This study aimed to improve the restorer line IR 42266–29-3R (A42) for multiple stress tolerance using integrated marker-assisted backcross breeding (MABB) and the doubled haploid (DH) approach. The primary objective was to introduce the abiotic stress tolerant QTL (qDTY1.1 and qHTSF4.1) into the background IR 42266–29-3R, which already harbors three bacterial blight (BB) resistance genes (xa5, xa13, and Xa21). The BC1F1 population was derived from crosses between IR 42266–29-3R and N22, leading to the development of 113 true DHs. Efficient callus induction (29.64

The three-line system of hybrid rice has been a widely adopted method used to develop high-yielding hybrid varieties. The system encompasses a cytoplasmic male sterile line (A line), a maintainer to the male sterile line (B line), and a fertility restorer line (R line). For the first time, the study validates a comparative assessment of an efficient anther culture technique utilizing F1 hybrids derived from crosses between (A × R) and (B × R) genotypes. In the above hybrid system, A × R leads to heterosis resulting in hybrid rice production while B × R crosses envisioned to develop superior maintainer or restorer lines. The ANOVA along with Duncan’s mean supported N6 medium fortified with 2.0 mg L−1 2,4-di-chlorophenoxyacetic acid and 0.5 mg L−1 6-benzylaminopurine resulted in maximum callusing on the 7th d with a callusing frequency of 47.63

Drought is one of the major abiotic stress factors affecting the growth and production of rice globally and it can cause an estimated yield loss up to 90% in rice. With the increasing population around the globe, a comprehensive approach for mitigating drought stress should be taken to develop drought-tolerant rice varieties to meet future food demands. One hundred and eighty-two rice genotypes were evaluated for six critical gene/QTLs associated with drought tolerance using SNP marker data. The results revealed that 172 genotypes carry at least one gene/QTL for drought tolerance. The six gene/QTLs, namely, DTY1.1, qDTY2.2, qDTY3.1, qDTY3.2, qDTY4.1 and qDTY12.1were found in 103, 26, 90, 25, 27 and 45 genotypes corresponding to 57, 49, 14, 14, 15 and 25% of the total screened genotypes, respectively. Remarkably, five genotypes (RL-32, RL-105, RL-110, RL-142 and RL-158) possessed a unique combination three major genes/QTLs and three genotypes (RL-21, RL-41 and RL-188) possessed a unique combination four major gene/QTLs for drought tolerance. Furthermore, both cluster and populationn structure analyses revealedd the distribution of the genotypes into two major clusters. The genotypes carrying valuable gene/QTLs either in single or combination, hold immense potential for deployment in drought tolerance rice breeding programs.

Rice blast disease is the most devastating disease constraining crop productivity. Vertical resistance to blast disease is widely studied despite its instability. Clusters of genes or QTLs conferring blast resistance that offer durable horizontal resistance are important in resistance breeding. In this study, we aimed to refine the reported QTLs and identify stable meta-QTLs (MQTLs) associated with rice blast resistance. A total of 435 QTLs were used to project 71 MQTLs across all the rice chromosomes. As many as 199 putative rice blast resistance genes were identified within 53 MQTL regions. The genes included 48 characterized resistance gene analogs and related proteins, such as NBS-LRR type, LRR receptor-like kinase, NB-ARC domain, pathogenesis-related TF/ERF domain, elicitor-induced defense and proteins involved in defense signaling. MQTL regions with clusters of RGA were also identified. Fifteen highly significant MQTLs included 29 candidate genes and genes characterized for blast resistance, such as Piz, Nbs-Pi9, pi55-1, pi55-2, Pi3/Pi5-1, Pi3/Pi5-2, Pikh, Pi54, Pik/Pikm/Pikp, Pb1 and Pb2. Furthermore, the candidate genes (42) were associated with differential expression (in silico) in compatible and incompatible reactions upon disease infection. Moreover, nearly half of the genes within the MQTL regions were orthologous to those in O. sativa indica, Z. mays and A. thaliana, which confirmed their significance. The peak markers within three significant MQTLs differentiated blast-resistant and susceptible lines and serve as potential surrogates for the selection of blast-resistant lines. These MQTLs are potential candidates for durable and broad-spectrum rice blast resistance and could be utilized in blast resistance breeding.

The unpolished whole rice grains having the pericarp intact are packed with nutrients and antioxidants. The colored pericarp provides health benefits against lifestyle diseases. The diversity in the pericarp color which can be red, brown or black in various shades is a reflection of differential antioxidants profile. However, a natural mutation in the Rc gene (coding for red pericarp) resulted in the production of rc allele (coding for white pericarp) which was subsequently selected during domestication. The objective of this study is to identify novel candidate genes for pericarp color using genome-wide association analysis. Three types of scoring systems were used for this work namely, the 1 to 8, 0 1 and 1 9 scoring systems. For the 1 to 8 and 0 1 scoring systems, 278 accessions of the 3K rice panel were visually sorted into eight pericarp groups (1 to 8 scoring system) having seeds with green, white, off-white, light red, red, dark red, brown, and black pericarp, respectively and later into two groups (0 1 scoring system) having seeds with colored and white pericarp, respectively. For the 1 9 scoring system, 254 accessions of the 278 accessions were sorted into two groups having seeds with white and red shaded pericarp colors, respectively. The genome wide association analysis revealed that a SNP in chromosome 7 corresponding to Rc gene along with a SNP in chromosome 1, which is novel, are significantly associated with the pericarp color with cumulative phenotypic variance of 80

Rice, a staple food for a significant portion of the global population, faces persistent threats from various pathogens and pests, necessitating the development of resilient crop varieties. Deployment of resistance genes in rice is the best practice to manage diseases and reduce environmental damage by reducing the application of agro-chemicals. Genome editing technologies, such as CRISPR-Cas, have revolutionized the field of molecular biology, offering precise and efficient tools for targeted modifications within the rice genome. This study delves into the application of these tools to engineer novel alleles of resistance genes in rice, aiming to enhance the plant’s innate ability to combat evolving threats. By harnessing the power of genome editing, researchers can introduce tailored genetic modifications that bolster the plant’s defense mechanisms without compromising its essential characteristics. In this study, we synthesize recent advancements in genome editing methodologies applicable to rice and discuss the ethical considerations and regulatory frameworks surrounding the creation of genetically modified crops. Additionally, it explores potential challenges and future prospects for deploying edited rice varieties in agricultural landscapes. In summary, this study highlights the promise of genome editing in reshaping the genetic landscape of rice to confront emerging challenges, contributing to global food security and sustainable agriculture practices.

Rice production faces a significant threat from the rice leaffolder, Cnaphalocrocis medinalis . To address this challenge, growing resistant varieties stands out as a sustainable and eco-friendly pest management strategy. This necessitates identifying resistant sources and understanding their inheritance patterns through employing DNA markers for marker-assisted resistance breeding. Our study involves screening for resistant cultivars following the SES of IRRI, assessing genetic diversity among landraces using molecular markers, and identifying genomic regions associated with resistance. Screening indicated that 33.33%, 27.08%, 19.79%, and 19.80% of genotypes were resistant, moderately resistant, susceptible, and admixture, respectively. Landraces were categorized into three clusters, with clusters I and II predominantly containing moderately resistant and resistant cultivars, and cluster III mainly susceptible types. Molecular variance analysis revealed 12% variation among populations and 88% within the population. Simple linear regression identified significant marker-trait associations, with markers RM 162 and RM 284 on chromosomes 6 and 8, respectively, found highly associated with leaffolder resistance. Phenotypic variation in leaffolder damage correlated highly with the allelic effects of these markers. Further confirmation of marker linkage with resistance loci was established through independent assays on highly resistant and susceptible genotypes. The information derived from genetic diversity and marker-trait associations will be useful for future marker-assisted resistance breeding programs, enhancing the sustainability of rice production.

A crucial phenotypic attribute for breeding rice for direct seeded condition is rapid uniform germination and build-up of biomass during the initial period of seedling establishment. Seed vigour constitutes such traits that have gained potential to meet the requirements of breeding for direct seeded rice. In the present study, a set of 295 markers, including 215 candidate gene-derived markers covering all chromosome, was used to discover the casual alleles for eight rice seed vigour-related traits. Using a mixed linear model, the study identified 99 significant associations for seed vigour traits. Many associated markers originated from diverse candidate genes in rice. Notably, alleles from genes like RSR1, OsSRS3 and OsSWEET15 exhibited pleiotropic effects, influencing multiple seed vigour traits. This discovery underscores the potential of certain genes to impact various facets of seed vigour simultaneously. The new candidate gene markers associated with seed vigour traits may be utilized to incorporate variable alleles for seed vigour traits through marker-assisted breeding programmes. Markers identified to be closely associated with more than one trait have significant application in the simultaneous improvement of multiple traits.

Rice grains are the major source of nutrition for more than half of the world's population. With increased frequencies of cyclones in the last decade during grain maturation stage of rice crop, most of the rice cultivars in lowland ecologies are getting affected by pre harvest sprouting due to flash flooding and incessant rains. Significant economic loss is incurred in the global food grain industry of cereals due to pre-harvest sprouting (PHS). It is very important to develop climate resilient varieties with PHS resistant traits introgressed in them. Well characterized PHS resistant rice genotypes with optimal dormancy that can serve as donors are need of the hour. We conducted an experiment to identify PHS resistant genotypes, and also determine to their physiological and biochemical characteristics. 96 diverse rice genotypes were evaluated for PHS resistance from 20 to 40 days after flowering (DAF). Based on their response, 16 contrasting genotypes were identified from 96 genotypes to further study the underlying mechanism of PHS resistance. The results revealed that, susceptible genotypes (8) exhibited very high germination percentage (4 to 87.5

Hybrid rice has a considerable yield advantage over inbred lines, but the adoption rate in India is quite slow. In a three-line hybrid rice breeding programme, the development of fertility restorer lines that have enhanced grain quality is crucial. Employment of doubled haploid (DH) technology will accelerate the development of improved R lines in a short period of time, thus hastening the pace of hybrid rice breeding. This investigation was carried out for the evaluation of genetic diversity and assessment of population differentiation in 113 DHs derived from BC1F1s of IMP. IR 42266-29-3R and Nagina 22. A total of 46 SSR (Simple Sequence Repeat) markers resulted in an average of 2.00 alleles per locus. Polymorphism information content (PIC) value ranged from 0.31 to 0.37 with an average of 0.36. RM496, RM25520, RM483 and RM553 were found to be the best markers for the identification of genetic diversity. Structure analysis classified 113 DHs into four groups, which matched the Neighbour-Joining method using UPGMA cluster analysis. The AMOVA results demonstrated substantial genetic variations within subpopulation than among sub-population. The SSR marker-based molecular fingerprinting could serve as a sound basis in the identification of genetically distant as well as in the duplicate sorting of the morphologically close population in future breeding programmes.

In cereals, pre-harvest sprouting (PHS) or vivipary is a key physiological and agronomic trait that causes huge economic loss. PHS triggered by typhoons, cyclones, and high relative humidity at the late seed maturation stage is becoming a major threat to rice production in India. To explore the mechanism of PHS in rice, we evaluated 96 rice genotypes for PHS resistance and discovered 12 PHS resistant genotypes. These genotypes were classified into two groups susceptible and resistant, based on their phenotype. From the 96 genotypes, 16 contrasting genotypes were chosen, to unravel the underlying mechanism associated with PHS resistance. The results revealed that resistant genotypes had 0% germination at all the flowering stages (20 to 40 DAF), while susceptible genotypes had 4 to 87.5% germination from 20 to 40 DAF. In terms of pericarp color, 7 out of 8 resistant genotypes had red/pigmented pericarp color while the susceptible genotypes had white/non-pigmented pericarp color. The carotenoid content of leaves and seeds from 20 to 40 DAF was also measured and found to be significantly higher in resistant genotypes than susceptible genotypes. Carotenoids have been demonstrated to increase resistance by assisting in the synthesis of ABA and thereby seed dormancy. The 12 resistant genotypes were examined for germination to decide the duration of dormancy. The duration of dormancy varied in these 12 resistant genotypes varying from 10 days up to 40 days after harvest. These findings suggest that these novel PHS resistant genotypes (PB-68, HT-81, PB-50(1), HT-86, HT-20, Mahulata, PB-285, PB-47, NHN-279, PB-65, PB-259 and Budidhan) may be exploited as donors in the crop improvement programmes to generate PHS resistant genotypes.

Cereal crops are the major contributors to global food and nutritional security. Cultivation of cereals is affected by various abiotic and biotic stresses, and diseases are one of the important biotic stresses leading to a reduction in the yield of cereal grain production worldwide. Effective management of diseases in these crops is subject to the availability of germplasm with resistance responses. The developments in the field of genomics and other omics tools have largely hastened our efforts to understand host-pathogen interactions and the mechanisms of virulence as well as resistance. In the present chapter, we have elaborated on the omics tools, such as genomics, transcriptomics, proteomics, metabolomics, and phenomics, and also highlighted how these tools are being used to devise modern approaches for understanding the complex nature of host-pathogen interactions and for the management of some of the most devastating diseases in cereal crops.

Blast pathogen, Magnaporthe spp., that infects ancient millet crops such pearl millet, finger millet, foxtail millet, barnyard millet, and rice was isolated from different locations of blast hotspots in India using single spore isolation technique and 136 pure isolates were established. Numerous growth characteristics were captured via morphogenesis analysis. Among the 10 investigated virulent genes, we could amplify MPS1 (TTK Protein Kinase) and Mlc (Myosin Regulatory Light Chain edc4) in majority of tested isolates, regardless of the crop and region where they were collected, indicating that these may be crucial for their virulence. Additionally, among the four avirulence (Avr) genes studied, Avr-Pizt had the highest frequency of occurrence, followed by Avr-Pia. It is noteworthy to mention that Avr-Pik was present in the least number of isolates (9) and was completely absent from the blast isolates from finger millet, foxtail millet, and barnyard millet. A comparison at the molecular level between virulent and avirulent isolates indicated observably large variation both across (44%) and within (56%) them. The 136 Magnaporthe spp isolates were divided into four groups using molecular markers. Regardless of their geographic distribution, host plants, or tissues affected, the data indicate that the prevalence of numerous pathotypes and virulence factors at the field level, which may lead to a high degree of pathogenic variation. This research could be used for the strategic deployment of resistant genes to develop blast disease-resistant cultivars in rice, pearl millet, finger millet, foxtail millet, and barnyard millet.

To obtain immediate homozygosity by androgenesis, the doubled haploid method is often used. As a result, a mapping population was created utilizing rice (Oryza sativa L.) cvs. Mahulata and IR 20 as parents in order to find QTLs/genes for drought tolerance at the vegetative stage. The effectiveness of the doubled haploids (DHs) approach, on the other hand, is largely dependent on the ability to distinguish haploids from diploids among the green regenerants. Although flow cytometry and cytological screening for pollen sterility can be used to identify haploids, these methods are expensive, time-consuming, and need a sophisticated laboratory with highly trained workers. Plant height and other spikelet features have also been used to differentiate haploids from doubled haploids. However, no systematic analysis of several morphological features for distinguishing haploids in doubled haploids has been published to date. As a result, a cost-effective approach for distinguishing haploids from true DHs obtained from anther culture is required. The goal of this work was to identify haploids using morphological features and simple microscopic examinations without the use of chemicals or complex laboratory facilities. The cross between the IR20 and Mahulata yielded a total of 198 anther culture (AC) derived plants. A group of 41 plantlets was chosen as putative haploids based on their shorter height and Cq values using qPCR-based genotyping and finally validated that, in addition to plant height, other morphological traits such as total number of leaves/plant, total number of tillers/plant, and floral characters can be used to successfully identify haploids. We report a variety of morphological signs as indicators of haploid plants, including smaller plants, higher tiller density, narrower and shorter leaf length, and partial exertion of panicle from the flag leaf sheath. Other morphological markers for identifying haploids from DHs include smaller florets and anthers, and small desiccated microspores.

Deployment of single or multiple blast resistance ( R ) genes in rice plant is considered to be the most promising approach to enhance resistance against blast disease caused by fungus Magnaporthe oryzae . At the proteome level, relatively little information about R gene mediated defence mechanisms for single and stacking resistance characteristics is available. The overall objective of this study is to look at the proteomics of rice plants that have R genes; Pi54, Pi54rh and stacked Pi54 + Pi54rh in response to rice blast infection. In this study ‘isobaric tag for relative and absolute quantification’ (iTRAQ)-based proteomics analysis was performed in rice plants at 72-h post inoculation with Magnaporthe oryzae and various differentially expressed proteins were identified in these three transgenic lines in comparison to wild type during resistance response to blast pathogen. Through STRING analysis, the observed proteins were further examined to anticipate their linked partners, and it was shown that several defense-related proteins were co-expressed. These proteins can be employed as targets in future rice resistance breeding against Magnaporthe oryzae . The current study is the first to report a proteomics investigation of rice lines that express single blast R gene Pi54 , Pi54rh and stacked ( Pi54 + Pi54rh ) during incompatible interaction with Magnaporthe oryzae . The differentially expressed proteins indicated that secondary metabolites, reactive oxygen species-related proteins, phenylpropanoid, phytohormones and pathogenesis-related proteins have a substantial relationship with the defense response against Magnaporthe oryzae .

It is hypothesized that the genome-wide genic markers may increase the prediction accuracy of genomic selection for quantitative traits. To test this hypothesis, a set of candidate gene-based markers for yield and grain traits-related genes cloned across the rice genome were custom-designed. A multi-model, multi-locus genome-wide association study (GWAS) was performed using new genic markers developed to test their effectiveness for gene discovery. Two multi-locus models, FarmCPU and mrMLM, along with a single-locus mixed linear model (MLM), identified 28 significant marker-trait associations. These associations revealed novel causative alleles for grain weight and pleiotropic associations with other traits. For instance, the marker YD91 derived from the gene OsAAP3 on chromosome 1 was consistently associated with grain weight, while the gene has a significant effect on grain yield. Furthermore, nine genomic selection methods, including regression-based and machine learning-based models, were used to predict grain weight using a leave-one-out five-fold cross-validation approach to optimize the genomic selection model with genic markers. Among nine prediction models, Kernel Hilbert Space Regression (RKHS) is the best among regression-based models, and Random Forest Regression (RFR) is the best among machine learning-based models. Genomic prediction accuracies with and without GWAS significant markers were compared to assess the effectiveness of markers. The rapid decreases in prediction accuracy upon dropping GWAS significant markers indicate the effectiveness of new genic markers in genomic selection. Apart from that, the candidate gene-based markers were found to be more effective in genomic selection programs for better accuracy.

Rice is a global food grain crop for more than one-third of the human population and a source for food and nutritional security. Rice production is subjected to various stresses; blast disease caused by Magnaporthe oryzae is one of the major biotic stresses that has the potential to destroy total crop under severe conditions. In the present review, we discuss the importance of rice and blast disease in the present and future global context, genomics and molecular biology of blast pathogen and rice, and the molecular interplay between rice–M. oryzae interaction governed by different gene interaction models. We also elaborated in detail on M. oryzae effector and Avr genes, and the role of noncoding RNAs in disease development. Further, rice blast resistance QTLs; resistance (R) genes; and alleles identified, cloned, and characterized are discussed. We also discuss the utilization of QTLs and R genes for blast resistance through conventional breeding and transgenic approaches. Finally, we review the demonstrated examples and potential applications of the latest genome-editing tools in understanding and managing blast disease in rice.

Rice genes namely TPP7 ( Trehalose Phosphate Phosphatase 7 ), Sub1A ( Submergence 1a ) and their interactions regulate tolerance to submergence at germination and seedling stage, respectively. Sequential stress of initial submergence during the germination and subsequent seedling stage water deficit stresses are not properly addressed in direct seeded rice cultivation. In our initial linkage disequilibrium and meta-QTL analysis, Sub1 locus and TPP7 genes co-segregated for tolerance to submergence at germination and seedling stage and were in linkage disequilibrium only in aus subpopulations of rice. Phenotypically, root traits were positively correlated (correlation coefficient = >0.8) with seedling growth in germination under submergence and also in subsequent water deficit stresses in recombinant inbred lines developed from N22 and Bhalum 2 cross. Further, favourable alleles of Sub1 in N22 and 3’-UTR allele of TPP7 in Bhalum 2 enhanced the root traits (>20 per cent) and seedling survival (>25 per cent), respectively in germination under submergence stress. Additionally, the interaction of N22 alleles of Sub1 and TPP7 significantly enhanced the culm diameter and root dry weight in submergence at germination stress. Interestingly, two QTLs with high additive effects associated with sixteen different traits for submerged germination and water deficit tolerance traits were identified within the genomic regions spanning Sub1 and TPP7 genes (~4 Mbp) in Chr09 indicative of genomic region effects on the trait response rather than Sub1 and TPP7. Further, favourable haplotype within the Sub1 and TPP7 genomic region had an epistatic effect on trait responses and enhanced the crown root number, root dry weight, and specific root area by 11.45%, 15.69%, and 33.15% respectively in flooded germination condition, indicative of haplo-allelic contribution in trait response. A wall-associated kinase 79 ( WAK79 ) and malectin-like receptor-like kinase 59 ( MRLK59 ) were identified as candidate genes, that through regulation of cell wall elongation might coordinate the ‘haplogenic model’ of quantitative trait response under flooded germination, recovery, and subsequent water deficit conditions and thus, favourable haplotypes could be employed in direct seeded rice improvement.