Rice Populations Research Articles

Trait Association Studies to Determine Selection Indices in F5 Segregating Populations of Rice (Oryza sativa L.)

The experiment consisted of 38 promising F5 breeding lines developed and evaluated for correlation coefficient, path coefficient and selection indices studies with four check varieties viz., NVSR-2435, Sardar, Lalkada Gold and GR-18 in RBD with three replications during kharif-2023 at RRRS, Vyara, Gujarat. Genotypic correlation analysis revealed that grain yield per plant appeared to be positively and significantly correlated with productive tillers per plant, plant height, panicle length, straw yield per plant and 100 grain weight, which suggested that these characters can be improved simultaneously towards higher grain yield per plant by direct selection. Genotypic path analysis revealed that positive and direct effects on grain yield per plant were exhibited by days to maturity, productive tillers per plant, panicle length, 100 grain weight and straw yield per plant. Among these traits, panicle length, productive tillers per plant, 100 grain weight and straw yield per plant exhibited direct effect along with highly significant and positive association with grain yield per plant. Therefore, selection for such traits may be considered as most important yield attributing characters. The negligible residual effect of 0.037 was observed in path analysis, indicates that the model explained large proportion of variance. Thirty-one selection indices were constructed in all possible combinations of grain yield per plant (X1) along with four components viz., productive tiller per plant (X2), panicle length (X3), 100 grain weight (X4) and straw yield per plant (X5) through equal weight method. Among all the selection indices, the relative efficiency (%) and expected genetic advance (GA) was noted maximum with four characters selection index (I1245) compared to grain yield per plant (I1).

Nested association mapping population in japonica rice: Development, characterization, and application in genome-wide association studies

Multiparental mapping populations hold great potential for dissecting quantitative traits and rapidly identifying genetic determinants. We developed a japonica nested association mapping population, KNU_NAM, comprising 880 lines derived from ten recombinant inbred lines (RILs) families of prominent varieties and the elite Korean variety Shindongjin. Genetic characterization of KNU_NAM revealed 48,159 polymorphic SNPs, with family counts ranging from 18,787 to 42,578, and an average of 30,019 SNPs per family. Further molecular diversity analysis of KNU_NAM indicated reduced population structure and broad genetic diversity. Genome-wide association studies (GWAS) on five morphological traits identified 47 significant marker-trait associations (MTAs), with a set of 18 MTAs located on chromosome 9. Linkage disequilibrium (LD) block analysis of this region revealed 15 haplotypes, and identified five key genes associated with panicle architecture: OsDEP1, OsEATB, OsLGD1, and OsSPL18. Additionally, two non-synonymous MTAs on chromosome 7 were located on exon of OsPRR37/Ghd7.1, a gene associated with plant height, heading date, and grain number per panicle. Further phenotypic performance analysis of haplotypes from these hotspot regions revealed significant differences in the targeted traits. The study validates the potential of KNU_NAM and GWAS for high-resolution genetic mapping in rice breeding programs, highlighting the utility of these populations for enhancing genetic diversity and improving trait selection in rice.

Grain Appearance Quality of Parental and \(F_2\) Segregating Populations of Aus Rice (Oryza sativa L.)

Longer grain length with smaller grain breadth, length-breadth ratio and 1000-grain weight is considered desirable character for the development of fine grain premium quality rice. In the present experiment, grain appearance quality of 15 F2 families and 10 parental genotypes were determined to select fine grain rice. The maximum mean value for thousand seed weight was found from the genotypes P2 (29.32g), P1 (28.89g), and F2 generations of P2 x P5 (32.77g), P2 x P1 (27.30g), P1 x P4 (26.04g) and were considered as high yielders in terms of grain weight. The highest mean values for grain length were found from the genotypes P6 (9.95 mm; grain breadth 2.23 mm), P7 (9.36 mm; grain breadth 2.62 mm), and F2 generations of P6 x P7 (9.46 mm; grain breadth 2.44 mm), P3 x P6 (9.40 mm; grain breadth 2.18 mm), P7 x P6 (9.37 mm; grain breadth 2.29 mm), P7 x P3 (9.36 mm; grain breadth 2.33 mm). The F2 progenies of the cross P1 x P4 (7.79 to 11.61 mm) and P6 x P3 (7.69 to 11.11 mm) showed extremes performance for grain length indicating transgressive segregation for this trait. The superior genotypes with desirable grain characters could be selected from transgressive segregation of F2 families for the development of new varieties of fine grain rice.

Evaluating the effect of organic NPK granules on yield, nutrient uptake, post-harvest soil fertility and soil microbial population in rice (Oryza sativa L.)

Rice is the most important and staple food crop for more than two third of population of India. India is the second largest rice producing country in the world after China. Although, rice planted area in India is 40 per cent higher than in China, Indian rice production is 30 percent below Chinese production because of lower yields. Among several constraints of production, nutrient management plays a key role in realizing sustainable yield from any given cultivation practices. Integrated nutrient management system plays a vital role in balancing the soil fertility and plant nutrient supply to an optimum level through the judicious and efficient use of chemical fertilizers, green manure, FYM and biofertilizers leading to an eco-friendly approach and economically viable solution for this problem. Continuous integrated use of organic manures with chemical fertilizers would be quite promising in assessing the sustainability of a cropping system vis-à-vis monitoring the soil properties. To investigate further, a field experiment was conducted at the Experimental Farm, Department of Agronomy, Annamalai University, Annamalai Nagar, Cuddalore district of Tamil Nadu from June to September 2023 with a key objective of evaluating the effect of combined application of graded levels of conventional fertilizers along with organic NPK granules in lowland rice. The experiment was laid out in randomized block design with seven treatments comprised of different levels of conventional fertilizers along with organic NPK granules. Among the nutrient management evaluated, all the yield attributes of lowland rice viz., grain yield, straw yield, uptake of nutrients and post-harvest soil available nutrients were significantly influenced by the application of 70% NPK through synthetic fertilizers and 30% NPK through organic granules. Combining conventional fertilizers along with organic NPK granules improved nitrogen use efficiency via metabolite production, enzyme activity stimulation, and microbial rhizosphere interactions significantly enhancing the yield attributes and yield.

Volatile Organic Compounds Produced by Bacillus sp. Strain R2 Inhibit Aspergillus flavus Growth In Vitro and in Unhulled Rice.

Volatile organic compounds (VOCs) produced by Bacillus species exhibit biocontrol activity against fungal pathogens of fruits and vegetables. However, research on the effect of VOCs on Aspergillus flavus in stored grains is limited. This study aimed to investigate the effects of VOCs extracted from the strain R2, which was isolated from unhulled rice and identified as Bacillus paramycoides on A. flavus in vitro and unhulled rice. R2 VOCs effectively inhibited conidial germination and the hyphal growth of A. flavus in vitro. Moreover, R2 VOCs reduced the fungal population, aflatoxin B1 (AFB1) levels, and free fatty acid (FFA) value by 90.8%, 67%, and 38.7%, respectively, in unhulled rice. Eighteen R2 VOCs were identified using headspace solid-phase micro-extraction gas chromatography-mass spectrometry, and the individual activity of the VOCs against A. flavus was tested in vitro. Benzaldehyde (Ben) and 3,7-dimethyl-1-octanol (Dmo) showed strong inhibitory activities against A. flavus on PDA plates, with inhibition rates of 100% and 91.2%, respectively, at a concentration of 20 μL/dish. Ben at the concentration of 0.09 mg/mL, Dmo at the concentration of 0.07 mg/mL, or a mixture of both at halved concentrations could reduce the fungal population, AFB1 levels, and FFA content in unhulled rice. Our findings suggest that R2 VOCs are good alternatives to traditional chemical fumigants for suppressing A. flavus in stored grains. However, further research is necessary to establish the optimal fumigation concentration of these two components in unhulled rice. The impact of their residues on grain quality should be explored through sensory evaluation and nutritional analysis, and their safety to the environment and human body should be evaluated through safety assessment.

Analysis of the Rice Raffinose Synthase (OsRS) Gene Family and Haplotype Diversity.

Based on the genome information of rice (Nipponbare), this study screened and identified six raffinose synthase (RS) genes and analyzed their physical and chemical properties, phylogenetic relationship, conserved domains, promoter cis-acting elements, and the function and genetic diversity of the gene-CDS-haplotype (gcHap). The results showed that these genes play key roles in abiotic stress response, such as OsRS5, whose expression in leaves changed significantly under high salt, drought, ABA, and MeJA treatments. In addition, the OsRS genes showed significant genetic variations in different rice populations. The main gcHaps of most OsRS loci had significant effects on key agronomic traits, and the frequency of these alleles varied significantly among different rice populations and subspecies. These findings provide direction for studying the RS gene family in other crops.

Substitutive Effects of Upland Rice and Soybean Plant Populations on the Performance of the Component Crops in Intercropping System

Substitutive Effects of Upland Rice and Soybean Plant Populations on the Performance of the Component Crops in Intercropping System

Multiomics of a rice population identifies genes and genomic regions that bestow low glycemic index and high protein content

To counter the rising incidence of diabetes and to meet the daily protein needs, we created low glycemic index (GI) rice varieties with protein content (PC) surpassing 14%. In the development of recombinant inbred lines using Samba Mahsuri and IR36 amylose extender (IR36ae) as parental lines, we identified quantitative trait loci and genes associated with low GI, high amylose content (AC), and high PC. By integrating genetic techniques with classification models, this comprehensive approach identified candidate genes on chromosome 2 (qGI2.1/qAC2.1 spanning the region from 18.62 Mb to 19.95 Mb), exerting influence on low GI and high amylose. Notably, the phenotypic variant with high value was associated with the recessive allele of the starch branching enzyme 2b (sbeIIb). The genome-edited sbeIIb line confirmed low GI phenotype in milled rice grains. Further, combinations of alleles created by the highly significant SNPs from the targeted associations and epistatically interacting genes showed ultralow GI phenotypes with high amylose and high protein. Metabolomics analysis of rice with varying AC, PC, and GI revealed that the superior lines of high AC and PC, and low GI were preferentially enriched in glycolytic and amino acid metabolisms, whereas the inferior lines of low AC and PC and high GI were enriched with fatty acid metabolism. The high amylose high protein recombinant inbred line (HAHP_101) was enriched in essential amino acids like lysine. Such lines may be highly relevant for food product development to address diabetes and malnutrition.

Analysis of Rice Demand in Klaten Regency

This study aims to analyze the influence of rice prices, population size, and income on rice demand, as well as to determine the elasticity of rice demand in Klaten Regency. A descriptive analysis method was employed using secondary time series data over a period of 10 years (2013-2022), which included rice demand and population data. The data analysis model applied was multiple linear regression and classical assumption tests. Hypotheses were tested using t-tests, F-tests, and R-squared tests. The results indicate that: 1) Rice prices have a negative influence on rice demand, with a p-value of 0.06; 2) Population size has a positive influence on rice demand, with a p-value of 0.003; 3) Per capita income positively influences rice demand, with a p-value of 0.004; and 4) Rice demand is inelastic, as the price elasticity coefficient (0 < Ep < 1) suggests that changes in rice demand are smaller than changes in rice prices. Income elasticity (EI > 1) indicates that rice demand increases significantly with higher income levels.

Landrace introgression contributed to the recent feralization of weedy rice in East China

This study leveraged knowledge of the specific known cultivar progenitor "Nanjing11" of a weedy rice population from East China, and discovered that the landrace introgression greatly contributed to the recent feralization of modern cultivars, including the introduction of the Rc gene that confers key weedy traits such as red pericarp and seed dormancy.

Analysis of Rice Blast Fungus Genetic Diversity and Identification of a Novel Blast Resistance OsDRq12 Gene.

The rice blast fungus Magnaporthe oryzae poses a significant challenge to maintaining rice production. Developing rice varieties with resistance to this disease is crucial for its effective control. To understand the genetic variability of blast isolates collected between 2015 and 2017, the 27 monogenic rice lines that carry specific resistance genes were used to evaluate blast disease reactions. Based on criteria such as viability, virulence, and reactions to resistance genes, 20 blast isolates were selected as representative strains. To identify novel resistance genes, a quantitative trait locus analysis was carried out utilizing a mixture of the 20 representative rice blast isolates and a rice population derived from crossing the blast-resistant cultivar 'Cheongcheong' with the blast-susceptible cultivar 'Nagdong'. This analysis revealed a significant locus, RM1227-RM1261 on chromosome 12, that is associated with rice blast resistance. Within this locus, 12 disease resistance-associated protein genes were identified. Among them, OsDRq12, a member of the nucleotide-binding, leucine-rich repeat disease resistance family, was chosen as the target gene for additional computational investigation. The findings of this study have significant implications for enhancing rice production and ensuring food security by controlling rice blast and developing resistant rice cultivars.

Impact of IPM practices on microbial population and disease development in transplanted and direct-seeded rice.

Integrated pest management (IPM) is a comprehensive approach to managing diseases, focusing on combining various strategies to reduce pathogen populations effectively and in an environmentally conscious way. We investigated the effects of IPM on beneficial microbial populations and its relationship with pathogen populations in both direct-seeded rice (DSR) and transplanted rice (TR) systems. This study demonstrates that IPM practices have significantly higher populations of beneficial microbes, such as Trichoderma harzianum and Pseudomonas fluorescens, and lower level of the pathogen Fusarium verticillioides compared to non-IPM (farmer practices). The average mean population of T. harzianum was 6.38 × 103 CFU/g in IPM compared to 3.22 × 103 CFU/g in non-IPM during 2019 in TR at Bambawad. P. fluorescens mean population in 2019 was significantly higher in IPM (4.67 × 103 CFU/g) than in non-IPM (3.82 × 103 CFU/g) at the Karnal location in DSR. The F. verticillioides populations were significantly lower in IPM fields (9.46 × 103 CFU/g) compared to non-IPM fields (11.48 × 103 CFU/g) during 2017 at Haridwar in TR. Over three years, a significant increase in the populations of beneficial microbes in IPM plots was observed in all three locations of both TR and DSR, highlighting the sustainable impact of IPM practices. Disease dynamics analysis revealed that IPM effectively managed key diseases in both DSR and TR systems, with significant correlations between microbial density and disease severity. A significant positive correlation was recorded between F. verticillioides population and bakanae incidence at all three locations. Sheath blight incidence was negatively correlated with P. fluorescens population in both TR and DSR. In DSR, bacterial blight and brown spot diseases are reduced with the increased population of T. harzianum. Bioagents T. harzianum and P. fluorescens reduced disease incidence, underscoring the role of beneficial microbes in disease suppression and their importance for sustainable production using IPM practices.

Inheritance pattern of Qualitative traits, Genetic analysis and association of yield attributes in F2 populations of Rice (Oryza sativa)

Understanding the extent of genetic variability within the segregating generations is crucial for identifying superior segregants with high yield and better market acceptability. Thus, the present study was carried out to quantify the extent of genetic variation available in the segregating population of rice. Three crosses, viz., CO 55 × IC 457996, CO 55 × IC 464685, and CO 55 × IC 115439 were evaluated using a non-randomized experimental design for six yield attributing and two physical grain quality traits in F2 generation. The inheritance pattern of basal leaf sheath colour and grain colour in CO 55 × IC 115439 indicate digenic complementary gene interaction (9:7), whereas grain colour in CO 55 × IC 464685 exhibits inhibitory gene action (13:3). The positively skewed nature of productive tillers per plant and single-plant yield in the F2 segregants emphasizes the need for intensive selection to facilitate rapid improvement due to the influence of complementary gene action. Moderate to high GCV with high heritability and GAM for traits such as plant height, productive tillers per plant, hundred seed weight, grain width, and single-plant yield in the F2 segregants underscore the prevalence of additive gene action and thus provide the most effective condition for simple phenotypic selection. Moreover, productive tillers per plant and single-plant yield showed a strong positive association in all the crosses. Therefore, productive tillers per plant can be considered an indicator trait when selecting high-yielding segregants for grain yield improvement.

Data Mining Forecasting Methods for Predicting the Availability of Sustainable Rice Commodities in Bali Province

This research aims to prepare the capacity of local governments to provide sufficient strategic food production, especially rice, which is the commodity most consumed by the people of Gianyar Regency every year. This research is descriptive research with a quantitative approach. The data used in the analysis is secondary data in the form of rice production data (tons), rice production (tons), harvested area (ha), public consumption of rice commodities (kg) and population (people) from 2018 to 2022. obtained from the Central Statistics Agency (BPS) and the Bali Province Agriculture and Food Security Service. The results of this research show that the forecasting method using the Backpropagation algorithm can be used to provide an approach to forecasting rice harvest area, rice production, rice production, community consumption levels, and population in 2023 and 2024 in Gianyar Regency. The Backpropagation architectural design uses 12 input layers, 10 hidden layers, and 1 output with Mean Absolute Percentage Error (MAPE) results of 0.22 and Mean Absolute Deviation (MAD) of 339 with a very good forecasting category. The average ratio of normative per capita consumption to food availability, especially rice commodities in Gianyar Regency in 2023 will experience a high deficit condition with a Cnorm Ratio value (z) = 1.52 and in 2024 will experience a high deficit condition with a Cnorm Ratio value (z) = 1.57. The forecasting method using the Backpropagation Algorithm can still be developed by focusing on each district by calculating the overall food commodities in that district.

Comparative histology of abscission zones reveals the extent of convergence and divergence in seed shattering in weedy and cultivated rice.

The modification of seed shattering has been a recurring theme in rice evolution. The wild ancestor of cultivated rice disperses its seeds, but reduced shattering was selected during multiple domestication events to facilitate harvesting. Conversely, selection for increased shattering occurred during the evolution of weedy rice, a weed invading cultivated rice fields that has originated multiple times from domesticated ancestors. Shattering requires formation of a tissue known as the abscission zone (AZ), but how the AZ has been modified throughout rice evolution is unclear. We quantitatively characterized the AZ characteristics of relative length, discontinuity, and intensity in 86 cultivated and weedy rice accessions. We reconstructed AZ evolutionary trajectories and determined the degree of convergence among different cultivated varieties and among independent weedy rice populations. AZ relative length emerged as the best feature to distinguish high and low shattering rice. Cultivated varieties differed in average AZ morphology, revealing lack of convergence in how shattering reduction was achieved during domestication. In contrast, weedy rice populations typically converged on complete AZs, irrespective of origin. By examining AZ population-level morphology, our study reveals its evolutionary plasticity, and suggests that the genetic potential to modify the ecologically and agronomically important trait of shattering is plentiful in rice lineages.

Predictive modelling of yellow stem borer population in rice using light trap: A comparative study of MLP and LSTM networks

AbstractThe yellow stem borer (YSB), Scirpophaga incertulas (Walker), is a major insect pest that significantly damages rice crop. This study investigates methods to predict YSB populations in rice fields, aiming to develop an early warning system. Traditionally, rice farmers rely on light traps to monitor YSB presence. However, this study goes beyond this approach by combining light‐trap data with weather information (temperature, humidity, rainfall) and utilizing powerful artificial intelligence (AI) techniques to forecast future YSB populations. Two AI methods, multilayer perceptron (MLP) and long short‐term memory (LSTM), were employed to estimate YSB populations and assess their performance. The results revealed that the LSTM model outperformed the MLP model based on statistical metrics like RMSE, MAE, and R2 values. Utilizing LSTM model with historical data, stakeholders in the Eastern Coastal Plains and Hills agro‐climatic zone of India can gain a significant advantage in predicting YSB populations well in advance. This early warning system can alert stakeholders of potential YSB outbreaks, allowing them to take timely management actions and protect their rice crops from substantial yield losses.

Marker assisted identification of improved restorer lines with yield enhancing genes adaptable for aerobic conditions

To feed the world's growing population, development and introduction of climate resilient rice varieties/hybrids with increased yield ability are the need of the hour. This can be accomplished through novel genetic approaches such as hybrid rice technology, using a diverse set of parental lines with high restoring ability and specific desirable traits. In our study, for perse genetic yield improvement in aerobic restorer line AR 9-18R, hybridization was carried out with yield enhancing donor YPK 198 possessing Gn1a and OsSPL14 during kharif, 2018 and generated F1s were fixed for its hybridity through morphological and molecular analysis. In kharif, 2019 two hundred and five F2 population obtained were screened for two yield-enhancing Gn1a and OsSPL14 genes along with two fertility restorer genes Rf3 and Rf4 at ICAR-IIRR, Hyderabad. c2 analysis revealed that the c2 value of both yield enhancing genes was non-significant as the population was segregated in a ratio of 1:2:1. whereas c2 value for fertility restorer genes was significant as population deviated from 1:2:1. Phenotypic evaluation of F2 population for yield related traits exhibited high GCV and PCV for number of productive tillers, number of grains per panicle and single plant yield. Plant height, number of productive tillers, number of grains per panicle and single plant yield displayed high heritability along with high genetic advance as per cent of mean. Correlation and path co-efficient analysis revealed that plant height, number of productive tillers and number of grains per panicle are very important traits as selection criteria for effective yield improvement.

Estimating genetic variance contributed by a quantitative trait locus: removing nuisance parameters.

The main objective of mapping quantitative trait loci (QTL) and genome-wide association studies (GWAS) is to identify and locate QTLs on the genome. Estimating the sizes of QTL is equally important as identifying the QTLs. The size of a QTL is often measured by the QTL variance, or the proportion of phenotypic variance explained by the QTL, known as the QTL heritability. The reported QTL heritability is biased upward for small-sized QTLs estimated from small samples, especially in GWAS with a very small P-value threshold accommodating to Bonferroni correction for multiple tests. The phenomenon is called the Beavis effect. Methods of correcting the Beavis effect have been developed for additive effect models. Corresponding methods are not available for QTLs with more than one effect, such as QTLs including dominance and other genetic effects. In this study, we developed explicit formulas for estimating the variances and heritability for QTL with multiple effects. We also developed a method to remove nuisance parameters via an annihilator matrix. Finally, biases in estimated QTL variances caused by the Beavis effect are investigated and corrected. The new method is demonstrated by analyzing the 1000 grain weight (KGW) trait in a hybrid rice population.

Modeling the spread of rice blast in rice plant group based on cellular automata

Studying and modeling the process of the disease and spread of blast can guide fertilization and reduce the amount of pesticide application. Since most of the existing research focuses on the pathogenesis of the rice blast fungus and the interaction between the plant structure and the fungus, this paper presents a method to simulate the spread of rice blast among rice populations. The method is divided into the following processes. First, based on the cellular automata grid dynamics model, the cell state corresponds to the degree of infection of the rice blast fungus, and its ability to simulate the spatiotemporal evolution of complex systems is used to simulate the spread of disease spots on the surface of rice leaves. Second, according to the biological mechanism of the rice blast fungus and the position of the first infected leaf in a single rice plant, the normal distribution function is used to calculate the infection probability of the remaining leaves, and then the transmission mode of the disease inside a single rice plant is simulated. Then, in view of the natural phenomenon that the blast fungus spores spread with the wind, the wind factor is added to propose a method for the spread of the rice blast fungus among the population of rice plants, and thus a model for the spread of the pathogen among the entire plant population was established. Finally, we set up a simulation system for the spread of rice blasts in rice fields and visualized the spread and spread trend of rice blasts in rice populations. In the simulation experiment, the infection process of rice blast on the surface of the rice leaf was simulated, and the change process of the shape of the diseased spot can be visually seen. This paper not only provides a new idea for the research on pathogen propagation and diffusion between plants in agricultural production but also provides a reference for how to realistically visualize the pathogen propagation model in the virtual agricultural scene.

Systems genomics of salinity stress response in rice.

Populations can adapt to stressful environments through changes in gene expression. However, the role of gene regulation in mediating stress response and adaptation remains largely unexplored. Here, we use an integrative field dataset obtained from 780 plants of Oryza sativa ssp. indica (rice) grown in a field experiment under normal or moderate salt stress conditions to examine selection and evolution of gene expression variation under salinity stress conditions. We find that salinity stress induces increased selective pressure on gene expression. Further, we show that trans-eQTLs rather than cis-eQTLs are primarily associated with rice's gene expression under salinity stress, potentially via a few master-regulators. Importantly, and contrary to the expectations, we find that cis-trans reinforcement is more common than cis-trans compensation which may be reflective of rice diversification subsequent to domestication. We further identify genetic fixation as the likely mechanism underlying this compensation/reinforcement. Additionally, we show that cis- and trans-eQTLs are under different selection regimes, giving us insights into the evolutionary dynamics of gene expression variation. By examining genomic, transcriptomic, and phenotypic variation across a rice population, we gain insights into the molecular and genetic landscape underlying adaptive salinity stress responses, which is relevant for other crops and other stresses.