Development Of Rice Varieties Research Articles

The Development of Multi-Resistant Rice Restorer Lines and Hybrid Varieties by Pyramiding Resistance Genes against Blast and Brown Planthopper

Rice blast, caused by the fungus Magnaporthe oryzae, and brown planthopper (BPH) infestation are two of the most destructive problems of rice production in China. The development of multi-resistant varieties is widely recognized as the most efficient and environmentally friendly approach to controlling crop diseases and pests. Functional molecular markers (FMMs) have been developed from functional variants in the genic region associated with trait variation, greatly enhancing the efficiency of identifying and pyramiding valuable genes in crop breeding. In this study, two FMMs and a multiplex PCR amplification system were developed for two major broad-spectrum BPH resistance genes, Bph6 and Bph9. With the assistance of FMMs in the multi-resistant rice restorer-line development pipeline, two lines (Huahui7713 and Huahui3006) with blast and BPH resistance were developed by pyramiding three resistance genes Pigm, Bph6 and Bph9. Two new hybrid rice varieties, Weiliangyou7713 and Xuanliangyou3006, derived from Huahui7713 and Huahui3006, have been developed and commercialized in China. Weiliangyou7713 and Xuanliangyou3006 exhibit enhanced resistance to both blast and BPH, while maintaining optimal yield and grain quality. The adoption of Weiliangyou7713 continues to expand, now being cultivated on a large scale, which is promising for its future role in reducing the dependence on chemical fungicides and pesticides in rice production. This suggests that the implementation of Huahui7713 and Huahui3006 in targeted breeding programs could be highly beneficial for developing rice varieties with strong resistance to blast and BPH.

Creation of Bacterial Blight Resistant Rice by Targeting Homologous Sequences of Xa13 and Xa25 Genes

Bacterial blight is a destructive disease in rice caused by Xanthomonas oryzae pv. oryzae (Xoo). Single resistance genes often have limitations in providing broad-spectrum resistance, as pathogens continuously evolve and vary. Breeding rice varieties with multiple disease resistance genes has proven to be an effective strategy for controlling bacterial blight. In this study, a single Cas9/gRNA construct was used to target the homologous sequences of Xa13 and Xa25 genes through destroying the target gene function, creating bacterial blight resistance in five rice varieties. These materials provide promising germplasm resources for the development of rice varieties with durable resistance to bacterial blight.

Pangenome-Wide Association Study and Transcriptome Analysis Reveal a Novel QTL and Candidate Genes Controlling both Panicle and Leaf Blast Resistance in Rice

Cultivating rice varieties with robust blast resistance is the most effective and economical way to manage the rice blast disease. However, rice blast disease comprises leaf and panicle blast, which are different in terms of resistance mechanisms. While many blast resistant rice cultivars were bred using genes conferring resistance to only leaf or panicle blast, mining durable and effective quantitative trait loci (QTLs) for both panicle and leaf blast resistance is of paramount importance. In this study, we conducted a pangenome-wide association study (panGWAS) on 9 blast resistance related phenotypes using 414 international diverse rice accessions from an international rice panel. This approach led to the identification of 74 QTLs associated with rice blast resistance. One notable locus, qPBR1, validated in a F4:5 population and fine-mapped in a Heterogeneous Inbred Family (HIF), exhibited broad-spectrum, major and durable blast resistance throughout the growth period. Furthermore, we performed transcriptomic analysis of 3 resistant and 3 sensitive accessions at different time points after infection, revealing 3,311 differentially expressed genes (DEGs) potentially involved in blast resistance. Integration of the above results identified 6 candidate genes within the qPBR1 locus, with no significant negative effect on yield. The results of this study provide valuable germplasm resources, QTLs, blast response genes and candidate functional genes for developing rice varieties with enduring and broad-spectrum blast resistance. The qPBR1, in particular, holds significant potential for breeding new rice varieties with comprehensive and durable resistance throughout their growth period.

The Function of SD1 on Shoot Length and its Pyramiding Effect on Shoot Length and Plant Height in Rice (Oryza sativa L.)

Strong seedling vigor is imperative to achieve stable seedling establishment and enhance the competitiveness against weeds in rice direct seeding. Shoot length (SL) is one of the important traits associated with seedling vigor in rice, but few genes for SL have been cloned so far. In the previous study, we identified two tightly linked and stably expressed QTLs for SL, qSL-1f and qSL-1d by genome-wide association study, and cloned the causal gene (LOC_Os01g68500) underlying qSL-1f. In the present study, we identify LOC_Os01g66100 (i.e. the semidwarf gene SD1), a well-known gene controlling plant height (PH) at the adult-plant stage, as the causal gene underlying qSL-1d through gene-based haplotype analysis and knockout transgenic verification. By measuring the phenotypes (SL and PH) of various haplotypes of the two genes and their knockout lines, we found SD1 and LOC_ Os01g68500 controlled both SL and PH, and worked in the same direction, which provided the directly genetic evidence for a positive correlation between SL and PH combined with the analysis of SL and PH in the diverse natural population. Moreover, the knockout transgenic experiments suggested that SD1 had a greater effect on PH compared with LOC_ Os01g68500, but no significant difference in the effect on SL. Further investigation of the pyramiding effects of SD1 and LOC_Os01g68500 based on their haplotype combinations suggested that SD1 may play a dominant role in controlling SL and PH when the two genes coexist. In this study, the effect of SD1 on SL at the seedling stage is validated. In total, two causal genes, SD1 and LOC_ Os01g68500, for SL are cloned in our studies, which controlled both SL and PH, and the suitable haplotypes of SD1 and LOC_ Os01g68500 are beneficial to achieve the desired SL and PH in different rice breeding objectives. These results provide a new clue to develop rice varieties for direct seeding and provide new genetic resources for molecular breeding of rice with suitable PH and strong seedling vigor.

Genome-wide association study and genomic prediction for resistance to brown planthopper in rice.

The brown planthopper (BPH) is the most destructive insect pest that threatens rice production globally. Developing rice varieties incorporating BPH-resistant genes has proven to be an effective control measure against BPH. In this study, we assessed the resistance of a core collection consisting of 502 rice germplasms by evaluating resistance scores, weight gain rates and honeydew excretions. A total of 117 rice varieties (23.31%) exhibited resistance to BPH. Genome-wide association studies (GWAS) were performed on both the entire panel of 502 rice varieties and its subspecies, and 6 loci were significantly associated with resistance scores (P value < 1.0e-8). Within these loci, we identified eight candidate genes encoding receptor-like protein kinase (RLK), nucleotide-binding and leucine-rich repeat (NB-LRR), or LRR proteins. Two loci had not been detected in previous study and were entirely novel. Furthermore, we evaluated the predictive ability of genomic selection for resistance to BPH. The results revealed that the highest prediction accuracy for BPH resistance reached 0.633. As expected, the prediction accuracy increased progressively with an increasing number of SNPs, and a total of 6.7K SNPs displayed comparable accuracy to 268K SNPs. Among various statistical models tested, the random forest model exhibited superior predictive accuracy. Moreover, increasing the size of training population improved prediction accuracy; however, there was no significant difference in prediction accuracy between a training population size of 737 and 1179. Additionally, when there existed close genetic relatedness between the training and validation populations, higher prediction accuracies were observed compared to scenarios when they were genetically distant. These findings provide valuable resistance candidate genes and germplasm resources and are crucial for the application of genomic selection for breeding durable BPH-resistant rice varieties.

Area coverage of BINA developed rice, pulse, oilseed and horticultural crop varieties in Bangladesh

The study was conducted to assess the area coverage of BINA developed rice, pulse, oilseed and horticultural crop varieties during 2022-23. Field survey data were collected from 64 districts through concern DD, DAE office. Both tabular and descriptive statistical analysis was used. It was observed that the overall area coverage of BINA developed rice varieties were 8.91%. Among the three seasons; Aus, Aman and Boro the highest area coverage was found in Aman season that was 14.54% followed by Aus 5.95% and Boro 2.93%, respectively. Among the 14 agricultural regions the highest area coverage of rice was found 15.41% in Rajshahi region (Reg-7) and the lowest was found 1.01% in Dhaka region (Reg-11). The overall area coverage of BINA developed pulse varieties were 16.32% and among the 14 regions the highest area coverage for pulses was found in Barishal region 58.51% (Reg-6). The overall area coverage of BINA developed oilseed varieties were 23.46% and among the 14 regions the highest area coverage for oilseed was found in Jashore region 16.32% (Reg-13). Among the BINA developed horticultural varieties the highest area coverage was found 4.46% for Binalebu-1 followed by Binahalud-1 (0.93%) and Binatomato-10 (0.36%). It was also observed that, among the 14 regions the highest area coverage for Binalebu-1 and Binahalud-1 were found in Rangamati agricultural region (region-4) about 483 ha (87.26%) and 45 ha (18.19%), respectively. The study identified that the overall area coverage of BINA developed rice, pulse and oilseed crops for distributed seed were 0.93%, 1.41% and 3.45%, respectively. The study also observed some constraints such as-non availability of seed, lack of training, demonstrations, field day, collaboration etc. For continuation of variety expansion, the institute should ensure quality seed supply in proper time and training, demonstration as well as collaboration among other research institutes, DAE, BADC and NGOs should be emphasized. Bangladesh J. Nuclear Agric, 37(2): 89-107, 2023

Genomic dissection of brown planthopper, Nilaparvata lugens (Hemiptera: Delphacidae) resistance in Indica rice genotypes

AbstractThe population growth and the regular breakout of Nilaparvata lugens pose a significant risk to rice cultivation. Four different N. lugens biotypes have been identified worldwide, with biotype 4 being the most destructive and prevalent throughout Asia, particularly in India. Therefore, a rice variety with multiple resistance genes/alleles is required for effective management of N. lugens. Hence, 191 rice genotypes collected from various parts of India were evaluated for resistance to N. lugens. Further, SSR markers representing 23 different N. lugens resistant (R) genes were assayed to identify genomic regions associated with resistance. The results of the genetic analysis showed that the average genetic diversity value of all markers was 0.165 and polymorphic information content of 0.145 for all the markers used. The population structure and cluster analysis divided the studied genotypes into three distinct groups, with resistant genotypes grouped separately. These findings were confirmed by the principal coordinate analysis, which categorized resistant genotypes, moderately resistant genotypes, and susceptible genotypes into distinct components. Additionally, 90% of the genetic variation was between individuals of populations and 10% between the populations. Marker‐trait association study through mixed linear model and generalized linear model identified six SSR markers such as RM6732 (Bph15), RM314 (Bph6), RM16999 (Bph6), RM7 (QBph3), RM401 (bph4), and RM7102 (Bph1), which were significantly associated with various phenotypic parameters, such as feeding mark, honeydew excretion, percent damage and nymphal survival. The resistant genes identified in these genotypes could help in the marker‐assisted rice variety development with durable resistance against N. lugens.

Analysis of Yield Stability in Diverse Rice Genotypes

Aims/ objectives: This study aims to improve stable and sustainable rice varieties adaptable to changing climatic conditions. It involves assessing genetic variability and Genotype X Environment interaction (G x E) among 186 diverse rice genotypes. The goal is to select genotypes with high breeding value, contributing to the development of rice varieties well-suited to varying climatic conditions. Study Design: The study employed an augmented design in a Randomized Complete Block Design (RCBD). Swarna, Madhuraj-55, Safri-17, Improved Samba Mahsuri, Thavalkannan, and IR64 checks were replicated across environments. Place and Duration of Study: The study took place in College of Agriculture, Raipur, IGKV over two years (wet season-2020 and 2021). Methodology: Analysis of genetic variability and G X E interaction among 186 rice genotypes. Execution of the experiment in an augmented design with a randomized complete block design. Replication of standard rice checks across different environments. Assessment of yield-attributing traits such as plant height, number of effective tillers, panicle length, number of grains per panicle, biological yield per plot, and grain yield. Evaluation of stability was done using univariate (Shukla stability variance, Wricke’s ecovalence, Kang stability statistic) and multivariate (AMMI yield stability index and GGE biplot) stability parameters. Selection of stable genotypes with high yield based on stability analyses. Results: Significant phenotypic variation was observed in yield-attributing traits across seasons. Genetic variability and G x E interaction effect demonstrated by variable genotype performance across environments. Univariate and multivariate stability parameters (S2i, W2i, KSi, AMMI stability value, GGE biplot) were used for stability analyses. Identification of stable genotypes with high yield across environments, including IR13f167, ARC13156, IR93354, F50, Ngalongyi, Giza 178, Arc 10159, Sadajira 19-317, Arith, IR 57920-Ac 25-2-B, Pesagro 102, Mekenzie small, Nasaenge, Kula Karuppan, Vary Gony, MR 69, Kanu Dam, IRRI 123, Sativa IRGC17083-1, Kalia, and Swarna. Conclusion: The study concludes that stability in genotype performance across diverse environments is crucial for the development of sustainable rice varieties. Genotypes with high stability and yield, as identified through stability analyses, hold potential breeding value for developing rice varieties adaptive to climate change. The stable genotypes listed, including IR13f167, ARC13156, IR93354, and others, are recommended for further breeding and development efforts to enhance rice productivity and adaptability.

Data-driven review on gender and rice varietal trait preferences in Bangladesh

In Bangladesh, farmers adapt to changing conditions through the adoption of improved varieties containing new or combined traits. The diverse varietal adoption decisions among farmers stem from gender-based differences in trait preferences. This review synthesizes existing knowledge to assess the nature, extent, and causes of gendered disparities in rice varietal trait preferences among farmers and consumers in Bangladesh. To enhance the data-driven nature of this review, we not only scrutinized secondary articles (45 documents) and databases but also incorporated and analyzed primary data on varietal adoption and trait preferences. The analysis revealed a pronounced need for rice breeding programs in Bangladesh to integrate both market and climate-smart traits, aligning with gender-specific needs in developing optimal rice product profiles. Analysis of primary data unveiled substantial variations in women and men farmers’ varietal trait preferences, influenced by factors like income, access to farming information, household size, land size, and decision-making. Consequently, addressing gender-differentiated trait preferences in the development of improved rice varieties is crucial to curtail farmers’ varietal adoption lag in Bangladesh. The findings underscore the necessity of systematic identification and integration of gender-differentiated varietal trait preferences into rice breeding programs. Failure to account for such preferences may disadvantage the gender-responsiveness of developed varieties and limit the anticipated impact. Therefore, understanding the biophysical, social, and cultural dynamics of diverse farmer groups from a gender perspective is imperative for achieving gender-responsive rice variety development in the context of Bangladesh. This process involves identifying key gender concerns for integration into rice breeding programs, ensuring a comprehensive approach to sustainable agriculture.

Characterization of Grain Quality Traits of Thai Highland Glutinous Rice Landraces

Glutinous rice is popularly consumed as a staple food, processed for the snack industry, and fermented for alcoholic beverages by people in the North and Northeast of Thailand. Cooking quality traits are an important factor used to select for consumption and utilization by farmers. The target outputs of future rice breeding programs should focus on developing rice varieties with superior grain quality, particularly in relation to their utilization. Therefore, this research aims to assess the morphological characteristics and cooking quality of four populations of Thai highland glutinous rice landraces: Pa Ai Khupe (PAKP4 and PAKP5) and Khao Hao (KH2 and KH5), comparing them to two elite varieties (RD4 and RD6). Additionally, it examines the partial nucleotide sequence of genes involved in amylopectin branch length, specifically SSII3, ISA3, and PUL3. The study illustrates that the four populations of glutinous rice landraces exhibit morphological variations between and within populations in plant type, and panicle exsertion. Variations in alkali spreading value, gel consistency, gelatinization temperature, amylose content, and seed elongation ratio were observed among and within the glutinous rice populations. PAKP5 and KH5 were classified as hard rice, similar to RD4. KH2 was classified as medium-hard texture after cooking, while PAKP4 was classified as soft rice after cooking, similar to RD6. The partial target sequences of the selected genes showed a similar nucleotide sequence among glutinous rice landraces. Therefore, further studies should focus on more nucleotide sequences of the selected genes and additional genes, as implications for marker-assisted selection in glutinous rice breeding programs. This study provides information to assist in breeding strategies for grain quality in Thai glutinous rice breeding programs.

Unveiling the Roles of LncRNA MOIRAs in Rice Blast Disease Resistance.

Rice blast disease, caused by the fungal pathogen Magnaporthe oryzae, is a major threat to rice production worldwide. This study investigates the role of long non-coding RNAs (lncRNAs) in rice's response to this destructive disease, with a focus on their impacts on disease resistance and yield traits. Three specific lncRNAs coded by M. oryzae infection-responsive lncRNAs (MOIRAs), MOIRA1, MOIRA2, and MOIRA3, were identified as key regulators of rice's response to M. oryzae infection. Strikingly, when MOIRA1 and MOIRA2 were overexpressed, they exhibited a dual function: they increased rice's susceptibility to blast fungus, indicating a negative role in disease resistance, while simultaneously enhancing tiller numbers and single-plant yield, with no adverse effects on other yield-related traits. This unexpected improvement in productivity suggests the possibility of overcoming the traditional trade-off between disease resistance and crop yield. These findings provide a novel perspective on crop enhancement, offering a promising solution to global food security challenges by developing rice varieties that effectively balance disease resistance and increased productivity.

Introgression of bacterial leaf blight (BLB) resistant gene, Xa7 into MARDI elite variety, MR219 by marker assisted backcrossing (MABC) approach.

Bacterial leaf blight (BLB) is one of the major rice diseases in Malaysia. This disease causes substantial yield loss as high as 70%. Development of rice varieties which inherited BLB resistant traits is a crucial approach to promote and sustain rice industry in Malaysia. Hence, this study aims were to enhance BLB disease resistant characters of high yielding commercial variety MR219 through backcross breeding approach with supporting tool of marker-assisted selection (MAS). Broad spectrum BLB resistance gene, Xa7 from donor parent IRBB7 were introgressed into the susceptible MR219 (recurrent parent) using two flanking markers ID7 and ID15. At BC3F4, we managed to generate 19 introgressed lines with homozygous Xa7 gene and showed resistant characteristics as donor parent when it was challenged with Xanthomonas oryzae pv. oryzae through artificial inoculation. Recurrent parent MR219 and control variety, MR263 were found to be severely infected by the disease. The improved lines exhibited similar morphological and yield performance characters as to the elite variety, MR219. Two lines, PB-2-107 and PB-2-34 were chosen to be potential lines because of their outstanding performances compared to parent, MR219. This study demonstrates a success story of MAS application in development of improved disease resistance lines of rice against BLB disease.

Root attributes governing drought stress adaptation and the associated molecular markers in chromosome segment substitution lines in rice (Oryza sativa L.)

The wild relatives of cultivated rice offer crucial resistance genes for combating stresses like drought. Developing rice varieties with drought tolerance is possible through chromosome segment substitution lines (CSSLs), which blend the genetic background of a high-yielding parent with specific chromosome segments from a donor parent. This study aimed to study the effect of drought stress on various root traits of chromosome segment substitution lines (CSSLs) and their relationship with specific molecular markers. Ninety-six genotypes, including 80 chromosome segment substitution lines (Curinga x O. rufipogon and Curinga x O. meridionalis), 9 New Rice for Africa (NERICAs) and 7 controls were grown in Basket and PVC pipe methods for phenotyping different root traits. Under drought stress (DS), MER16, MER20, RUF10, RUF16, RUF44, NERICA1, and NERICA3 showed superior performance for most of the root traits. These evaluations were supplemented with association analysis of 17 root trait-linked simple sequence repeat (SSR) markers with root phenotypic traits. The marker RM201 is strongly associated with multiple root traits, found to be independent of three growth conditions (well-watered “WW” under Basket, WW condition and DS conditions under PVC pipe). The marker RM316 is associated with root volume, and the marker RM7424 and RM1054 show maximum root length. In conclusion, these markers can be used in marker-assisted breeding programs, and the lines carrying them can be used as parental lines in variety-development programs for drought tolerance.

Molecular Diversity Analysis of Some Selected Brri Developed Rice Varieties Using Ssr Markers

Molecular characterization of 26 modern rice varieties of Bangladesh was performed using 52 simple sequence repeat markers (SSRs) to estimate the genetic diversity and to reveal genetic relationships among rice cultivars. A total of 156 alleles were detected where the number of alleles per locus generated by each marker varied from 2 to 7, with an average of 3. The band size for a given microsatellite locus ranged from 79 to 278 bp. The polymorphism information content (PIC) for the SSR loci ranged from 0.08 to 0.79, with an average of 0.35. RM566 was the best marker for identification and variability assessment of varieties as revealed by PIC values. A UPGMA dendrogram generated using the NTSYS-pc revealed four clusters with a similarity coefficient of 0.55, whereas phylogenetic cluster analysis of the SSR data based on Nei-genetic distance divided the varieties into three groups. Two- and three-dimensional graphical views of principal coordinate analysis showed the spatial distribution of the varieties and revealed that BRRI dhan56, BRRI dhan51, BRRI dhan52, BRRI dhan61, BRRI dhan62 and BRRI dhan66 were found far away from the centroid of the cluster. The findings of this study are helpful for varietal identification, background selection during backcross breeding and for selecting the suitable genetically diverse parents for crossing programs. SAARC J. Agric., 21(2): 1-14 (2023)

A comparative study of state-of-the-art deep learning architectures for rice grain classification

Accurate and efficient automated rice grain classification systems are vital for rice producers, distributors, and traders, offering improved quality control, cost optimization, and supply chain management. They also hold the potential to aid in the development of rice varieties that are more resistant to disease, pests, and environmental stress. While most existing studies in the rice classification domain rely on traditional machine-learning techniques that necessitate feature extraction engineering processes, our research explores the effectiveness of novel deep-learning models for this task. We evaluated the performance of various contemporary deep-learning models, including Residual Network (ResNet), Visual Geometry Group (VGG) network, EfficientNet, and MobileNet. These models were tested on a dataset comprising 75,000 images, classified into five different rice categories. We assessed each model using established evaluation metrics such as accuracy, F1 score, precision, recall, and per-class accuracy. Our findings showed that the EfficientNet-based model delivered the highest accuracy (99.67%), while the MobileNet-based model excelled in the speed of classification (2556 s). We concluded that, compared to traditional machine learning methods, the models employed in our study are highly scalable and capable of managing large volumes of complex data with millions of features and samples.

Dissecting genomic regions and underlying sheath blight resistance traits in rice (Oryza sativa L.) using a genome-wide association study.

The productivity of rice is greatly affected by the infection of the plant pathogenic fungus Rhizoctonia solani, which causes a significant grain yield reduction globally. There exist a limited number of rice accessions that are available to develop sheath blight resistance (ShB). Our objective was to identify a good source of the ShB resistance, understand the heritability, and trait interactions, and identify the genomic regions for ShB resistance traits by genome-wide association studies (GWAS). In the present study, a set of 330 traditional landraces and improved rice varieties were evaluated for ShB resistance and created a core panel of 192 accessions used in the GWAS. This panel provides a more considerable amount of genetic variance and found a significant phenotypic variation among the panel of rice accessions for all the agro-morphological and disease-resistance traits over the seasons. The infection rate of ShB and disease reaction were calculated as percent disease index (PDI) and area under the disease progress curve (AUDPC). The correlation analysis showed a significant positive association between PDIs and AUPDC and a negative association between PDI and plant height, flag leaf length, and grain yield. The panel was genotyped with 133 SSR microsatellite markers, resulting in a genome coverage of 314.83 Mb, and the average distance between markers is 2.53 Mb. By employing GLM and MLM (Q + K) models, 30 marker-trait associations (MTAs) were identified with targeted traits over the seasons. Among these QTLs, eight were found to be novel and located on 2, 4, 8, 10, and 12 chromosomes, which explained the phenotypic variation ranging from 5% to 15%. With the GWAS approach, six candidate genes were identified. Os05t0566400, Os08t0155900, and Os09t0567300 were found to be associated with defense mechanisms against ShB. These findings provided insights into the novel donors of IC283139, IC 277248, Sivappuchithirai Kar, and Bowalia. The promising genomic regions on 10 of 12 chromosomes associated with ShB would be useful in developing rice varieties with durable disease resistance.

Marker-assisted enhancement of bacterial blight (Xanthomonas oryzae pv. oryzae) resistance in a salt-tolerant rice variety for sustaining rice production of tropical islands.

Bacterial blight (BB) caused by Xanthomonas oryzae pv. oryzae is a major disease of rice, specially in the tropical regions of the world. Developing rice varieties with host resistance against the disease is the most effective and economical solution for managing the disease. Pyramiding resistance genes (Xa4, xa5, xa13,and Xa21) in popular rice varieties using marker-assisted backcross breeding (MABB) has been demonstrated as a cost-effective and sustainable approach for establishing durable BB resistance. Here, we report our successful efforts in introgressing four resistance genes (Xa4, xa5, xa13, and Xa21) from IRBB60 to CARI Dhan 5, a popular salt-tolerant variety developed from a somaclonal variant of Pokkali rice, through functional MABB. Both BB and coastal salinity are among the major challenges for rice production in tropical island and coastal ecosystems. Plants with four, three, and two gene pyramids were generated, which displayed high levels of resistance to the BB pathogen at the BC3F2 stage. Under controlled salinity microplot environments, the line 131-2-175-1223 identified with the presence of three gene pyramid (Xa21+xa13+xa5) displayed notable resistance across locations and years as well as exhibited a salinity tolerance comparable to the recurrent parent, CARI Dhan 5. Among two BB gene combinations (Xa21+xa13), two lines, 17-1-69-334 and 46-3-95-659, demonstrated resistance across locations and years, as well as salt tolerance and grain production comparable to CARI Dhan 5. Besides salinity tolerance, five lines, 17-1-69-179, 46-3-95-655, 131-2-190-1197, 131-2-175-1209, and 131-2-175-1239, exhibited complete resistance to BB disease. Following multilocation testing, potential lines have been identified that can serve as a prospective candidate for producing varieties for the tropical Andaman and Nicobar Islands and other coastal locations, which are prone to BB and coastal salinity stresses.

Estabilidad fenotípica de cuarenta líneas avanzadas de arroz en Babahoyo, Ecuador

The crosses between Oryza sativa L. and O. rufipogon Griff., create a high genetic diversity to develop rice varieties with high yield and phenotypic stability. In the present investigation, forty advanced lines of rice were evaluated in subsidiaries F5 (dry season) and F6 (rainy season), together with three commercial controls in the town of Babahoyo, Ecuador. A Randomized Complete Block Design (DBCA) was applied with three repetitions, recording morphoagronomic and productive characters. Statistical analyzes were applied and phenotypic stability was determined using the Eberhart and Russell, AMMI, Lin and Binns, PROMVAR models. The average morphoagronomic results were: days to flowering (72), vegetative cycle (98 days), plant height (111 cm), panicle sterility (6 %); the productive variables the results were: tillers per plant (32), panicles per plant (31), panicle length (27 cm), grains per panicle (168) and yield (8,100 kg.ha-1). The stable lines identified by the models: Eberhart and Russell were 1, 2, 10, 11, 13, 18, 25, 26, 30 and 37; AMMI identified lines 8 and 22; Lin and Binns to lines 2, 12, 18, 27, 37 and 40; and PROMOTE lines 2, 10, 13, 18, 25, 30, 38, 40 and 43; concluding that seven lines (2, 10, 13, 18, 25, 30 and 40) coincided with the applied models except AMMI. The average yield of the lines mentioned in the two seasons was 7,797 kg.ha-1, higher than the average of the commercial controls that obtained 6,809 kg.ha-1.

MG1 interacts with a protease inhibitor and confers resistance to rice root-knot nematode

The rice root-knot nematode (Meloidogyne graminicola) is one of the most destructive pests threatening rice (Oryza sativa L.) production in Asia; however, no rice resistance genes have been cloned. Here, we demonstrate that M. GRAMINICOLA-RESISTANCE GENE 1 (MG1), an R gene highly expressed at the site of nematode invasion, determines resistance against the nematode in several rice varieties. Introgressing MG1 into susceptible varieties increases resistance comparable to resistant varieties, for which the leucine-rich repeat domain is critical for recognizing root-knot nematode invasion. We also report transcriptome and cytological changes that are correlated with a rapid and robust response during the incompatible interaction that occurs in resistant rice upon nematode invasion. Furthermore, we identified a putative protease inhibitor that directly interacts with MG1 during MG1-mediated resistance. Our findings provide insight into the molecular basis of nematode resistance as well as valuable resources for developing rice varieties with improved nematode resistance.

Genome wide association studies and candidate gene mining for understanding the genetic basis of straw silica content in a set of Oryza nivara (Sharma et Shastry) accessions.

Rice is a high-silica (SiO2·nH2O) accumulator. Silicon (Si) is designated as a beneficial element associated with multiple positive effects on crops. However, the presence of high silica content is detrimental to rice straw management, hampering its use as animal feed and as raw material in multiple industries. Rice straw management is a serious concern in north-western India, and it is eventually burned in situ by farmers, contributing to air pollution. A practical solution could lie in reducing the silica content in rice while also attaining sound plant growth. A set of 258 Oryza nivara accessions along with 25 cultivated varieties of Oryza sativa was used to assess the variation in straw silica content using the molybdenum blue colorimetry method. A large continuous variation was observed for straw silica content in O. nivara accessions, ranging from 5.08% to 16%, while it varied from 6.18% to 15.81% in the cultivated varieties. The O. nivara accessions containing 43%-54% lower straw silica content than the currently prominent cultivated varieties in the region were identified. A set of 22,528 high-quality single nucleotide polymorphisms (SNPs) among 258 O. nivara accessions was used for estimating population structure and genome-wide association studies (GWAS). A weak population structure with 59% admixtures was identified among O. nivara accessions. Further, multi-locus GWAS revealed the presence of 14 marker-trait associations (MTAs) for straw silica content, with six of them co-localizing with previously reported quantitative trait loci (QTL). Twelve out of 14 MTAs showed statistically significant allelic differences. Thorough candidate gene analyses revealed the presence of promising candidate genes, including those encoding the ATP-binding cassette (ABC) transporter, Casparian thickening, multi-drug and toxin extrusion (MATE) protein, F-box, and MYB-transcription factors. Besides, ortho-QTLs among rice and maize genomes were identified, which could open ways for further genetic analysis of this trait. The findings of the study could aid in further understanding and characterizing genes for Si transport and regulation in the plant body. The donors carrying the alleles for lower straw silica content can be used in further marker-assisted breeding programs to develop rice varieties with lower silica content and higher yield potential.