The recent advancements in forward genetics have expanded the applications of mutation techniques in advanced genetics and genomics, ahead of direct use in breeding programs. The advent of next-generation sequencing (NGS) has enabled easy identification and mapping of causal mutations within a short period and at relatively low cost. Identifying the genetic mutations and genes that underlie phenotypic changes is essential for understanding a wide variety of biological functions. To accelerate the mutation mapping for crop improvement, several high-throughput and novel NGS based forward genetic approaches have been developed and applied in various crops. These techniques are highly efficient in crop plants, as it is relatively easy to grow and screen thousands of individuals. These approaches have improved the resolution in quantitative trait loci (QTL) position/point mutations and assisted in determining the functional causative variations in genes. To be successful in the interpretation of NGS data, bioinformatics computational methods are critical elements in delivering accurate assembly, alignment, and variant detection. Numerous bioinformatics tools/pipelines have been developed for such analysis. This article intends to review the recent advances in NGS based forward genetic approaches to identify and map the causal mutations in the crop genomes. The article also highlights the available bioinformatics tools/pipelines for reducing the complexity of NGS data and delivering the concluding outcomes.

Rice production needs to be sustained in the coming decades, as the changeable climatic conditions are becoming more conducive to disease outbreaks. The majority of rice diseases cause enormous economic damage and yield instability. Among them, rice blast caused by Magnaportheoryzae is a serious fungal disease and is considered one of the major threats to world rice production. This pathogen can infect the above-ground tissues of rice plants at any growth stage and causes complete crop failure under favorable conditions. Therefore, management of blast disease is essentially required to sustain global food production. When looking at the drawback of chemical management strategy, the development of durable, resistant varieties is one of the most sustainable, economic, and environment-friendly approaches to counter the outbreaks of rice blasts. Interestingly, several blast-resistant rice cultivars have been developed with the help of breeding and biotechnological methods. In addition, 146 R genes have been identified, and 37 among them have been molecularly characterized to date. Further, more than 500 loci have been identified for blast resistance which enhances the resources for developing blast resistance through marker-assisted selection (MAS), marker-assisted backcross breeding (MABB), and genome editing tools. Apart from these, a better understanding of rice blast pathogens, the infection process of the pathogen, and the genetics of the immune response of the host plant are very important for the effective management of the blast disease. Further, high throughput phenotyping and disease screening protocols have played significant roles in easy comprehension of the mechanism of disease spread. The present review critically emphasizes the pathogenesis, pathogenomics, screening techniques, traditional and molecular breeding approaches, and transgenic and genome editing tools to develop a broad spectrum and durable resistance against blast disease in rice. The updated and comprehensive information presented in this review would be definitely helpful for the researchers, breeders, and students in the planning and execution of a resistance breeding program in rice against this pathogen.

Fast neutron (FN) radiation mediated mutagenesis is a unique approach among the several induced mutagenesis methods being used in plant science in terms of impacted mutations. The FN mutagenesis usually creates deletions from few bases to several million bases (Mb). A library of random deletion generated using FN mutagenesis lines can provide indispensable resources for the reverse genetic approaches. In this review, information from several efforts made using FN mutagenesis has been compiled to understand the type of induced mutations, frequency, and genetic stability. Concerns regarding the utilization of FN mutagenesis technique for a plant with different level of ploidy and genome complexity are discussed. We have highlighted the utility of next-generation sequencing techniques that can be efficiently utilized for the characterization of mutant lines as well as for the mapping of causal mutations. Pros and cons of mapping by mutation (MutMap), mutant chromosome sequencing (MutChromSeq), exon capture, whole genome sequencing, MutRen-Seq, and different tilling approaches that can be used for the detection of FN-induced mutation has also been discussed. Genomic resources developed using the FN mutagenesis have been catalogued wooing to meaningful utilization of the available resources. The information provided here will be helpful for the efficient exploration for the crop improvement programs and for better understanding of genetic regulations.

Salt stress is one of the most severe environmental stresses limiting the productivity of crops, including rice. However, there is a lack of information on how salt-stress sensitivity varies across different developmental stages in rice. In view of this, a comparative evaluation of contrasting rice varieties CSR36 (salt tolerant) and Jaya (salt sensitive) was conducted, wherein NaCl stress (50 mM) was independently given either at seedling (S-stage), tillering (T-stage), flowering (F-stage), seed-setting (SS-stage) or throughout plant growth, from seedling till maturity. Except for S-stage, CSR36 exhibited improved NaCl stress tolerance than Jaya, at all other tested stages. Principal component analysis (PCA) revealed that the improved NaCl stress tolerance in CSR36 coincided with enhanced activities/levels of enzymatic/non-enzymatic antioxidants (root ascorbate peroxidase for T- (2.74-fold) and S+T- (2.12-fold) stages and root catalase for F- (5.22-fold), S+T- (2.10-fold) and S+T+F- (2.61-fold) stages) and higher accumulation of osmolytes (shoot proline for F-stage (5.82-fold) and S+T+F- (2.31-fold) stage), indicating better antioxidant capacitance and osmotic adjustment, respectively. In contrast, higher shoot accumulation of Na⁺ (14.25-fold) and consequent increase in Na⁺/K⁺ (14.56-fold), Na⁺/Mg⁺² (13.09-fold) and Na⁺/Ca⁺² (8.38-fold) ratio in shoot, were identified as major variables associated with S-stage salinity in Jaya. Higher root Na⁺ and their associated ratio were major deriving force for other stage specific and combined stage salinity in Jaya. In addition, CSR36 exhibited higher levels of Fe³⁺, Mn²⁺ and Co³⁺ and lower Cl⁻ and SO₄²⁻, suggesting its potential to discriminate essential and non-essential nutrients, which might contribute to NaCl stress tolerance. Taken together, the findings provided the framework for stage-specific salinity responses in rice, which will facilitate crop-improvement programs for specific ecological niches, including coastal regions.

Mutation breeding offers a simple, fast and efficient way to rectify major defects without altering their original identity. The present study deployed radiation (gamma rays @ 300Gy)-induced mutation breeding for the improvement and revival of three traditional rice landraces, viz., Samundchini, Vishnubhog and Jhilli. Among the various putative mutants identified in the M2 generation, only three, ten and five rice mutants of Samundchini, Vishnubhog and Jhilli, respectively, were advanced to the M4, M5 and M6 generations, along with their parents and three checks for evaluations based on 13 agro-morphological and 16 grain quality traits. Interestingly, all the mutants of the three landraces showed a reduction in days to 50% flowering and plant height as compared to their parents in all the three generations. The reduction in days to 50% flowering ranges from 4.94% (Vishnubhog Mutant V-67) to 21.40% (Jhilli Mutant J-2-13), whereas the reduction in plant height varies from 11.28% (Vishnubhog Mutant V-45-2, Vishnubhog Mutant V-67) to 37.65% (Jhilli Mutant J-15-1). Furthermore, two, six and three mutants of Samundchini, Vishnubhog and Jhilli have increased their yield potential over their corresponding parents, respectively. Interestingly, Samundchini Mutant S-18-1 (22.45%), Vishnubhog Mutant V-74-6 (36.87%) and Jhilli Mutant J-13-5 (25.96%) showed the highest yield advantages over their parents. Further, a pooled analysis of variance based on a randomized complete block design revealed ample variations among the genotypes for the studied traits. In addition, all the traits consistently showed high to moderate PCV and GCV and a slight difference between them in all three generations indicated the negligible effect of the environment. Moreover, in the association analysis, the traits, viz., fertile spikelets/panicle, panicle length, total tillers/plant, spikelet fertility percent and 100-seed weight showed the usual grain yield/plant, whereas the traits hulling (%) and milling (%) with HRR (%) consistently showed high direct effects and significant positive correlations. The SSR marker-based genome similarity in rice mutants and corresponding parents ranged from 95.60% to 71.70% (Vishnubhog); 95.62% to 89.10% (Samundchini) and 95.62% to 80.40% (Jhilli), indicating the trueness of the mutants. Moreover, the UPGMA algorithm and Gower distance-based dendrogram, neighbour joining tree and PCA scatter diagram assured that mutants were grouped with their respective parents and fell into separate clusters showing high similarity between mutants and parents and dissimilarity among the 24 genotypes. Overall, the information and materials generated from the current study will be very useful and informative for students, researchers and plant breeders. Additionally, our results also showed that irradiation could generate a considerable amount of genetic variability and provide new avenues for crop improvement and diversification.