), grain width (GW), grain aroma (Aro), and length–width ratio (LWR). Notably, 16 QTNs were simultaneously identified using two ML-GWAS methods, distributed across multiple chromosomes. Nearly 258 genes were found near the 16 significant QTNs. Gene annotation study revealed that sixty of these genes exhibited elevated expression levels in specific tissues and were implicated in pathways influencing grain quality. Gene ontology (GO), trait ontology (TO), and enrichment analysis pinpointed 60 candidate genes (CGs) enriched in relevant GO terms. Among them, LOC_Os05g06470, LOC_Os06g06080, LOC_Os08g43470, and LOC_Os03g53110 were confirmed as key contributors to GL, GW, Aro, and LWR. Insights from QTNs and CGs illuminate rice trait regulation and genetic connections, offering potential targets for future studies. [ABSTRACT FROM AUTHOR]

Rice blast is a destructive fungal disease affecting rice plants at various growth stages, significantly threatening global yield stability. Development of resistant rice cultivars stands as a practical means of disease control. Generally, association mapping with a diversity panel powerfully identifies new alleles controlling trait of interest. On the other hand, utilization of a breeding panel has its advantage that can be directly applied in a breeding program. In this study, we conducted a genome-wide association study (GWAS) for blast resistance using 296 commercial rice cultivars with low population structure but large phenotypic diversity. We attempt to answer the genetic basis behind rice blast resistance among early maturing cultivars by subdividing the population based on its Heading date 1 (Hd1) functionality. Subpopulation-specific GWAS using the mixed linear model (MLM) based on blast nursery screening conducted in three years revealed a total of 26 significant signals, including three nucleotide-binding site leucine-rich repeat (NBS-LRR) genes (Os06g0286500, Os06g0286700, and Os06g0287500) located at Piz locus on chromosome 6, and one at the Pi-ta locus (Os12g0281300) on chromosome 12. Haplotype analysis revealed blast resistance associated with Piz locus was exclusively specific to Type 14 hd1 among japonica rice. Our findings provide valuable insights for breeding blast resistant rice and highlight the applicability of our elite cultivar panel to detect superior alleles associated with important agronomic traits. [ABSTRACT FROM AUTHOR]

[Objective] The present paper aimed to explore the pathogenicity and dominant physiological groups and physiological races of Magnaporthe oryzae in Guangxi, analyze avirulence genes, find out the composition and distribution of physiological races and avirulence genes, providing reference for resistance breeding and variety promotion. [Method] Pathogenicity of 128 M. oryzae single spore isolates from 4 rice growing regions of southern Guangxi (Guinan), central Guangxi (Guizhong), northern Guangxi (Guibei) and alpine region were deter- mined by artificial spraying inoculation on the 7 unified identification of varieties in China and 26 near-isogenic lines (NILs) that contained only one resistance gene. (Result) Among the 128 rice blast strains, the proportion of strong pathogenic strains was 60.16%. The 128 M. oryzae strains could be divided into 7 groups and 26 physiological races, and the dominant group was ZB with a frequency of 69.53%. Dominant physiological races were ZB13 and ZB,, whose frequencies were 25.00% and 14.84%. Virulence frequency of the tested isolates ranged from 28.12% to 100.00%. Among them, the virulence frequency of the isolates group to resistance genes Pik, Pikm, Pil and Pi9 was lower, with frequencies of 28. 12%, 28.91%, 35.94% and 37.50%, respectively. Avirulence genes corresponding to the tested resistance genes were detected in the collected rice blast fungi, and 15 avirulence genes were detected in the four regions. Avirulence genes Aur-Pia (1), Aur-Pia(2), Aur-Pii, Aur-Pik, Aur-Pib, Aur-Pit, Aur-Pish (2), Aur-Pi3(1), Aur-Pi5 (1), Aur-Pil2(t) and Avr-Pi19(t) occurred at a frequency less than 20.00%. Most of isolates contained 5, 6, 7, 8, 10 avirulence genes with combination frequency of 19.53%, 11.72%, 11.72%, 15.63% and 10. 16% in the tested strains. [Conclusion] Rice blast fungi in Guangxi from 2021 have strong pathogenicity. The dominant physiological group is ZB and dominant physiological races are ZB13 and ZB9. Avirulence genes Aur-Pia (1), Avr-Pia (2), Aur-Pii, Aur-Pik, Aur-Pib, Aur-Pit, Avr-Pish (2), Aur-Pi3 (1), Aur-Pi5(1), Aur-Pil2(t) and Aur-Pil9(t) occurr at low frequency, which suggests that resistance genes corresponding to the avirulence genes should not be suitable for applying rice breeding and variety distribution in Guangxi. [ABSTRACT FROM AUTHOR]

Simple Summary: Although the geographic distribution and production of rice are significantly influenced by temperature fluctuations, rice plants have developed a wide range of physiological, biochemical, and molecular responses to cope with and adapt to temperature stresses, including cold stress resulting from low temperatures. Deciphering cold-responsive genes and the underlying mechanisms may accelerate the development of new cold-resistant rice varieties and ensure stable rice production in adverse temperature conditions. This review aims to provide a straightforward summary of the previous progress in understanding the functions and molecular mechanisms of cold-responsive genes in rice. Rice (Oryza sativa L.) production is highly susceptible to temperature fluctuations, which can significantly reduce plant growth and development at different developmental stages, resulting in a dramatic loss of grain yield. Over the past century, substantial efforts have been undertaken to investigate the physiological, biochemical, and molecular mechanisms of cold stress tolerance in rice. This review aims to provide a comprehensive overview of the recent developments and trends in this field. We summarized the previous advancements and methodologies used for identifying cold-responsive genes and the molecular mechanisms of cold tolerance in rice. Integration of new technologies has significantly improved studies in this era, facilitating the identification of essential genes, QTLs, and molecular modules in rice. These findings have accelerated the molecular breeding of cold-resistant rice varieties. In addition, functional genomics, including the investigation of natural variations in alleles and artificially developed mutants, is emerging as an exciting new approach to investigating cold tolerance. Looking ahead, it is imperative for scientists to evaluate the collective impacts of these novel genes to develop rice cultivars resilient to global climate change. [ABSTRACT FROM AUTHOR]

Genetic variability in rice breeding programs plays a very crucial role. It provides an outstanding pool of superior alleles governing better agronomic and quality characters through association mapping. For a greater understanding of population structure, the genetic relationship among different rice lines is indispensable prior to the setting of a correlation among dynamic alleles and traits. In the present investigation, the genetic diversity and population structure of 116 rice accessions were studied to understand genetic relatedness and diversity among them using 64 polymorphic SSR markers. A genotyping assessment based on SSR markers revealed a total of 225 alleles, with an average PIC value of 0.755. The germplasm lines were classified into three distinct subgroups through population structure analysis, utilizing both model- and distance-based approaches. AMOVA analysis showed that 11% of the total variation could be attributed to differences between groups, while the remaining 89% was likely due to differences within groups. This study suggested that population structure and genetic relatedness should be considered to establish marker–trait associations for association mapping when working with the core collection of germplasm lines. [ABSTRACT FROM AUTHOR]

Hybrid rice needs to prevent lodging due to excessive grain weight during maturity, which can lead to yield loss, grain quality deterioration and difficulty in harvesting. Breeding excellent parents (restorer and male-sterile lines) is the foundation for cultivating lodging-resistant hybrid rice. However, there is still limited information about restorers with improved lodging resistance. To identify a new restorer with significantly enhanced resistance to lodging, the restorer line Huazhan, which has been used for many years in hybrid rice breeding in China, was used as the control, to evaluate the lodging resistance of the new restorer R382. A two-year field experiment was executed to investigate the difference on lodging-related traits of the basal two internodes above-ground, such as out diameters of stems with or without leaf sheath (DWS, DWOS), culm thickness (CT), the section modulus (SM), bending stress (BS), and bending moment at break (M). The results indicated that DWS, CT, BS, M of R382 was at least 19.9%, 13.3%, 36.5% and 52.6% higher than that of Huazhan. However, the negative indicator lodging index of R382 was over 17.5% lower. The number and area of vascular bundles, and the contents of the chemical components of the cell wall including cellulose, lignin, and hemicellulose, together with the accumulation of starch granules, were significantly greater in R382. Furthermore, in the basal stems during the jointing stage, a series of genes that promote cell wall formation exhibited significantly higher expression levels in R382. Meanwhile, there was no significant difference in the yield of R382 and Huazhan. Thus, this new restorer could be a valuable donor in the future hybrid rice breeding programs for improving lodging resistance. [ABSTRACT FROM AUTHOR]

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

Summary: The exploitation of heterosis to integrate parental advantages is one of the fastest and most efficient ways of rice breeding. The genomic architecture of heterosis suggests that the grain yield is strongly correlated with the accumulation of numerous rare superior alleles with positive dominance. However, the improvements in yield of hybrid rice have shown a slowdown or even plateaued due to the limited availability of complementary superior alleles. In this study, we achieved a considerable increase in grain yield of restorer lines by inducing an alternative splicing event in a heterosis gene OsMADS1 through CRISPR‐Cas9, which accounted for approximately 34.1%–47.5% of yield advantage over their corresponding inbred rice cultivars. To achieve a higher yield in hybrid rice, we crossed the gene‐edited restorer parents harbouring OsMADS1GW3p6 with the sterile lines to develop new rice hybrids. In two‐line hybrid rice Guang‐liang‐you 676 (GLY676), the yield of modified hybrids carrying the homozygous heterosis gene OsMADS1GW3p6 significantly exceeded that of the original hybrids with heterozygous OsMADS1. Similarly, the gene‐modified F1 hybrids with heterozygous OsMADS1GW3p6 increased grain yield by over 3.4% compared to the three‐line hybrid rice Quan‐you‐si‐miao (QYSM) with the homozygous genotype of OsMADS1. Our study highlighted the great potential in increasing the grain yield of hybrid rice by pyramiding a single heterosis gene via CRISPR‐Cas9. Furthermore, these results demonstrated that the incomplete dominance of heterosis genes played a major role in yield‐related heterosis and provided a promising strategy for breeding higher‐yielding rice varieties above what is currently achievable. [ABSTRACT FROM AUTHOR]

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

Knowledge of interspecific and spatiotemporal variation in demography–environment relationships is key for understanding the population dynamics of sympatric species and developing multispecies conservation strategies. We used hierarchical random‐effects models to examine interspecific and spatial variation in annual productivity in six migratory ducks (i.e., American wigeon [Mareca americana], blue‐winged teal [Spatula discors], gadwall [Mareca strepera], green‐winged teal [Anas crecca], mallard [Anas platyrhynchos] and northern pintail [Anas acuta]) across six distinct ecostrata in the Prairie Pothole Region of North America. We tested whether breeding habitat conditions (seasonal pond counts, agricultural intensification, and grassland acreage) or cross‐seasonal effects (indexed by flooded rice acreage in primary wintering areas) better explained variation in the proportion of juveniles captured during late summer banding. The proportion of juveniles (i.e., productivity) was highly variable within species and ecostrata throughout 1961–2019 and generally declined through time in blue‐winged teal, gadwall, mallard, pintail, and wigeon, but there was no support for a trend in green‐winged teal. Productivity in Canadian ecostrata declined with increasing agricultural intensification and increased with increasing pond counts. We also found a strong cross‐seasonal effect, whereby more flooded rice hectares during winter resulted in higher subsequent productivity. Our results suggest highly consistent environmental and anthropogenic effects on waterfowl productivity across species and space. Our study advances our understanding of current year and cross‐seasonal effects on duck productivity across a suite of species and at finer spatial scales, which could help managers better target working‐lands conservation programs on both breeding and wintering areas. We encourage other researchers to evaluate environmental drivers of population dynamics among species in a single modeling framework for a deeper understanding of whether conservation plans should be generalized or customized given limited financial resources. [ABSTRACT FROM AUTHOR]

Rice production is severely threatened by drought stress. To develop drought-tolerant varieties, the selection of donors for the breeding programme is crucial. Twenty-one rice genotypes were evaluated at the vegetative and reproductive stages under drought. Higher relative water content (> 65%) and leaf water potential (> − 3.50 MPa) in Danteshwari, Mahamaya, Samleshwari, Poornima, IBD-1, Safri 17, Sahabhagidhan, Vandana and N22 explained their drought tolerance with higher biomass production, lower drought score and early stress recovery rate of 1 and 3 under vegetative stage drought. At the reproductive stage drought, higher grain yield and less relative yield reduction was found in Mahamaya (2.42 t/ha, 46.37%), Samleshwari (2.05 t/ha, 42.88%), Poornima (1.86 t/ha, 42.67%), Sahabhagidhan (2 t/ha, 57.72%) and Danteshwari (2 t/ha, 39.11%), showed higher tolerance due to greater leaf water potential and biomass with a lower reduction in grain filling percentage due to more remobilization of assimilates to the grains. Though, N22 and Anjali flowered 5–7 days earlier in drought stress compared to well-watered condition, partially responsible for increased grain filling under drought. Therefore, visual selection for a large sink size under favorable conditions and higher biomass accumulation under vegetative drought stress with greater fertility under reproduction stage is favorable for maintaining higher grain yield in rice. Further, higher expression of OsAP37, EDT1, OsLEA3-1, OsDIL, OsDRAP1, OsNAC14, OsNAR2.1, OsWRKY30 and OsRab7 in Mahamaya, Samleshwari, Poornima, Sahabhagidhan, and Danteshwari supported the higher grain yield under drought stress. [ABSTRACT FROM AUTHOR]

Rice black-streaked dwarf disease (RBSDD) is one of the most serious crop diseases in Asia, causing serious damage to rice production. Therefore, reducing the harmful effects of RBSDD is vital to the food security of China and other Asian countries. In this study, 248 rice varieties from different countries were screened for resistance to RBSDD, and 19 varieties with high resistance to RBSDD were found. Among them, H185, an indica variety, showed stable and high resistance to RBSDD. Using an F2:3 population of H185 and Wuyujing 3 (WYJ3, a highly susceptible japonica rice variety), three QTL conferring resistance to RBSDD, namely qRBSDD2, qRBSDD7, and qRBSDD11 were identified, and they explained 53.6% of the total phenotypic variation. Among them, qRBSDD2 and qRBSDD7, with LOD scores of 4.26 and 4.25, respectively, were repeatedly detected in artificial inoculation conditions, accounting for 28.0% and 29.8% of the total phenotypic variation, respectively. Resistant alleles of the two QTL were all derived from H185, and several BC5F2 lines possessing single or two QTL of qRBSDD2 and qRBSDD7 exhibited higher resistance for RBSDD. The QTL detected in our study open new possibilities for breeding rice cultivars with RBSDD resistance through resistance gene pyramiding. [ABSTRACT FROM AUTHOR]

Rice (Oryza sativa L.) yield, quality and resistance to various biotic and abiotic stresses are the major barriers of rice production worldwide. Bacterial blight (BB), caused by Xanthomonas oryzae pv. oryzae, is a major cause of reduced yield in rice. In the present study, a set of 43 advance breeding lines along with 6 check varieties was evaluated for yield attributes, milling quality traits and BB resistance. The results indicated a significant variation for various morpho-physiological and milling traits. Disease screening was carried out in field at maximum tillering stage under artificial inoculation conditions. Based on pathogenicity test, 36 genotypes showed resistance to all the ten BB pathotypes prevalent in northern India (Punjab). Further, these lines were characterized for known BB resistance gene(s); Xa4, xa5, xa13 and Xa21 using linked molecular markers and molecular analysis showed a wide range of gene combinations and indicated the presence of single (6), two (23), and three (13) gene combinations while one line (PAU 5285-23-1-2) showed none of the known gene tested. The genotypes PAU 7261-19-1, PAU 6998-110-3-1, PAU 6516-11-1-2-1-1, PAU 6554-1-1-1-2-3, PAU 6970-18-1-3, PAU 6707-33-6-1-1-1-3 had significantly and consistently high yield with early maturity, semi dwarf, good tillering along with desirable quality traits. Moreover, these are resistant to all ten pathotypes of BB presently prevalent in the Punjab state. Therefore, it is recommended that these can be utilized further to identify and develop improved varieties with high yield, early to mid-maturity, desirable milling quality and BB resistance. [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]

A diverse set of 275 rice germplasm lines including 159 lines from global rice diversity panel, 10 Oryza glaberrima Steud accessions; 22 basmati and non-basmati varieties, 67 aromatic germplasm lines and 17 advanced breeding lines were screened along with susceptible and resistant checks for foot rot disease caused by Fusarium moniliforme Sheldon through artificial inoculation. The screening was conducted in trays under less humid condition (50% RH) in April 2019 (referred as E1) and in the field under high humid condition (72% RH) in July 2019 (referred as E2). The susceptible plants showed stunting in E1 and elongation in E2. Based on screening in E1 and E2, thirty-three lines including eighteen of global rice diversity panel, five of O. glabberrima, two aromatic and ten released varieties showed complete resistance to foot rot. Multi-locus GWAS using 159 lines of global rice diversity panel identified 11 QTLs on seven different chromosomes. In the 11 QTL regions, 40 putative genes were identified based on stringent filtering and relevance to the disease. The QTL present on chromosome 1 (qbk1) that co-localized with many studies is proposed for further studies. In addition, the expression analysis of GA-related genes, viz. OsXTH8, OsGAE1, EUI, G-alpha-(D1), GID1, GID2 and SLR1, showed no association with foot rot resistance/susceptibility. However, 24 DAS was identified as the most important stage for expression analysis. The highly resistant lines are suggested to use in the rice breeding program particularly basmati rice. Besides, the genomic region flanking the associated SNPs and the candidate genes within them could be studied further to identify underlying genes and markers associated with foot rot resistance. [ABSTRACT FROM AUTHOR]