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This study aimed to understand the maternal influence on the inheritance of pericarp colour and grain dimensions in rice, serving as a model for maternal effects in plants. Four crosses, namely Kalarata (red pericarp) × DRR Dhan 58 (white pericarp), DRR Dhan 58 × Kalarata, Kalarata × Pusa 44 (white pericarp), and Pusa 44 × Kalarata, were attempted and their F1, F2 and F3 seeds were analysed. All F1 seeds of all crosses exhibited the pericarp colour of their corresponding maternal parent, confirming a strong maternal influence. In subsequent generations, F2 seeds uniformly exhibited red pericarp colour across all crosses, thus reinforcing the influence of maternal genotype on inheritance. However, F3 seeds were segregated into 9 red: 3 medium red: 4 white, suggesting digenic recessive epistasis (supplementary gene action). Phenotypic assessments indicated nuclear inheritance with maternal effects, while genotypic analysis using gene-based markers revealed polymorphisms at ‘Rc’ locus and monomorphism at ‘Rd’ locus, indicating the presence of specific genetic factors in the parental materials used in the study. Additionally, analysis of the grain L/B ratio revealed a similar trend to pericarp colour inheritance, with direct maternal genetic effects in F1 seeds, consistent uniformity in F2 seeds and continuous variation in F3 seeds across all crosses. Welch’s test comparisons of L/B ratios suggested a significant maternal impact, particularly in F3 and F2 generations, with paternal influence remaining consistent across generations. Deviations in the L/B ratios in certain F3 segregants suggest environmental influences on grain development. These findings contribute to the understanding of maternal effects in plants and have important implications for rice breeding. The significance of this research lies in its contribution to the relatively unexplored field of maternal effects in plant genetics. [ABSTRACT FROM AUTHOR]

This study estimates genetic variability and correlations among germination and seedling traits conferring salinity tolerance in rice accessions. Five rice accessions were screened under salinity levels of 0, 50, 100, and 200 mM NaCl in a controlled laboratory setting. Traits such as germination energy, capacity, shoot and root length, and biomass were measured. Data were analyzed for variance and correlations to assess variability and trait relationships. Significant genetic variability was found among accessions for all traits. Germination energy showed the highest coefficient of variation (CV) at 22.29% under control conditions, while fresh shoot weight had the highest CV (34.35%) under 200 mM salinity. Accessions ACC2 and ACC5 consistently demonstrated higher performance in germination energy (23.33 to 53.33% and 10.00 to 41.67%), germination capacity (40.00 to 60.00% and 28.33 to 46.67%), and shoot length (0.67 to 2.97 cm and 0.40 to 3.93 cm) under various salinity stress levels. ACC1, ACC3, and ACC4 showed more variability but maintained some consistency in specific traits, with ACC4 generally showing lower performance across most traits. Genetic parameter estimates indicated high heritability (>60%) for all traits, with the highest in germination capacity (96.88%). High genetic advance (GAM) was observed for all traits (>20%), with germination energy showing the highest (107.00%). Traits with high heritability and genetic advance, such as germination energy, germination capacity, and root length, suggest strong genetic control and potential for improvement through selective breeding. Significant correlations were found between germination energy and capacity (r= 0.89 to 0.96) and between shoot length and leaf length (r= 0.92) under stress conditions. Stress tolerance indices identified accessions ACC2 and ACC5 as the most tolerant, with ACC1 showing consistent performance across traits. This study underscores the importance of identifying resilient traits and accessions to enhance salinity tolerance in rice, contributing to improved productivity in saline-affected regions. [ABSTRACT FROM AUTHOR]

Spring rice (Oryza sativa L.) plays a crucial role as Nepal's primary staple cereal crop. It has a high potential as an alternative during low rice production in the main season, ensuring food self-sufficiency. A field study was conducted on spring rice at a farmer field school, Kailari Rural Municipality-09, Kailali district, Nepal to identify the best-performing and the most preferred genotypes by the farmers through the participatory approach. The experiment was laid out in randomized complete block design (RCBD) with twelve spring rice genotypes including a local check variety. Each treatment was replicated thrice. Statistically significant differences in yield and yield-attributing traits were observed among the genotypes under observation. Average plant height was recorded as the highest in Hardinath-3 (101.75 cm) followed by IR17L1387 (99.78 cm), Jhumka (98.74 cm), and IR17A3019 (96.55 cm) with the lowest in IR16A3838 (84.79 cm). Similarly, the total number of tillers and effective tillers were found to be the greatest in IR18A1451 and IR17A3019 respectively at harvest. The sterility percentage was lowest in IR17A3012 followed by IR17A3019 whereas highest in Hardinath-4. Similarly, the Hardinath-1 variety matured earlier than, IR16A3838 and IR17A3019. Hardinath-4 variety followed by Jhumka was a late maturing variety. Maximum grain yield was found in IR17A3012 (6.06 t ha-1) which was followed by IR17A3019 (5.97 t ha-1) and superior to the local check variety (Jhumka). Thus, the farmers' preference score was found to be maximum (0.09) in the IR17A3019 genotype which signifies that this genotype has certain preferable traits such as early and uniform maturity, low disease and pest attack, a high number of effective tillers, panicle length, and sterility percentage. [ABSTRACT FROM AUTHOR]

Transplanted (T.) aman rice (Oryza sativa L.) covers the largest cultivated area in Bangladesh while very little information on molecular level characterization of T. aman genotypes persists. The major aim of this study was to dissect molecular characterization and genetic diversity of 25 T. aman rice genotypes using twelve simple sequences repeats (SSRs) markers. The rice genotypes comprised local landraces that were collected from twelve districts of Bangladesh. A total of twelve SSR primer pairs covering all 12 chromosomes of rice were selected for the study. The molecular characterization, genetic diversity, population structure and principal component analysis (PCA) were estimated and the results revealed a total of fifty alleles across 12 loci ranged from 2 (RM411) to 7 (RM252) per locus. The maximum gene diversity exhibited in RM252 (0.7) while the minimum was in RM320 (0.15). The polymorphism information content (PIC) values ranged from 0.14 to 0.67 while RM252 and RM206 identified as the most suitable markers. Clustering based on unweight pair group method with arithmetic mean (UPGMA) analysis clustered 25 genotypes into six major clusters (IVI) with similarity coefficient value of 0.34. Cluster V contained a maximum seven genotypes with 5 subgroups. Again, the population structure displayed 3 populations namely population 1, 2 and 3. These populations were clustered into the 3 major groups in the Principle Component Analysis (PCA) 2D plot. Here, PC1 and PC2 contributed 32.7% variations. However, the overall hybridization suggested between the genotypes of the population 1 and 3, specifically between clusters I and cluster VI, and between the diverse parents such as, genotypes Bohi Trimota and Ranga, Bohi Trimota and Purple Rice-2, Bohi Trimota and Purple Rice-3. These diverse clusters and genotypes identified through SSR makers are lay foundation of molecular characterization of T. aman rice genotypes in Bangladesh and further marker-assisted studies will be suggested. [ABSTRACT FROM AUTHOR]

The article presents a study which identified the role that environmental factors play in explaining the heritability of important economic traits across a range of rice bean genotypes cultivated under different settings. Topics include genotypic and phenotypic coefficient of correlation, genotypic character association among yield and yield contributing traits in rice bean, and phenotypic path coefficient analysis among yield and yield contributing traits in rice bean.

This article, published in the journal Environment & Ecology, presents a study on genetic variability and cause-effect relationships in aromatic rice. The study analyzed twenty different rice genotypes to determine the genetic variability and correlation between various agro-morphological characters. The results showed that selecting for certain traits such as flag leaf angle, panicle exertion, and test weight could effectively improve rice yield. The study also emphasized the importance of maintaining a balance between morphological architecture and physiological rhythm for optimal yield. The document provides data on quantitative characters and their correlation with grain yield, as well as a table showing the correlation between various traits and grain yield in rice. The conclusion suggests that selecting for larger flag leaf area, higher spikelet fertility, and greater grain weight while restricting selection for panicle number, plant height, and flag leaf angle would increase rice grain yield. The document also references other studies on genetic variability and yield analysis in rice. [Extracted from the article]

This research focused on the evaluation of twelve newly bred rice genotypes with diverse morphological traits under aerobic cultivation to develop strategies for water conservation while maintaining grain productivity and quality. The experiment was conducted during the summer season of 2016, employing a Randomized Complete Block Design (RCBD) with wetland cultivation as a control. For analysis, various vegetative and reproductive traits namely, Plant height, Number of Tillers, Shoot Weight, Days to 50% flowering, Days to Maturity, Number of Productive Tillers, Panicle Length, Grain Weight, Length of the seed, Breadth of the seed, Ratio of Length and Breadth of the Seed, and Test weight of 100 seeds were recorded. Data on analysis of variance revealed the significant difference for days to flowering, maturity, plant height, panicle length, test weight, and grain yield under aerobic and wetland cultivation methods during the summer season, 2016, suggesting these traits are under high genetic control. Genetic parameters such as percentage of GCV, PCV, Heritability, and GAM were estimated across 13 parameters comprising vegetative and reproductive characters. The findings suggest a considerable amount of genetic variability for most traits, providing a foundation for the potential implementation of an effective selection procedure in breeding new rice varieties within the selected genotypes. [ABSTRACT FROM AUTHOR]

This article discusses a study on the genetic diversity of rice genotypes under normal and flash flood conditions. The study analyzed 30 rice genotypes and found significant variability in traits such as flowering time, plant height, and grain yield. The genotypes were categorized into clusters based on their genetic diversity, and certain genotypes were identified as superior parents for flash flood tolerance. The article emphasizes the importance of genetic diversity in rice cultivation, particularly in the face of climate change and the risk of flash flooding. The study provides insights into potential strategies for improving rice varieties in flash flood-prone areas. [Extracted from the article]

In Asia, the rice crop sustains millions of people. However, growing demand for this crop needs to be met while simultaneously reducing its water consumption to cope with the effects of climate change. Lowland cropping systems are the most common and productive but have particularly high water requirements. High-yielding rice genotypes adapted to drier environments (such as rainfed or aerobic rice ecosystems) are needed to increase the water use efficiency of cropping. Identifying these genotypes requires fast and more accurate selection methods. It is hypothesized that applying a new quantitative selection method (the score index selection method), can usefully compare rice yield responses over different years and stress intensities to select genotypes more rapidly and efficiently. Applying the score index to previously published rice yield data for 39 genotypes grown in no-stress and two stress environments, identified three genotypes (ARB 8, IR55419-04 and ARB 7) with higher and stable yield under moderate to severe stress conditions. These genotypes are postulated to be better adapted to stress environment such as upland and aerobic environments. Importantly, the score index selection method offers improved precision than the conventional breeding selection method in identifying genotypes that are well-suited to a range of stress levels within the target environment. [ABSTRACT FROM AUTHOR]

Poor seedling emergence is a challenge for direct seeding of rice under deep-sowing field conditions. Here we reveal that UDP-glucosyltransferase OsUGT75A promotes rice seedling emergence under deepsowing conditions by increasing shoot length. Expression of OsUGT75A was higher in the middle regions of the shoot and in shoots under deep-sowing conditions. Levels of free abscisic acid (ABA) and jasmonates (JA) were higher in shoots of OsUGT75A mutants than in those of wild-type plants, and OsUGT75A mutants were more sensitive to ABA and JA treatments. Reduced shoot length was attributed to higher ABA INSENSITIVE 3 (OsABI3) expression and lower JASMONATE-ZIM domain protein (OsJAZ) expression in shoots. Shoot extension by OsUGT75A is achieved mainly by promotion of cell elongation. An elite haplotype of OsUGT75A associated with increased shoot length was identified among indica rice accessions. OsUGT75A acts to increase seedling emergence under deep-sowing conditions. [ABSTRACT FROM AUTHOR]

Doubled haploid (DH) technology is an important tool in crop breeding because it can significantly accelerate the breeding process. ZmPLA1/MATL/NLD and ZmDMP are two key genes controlling haploid induction (HI) in maize, exhibiting a synergistic effect. However, it is unknown whether knock out of ZmDMP orthologs can stimulate HI in rice. In this study, a ZmPLA1 ortholog (OsPLA1) and two ZmDMP orthologs (OsDMP3 and OsDMP6) were identified in rice. All three genes encode plasma membrane-localized proteins and were highly expressed in mature anthers. Knockout of OsPLA1 in both Minghui 63 and Nipponbare resulted in reduced seed setting rate (SSR) and caused HI. The osdmp3, osdmp6 and the double mutant failed to trigger HI independently, nor increased the haploid induction rate (HIR) when combined with ospla1. Repeated pollinations operations of QX654A with the ospla1 mutant significantly improve SSR, while reducing HIR. RNA-seq profiling of mature ospla1 mutant anthers indicated that a large number of differentially expressed genes (DEGs) were enriched in redox homeostasis and lipid metabolic GO terms, plant hormone signal transduction, and MAPK signaling pathways. These findings provide important insights towards construction of an efficient DH breeding technology and study of the molecular mechanism of HI in rice. [ABSTRACT FROM AUTHOR]

Plasma membrane intrinsic proteins (PIPs) are conserved plant aquaporins that transport small molecules across the plasma membrane to trigger instant stress responses and maintain cellular homeostasis under biotic and abiotic stress. To elucidate their roles in plant immunity to pathogen attack, we characterized the expression patterns, subcellular localizations, and H2O2-transport ability of 11 OsPIPs in rice (Oryza sativa), and identified OsPIP2;6 as necessary for rice disease resistance. OsPIP2;6 resides on the plasma membrane and facilitates cytoplasmic import of the immune signaling molecule H2O2. Knockout of OsPIP2;6 increases rice susceptibility to Magnaporthe oryzae, indicating a positive function in plant immunity. OsPIP2;6 interacts with OsPIP2;2, which has been reported to increase rice resistance to pathogens via H2O2 transport. Our findings suggest that OsPIP2;6 cooperates with OsPIP2;2 as a defense signal transporter complex during plant–pathogen interaction. [ABSTRACT FROM AUTHOR]

Improving the grain yield in rice can be done more efficiently by selecting the yield components than selecting the grain yield itself, provided that these traits have a desirable genetic correlation with the grain yield trait. A field experiment was carried out in the rice research station in Al-Mashkhab/ Najaf/ IRAQ to determine the traits correlated with grain yield and to select the superior genotypes with their selection index among the sixteen genotypes planted during the growing season of 2021. During the 2022 season six genotypes were selected to evaluate the path coefficient analysis for the grain yield and its components according to randomized complete block design (RCBD) with three replicates. The results showed that the mean squares of the genotypes were significant for all studied traits(P<0.1). The superiority of the genotypes Furat1, Jasmine and K2 over the rest of six genotypes that were selected for having a high selection index, especially in the trait of grain yield, number of tillers.m-2 and number of grains.panicle-1. The genetic and phenotypic path coefficient analysis revealed that there was a high direct effect of the yield components on the grain yield due to the high positive and desirable values of the genetic and phenotypic correlation between the grain yield and its components including the number of tillers.m-2, the number of grains.panicle-1 and the panicle length, which are selective indicators for improving grain yield. Furthermore, the aforementioned traits showed high values of heritability in the broad sense and good stability during the two study seasons. Thus, the characteristics of the number of tillers.m-2 and the number of grains per panicle can be considered as one of the best criteria to be adopted as a selection index in the breeding programs for the rice crop. Moreover, further investigations are required for these criteria at different experimental conditions in other to testing their efficiency. [ABSTRACT FROM AUTHOR]

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Bacterial leaf streak (BLS), caused by Xanthomonas oryzae pv. oryzicola (Xoc), is a bacterial disease affecting rice production in Asia and Africa, whose severity is expected to increase with climate change. Identification of new quantitative-trait loci (QTL) or resistance genes for BLS resistance is essential for developing resistant rice. A genome-wide association study to identify QTL associated with BLS resistance was conducted using phenotypic and genotypic data from 429 rice accessions. Of 47 QTL identified, 45 were novel and two co-localized with previously reported QTL or genes conferring BLS resistance. qBLS6.2 on chromosome 6 explained the greatest phenotypic variation. Combined analysis of differential expression and annotations of predicted genes near qBLS6.2 based on haplotype and disease phenotype identified OsBLS6.2 (LOC_Os06g02960) as a candidate gene for qBLS6.2. OsBLS6.2 knockout plants showed higher resistance to Xoc than wild-type plants. Many other candidate genes for resistance to Xoc were identified. [ABSTRACT FROM AUTHOR]

In animals, serotonin is a neurotransmitter and mood regulator. In plants, serotonin functions in energy acquisition, tissue maintenance, delay of senescence, and response to biotic and abiotic stresses. In this study, we examined the effect of serotonin enrichment of rice endosperm on plant growth, endosperm development, and grain quality. To do so, TDCs and T5H were selected as targets for serotonin fortification. Overexpression of TDC1 or TDC3 increased serotonin accumulation relative to overexpression of T5H in rice grain. Transgenic lines of target genes driven by the Gt1 promoter showed better field performance than those driven by the Ubi promoter. Overexpression of T5H showed little effect on plant growth or grain physicochemical quality. In neuronal cell culture assays, serotonin induced neuroprotective action against apoptosis. Breeding of rice cultivars with high serotonin content may be beneficial for health and nutrition. [ABSTRACT FROM AUTHOR]

Plant trichomes are a specialized cellular tissue that functions in resistance to biotic and abiotic stresses. In rice, three transcription-factor genes: OsWOX3B, HL6, and OsSPL10, have been found to control trichome development. Although studies have shown interactions between the three genes, their full relationship in trichome development is unclear. We found that the expression levels of OsWOX3B and HL6 were both reduced in OsSPL10-knockout plants but increased in OsSPL10-overexpression plants, suggesting that OsSPL10 positively regulates their expression. Physical interaction between OsSPL10 and OsWOX3B was found both in vivo and in vitro and attenuated their abilities to bind to the promoter of HL6 to activate its transcription. This mechanism may regulate trichome length by adjusting the expression of HL6. A rice gene network regulating trichome development is proposed. [ABSTRACT FROM AUTHOR]

Nuclear factor Y (NF-Y), a group of conserved transcription-factor complexes that consist of NF-YA, B, and C subunits, is essential for developmental regulation and for responses to environmental changes in eukaryotes. We previously found that some NF-Y genes, such as OsNF-YA8, were expressed specifically in the endosperm of rice. In the present study, overexpression of OsNF-YA8 in rice resulted in reduced plant height due to suppressed cell elongation in internodes. Gibberellin (GA) biosynthetic genes, including OsCPS1, OsGA20ox1, and OsGA20ox2, were down-regulated. OsNF-YA8 bound to the promoters of these genes to repress their expression. Endogenous GA content was decreased in OsNF-YA8 overexpressors, whose dwarf phenotype could be partially rescued by exogenous GA treatment. The findings suggested that ectopic expression of OsNF-YA8 causes defective GA biosynthesis in vegetative stage. Heading date in OsNF-YA8 overexpressors was delayed, especially under short-day conditions. OsNFYA8 bound to the promoter of Heading Date 3a (Hd3a), the florigen gene in rice, to negatively regulate flowering. Either ectopic activation or knockout of OsNF-YA8 impaired seed development, as indicated by reduced seed size and increased grain chalkiness. These results suggest that ectopic expression of the endosperm-specific OsNF-YA8 in rice disrupts both vegetative and reproductive development. [ABSTRACT FROM AUTHOR]

As a natural genetic reservoir, wild rice contains many favorable alleles and mutations conferring high yield and resistance to biotic and abiotic stresses. However, there are few reports describing favorable genes or QTL from the AA genome wild rice O. longistaminata, which is characterized by tall and robust habit and long tassels and anthers and shows high potential for use in cultivated rice improvement. We constructed a stable BC2F20 backcross inbred line (BIL) population of 152 lines from the cross of 9311 × O. longistaminat. Some BILs showed large panicles, large seeds, and strong resistance to rice false smut, bacterial leaf blight, rice blast spot, and brown planthopper. Genomic resequencing showed that the 152 BILs covered about 99.6% of the O. longistaminata genome. QTL mapping with 2432 bin markers revealed 13 QTL associated with seven yield traits and eight with resistance to brown planthopper and to four diseases. Of these QTL, 12 for grain yield and 11 for pest and disease resistance are novel in Oryza species. A large-panicle NIL1880 line containing QTL qPB8.1 showed a nearly 50% increase in spikelet number and 27.5% in grain yield compared to the recurrent parent 9311. These findings support the potential value of O. longistaminata for cultivated rice improvement. [ABSTRACT FROM AUTHOR]

Increasing tiller number is a target of high-yield rice breeding. Identification of tiller-defect mutants and their corresponding genes is helpful for clarifying the molecular mechanism of rice tillering. Summarizing research progress on the two processes of rice tiller formation, namely the formation and growth of axillary meristem, this paper reviews the effects of genetic factors, endogenous hormones, and exogenous environment on rice tillering, finding that multiple molecular mechanisms and signal pathways regulating rice tillering cooperate rice tillering, and discusses future research objectives and application of its regulatory mechanism. Elucidation of theis mechanism will be helpful for breeding high-yielding rice cultivars with ideal plant type via molecular design breeding. [ABSTRACT FROM AUTHOR]

Rice production is a critical component of global food security. To date, rice is grown in over 100 countries and is the primary source of food for more than 3 billion people. Despite its importance, rice production is facing numerous challenges that threaten its future viability. One of the primary problems is the advent of climate change. The changing climatic conditions greatly affect the growth and productivity of rice crop and the quality of rice yield. Similarly, biotic stresses brought about by pathogen and pest infestations are greatly affecting the productivity of rice. To address these issues, the utilization of rice genetic resources is necessary to map, identify, and understand the genetics of important agronomic traits. This review paper highlights the role of rice genetic resources for developing high-yielding and stress-tolerant rice varieties. The integration of genetic, genomic, and phenomic tools in rice breeding programs has led to the development of high-yielding and stress-tolerant rice varieties. The collaboration of multidisciplinary teams of experts, sustainable farming practices, and extension services for farmers is essential for accelerating the development of high-yielding and stress-tolerant rice varieties. [ABSTRACT FROM AUTHOR]

Single nucleotide polymorphism (SNP) genotyping arrays provide an optimal high-throughput platform for genetic research and molecular breeding programs in both animals and plants. In this study, a highquality and custom-designed Rice3K56 SNP array was developed with the resequencing data of 3024 rice accessions worldwide, which was then tested extensively in 192 representative rice samples. Printed on the GeneTitan chips of Affymetrix Axiom each containing 56,606 SNP markers, the Rice3K56 array has a high genotyping reliability (99.6%), high and uniform genome coverage (an average of 6.7-kb between adjacent SNPs), abundant polymorphic information and easy automation, compared with previously developed rice SNP arrays. When applied in rice varietal differentiation, population diversity analysis, gene mapping of 13 complex traits by a genome-wide association study analysis (GWAS), and genome selection experiments in a recombinant inbred line and a multi-parent advanced generation inter-cross populations, these properties of the Rice3K56 array were well demonstrated for its power and great potential to be a highly efficient tool for rice genetic research and genomic breeding. [ABSTRACT FROM AUTHOR]

The wild abortive (WA)-type cytoplasmic male sterility (CMS) derived from the wild rice species Oryza rufipogon Griff. is used widely in three-line indica hybrids. The identification and mapping of restorer of fertility (Rf) genes aided in the development of WA-type hybrids. Here we report that testcross F1 plants from the WA-type CMS line and 9311 exhibited stainable pollen grains with no seed set, indicating that 9311 carries minor-effect Rfs for WA-type CMS. We developed an advanced backcross population consisting of plants harboring small regions of donor chromosomal segments from 9311 in the WATianfengA genetic background with moderate seed setting rates. Genetic analysis showed that the pollen fertility levels of the backcross individuals are governed by a single gene from 9311 that we named Rf19 (t). By use of the RICE 40 K gene chip, three introduced segments were identified in the fertile lines, and a candidate region spanning 4.37–8.29 Mb on chromosome 1 was identified for Rf19(t). Finally, Rf19(t) was fine-mapped to a region of 90 kb between the DNA marker loci STS1-163 and STS1-183, in which eight ORFs were predicted. Also, using relative expression analyses, comparative sequence analyses and functional domain analyses, we identified LOC_Os01g10530 as the most likely candidate gene for Rf19(t). Furthermore, Rf19(t) was found to function in fertility restoration, most probably by regulating the degradation of mRNA transcribed from the mitochondrial gene WA352. These results increase our knowledge of fertility restoration in WA-type CMS lines and will facilitate the development of high-quality pairs of WAtype CMS and maintainer lines. [ABSTRACT FROM AUTHOR]

Nitrogen (N) fertilization is necessary for obtaining high rice yield. But excessive N fertilizer reduces rice plant N efficiency and causes negative effects such as environmental pollution. In this study, we assembled key genes involved in different nodes of N pathways to boost nitrate and ammonium uptake and assimilation, and to strengthen amino acid utilization to increase grain yield and nitrogen use efficiency (NUE) in rice. The combinations OsNPF8.9a x OsNR2, OsAMT1;2 x OsGS1;2 x OsAS1, and OsGS2 x OsAS2 x OsANT3 optimized nitrate assimilation, ammonium conversion, and N reutilization, respectively. In co-overexpressing rice lines obtained by co-transformation, the tiller number, biomass, and grain yield per plant of the OsAMT1;2 x OsGS1;2 x OsAS1-overexpressing line exceeded those of wild-type ZH11, the OsNPF8.9a x OsNR2 x OsGS1;2 x OsAS1-overexpressing line, and the OsGS2 x OsAS2 x OsANT3-overexpressing line. The glutamine synthase activity, free amino acids, and nitrogen utilization efficiency (NUtE) of the OsAMT1;2 x OsGS1;2 x OsAS1-overexpressing line exceeded those of ZH11 and other lines that combined key genes. N influx efficiency was increased in the OsAMT1;2 x OsGS1;2 x OsAS1-overexpressing line and OsNPF8.9a x OsNR2 x OsGS1;2 x OsAS1- overexpressing line under a low ammonium and a low nitrate treatment, respectively. We propose that combining overexpression of OsAMT1;2, OsGS1;2, and OsAS1 is a promising breeding strategy for systematically increasing rice grain yield and NUE by focusing on key nodes in the N pathway. [ABSTRACT FROM AUTHOR]

Abiotic stresses are among the major limiting factors for plant growth and crop productivity. Among these, salinity is one of the major risk factors for plant growth and development in arid to semi-arid regions. Cultivation of salt tolerant crop genotypes is one of the imperative approaches to meet the food demand for increasing population. The current experiment was carried out to access the performance of different rice genotypes under salinity stress and Zinc (Zn) sources. Four rice genotypes were grown in a pot experiment and were exposed to salinity stress (7 dS m-1), and Zn (15 mg kg-1 soil) was applied from two sources, ZnSO4 and Zn-EDTA. A control of both salinity and Zn was kept for comparison. Results showed that based on the biomass accumulation and K+/Na+ ratio, KSK-133 and BAS-198 emerged as salt tolerant and salt sensitive, respectively. Similarly, based on the Zn concentration, BAS-2000 was reported as Zn-in-efficient while IR-6 was a Zn-efficient genotype. Our results also revealed that plant growth, relative water content (RWC), physiological attributes including chlorophyll contents, ionic concentrations in straw and grains of all rice genotypes were decreased under salinity stress. However, salt tolerant and Zn-in-efficient rice genotypes showed significantly higher shoot K+ and Zn concentrations under saline conditions. Zinc application significantly alleviates the harmful effects of salinity by improving morpho-physiological attributes and enhancing antioxidant enzyme activities, and the uptake of K and Zn. The beneficial effect of Zn was more pronounced in salt-tolerant and Zn in-efficient rice genotypes as compared with salt-sensitive and Zn-efficient genotypes. In sum, our results confirmed that Zn application increased overall plant's performance under saline conditions, particularly in Zn in-efficient and tolerant genotypes as compared with salt-sensitive and Zn efficient rice genotypes. [ABSTRACT FROM AUTHOR]

Grain size influences the yield and quality of rice (Oryza sativa L.), and grain length is one of the component traits of grain size. In this study, a near-isogenic line LB3 with long grain size was constructed using japonica rice cultivar 02428, with short grain size, as the recipient parent and indica rice cultivar ZYX, with long grain size, as the donor parent, by multi-generation backcrossing and selfing. BSA-seq was used for preliminary QTL mapping and InDel markers were developed to fine map the locus. The major QTL, tentatively named qGL10, for grain length was located in a 128.45 kb region of chromosome 10. Combined with haplotype analysis of rice varieties, expression pattern analysis of candidate genes suggested LOC_Os10g39130 (OsMADS56) as a candidate gene. Sequence alignment of OsMADS56 in 02428 and LB3 revealed that there were 15 SNPs in the promoter region and four in the coding region. Further haplotype analysis suggested that SNP9 (G/A) located in the TGTCACA motif might account for the different expression levels of OsMADS56 in 02428 and LB3. These results lay a foundation for the application of qGL10 in molecular breeding of new rice varieties. [ABSTRACT FROM AUTHOR]

The present study high-lighted on the yet-explored extensive analyses of eating and cooking quality parameters in fifteen indigenous rice varieties. As rice is a vital staple crop globally that can feed one-third world's population solely, it is an imperious task to develop research for enhancement of its nutritional as well as eating and cooking quality (ECQ). The exploitation of identified nutrient-enriched rice germplasm for breeding application is the easiest way to get better quality rice. Satabdi IET-4786 (SAT) appeared to be very demanding by virtue of having sufficient level of amylose which is considered as key determinant of grain quality. The importance of Sabita (SAB), with regards to higher content of amylose and maltose with higher a-amylase activity and of Dudheshwar (DUD) with respect to protein and total free amino acid content in rice grain was also significant. Here we analyzed fifteen different local rice germplasms including aromatic and some high yielding cultivars to identify some qualitative as well as some quantitative traits related to nutrition and consumers' acceptance. The knowledge gained from this study will largely provide a path direction for the making a proper decision of considering germplasms for large-scale cultivation and dietary consumption. [ABSTRACT FROM AUTHOR]

Grain size is a key factor influencing grain yield and appearance quality in rice. We identified twelve quantitative trait loci (QTL) for grain length (GL), nine for grain width (GW), and nine for 1000-kernel weight (TKW) using GLU-SSSLs, which are single-segment substitution lines with Oryza glumaepatula as donor parent and Huajingxian 74 (HJX74) as recipient parent. Among the QTL, qGL1-2, qGL1-4, qGL9-2, qGW2-2, qGW9-1 and qTKW9-2 contributed to high grain yield. GL9 was identified as a candidate gene for qGL9-2 by map-based cloning and sequencing, and is a novel allele of GS9. The kernel of NIL-gl9 was slenderer and longer than that of HJX74, and the TKW and grain yield per plant of NIL-gl9 were higher than those of HJX74. The proportion of grain chalkiness of NIL-gl9 was much lower than that of HJX74. Thus, gl9 increased grain yield and appearance quality simultaneously. Three pyramid lines, NIL-gs3/gl9, NIL-GW7/gl9 and NIL-gw8/gl9, were developed and the kernel of each was longer than that of the corresponding recipient parent lines. The gl9 allele may be beneficial for breeding rice varieties with high grain yield and good appearance quality. [ABSTRACT FROM AUTHOR]

Somatic embryogenesis is an asexual reproduction process that occurs in many plant species, including rice. This process contains several totipotency markers such as Somatic Embryogenesis Receptor-like Kinase (SERK), Leafy Cotyledon1 (LEC1) and WUSCHEL-Related Homeobox4 (WOX4) and also a helpful model for embryo development and clones and transformations. Here, we report the gene expression during somatic embryo development correlates with regeneration frequency in 14 Javanica rice (pigmented and non-pigmented) using modified N6 media supplemented with Kinetin (2.0 mg/L) and NAA (1.0 mg/L). Although there have been advances in understanding the genetic basis of somatic embryogenesis in other varieties, rice is still unexplored, especially during somatic embryo development. Moreover, for the formation of callus induction from immature embryos, 2,4-D (2.0 mg/L, 3.0 mg/L) was used. This study analysed the gene expression of OsSERK, OsWOX4 and OsLEC1 genes through RT-PCR analysis. Higher expression of the OsLEC1 gene indicates that their function may correlate in the in vitro with the high response of rice after transfer to regeneration media. This study found that rice varieties of pigmented rice (MS Pendek and Gogoniti II) and non-pigmented rice (Pandan Ungu) showed high regeneration frequency, showing higher OsLEC1 expression than other varieties because OsLEC1 promotes the maturation of somatic embryos in plant regeneration on day 14. However, the contrast with Genjah nganjuk may be effective because of other regulatory genes. RT-PCR analysis showed OsSERK had less expression level than OsLEC1 and OsWOX4 in the varieties, which correlate with the percentage of plant regeneration, but not for Gogoniti II. In conclusion, the higher percentage of plant regeneration correlates with the higher expression level of OsLEC1 at day 14 of media regeneration of rice. [ABSTRACT FROM AUTHOR]

Serotonin is ubiquitous across all forms of life and functions in responses to biotic and abiotic stresses. In rice, the conversion of tryptamine to serotonin is catalyzed by Sekiguchi lesion (SL). Previous studies have identified an sl mutation (a null mutation of SL) in several rice varieties and confirmed its increase of resistance and cell death. However, a systematic understanding of the reprogrammed cellular processes causing cell death and resistance is lacking. We performed a multi-omics analysis to clarify the fundamental mechanisms at the protein, gene transcript, and metabolite levels. We found that cell death and Magnaporthe oryzae (M. oryzae) infection of the sl-MH-1 mutant activated plant hormone signal transduction involving salicylic acid (SA), jasmonic acid (JA), and abscisic acid (ABA) in multiple regulatory layers. We characterized the dynamic changes of several key hormone levels during disease progression and under the cell death conditions and showed that SA and JA positively regulated rice cell death and disease resistance. SL-overexpressing lines confirmed that the sl-MH-1 mutant positively regulated rice resistance to M. oryzae. Our studies shed light on cell death and facilitate further mechanistic dissection of programmed cell death in rice. [ABSTRACT FROM AUTHOR]

Development of hybrid rice with high yield and grain quality is a goal of rice breeding. To investigate the genetic mechanism of heterosis for rice milling and appearance quality in indica/xian rice, QTL mapping was conducted using 1061 recombinant inbred lines (RILs) derived from a cross of the xian rice cultivars Quan9311B (Q9311B) and Wu-shan-si-miao (WSSM), and a backcross F1 (BC1F1) population developed by crossing the RILs with Quan9311A (Q9311A), combined with phenotyping in two environments. The F1 hybrid (Q9311A - WSSM) showed various degrees of heterosis for milling and appearance quality. A total of 142 main-effect QTL (M-QTL) and 407 pairs of epistatic QTL (E-QTL) were identified for five milling and appearance quality traits and grain yield per plant (GYP) in the RIL, BC1F1 and mid-parental heterosis (HMP) populations. Differential detection of QTL in three populations revealed that most additive loci detected in the RILs did not show heterotic effects, but some of them did contribute to BC1F1 trait performance. Unlike heterosis of GYP, single-locus overdominance and epistasis were the main contributors to heterosis for milling and appearance quality. Epistasis contributed more to the heterosis for milling quality than to that for appearance quality. Three (four) QTL regions harboring opposite (consistent) directions of favorable allele effects for GYP and grain quality were identified, indicating the presence of partial genetic overlaps between GYP and grain quality. Three strategies are proposed to develop hybrid rice with high yield and good grain quality: 1) pyramiding favorable alleles with consistent directions of gene effects for GYP and grain quality at the M-QTL on different chromosomes; 2) introgressing favorable alleles for GYP and grain quality into the parents and then pyramiding and fixing these additive effects in hybrids; and 3) pyramiding overdominant and dominant loci and minimizing or eliminating underdominant loci from the parents. [ABSTRACT FROM AUTHOR]

Because high temperatures impair rice production, it is desirable to elucidate the regulatory mechanisms involved in rice response to heat stress. The objectives of this study were to identify candidate genes and characterize their response patterns during rice adaptation to high temperatures at the seedling stage. Ten heat-associated quantitative-trait loci were identified in a genome-wide association study. Comparison of transcript abundances in heat-sensitive and heat-tolerant rice pools under heat stress revealed approximately 400 differentially expressed genes. The expression of genes from heatsensitive accessions changed more than those from heat-tolerant accessions under heat stress. Alternative splicing (AS) events responded to heat stress in rice. The types of AS variants significant different between the heat-sensitive and heat-tolerant accessions. Expression patterns differing between the heat-sensitive and heat-tolerant accessions were identified for genes known to be involved in heat stress. We identified eleven genes associated with rice heat stress response. These genes could be pyramided to breed heat-tolerant rice accessions. [ABSTRACT FROM AUTHOR]

Nitrate (NO3-) uptake involves a finely regulated and complex multilevel response system. Elucidating the molecular mechanism of nitrate uptake may lead to improving the growth and productivity of plants in the presence of dynamic variation in nitrate concentration. In this study, we identified three lateral organ boundaries domain (LBD) transcription factors, OsLBD37, OsLBD38, and OsLBD39, as regulators of nitrate uptake in response to nitrogen (N) availability. OsLBD37, OsLBD38, and OsLBD39 were induced by ammonium and glutamine in rice roots. Individual or collective knockout of OsLBD37, OsLBD38, and OsLBD39 led to increased concentrations of nitrate and increased expression of OsNRT2.1, OsNRT2.2, and OsNRT2.3 respectively under high-N conditions, whereas overexpression of each of these three LBD genes produced opposite effects where N accumulation was reduced. Dual-luciferase reporter assay further confirmed that OsLBD37, OsLBD38, and OsLBD39 possessed transcription inhibitory activities in rice protoplast cells, downregulating the expression of OsNRT2.1/OsNRT2.2/OsNRT2.3. Yeast two-hybrid and bimolecular fluorescence complementation assays showed that OsLBD37 interacted with OsLBD37, OsLBD38, and OsLBD39 in the nucleus. Together, these results show that OsLBD37, OsLBD38, and OsLBD39 collaborate to inhibit the expression of OsNRT2.1/OsNRT2.2/OsNRT2.3 transporters under N-sufficient conditions, thereby helping rice plants avoid excessive nitrate accumulation that may affect their growth. [ABSTRACT FROM AUTHOR]

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The development of mutants and their further characterization offers an ample scope to isolate genes and genotypes with desire trait of interest. Ethyl methanesulphonate (EMS) is a widely used chemical mutagen applied for generating genetic variability in different crop species. This study aimed to assess the agronomic performance, genetic variability and character association of 11 EMS mutants (M3 generation) of rice derived from a promising local rice genotype (Fatemadhan). Seeds of the selected mutants, original parent and two popular varieties were grown at the field experimental farm of the Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh, Bangladesh. Significant inter-population differences for seven yield and yield contributing traits (viz., days to first flowering; days to maturity, DM; plant height, PH; number of effective tiller per plant, ET; panicle length; 100-seed weight, 100-SW; yield per plant) were observed. EMS Line 2 was found to be the most early maturing and high-yielding than those of the other mutants and check varieties. Analysis of heritability and genetic parameters revealed that all the traits are mostly controlled by genetic components while environment has little influence on them. The higher phenotypic and genotypic co-efficient of variation, heritability and genetic advance as percentage of mean confirmed the possibilities of rice yield improvement through phenotypic selection. Yield per plant showed significant positive correlation with ET whereas it showed negative correlation with DM, PH, and 100-SW. The first three components explained 81.4% of the total variation among the genotypes as revealed through principal component analysis. Thus, the promising mutant (EMS Line 2) isolated from this study can be released as an early maturing high-yielding rice variety. [ABSTRACT FROM AUTHOR]

This study has been conducted to determine genetic diversity of the common vetch lines and cultivars by using pairwise combinations of universal rice primers (URPs). A total number of 37 URP marker pairs were tested and twenty of those provided amplicons in the common vetch genome. The pairs of amplified URP markers provided a total of 83 bands and 62 of them were determined as polymorphic and were scattered to the whole genome. The average polymorphism rate of the primers was calculated as 73.5% while the polymorphism information content (PIC) values have ranged from 0.11 to 0.47 with an average of 0.24. The phylogenetic tree constructed based on UPGMA analysis provided three main clades. Two-dimensional plot of PCA and the UPGMA analysis showed that the URP markers successfully distinguished the genetic material based on their genetic origin. In conclusion, this study revealed that the use of pairwise combinations of URP markers could have a better power to reveal the level of polymorphism in plant genome. [ABSTRACT FROM AUTHOR]

Grain size is one of the most important factors affecting rice grain quality and yield, and attracts great attention from molecular biologists and breeders. In this study, we engineered a CRISPR/Cas9 system targeting the miR396 recognition site of the rice GS2 gene, which encodes growth-regulating factor 4 (OsGRF4) and regulates multiple agronomic traits including grain size, grain quality, nitrogen use efficiency, abiotic stress response, and seed shattering. In contrast to most previous genome editing efforts in which indel mutations were chosen to obtain null mutants, a mutant named GS2E carrying an in-frame 6-bp deletion and 1-bp substitution within the miR396-targeted sequence was identified. GS2E plants showed increased expression of GS2 in consistent with impaired repression by miR396. As expected, the gain-of-function GS2E mutant exhibited multiple beneficial traits including increased grain size and yield and bigger grain length/width ratio. Thousand grain weight and grain yield per plant of GS2E plants were increased by 23.5% and 10.4%, respectively. These improved traits were passed to hybrids in a semidominant way, suggesting that the new GS2E allele has great potential in rice improvement. Taken together, we report new GS2 germplasm and describe a novel gene-editing strategy that can be widely employed to improve grain size and yield in rice. This trait-improvement strategy could be applied to other genes containing miRNA target sites, in particular the conserved miR396-GRF/GIF module that governs plant growth, development and environmental response. [ABSTRACT FROM AUTHOR]

Germplasm conserved in gene banks is underutilized, owing mainly to the cost of characterization. Genomic prediction can be applied to predict the genetic merit of germplasm. Germplasm utilization could be greatly accelerated if prediction accuracy were sufficiently high with a training population of practical size. Large-scale resequencing projects in rice have generated high quality genome-wide variation information for many diverse accessions, making it possible to investigate the potential of genomic prediction in rice germplasm management and exploitation. We phenotyped six traits in nearly 2000 indica (XI) and japonica (GJ) accessions from the Rice 3K project and investigated different scenarios for forming training populations. A composite core training set was considered in two levels which targets used for prediction of subpopulations within subspecies or prediction across subspecies. Composite training sets incorporating 400 or 200 accessions from either subpopulation of XI or GJ showed satisfactory prediction accuracy. A composite training set of 600 XI and GJ accessions showed sufficiently high prediction accuracy for both XI and GJ subspecies. Comparable or even higher prediction accuracy was observed for the composite training set than for the corresponding homogeneous training sets comprising accessions only of specific subpopulations of XI or GJ (within-subspecies level) or pure XI or GJ accessions (across-subspecies level) that were included in the composite training set. Validation using an independent population of 281 rice cultivars supported the predictive ability of the composite training set. Reliability, which reflects the robustness of a training set, was markedly higher for the composite training set than for the corresponding homogeneous training sets. A core training set formed from diverse accessions could accurately predict the genetic merit of rice germplasm. [ABSTRACT FROM AUTHOR]

The development of rice cultivars with improved nitrogen use efficiency (NUE) is desirable for sustainable agriculture. Achieving this goal depends in part on understanding how rice responds to low soil nitrogen (N) and identifying causative genes underlying this trait. To identify quantitative trait loci (QTL) or genes associated with low N response, we conducted a genome-wide association study (GWAS) using a diverse panel of 230 rice accessions and performed a transcriptomic investigation of rice accessions with differential responses to low N stress at two N levels. We detected 411 GWAS-associated genes in 5 QTL and 2722 differentially expressed genes in response to low N, of which 24 were identified by both methods and ranked according to gene annotations, literature queries, gene expression, and genetic diversity analysis. The large-scale datasets obtained from this study reveal low N-responsive characteristics and provide insights towards understanding the regulatory mechanisms of N-deficiency tolerance in rice, and the candidate genes or QTL would be valuable resources for increasing rice NUE via molecular biotechnology. [ABSTRACT FROM AUTHOR]

The Asian cultivated rice Oryza sativa can be classified into two major subspecies: japonica/geng and indica/xian. There are large physiological and phenotypic differences between the two subspecies, with each having its advantages and disadvantages. Understanding the differences between xian and geng could provide a foundation for cultivar improvement based on hybridization between subspecies in order to synthesize favorable traits. We review the origin and domestication of xian and geng rice, compare their differences in terms of physiological and phenotypical traits, and describe the molecular mechanism differences between the subspecies. Based on this knowledge, we propose an ideal plant architecture of geng rice varieties for northern regions. [ABSTRACT FROM AUTHOR]

Plant height is an important morphological trait that affects crop yield. Several genes related to plant height and yield have been reported in rice (Oryza sativa L.), however, the molecular mechanism underlying the regulation of these traits is still not completely understood. VP64 is widely used as a transcriptional activator to investigate the biological function of genes encoding transcription factors. Here, we identified a novel bZIP transcription factor OsbZIP62 that is involved in modulating agronomic traits in rice. Overexpression of OsbZIP62-VP64 (Osb-ZIP62V) significantly increases the plant height and yield per plant in rice. RNA-seq analysis showed that some plant height and panicle development related genes (i.e., OsEATB, OsDSS1 and OsGA3ox2) were up-regulated in OsbZIP62V overexpressing rice plants. Besides, OsbZIP62 could also bind to the promoters of several putative target genes. These results suggested that OsbZIP62 plays a role as transcriptional regulator in regulating the expression of genes associated with agronomic traits, and OsbZIP62 fused with VP64 would be useful in crop genetic modification with improved plant architecture and yield. [ABSTRACT FROM AUTHOR]

Brown planthopper (BPH) Nilaparvata lugens (Stål.) is considered the most destructive rice pest in rice-growing countries including Sri Lanka. Resistance breeding considered the most economical management strategy, starts by identifying new genetic resources for BPH resistance and comparative analysis with existing donors. So far, scientists have identified 38 genes/QTLs responsible for BPH resistance. This study explored the BPH resistance in five wild rice species in Sri Lanka, including the endemic species Oryza rhizomatis. One recommended rice variety; Bg 352, fourteen O. rhizomatis accessions, and one accession from Oryza nivara, Oryza rufipogon, Oryza granulata and Oryza eichingeri screened by the honeydew test. The experiment was arranged in a complete randomized design with fifteen replicates with Bg 380 and Ptb 33 as susceptible and resistant checks respectively. The lower amount of honeydew excretion recorded in all tested O. rhizomatis accessions, O. nivara, O. granulata, and O. eichingeri accessions suggested BPH resistance. Both Ptb 33 and O. rufipogon showed a similar level of resistance with low honeydew excretion. The varieties Bg 352 and Bg 380 showed a high amount of honeydew excretions confirming higher susceptibility to the BPH. Therefore, all fourteen accessions of O. rhizomatis and the selected accessions of O. nivara and O. eichingeri are potential donors for rice breeding programs. Further, the coding sequences (CDS) of known BPH genes of O. sativa were used as queries to search similar genes in wild rice genomes. The CDS coverage and phylogenetic analysis suggest, of known BPH resistance genes, at least BPH6, BPH9, BPH14-1, and BPH18 are present in O. rhizomatis, O. eichingeri, O. nivara, and O. rufipogon genomes. This information will assist in marker-assisted breeding attempts. [ABSTRACT FROM AUTHOR]

Genetic resistance in rice through native traits is an important tactic to manage Brown planthopper (BPH), Nilaparvata lugens Staal (Homoptera: Delphacidae) which is one of the most dreaded pests in the farmer's field causing serious crop losses. Many sources of resistance, both from cultivated and wild accessions, are known with almost 36 resistance genes mapped to different chromosomes through phenotypic and genotypic selections. A majority of resistance genes identified are effective for BPH biotypes prevailing in Southeast Asia and China. For South Asia, very few BPH resistance genes are effective but without their utilization for the development of commercial hybrids and varieties. A new source of resistance HSPP 6417 has been identified in the present paper, which displayed resistance to 11 populations of BPH collected from different rice ecologies of India. The new source HSPP 6417 had an adverse effect on the population dynamics of BPH by inhibiting the population build-up on the plants. The resistance of HSPP 6417 was equivalent to the only source of resistance in India, G7253 used to develop a commercial rice hybrid AZ8433 DT. On crossing HSPP 6417 with other prolific restorer lines of the commercial hybrids, the major genes were found to control its modes of inheritance. Field trials with F4 generation revealed that resistance was stable with good agronomic performance under infestations. The implications of using such a source of resistance for developing BPH resistant hybrids are discussed in the paper. [ABSTRACT FROM AUTHOR]