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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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

One strategy currently being developed to increase rice (Oryza sativa L.) productivity is using a multi-canopy cropping system in rice cultivation. This method involves planting tall and short rice genotypes in the same hill. The objective of this experiment was to estimate the genetic parameters and response to selection in multi-canopy rice. Each experiment was arranged in an augmented randomized complete block design with five replications for the checks. In the first planting season, 200 F3 families from IPB196 and IPB197 populations were planted in monoculture and multi-canopy as the short genotypes. IPB187-F-40-1-1 was used in multi-canopy as the tall genotype. Selection of 25% based on grain weight per hill of short genotype in multi-canopy was performed, and 50 families were selected and their F4 seeds were planted in the second season along with the same tall genotype. The results indicated the genotype × cropping system was significant for grain weight per hill in the F3 and F4 generations. Grain weight per hill has a similar realized h² ns in the multi-canopy (0.58) with monoculture (0.54). Meanwhile, the response to selection in multi-canopy (3.60) was higher compared to monoculture (2.09), and therefore the selection of rice lines for a multi-canopy system should be conducted in the multicanopy environment. A selection percentage of 5% resulted in a higher response to selection. These findings may provide insight into the acceleration of breeding rice varieties for the multi-canopy system. [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: 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]

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]

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]

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]

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]

The article in the Plant Biotechnology Journal discusses the CRISPR/Cas9-mediated editing of the OsFd1 gene in rice to enhance broad-spectrum resistance without affecting growth and yield. The study identifies specific mutations, OsFd1D3bp and OsFd1D15bp, that confer resistance to pathogens without growth penalties. The research highlights the potential of utilizing OsFd1 gene editing in rice disease resistance breeding to balance growth and defense effectively. [Extracted from the article]

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]

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]

Summary: Root architecture and function are critical for plants to secure water and nutrient supply from the soil, but environmental stresses alter root development. The phytohormone jasmonic acid (JA) regulates plant growth and responses to wounding and other stresses, but its role in root development for adaptation to environmental challenges had not been well investigated. We discovered a novel JA Upregulated Protein 1 gene (JAUP1) that has recently evolved in rice and is specific to modern rice accessions. JAUP1 regulates a self‐perpetuating feed‐forward loop to activate the expression of genes involved in JA biosynthesis and signalling that confers tolerance to abiotic stresses and regulates auxin‐dependent root development. Ectopic expression of JAUP1 alleviates abscisic acid‐ and salt‐mediated suppression of lateral root (LR) growth. JAUP1 is primarily expressed in the root cap and epidermal cells (EPCs) that protect the meristematic stem cells and emerging LRs. Wound‐activated JA/JAUP1 signalling promotes crosstalk between the root cap of LR and parental root EPCs, as well as induces cell wall remodelling in EPCs overlaying the emerging LR, thereby facilitating LR emergence even under ABA‐suppressive conditions. Elevated expression of JAUP1 in transgenic rice or natural rice accessions enhances abiotic stress tolerance and reduces grain yield loss under a limited water supply. We reveal a hitherto unappreciated role for wound‐induced JA in LR development under abiotic stress and suggest that JAUP1 can be used in biotechnology and as a molecular marker for breeding rice adapted to extreme environmental challenges and for the conservation of water resources. [ABSTRACT FROM AUTHOR]

Summary: To increase rice yields and feed billions of people, it is essential to enhance genetic gains. However, the development of new varieties is hindered by longer generation times and seasonal constraints. To address these limitations, a speed breeding facility has been established and a robust speed breeding protocol, SpeedFlower is developed that allows growing 4–5 generations of indica and/or japonica rice in a year. Our findings reveal that a high red‐to‐blue (2R > 1B) spectrum ratio, followed by green, yellow and far‐red (FR) light, along with a 24‐h long day (LD) photoperiod for the initial 15 days of the vegetative phase, facilitated early flowering. This is further enhanced by 10‐h short day (SD) photoperiod in the later stage and day and night temperatures of 32/30 °C, along with 65% humidity facilitated early flowering ranging from 52 to 60 days at high light intensity (800 μmol m−2 s−1). Additionally, the use of prematurely harvested seeds and gibberellic acid treatment reduced the maturity duration by 50%. Further, SpeedFlower was validated on a diverse subset of 198 rice accessions from 3K RGP panel encompassing all 12 distinct groups of Oryza sativa L. classes. Our results confirmed that using SpeedFlower one generation can be achieved within 58–71 days resulting in 5.1–6.3 generations per year across the 12 sub‐groups. This breakthrough enables us to enhance genetic gain, which could feed half of the world's population dependent on rice. We've developed a robust SpeedFlower protocol for rapid rice breeding, enabling 4–5 generations of indica and/or japonica rice annually. The SpeedFlower protocol was validated on 198 diverse rice accessions, representing all 12 sub‐groups of Oryza sativa L. With a timeframe of 58–71 days per generation, we achieved 5.1–6.3 generations per year. Therefore, SpeedFlower has shown a transformative potential in enhancing genetic gain with the pace of climate change. [ABSTRACT FROM AUTHOR]

Geographic and seasonal effects are important in driving selection decisions in rice breeding research. Adopting new strategies for characterizing environmental–phenotype associations is critical to understanding these effects, and the outcomes of their study could reflect the benefits of developing locally adapted cultivars. This study aimed to characterize Brazil's tropical irrigated rice (IR) environment, Latin America's largest rice production system. We integrated unsupervised (K‐means clustering) and supervised (decision tree classifier) algorithms to identify environmental clusters (EC) based on historical yield data. The data set included 31 locations and 471 genotypes from 1982 to 2017. We used environmental features (EF), such as weather and geography, as input variables for our analysis, assuming the model as EC ∼ f (EF). Results indicate that the tropical IR production region can be divided into four primary breeding zones, with temperature emerging as a significant factor in the study area. After employing a linear mixed model analysis, we observed that the current relationship between genetics (G), environmental variation (E), and their interaction (G×E) in Brazil's tropical IR has a 1:6:2 ratio. However, when introducing our data‐driven model based on EC, we reduced this ratio to 1:5:1. Therefore, the selection for local adaptability across a large region became more reliable. Our approach successfully identified EC in Brazil's tropical production region of IR, providing valuable insights for defining breeding zones and identifying more productive and stable seed production fields. Core Ideas: Machine learning links phenotypic and environmental features to cluster trialing locations for rice breeding.This approach also revealed the climatic causes of environmental quality for a group of genotypes or cultivars.As an alternative approach to reducing costs, the strategy benefits many stages of breeding and postbreeding.This approach facilitates postbreeding (cultivar recommendations and optimization of seed production sites). [ABSTRACT FROM AUTHOR]

Salt stress is one of the major factors that limits rice production. Therefore, identification of salt-tolerant alleles from wild rice is important for rice breeding. In this study, we constructed a set of chromosome segment substitution lines (CSSLs) using wild rice as the donor parent and cultivated rice Nipponbare (Nip) as the recurrent parent. Salt tolerance germinability (STG) was evaluated, and its association with genotypes was determined using this CSSL population. We identified 17 QTLs related to STG. By integrating the transcriptome and genome data, four candidate genes were identified, including the previously reported AGO2 and WRKY53. Compared with Nip, wild rice AGO2 has a structure variation in its promoter region and the expression levels were upregulated under salt treatments; wild rice WRKY53 also has natural variation in its promoter region, and the expression levels were downregulated under salt treatments. Wild rice AGO2 and WRKY53 alleles have combined effects for improving salt tolerance at the germination stage. One CSSL line, CSSL118 that harbors these two alleles was selected. Compared with the background parent Nip, CSSL118 showed comprehensive salt tolerance and higher yield, with improved transcript levels of reactive oxygen species scavenging genes. Our results provided promising genes and germplasm resources for future rice salt tolerance breeding. [ABSTRACT FROM AUTHOR]

Summary: Upland rice is a distinctive drought‐aerobic ecotype of cultivated rice highly resistant to drought stress. However, the genetic and genomic basis for the drought‐aerobic adaptation of upland rice remains largely unclear due to the lack of genomic resources. In this study, we identified 25 typical upland rice accessions and assembled a high‐quality genome of one of the typical upland rice varieties, IRAT109, comprising 384 Mb with a contig N50 of 19.6 Mb. Phylogenetic analysis revealed upland and lowland rice have distinct ecotype differentiation within the japonica subgroup. Comparative genomic analyses revealed that adaptive differentiation of lowland and upland rice is likely attributable to the natural variation of many genes in promoter regions, formation of specific genes in upland rice, and expansion of gene families. We revealed differentiated gene expression patterns in the leaves and roots of the two ecotypes and found that lignin synthesis mediated by the phenylpropane pathway plays an important role in the adaptive differentiation of upland and lowland rice. We identified 28 selective sweeps that occurred during domestication and validated that the qRT9 gene in selective regions can positively regulate drought resistance in rice. Eighty key genes closely associated with drought resistance were appraised for their appreciable potential in drought resistance breeding. Our study enhances the understanding of the adaptation of upland rice and provides a genome navigation map of drought resistance breeding, which will facilitate the breeding of drought‐resistant rice and the "blue revolution" in agriculture. [ABSTRACT FROM AUTHOR]

Ecological divergence due to habitat difference plays a prominent role in the formation of new species, but the genetic architecture during ecological speciation and the mechanism underlying phenotypic divergence remain less understood. Two wild ancestors of rice (Oryza rufipogon and Oryza nivara) are a progenitor‐derivative species pair with ecological divergence and provide a unique system for studying ecological adaptation/speciation. Here, we constructed a high‐resolution linkage map and conducted a quantitative trait locus (QTL) analysis of 19 phenotypic traits using an F2 population generated from a cross between the two Oryza species. We identified 113 QTLs associated with interspecific divergence of 16 quantitative traits, with effect sizes ranging from 1.61% to 34.1% in terms of the percentage of variation explained (PVE). The distribution of effect sizes of QTLs followed a negative exponential, suggesting that a few genes of large effect and many genes of small effect were responsible for the phenotypic divergence. We observed 18 clusters of QTLs (QTL hotspots) on 11 chromosomes, significantly more than that expected by chance, demonstrating the importance of coinheritance of loci/genes in ecological adaptation/speciation. Analysis of effect direction and v‐test statistics revealed that interspecific differentiation of most traits was driven by divergent natural selection, supporting the argument that ecological adaptation/speciation would proceed rapidly under coordinated selection on multiple traits. Our findings provide new insights into the understanding of genetic architecture of ecological adaptation and speciation in plants and help effective manipulation of specific genes or gene cluster in rice breeding. [ABSTRACT FROM AUTHOR]

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

BACKGROUND: Rice taste is closely associated with endosperm composition, which varies among different rice layers. Although clarifying the relationship between this difference and nutritional taste can guide rice breeding and cultivation practices, research on this topic is limited. RESULTS: Here, typical rice varieties having excellent and poor taste characteristics were selected to analyze the distribution characteristics and differences of their components. The varieties with excellent taste exhibited lower apparent amylose content (AAC) and protein content (PC), lesser short‐chain (Fa) and long‐chain (Fb3) amylopectin (AP) and more medium‐chain (Fb1+2) AP, higher long‐to‐short chain ratio (Fa:Fb3), and higher nitrogen (N), magnesium (Mg) and calcium (Ca) content in layer 1 (L1) than the varieties with poor taste. Layer 2 (L2) played a key role in AAC and PC regulation in the varieties with excellent taste by reducing AAC and appropriately increasing PC, consequently improving rice taste. AP structure in layer 3 (L3) substantially affected the taste of the two types of varieties. The mineral content was the highest in L1, and increased potassium (K), Ca, and Mg content improved taste in all varieties. CONCLUSION: AAC in each layer contributes to rice taste. PC and minerals primarily act on L1 and L2, whereas AP acts on L2 and L3. Therefore, the endosperm formation process should be exploited for improving rice taste. Furthermore, key resources and cultivation should be identified and regulated, respectively, to improve rice taste. © 2023 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

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

Summary: Seed germination is a critical trait for the success of direct seeding in rice cultivation. However, the underlying mechanism determining seed germination is largely unknown in rice.Here, we report that NAC transcription factor OsNAC3 positively regulates seed germination of rice. OsNAC3 regulates seed germination involving abscisic acid (ABA) pathway and cell elongation. OsNAC3 can directly bind to the promoter of ABA catabolic gene OsABA8ox1 and cell expansion gene OsEXP4, which consequently activates their expressions during seed germination.We also find that the expression of OsEXP4 is reduced by ABA during seed germination in rice. OsNAC3 regulates seed germination by influencing cell elongation of the embryo through directly affecting OsEXP4 expression and indirectly ABA‐medicated OsEXP4 expression. The OsNAC3 elite haplotype is useful for genetic improvement of seed germination, and overexpression of OsNAC3 can significantly increase seed germination.We therefore propose that OsNAC3 is a potential target in breeding of rice varieties with high seed germination for direct seeding cultivation. [ABSTRACT FROM AUTHOR]

Summary: COLD is a major naturally occurring stress that usually causes complex symptoms and severe yield loss in crops. R‐loops function in various cellular processes, including development and stress responses, in plants. However, how R‐loops function in COLD responses is largely unknown in COLD susceptible crops like rice (Oryza sativa L.).We conducted DRIP‐Seq along with other omics data (RNA‐Seq, DNase‐Seq and ChIP‐Seq) in rice with or without COLD treatment.COLD treatment caused R‐loop reprogramming across the genome. COLD‐biased R‐loops had higher GC content and novel motifs for the binding of distinct transcription factors (TFs). Moreover, R‐loops can directly/indirectly modulate the transcription of a subset of COLD‐responsive genes, which can be mediated by R‐loop overlapping TF‐centered or cis‐regulatory element‐related regulatory networks and lncRNAs, accounting for c. 60% of COLD‐induced expression of differential genes in rice, which is different from the findings in Arabidopsis. We validated two R‐loop loci with contrasting (negative/positive) roles in the regulation of two individual COLD‐responsive gene expression, as potential targets for enhanced COLD resistance.Our study provides detailed evidence showing functions of R‐loop reprogramming during COLD responses and provides some potential R‐loop loci for genetic and epigenetic manipulation toward breeding of rice varieties with enhanced COLD tolerance. [ABSTRACT FROM AUTHOR]

Sheath rot is a widespread rice disease that affects rice crops worldwide. It is particularly prevalent in Ethiopia, with the Fogera plains exhibiting the highest incidence and severity. However, the lack of reliable molecular‐level identification of rice fungal pathogens in Ethiopia has hindered the development of effective management practices. This study aimed to assess the diversity of fungal agents causing sheath rot disease in rice crops around the Fogera plains, Ethiopia, using both morphology and nucleotide sequences of the ITS1 rDNA region. Additionally, the pathogenicity of the isolates was evaluated using attached tiller assay methods. A total of 16 fungal isolates were recovered from diseased plant samples. Among these, five species; Phoma spp., Phoma herbarium, Epicoccum sorghinum, Epicoccum lantuscollum and Microdochium seminicola were identified and reported as new records of sheath rot disease in rice. The predominant genus was Phoma (75%) followed by Epicoccum (18.75%). The pathogenicity caused by E. sorghinum was particularly severe and significantly different from the symptoms caused by other isolates, resulting in a mean lesion length of 167.7 mm and a disease severity of 55.7%. These findings suggest that E. sorghinum is the most important rice pathogen in the region. Our results have identified the most predominant and pathogenic fungal species associated with sheath rot disease in the region. Importantly, this study marks the first report of sheath rot‐causing fungi identified in rice using the ITS rDNA‐sequencing technique in Ethiopia. Therefore, this research may contribute to the development of fungal disease management strategies in rice and provide evidence to initiate a rice breeding program focused on developing sheath‐rot‐resistant rice varieties. [ABSTRACT FROM AUTHOR]

This article, published in the Journal of Integrative Plant Biology, discusses the molecular bases for the three-line hybrid rice breeding system. The authors focus on the fertility restoration gene Rf4 and its impact on the Wild Abortive (WA) cytoplasmic male sterility type three-line system. They identify a two-copy haplotype of Rf4 (H1) as the most valuable for future hybrid rice breeding. The study provides insights into the evolutionary trajectory of Rf genes and the origin of cytoplasmic male sterility and fertility restoration systems in rice breeding. The findings contribute to our understanding of the CMS/Rf system and offer guidance for the molecular design breeding of three-line hybrid rice. [Extracted from the article]

Summary: Starch accounts for up to 90% of the dry weight of rice endosperm and is a key determinant of grain quality. Although starch biosynthesis enzymes have been comprehensively studied, transcriptional regulation of starch‐synthesis enzyme‐coding genes (SECGs) is largely unknown. In this study, we explored the role of a NAC transcription factor, OsNAC24, in regulating starch biosynthesis in rice. OsNAC24 is highly expressed in developing endosperm. The endosperm of osnac24 mutants is normal in appearance as is starch granule morphology, while total starch content, amylose content, chain length distribution of amylopectin and the physicochemical properties of the starch are changed. In addition, the expression of several SECGs was altered in osnac24 mutant plants. OsNAC24 is a transcriptional activator that targets the promoters of six SECGs; OsGBSSI, OsSBEI, OsAGPS2, OsSSI, OsSSIIIa and OsSSIVb. Since both the mRNA and protein abundances of OsGBSSI and OsSBEI were decreased in the mutants, OsNAC24 functions to regulate starch synthesis mainly through OsGBSSI and OsSBEI. Furthermore, OsNAC24 binds to the newly identified motifs TTGACAA, AGAAGA and ACAAGA as well as the core NAC‐binding motif CACG. Another NAC family member, OsNAP, interacts with OsNAC24 and coactivates target gene expression. Loss‐of‐function of OsNAP led to altered expression in all tested SECGs and reduced the starch content. These results demonstrate that the OsNAC24‐OsNAP complex plays key roles in fine‐tuning starch synthesis in rice endosperm and further suggest that manipulating the OsNAC24‐OsNAP complex regulatory network could be a potential strategy for breeding rice cultivars with improved cooking and eating quality. [ABSTRACT FROM AUTHOR]

BACKGROUND: To gain a better understanding of how Pyricularia oryzae population shifts is important for selecting suitable resistance genes for rice breeding programs. However, the relationships between P. oryzae pathogenic dynamics, geographic distribution, rice varieties, and timeline are not well studied. RESULTS: Resistance genes Piz‐5, Pi9(t), Pi12(t), Pi20(t), Pita‐2, and Pi11 showed stable resistance to the Taiwan rice blast fungus over 8 years of observations. Furthermore, 1749 rice blast isolates were collected from 2014 to 2021 and categorized into five pathotype clusters based on their correlation analysis between the geographic sources and virulence of Lijiangxintuanheigu monogenic lines. A detailed map of their distributions in Taiwan is presented. Isolates collected from the western region of Taiwan had greater pathotype diversity than those from the east region. Isolates collected from the subtropical region had greater diversity than those from the tropical region. Rice cultivars carrying Pik alleles were highly susceptible to pathotype L4. Cultivars with Piz‐t were highly susceptible to pathotype L5, and those with Pish were highly susceptible to pathotype L1. The geographical distribution of each pathotype was distinct, and the population size of each pathotype fluctuated significantly each year. CONCLUSION: The regional mega cultivars significantly impact the evolution of Pyricularia oryzae in Taiwan within the span of 8 years. However, the annual fluctuation of pathotype populations likely correlate to the rising annual temperatures that selected pathotype clusters by their optimal growth temperature. The results will provide useful information for effective disease management, and enable the R‐genes to prolong their function in the fields. © 2023 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

Exploiting novel endogenous glyphosate‐tolerant alleles is highly desirable and has promising potential for weed control in rice breeding. Here, through fusions of different effective cytosine and adenine deaminases with nCas9‐NG, we engineered an effective surrogate two‐component composite base editing system, STCBE‐2, with improved C‐to‐T and A‐to‐G base editing efficiency and expanded the editing window. Furthermore, we targeted a rice endogenous OsEPSPS gene for artificial evolution through STCBE‐2‐mediated near‐saturated mutagenesis. After hygromycin and glyphosate selection, we identified a novel OsEPSPS allele with an Asp‐213‐Asn (D213N) mutation (OsEPSPS‐D213N) in the predicted glyphosate‐binding domain, which conferred rice plants reliable glyphosate tolerance and had not been reported or applied in rice breeding. Collectively, we developed a novel dual base editor which will be valuable for artificial evolution of important genes in crops. And the novel glyphosate‐tolerant rice germplasm generated in this study will benefit weeds management in rice paddy fields. [ABSTRACT FROM AUTHOR]

SUMMARY: Grain size is a key factor in determining rice (Oryza sativa) yield, and exploring new pathways to regulate grain size has immense potential to improve yield. In this study, we report that OsCBL5 encodes a calcineurin B subunit protein that significantly promotes grain size and weight. oscbl5 plants produced obviously smaller and lighter seeds. We further revealed that OsCBL5 promotes grain size by affecting cell expansion in the spikelet hull. Biochemical analyses demonstrated that CBL5 interacts with CIPK1 and PP23. Furthermore, double and triple mutations were induced using CRISPR/Cas9 (cr) to analyze the genetic relationship. It was found that the cr‐cbl5/cipk1 phenotype was similar to that of cr‐cipk1 and that the cr‐cbl5/pp23, cr‐cipk1/pp23, and cr‐cbl5/cipk1/pp23 phenotype was similar to that of cr‐pp23, indicating that OsCBL5, CIPK1, and PP23 act as a molecular module influencing seed size. In addition, the results show that both CBL5 and CIPK1 are involved in the gibberellic acid (GA) pathway and significantly affect the accumulation of endogenous active GA4. PP23 participates in GA signal transduction. In brief, this study identified a new module that affects rice grain size, OsCBL5–CIPK1–PP23, which could potentially be targeted to improve rice yield. Significance Statement: The discovery of the OsCBL5–CIPK1–PP23 module and its role in rice (Oryza sativa) yield represents a significant breakthrough not only in reproductive biology but also in the agricultural field for rice breeding. [ABSTRACT FROM AUTHOR]

Water‐saving attempts for rice cultivation often reduce yields. Maintaining productivity under drought is possible when rice genotypes are bred with improved metabolism and spikelet fertility. Although attempts have been made to introgress water mining and water use efficiency traits, combining acquired tolerance traits (ATTs), that is, specific traits induced or upregulated to better tolerate severe stress, appears equally important. In our study, we screened 90 rice germplasm accessions that represented the molecular and phenotypic variations of 851 lines of the 3 K rice panel. Utilising phenomics, we identified markers linked to ATTs through association analysis of over 0.2 million SNPs derived from whole‐genome sequences. Propensity to respond to 'induction' stress varied significantly among genotypes, reflecting differences in cellular protection against oxidative stress. Among the ATTs, the hydroxyl radical and proline contents exhibited the highest variability. Furthermore, these significant variations in ATTs were strongly correlated with spikelet fertility. The 43 significant markers associated with ATTs were further validated using a different subset of contrasting genotypes. Gene expression studies and metabolomic profiling of two well‐known contrasting genotypes, APO (tolerant) and IR64 (sensitive), identified two ATT genes: AdoMetDC and Di19. Our study highlights the relevance of polyamine biosynthesis in modulating ATTs in rice. Genotypes with superior ATTs and the associated markers can be effectively employed in breeding rice varieties with sustained spikelet fertility and grain yield under drought. [ABSTRACT FROM AUTHOR]

Drought is becoming a major threat to rice farming across the globe owing to the depletion of water tables in rice‐growing belts. Drought affects rice plants at multiple stages, causing damage at morphological and physio‐biochemical levels, leading to severe losses that exceed losses from all other stresses. The amalgamation of conventional breeding methods with modern molecular biology tools and biometrical methods could help accelerate the genetic gain for drought tolerance in rice. Many drought‐tolerance traits with genetic determinants have been identified and exploited for tolerance rice variety breeding. The integration of genome‐wide association study and genomic selection tools with speed breeding shortened the breeding cycle and aided in rapid improvement of genetic gain. In this review, we emphasized the progress made through classical breeding as well as the limitations and usefulness of current genomic methods in improving drought tolerance. We briefly addressed methods for identifying genetic determinants for drought tolerance and deploying them through genomics‐assisted breeding programmes to develop high‐yielding drought‐tolerant rice cultivars. [ABSTRACT FROM AUTHOR]