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In order to give wide-ranging and long-lasting disease resistance that reduces rice output, breeding techniques are used such as the importance of selection assisted by markers and gene pyramiding. Bacterial leaf blight (BLB), which is carried on by the pathogen Xanthomonas oryzae pv. oryzae, is one such disease that significantly reduces rice yield. Numerous molecular marker techniques have already been developed because molecular markers are crucial for both marker-assisted selection and gene pyramiding. Currently, DNA-based markers, sometimes referred to as molecular markers, are the most frequently employed ones. Based on the methods used to find them, the molecular markers are divided into two main types. These markers are based on hybridization and polymerase chain reaction. The morphological (traditionally based) and biochemical (enzyme-based) markers are two more types of markers that are available. The best method for preventing rice BLB disease is host plant/varietal resistance. Gene pyramiding with the help of markers offers the potential to speed up breeding operations and ensure that the host plant's acquired resistance will last. This research explores the use, economic significance, constraints, and potential of marker-assisted selection and gene pyramiding for rice BLB disease resistance. [ABSTRACT FROM AUTHOR]

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

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

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

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

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

Previous studies have modified rice's resistant starch (RS) content by mutating single and double genes. These mutations include knocking out or reducing the expression of sbe1 or sbe2b genes, as well as overexpressing Wxa. However, the impact of triple mutant sbe2b/sbe1/OE-Wxa on RS contents remained unknown. Here, we constructed a double mutant with sbe2b/RNAi-sbe1, based on IR36ae with sbe2b, and a triple mutant with sbe2b/RNAi-sbe1/OE-Wxa, based on the double mutant. The results showed that the amylose and RS contents gradually increased with an increase in the number of mutated genes. The triple mutant exhibited the highest amylose and RS contents, with 41.92% and 4.63%, respectively, which were 2- and 5-fold higher than those of the wild type, which had 22.19% and 0.86%, respectively. All three mutants altered chain length and starch composition compared to the wild type. However, there was minimal difference observed among the mutants. The Wxa gene contributed to the improvement of 1000-grain weight and seed-setting rate, in addition to the highest amylose and RS contents. Thus, our study offers valuable insight for breeding rice cultivars with a higher RS content and yields. [ABSTRACT FROM AUTHOR]

Tandem repeats (TRs) are genomic regions that tandemly change in repeat number, which are often multiallelic. Their characteristics and contributions to gene expression and quantitative traits in rice are largely unknown. Here, we survey rice TR variations based on 231 genome assemblies and the rice pan-genome graph. We identify 227,391 multiallelic TR loci, including 54,416 TR variations that are absent from the Nipponbare reference genome. Only 1/3 TR variations show strong linkage with nearby bi-allelic variants (SNPs, Indels and PAVs). Using 193 panicle and 202 leaf transcriptomic data, we reveal 485 and 511 TRs act as QTLs independently of other bi-allelic variations to nearby gene expression, respectively. Using plant height and grain width as examples, we identify and validate TRs contributions to rice agronomic trait variations. These findings would enhance our understanding of the functions of multiallelic variants and facilitate rice molecular breeding. Tandem repeats (TRs) have unique ability to drive a range of phenotype variations. Here, the authors survey rice TR variations based on 231 genome assemblies and the rice pan-genome graph, identify TR variations associated with expressed genes, and reveal expression TRs contributed to rice agronomic trait variations. [ABSTRACT FROM AUTHOR]

In the past decade, the exploration of genetic resources in rice has significantly enhanced the efficacy of rice breeding. However, the exploration of genetic resources is hindered by the identification of candidate genes. To expedite the identification of candidate genes, this study examined tapetum programmed cell death-related genes OsiWAK1, OsPDT1, EAT1, TDR, and TIP2 to assess the efficacy of the Dual-Luciferase (Dual-LUC) assay in rapidly determining gene relationships. The study found that, in the Dual-LUC assay, OsiWAK1 and its various recombinant proteins exhibit comparable activation abilities on the EAT1 promoter, potentially indicating a false positive. However, the Dual-LUC assay can reveal that OsiWAK1 impacts both the function of its upstream regulatory factor OsPDT1 and the TDR/TIP2 transcription complex. By rapidly studying the relationship between diverse candidate genes and regulatory genes in a well-known trait via the Dual-LUC assay, this study provides a novel approach to expedite the determination of candidate genes such as genome-wide association study. [ABSTRACT FROM AUTHOR]

Discovering and engineering herbicide-resistant genes is a crucial challenge in crop breeding. This study focuses on the 4-hydroxyphenylpyruvate dioxygenase Inhibitor Sensitive 1-Like (HSL) protein, prevalent in higher plants and exhibiting weak catalytic activity against many β-triketone herbicides (β-THs). The crystal structures of maize HSL1A complexed with β-THs were elucidated, identifying four essential herbicide-binding residues and explaining the weak activity of HSL1A against the herbicides. Utilizing an artificial evolution approach, we developed a series of rice HSL1 mutants targeting the four residues. Then, these mutants were systematically evaluated, identifying the M10 variant as the most effective in modifying β-THs. The initial active conformation of substrate binding in HSL1 was also revealed from these mutants. Furthermore, overexpression of M10 in rice significantly enhanced resistance to β-THs, resulting in a notable 32-fold increase in resistance to methyl-benquitrione. In conclusion, the artificially evolved M10 gene shows great potential for the development of herbicide-resistant crops. [ABSTRACT FROM AUTHOR]

Rice is the leading global staple crop. Low temperatures pose negative impacts on rice's optimal growth and development. Rice cultivars acclimating to low temperatures exhibited improved seedling emergence under direct-seeded sowing conditions, yet little is known about the genes that regulate germination at low temperatures (LTG). In this research investigation, we've performed whole genome sequencing for the 273 rice plant materials. Using the best linear unbiased prediction (BLUP) values for each rice material, we identified 7 LTG-related traits and performed the efficient genetic analysis and genome-wide association study (GWAS). As a result of this, 95 quantitative trait loci (QTLs) and 1001 candidate genes associated with LTG in rice were identified. Haplotype analysis and functional annotation of the candidate genes resulted in the identification of three promising candidate genes (LOC_Os08g30520 for regulating LTG4 and LTG5, LOC_Os10g02625 for regulating LTG6, LTg7 and LTG8, and LOC_Os12g31460 for regulating LTG7, LTg8 and LTG9) involving in the regulation of LTG in rice. This research provides a solid foundation for addressing the LTG issue in rice and will be valuable in future direct-seeded rice breeding programs. [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]

Polyploid rice and its reverted diploid show rich phenotypic variation and strong heterosis, showing great breeding value. However, the genomic differences among tetraploids, counterpart common diploids, tetraploid-revertant diploids, and hybrid descendants are unclear. In this work, we bred a new excellent two-line hybrid rice variety, Y Liang You Duo Hui 14 (HTRM12), using Haitian tetraploid self-reverted diploid (HTRM2). Furthermore, we comparatively analyzed the important agronomic traits and genome-wide variations of those closest relatives, Haitian diploid (HT2), Haitian tetraploid (HT4), HTRM2, and HTRM12 in detail, based on multiple phenotypic investigations, genome resequencing, and bioinformatics analysis. The results of agronomic traits analysis and genome-wide variation analysis of single nucleotide polymorphism (SNP), insertion–deletion (InDel), and copy number variation (CNV) show that HT4 and HTRM2 had abundant phenotypic and genomic variations compared to HT2. HTRM2 can inherit important traits and variations from HT4. This implies that tetraploid self-reverted diploid has high potential in creating excellent breeding materials and in breeding breakthrough hybrid rice varieties. Our study verifies the feasibility that polyploid rice could be used as a mutation carrier for creating variations and provides genomic information, new breeding materials, and a new way of application for tetraploid rice breeding. [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]

【Objective】The current status of rice varieties in Guizhou and the role of DUS（distinctness, uniformity and stability) test traits in variety evaluation were clarified, so as to provide guidance to breeders in phenotypic selection when breeding rice varieties with excellent integrated traits and to provide theoretical support for testing institutions to efficiently conduct rice DUS tests.【Method】Genetic diversity, correlation, clustering and principal component analysis were used to investigate the genetic diversity, integrated performance and test performance of the traits tested in 250 rice varieties in Guizhou.【Result】Phenotypic analysis revealed that the partial visual traits were concentrated. The ligule shape of the reciprocal second leaves was bilobed in all cases. Additionally, 96.8% of the rice varieties had an erect or semi-erect growth habit with a compact plant shape. At the initial stage of the flag leaf, 99.2% of the varieties showed an erect or semi-erect state, while 96.0% of the varieties had their basal stem nodes wrapped. At maturity stage, 91.2% of the spikes will be significantly recurved, and 97.2% of the grain’s outer glumes showed light yellow in colour. Only one copy of the variety had a modified colour on the outer glume. The analysis of phenotypic variation and diversity to the 14 testing traits revealed that, apart from fruiting percentage, the other traits exhibited significant genetic variation. The coefficients of variation ranged from 6.51% to 20.82%, with the highest coefficient of variation observed for the number of grains per spike and the lowest for the fruiting percentage. Correlation analysis showed that all traits exhibited different levels of correlation. Eight pairs of traits reached significant levels, while another 43 pairs of traits showed highly significant levels. The tested varieties were classified into four main groups through cluster analysis. Group I had the highest mean values for yield-related traits, containing 68 samples. Group II had 25 samples with a significantly higher number of grains per spike than the other groups. Group III contained 67 samples with the shortest stalks. Group IV, which accounted for 36% of the total number of varieties, had the highest mean values for spike length, grain（brown rice) length and the best overall performance. The analysis using the affiliation function method revealed that 10 traits, including length of flag leaf, spike length and grain length, significantly affected the comprehensive characteristics of the tested varieties. The top 10 varieties with the highest composite evaluation (D value) included eight restoration lines and two hybrids. The optimal regression equation for variety evaluation was established through stepwise regression analysis. The equation was Y＝－0.707＋0.032X13＋0.003X7＋0.008X10＋0.003X5＋0.04X1＋0.02X3＋0.025X11－0.003X2＋0.001X4－0.1156×10-3X8. The results of the multiple linear regression analyses indicated that the distribution of grains per spike was scattered and did not fit well, while the remaining 13 traits fitted better.【Conclusion】The rice testing guidelines indicate that partial visual traits are effective in distinguishing different varieties, except for the ligule shape of the reciprocal second leaf. Among the measured traits, the number of grains per spike shows the largest coefficient of variation and genetic diversity index, making it an effective index for judging variety specificity. Furthermore, the overall evaluation value of the tested varieties is primarily influenced by 10 traits, including length of flag leaf, spike length and grain characteristics. [ABSTRACT FROM AUTHOR]

Simple Summary: Chalk5 is an important gene used in rice breeding to improve rice chalkiness, which greatly affects rice quality. For this study, the first exon of Chalk5 was edited, and two different knockout mutants were obtained. These two lines showed a decreased percentage of grains with chalkiness, chalkiness degree, and seed setting ratio. Moreover, their chalkiness was insensitive to temperature during the grain-filling stage, and the head milled rice rate was improved even under high-temperature conditions. The two lines showed significantly reduced PGWC and DEC without changes in other agronomic traits in the hybrid background. These results indicate that Chalk5 gene-edited lines are useful in indica hybrid rice breeding for a high yield and superior grain quality in high-temperature growing environments. Chalkiness is an important grain quality trait in rice. Chalk5, encoding a vacuolar H+-translocating pyrophosphatase, is a major gene affecting both the percentage of grains with chalkiness (PGWC) and chalkiness degree (DEC) in rice. Reducing its expression can decrease both PGEC and DEC. In this study, the first exon of Chalk5 was edited in the elite restorer line 9311 using the CRISPR/Cas9 system and two knockout mutants were obtained, one of which did not contain the exogenous Cas9 cassette. PGWC and DEC were both significantly reduced in both mutants, while the seed setting ratio (SSR) was also significantly decreased. Staggered sowing experiments showed that the chalkiness of the mutants was insensitive to temperature during the grain-filling stage, and the head milled rice rate (HMRR) could be improved even under high-temperature conditions. Finally, in the hybrid background, the mutants showed significantly reduced PGWC and DEC without changes in other agronomic traits. The results provide important germplasm and allele resources for breeding high-yield rice varieties with superior quality, especially for high-yield indica hybrid rice varieties with superior quality in high-temperature conditions. [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]

Simple Summary: Hybrid rice is grown by millions of Asian farmers and has normally higher yields compared to inbred varieties. However, hybrid rice has been associated with high damage from herbivores. This susceptibility could be due to the physiology of the hybrid plant type or due to a limited availability of male sterile parents that are necessary for hybrid seed production. We examined how plant type and breeding affect the relative susceptibilities of hybrid and inbred rice by exposing 32 rice genotypes to the brown planthopper, whitebacked planthopper, and yellow stemborer in controlled environments and field plots. We compared insect fitness on the plants and related this to the type and genetic similarity of genotypes. Despite their diverse origins (China, Colombia, India, and the Philippines), the hybrids and inbreds formed two distinct genetic groups, thereby confounding plant type and phylogeny. Hybrids were generally more susceptible to stemborers but not to planthoppers. Relative herbivore fitness was strongly influenced by plant origin (i.e., breeding program) with one group of related genotypes being relatively susceptible to all three herbivores. Our results indicate that hybrids are not inherently more susceptible than inbreds to insect herbivores and that careful screening with the elimination of the most susceptible genotypes is necessary to reduce herbivore damage to hybrid and inbred rice in Asia. Several studies have reported higher damage from insect herbivores to hybrid compared to inbred (pure line) rice. We used a collection of 20 hybrid and 12 inbred genotypes from diverse origins to test the hypotheses that hybrid rice susceptibility is due to (a) the hybrid plant type and/or (b) rice phylogeny. We challenged the genotypes with Nilaparvata lugans (BPH), Sogatella furcifera (WBPH) and Scirpophaga incertulas (YSB) in greenhouse and screenhouse bioassays and monitored herbivores in field plots. We used single nucleotide polymorphic (SNP) markers to assess genetic similarities between the genotypes and found that the hybrids and inbreds formed two distinct clusters regardless of origin. In the screenhouse, hybrids were more susceptible than inbreds to YSB; however, resistant hybrids and susceptible inbreds were also apparent from both the screenhouse and field plots. Plant biomass was the best predictor of susceptibility to YSB. Plant origin had a greater effect than plant type on susceptibility to BPH and WBPH. WBPH was the most abundant planthopper in the field plots where numbers were highly correlated with planthopper fitness in the greenhouse bioassays. Our results provide evidence that high-yielding hybrids that are relatively resistant to herbivores can be achieved through careful breeding. The avoidance of susceptible genotypes during breeding should remain a key element of integrated rice pest management. [ABSTRACT FROM AUTHOR]

This review mainly focuses on the rice grain quality based on which rice varieties are distinguished into several quality classes like, physical quality, eating and cooking quality and nutritional quality. The rice breeding programme needs to focus on the development of nutrient-dense rice for value addition, helping in reducing malnutrition and Vitamin-A deficiency (VAD). There is enough scope to enhance the nutritional and cooking quality in small and medium grain rice germplasm by bringing them into the breeding programme through Fe and Zn and Vitamin-A biofortification, aided with molecular techniques. Many studies have been conducted to find out the quantitative trait locus (QTL) for enhancing the quality of grain. The QTL qBRR5 and qBRR3 are responsible for brown rice grain width and length found on chromosome 5 and on chromosome number 3, respectively and for head rice on chromosome number 1, 5, and 6. The QTLs present on chromosomes 3, 5, and 6 are responsible for head rice recovery, chalky appearance of rice grain as well as grain size and shape. The gene Wx, located on chromosome 6 linked with the QTL qAC6 regulate amylose content and gel consistency. The QTL SSIIa on chromosome 6, control both the amylopectin and gelatinization temperature. The QTLs for Fe and Zn content in rice grain are located on chromosome 2, 3, 8, 11 and 12. Development of “Golden rice” and innovations with Arabidopsis genes can significantly enhance β-carotene levels and address Vitamin-A deficiency, while RNAi techniques improve storage quality. [ABSTRACT FROM AUTHOR]

The experiment was conducted during kharif season ( June-October, 2022) at Rice Research Station, Kaul, CCSHAU, Hisar using 48 rice genotypes to evaluate the genetic variability and character association under aerobic conditions. Analysis of variance revealed that the mean sum of squares was highly significant for all the traits examined. The magnitude of phenotypic coefficient of variation exceeded the genotypic coefficient of variation for all the traits analysed in the study. High genotypic coefficient of variation and phenotypic coefficient of variation were observed for root dry weight plant-1 followed by number of grains panicle-1, grain yield plant-1, biological yield plant-1, number of effective tillers plant-1 and flag leaf length. High heritability coupled with high genetic advance as per cent of mean was observed for grain yield plant-1, number of grains panicle-1, biological yield plant-1, root fresh weight plant-1 and root dry weight plant-1 indicating the presence of additive gene action. Grain yield plant-1 showed a highly significant and positive association with biological yield plant-1, harvest index percentage, root fresh weight plant-1, number of effective tillers plant-1 and 1000 seed weight. Path analysis revealed that biological yield plant-1 and harvest index percentage showed highest positive direct effect on grain yield plant-1. Furthermore, regression analysis revealed that biological yield plant-1, harvest index percentage, numbers effective of tillers plant-1, number of grains panicle-1, plant height and head rice recovery % as important traits contributing to grain yield plant-1. Therefore, phenotypic selection could be a viable approach for genetically improving these traits to obtain promising genotypes for future rice breeding programs. [ABSTRACT FROM AUTHOR]

Salinity is a common abiotic stress that limits crop productivity. Although there is a wealth of evidence suggesting that miRNA and lncRNA play important roles in the response to salinity in rice seedlings and reproductive stages, the mechanism by which competing endogenous RNAs (ceRNAs) influence salt tolerance and yield in rice has been rarely reported. In this study, we conducted full whole-transcriptome sequencing of rice panicles during the reproductive period to clarify the role of ceRNAs in the salt stress response and yield. A total of 214 lncRNAs, 79 miRNAs, and 584 mRNAs were identified as differentially expressed RNAs under salt stress. Functional analysis indicates that they play important roles in GO terms such as response to stress, biosynthesis processes, abiotic stimuli, endogenous stimulus, and response to stimulus, as well as in KEGG pathways such as secondary metabolite biosynthesis, carotenoid biosynthesis, metabolic pathways, and phenylpropanoid biosynthesis. A ceRNA network comprising 95 lncRNA–miRNA–mRNA triplets was constructed. Two lncRNAs, MSTRG.51634.2 and MSTRG.48576.1, were predicted to bind to osa-miR172d-5p to regulate the expression of OsMYB2 and OsMADS63, which have been reported to affect salt tolerance and yield, respectively. Three lncRNAs, MSTRG.30876.1, MSTRG.44567.1, and MSTRG.49308.1, may bind to osa-miR5487 to further regulate the expression of a stress protein (LOC_Os07g48460) and an aquaporin protein (LOC_Os02g51110) to regulate the salt stress response. This study is helpful for understanding the underlying molecular mechanisms of ceRNA that drive the response of rice to salt stress and provide new genetic resources for salt-resistant rice breeding. [ABSTRACT FROM AUTHOR]

Fragrance is a valuable trait in rice varieties, with its aroma significantly influencing consumer preference. In this study, we conducted comprehensive metabolome and transcriptome analyses to elucidate the genetic and biochemical basis of fragrance in the Shangsixiangnuo (SSXN) variety, a fragrant indica rice cultivated in Guangxi, China. Through sensory evaluation and genetic analysis, we confirmed SSXN as strongly fragrant, with an 806 bp deletion in the BADH2 gene associated with fragrance production. In the metabolome analysis, a total of 238, 233, 105 and 60 metabolic compounds exhibited significant changes at the seedling (S), reproductive (R), filling (F), and maturation (M) stages, respectively. We identified four compounds that exhibited significant changes in SSXN across all four development stages. Our analyses revealed a significant upregulation of 2-acetyl-1-pyrroline (2AP), the well-studied aromatic compound, in SSXN compared to the non-fragrant variety. Additionally, correlation analysis identified several metabolites strongly associated with 2AP, including ethanone, 1-(1H-pyrrol-2-yl)-, 1H-pyrrole, and pyrrole. Furthermore, Weighted Gene Co-expression Network Analysis (WGCNA) analysis highlighted the magenta and yellow modules as particularly enriched in aroma-related metabolites, providing insights into the complex aromatic compounds underlying the fragrance of rice. In the transcriptome analysis, a total of 5582, 5506, 4965, and 4599 differential expressed genes (DEGs) were identified across the four developmental stages, with a notable enrichment of the common pathway amino sugar and nucleotide sugar metabolism in all stages. In our correlation analysis between metabolome and transcriptome data, the top three connected metabolites, phenol-, 3-amino-, and 2AP, along with ethanone, 1-(1H-pyrrol-2-yl)-, exhibited strong associations with transcripts, highlighting their potential roles in fragrance biosynthesis. Additionally, the downregulated expression of the P4H4 gene, encoding a procollagen-proline dioxygenase that specifically targets proline, in SSXN suggests its involvement in proline metabolism and potentially in aroma formation pathways. Overall, our study provides comprehensive insights into the genetic and biochemical mechanisms underlying fragrance production in rice, laying the foundation for further research aimed at enhancing fragrance quality in rice breeding programs. [ABSTRACT FROM AUTHOR]

Salt stress is an environmental factor that limits plant growth and crop production. With the rapid expansion of salinized arable land worldwide, investigating the molecular mechanisms underlying the salt stress response in plants is urgently needed. Here, we report that GROWTH REGULATING FACTOR 7 (OsGRF7) promotes salt tolerance by regulating arbutin (hydroquinone-β-D-glucopyranoside) metabolism in rice (Oryza sativa). Overexpression of OsGRF7 increased arbutin content, and exogenous arbutin application rescued the salt-sensitive phenotype of OsGRF7 knockdown and knockout plants. OsGRF7 directly promoted the expression of the arbutin biosynthesis genes URIDINE DIPHOSPHATE GLYCOSYLTRANSFERASE 1 (OsUGT1) and OsUGT5, and knockout of OsUGT1 or OsUGT5 reduced rice arbutin content, salt tolerance, and grain size. Furthermore, OsGRF7 degradation through its interaction with F-BOX AND OTHER DOMAINS CONTAINING PROTEIN 13 reduced rice salinity tolerance and grain size. These findings highlight an underexplored role of OsGRF7 in modulating rice arbutin metabolism, salt stress response, and grain size, as well as its broad potential use in rice breeding. Transcription factor control of arbutin biosynthesis gene expression regulates grain size and salt stress response in rice (Oryza sativa). [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]

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]

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]

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]

Heading date determines rice seasonal and regional adaptation, while plant height is an important trait related to rice lodging resistance. In this study, a recombinant inbred line population was used to detect quantitative trait loci (QTLs) for both traits in long-day (LD) and short-day (SD) environments. Three and two QTLs for heading date were detected in LD and SD environments, respectively. Notably, qHD8 and qHD10 were commonly detected in both environments. Five and four QTLs for plant height were identified in LD and SD environments, respectively. Among them, qPH3, qPH5 and qPH6 showed no pleiotropic effects on heading date and were detected in both environments. These three QTLs are considered to be the primary targets for improving rice plant height. Additionally, two genomic regions exhibited pleiotropic effects on both heading date and plant height. The alleles delayed the heading date while simultaneously increasing plant height. This study indicated that most QTLs for heading date are sensitive to photoperiod and have pleiotropic effects on plant height, thereby complicating their application in breeding programs. These findings provide useful information for the breeding of rice varieties with desired heading dates and plant heights. [ABSTRACT FROM AUTHOR]

In Bangladesh, where rice plays a crucial role in both sustenance and economy, aromatic rice varieties have gained prominence due to their distinct taste and fragrance. This study evaluated the agronomic performance, grain quality, and cooking properties of four advanced breeding lines of small-grain aromatic rice that we developed at the Advanced Seed Research and Biotech Centre (ASRBC), ACI Limited, Bangladesh, alongside eighteen locally popular aromatic rice varieties and three check varieties. The study identified ASRBCR 1017-B-12-3 and ASRBCR 1017-B-13-2 as superior genotypes, exhibiting excellent results in terms of effective tillers, grains per panicle, aroma and overall yield. A greater plant height (168cm) was observed in Chinigura, while ASRBCR 1017-B-13-1 had the lowest height (90cm). ASRBCR 1017-B-13-2 had the maximum tiller count (12), and ASRBCR 1017-B-18-2 had the highest number of grains per panicle (350). Bashful (Golden) had the highest thousand-grain weight (19.17g). Detailed assessments of grain quality parameters revealed significant variations in grain length, length-tobreadth ratio, aroma intensity, and cooked rice elongation among the tested genotypes. The Bashful variety (golden) had the longest grain length (7.13mm), and the Madhumala variety had the highest length-tobreadth ratio. All four advanced breeding lines exhibited a grain length of approximately 4mm and a grain breadth ranging from 2.12 to 2.48mm, with a cooked rice elongation ratio ranging from 1.72 to 1.85. In addition, aroma/fragrance genotyping using SSR marker BADEX7-5 showed the presence of fragrance in all the test advanced lines, with common banding patterns, but absence of bands for aroma in Madhumala and BRRI dhan90. Results provide insights into trait interactions, choice of genotypes, and breeding for optimum yields as well as quality in aromatic rice. [ABSTRACT FROM AUTHOR]

The purple glume-tip is an essential morphological marker for selective rice breeding, aiding in assisted selection and variety purification. However, the inheritance of purple glume-tip in japonica rice landrace Donglan Black Rice (DBR) has not yet been explored deeply. The F2 and F4 populations were constructed from crossing between Huazhan with colorless glume-tip and DBR to identify the associated genomic region(s). Genetic analysis displayed two highly comparable and perplexing phenotypes in the purple glume-tip of rice. Two significant genes with recessive epistasis predominantly regulated the two phenotypes. The two target gene loci were located in the intervals of 5315163-5316875 bp on chr6 and 27915598-27939357 bp on chr4, respectively, where reported genes associated with the purple color trait in rice, Os06g0205100 and Os04g0557500, are present. The two genes may be potential target genes. However, the role of Os04g0557500 in the glume-tip coloration remains unreported. [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]

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]

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]

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]

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]

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]

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]

【Objective】Rice lodging resistance is an important trait in current rice breeding. The systematic evaluation of lodging resistance of germplasm resources is of great significance for breeding lodging-resistant varieties.【Method】200 germplasm resources in China were taken as materials, 9 traits related to lodging resistance of rice were systematically investigated, and the breeding value of these traits was evaluated by morphological clustering and path analysis.【Result】According to the lodging index, the tested materials were divided into three types: high fall-resistant type, fall-resistant type and lodging type, among which 81.5% of breeding resources had good fall-resistant ability. The correlation coefficient between stalk physical traits and lodging index of different lodging resistant germplasm resources was significantly different. The plant height, bending moment and second pitch length of restorer were positively correlated with lodging index, and the correlation coefficient between bending moment and lodging index d lodging index reached 0.789. The folding resistance of base and sheath leaf thickness were negatively correlated with lodging index, and the correlation coefficients were-0.754** and-0.659**, respectively. There was a significant positive correlation between plant height and basal segment length and lodging index, and the correlation coefficient between plant height and lodging index was 0.681**. The correlation coefficient between buckling resistance and lodging index was-0.841**.The path analysis results showed that the bending moment of the restorer line and other materials had a direct positive effect on the lodging index (Py=0.519), the plant height of the sterile line had a direct positive effect on the lodging index (Py=0.737), and the base bending force of both parents had a direct negative effect on the lodging index, with direct path coefficients of-0.331 and-0.702, respectively.【Conclusion】The lodging resistance of rice is a complex trait, and different germplasm resources have different lodging resistance characteristics. Scientific utilization of breeding resources is the key to rice lodging resistance breeding. [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]

A study was conducted in the Odisha region of India to assess genetic parameters, heritability, and trait associations in twenty traditional pigmented and non-pigmented rice landraces. The evaluation focused on twenty-five physical, phytochemical, and antioxidant properties. The results showed potential for enhancing desired traits in pigmented rice due to a wide range of genotypic variation, high heritability, and substantial genetic advances. These improvements were particularly observed in characteristics such as porosity, total soluble sugar, phytochemicals, and antioxidant properties in pigmented rice. Additionally, properties like the length-breadth ratio of grains, thickness, diameter, thousand grain weight, and bulk density of grains can be used for trait improvement in non-pigmented rice. Physical attributes like thickness, grain weight, and porosity, as well as phytochemical traits like total soluble sugar and protein content, were notably higher in pigmented rice. Correlations between traits indicated that Pigmented rice was associated with phytochemical and antioxidant properties, while Nonpigmented rice was linked to amylose content, density, and the length-breadth ratio of grains. Two promising pigmented genotypes, Bodikaberi and Mahipaljeera, were identified and could be valuable for future rice breeding programs. Moreover, these genotypes have potential applications in the food industry for creating value-added products to enhance nutritional quality and could also be relevant to the cosmetic industry due to their superior antioxidant properties. [ABSTRACT FROM AUTHOR]