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To combat the dreaded diseases in rice like bacterial blight (BB) and blast, host plant resistance has been advocated as the most suitable and sustainable method. Through the present study, we have successfully incorporated three major BB resistance genes, namely

A significant increase in genetic gains of different crops can be achieved by the pragmatic use of modern breeding techniques. The improvement in “omics” technologies makes an opportunity to generate different datasets for several crop species. The “omics” approach coordinates information gathered from the genome, transcriptome, proteome, and metabolome into a solitary informational collection which can rapid the recognizable proof of doubtful qualities and their administrative organizations related with metabolic pathways of interest. The analysis of genetic and phenotypic data using genomics and functional omics together is the main method to identify genes and pathways responsible for important phenotypic traits. The screening of large number of germplasm pools to identify unique alleles from various sources through high-throughput genotyping technologies. This approach enhances the availability of variation for breeding. The various omics tools and approaches like high-throughput genotyping platforms such as whole genome re-sequencing, proteomics, and metabolomics give more significant prospects to explore molecular phenomenon and the exposure of important genes for developing ideal genotypes which can survive in the rapidly changing climate. This book chapter provides an introduction to the core omics technologies, their relevant tools and methodologies, and application for developing and screening of breeding lines to accelerate precision breeding efforts in crops.

Background: Rice, being the principal food crop and major nutritional source for more than half of the global population, is also an important source of livelihood in many South and South-East Asian countries. Amidst diminishing natural resources and many biotic-abiotic stresses, increasing the yield of rice varieties remains a challenging task. Identification of novel and yield augmenting alleles from stable rice hybrids is crucial to facilitate their marker-assisted transfer into various genetic backgrounds. Results: Quantitative trait loci (QTL) mapping using a population of 125 doubled haploid (DH) lines developed from the cross IR58025A/KMR3R and 126 polymorphic SSR; EST-derived SSR markers led to the identification of 12 each of major-minor effect QTLs for yield related traits. Major effect QTLs were detected for traits namely days to fifty percent flowering, test (1,000) grain weight, plant height, panicle weight, panicle length, flag leaf width, flag leaf length, biomass and total grain yield/plant explaining the phenotypic variability in the range of 29.95%-56.75%. QTL hotspots were detected on chromosome 3 for the traits, panicle length and total grain yield/plant and on chromosome 6 for the traits, panicle length, flag leaf length and total grain yield/plant. Though many of these QTLs were noted to co-localize with the QTL regions reported in earlier studies, five novel and major effect QTLs for panicle length, biomass, flag leaf width, panicle weight, plant height and three novel minor effect QTLs for panicle weight and fertile grains per panicle, were identified in this study. Conclusions: Through this study, both major-minor effect novel QTLs for crucial yield related traits, viz., fertile grains per panicle, panicle length, panicle weight were identified. Further, the QTL hotspots identified on two different chromosomes for flag leaf length, panicle length and total grain yield/plant shall not only help in understanding the underlying genetic mechanisms of yield regulation but also would provide an insight into the genetic synchrony among the various yield related traits in contributing for yield heterosis. The identified QTL hotspots after their validation can be deployed in breeding programs targeted towards improvement of yield heterosis.

A major dwarfing region for plant height, asd1, was identified employing the next-generation sequencing-based QTL-Seq approach from a dwarf mutant and is demonstrated to be responsible for the dwarf nature with least penalty on yield in rice. The yield plateauing of modern rice is witnessed since many decades due to the narrow genetic base owing to the usage of a single recessive gene, i.e., semi-dwarf-1 (sd-1) for development of short-statured varieties throughout the world. This calls for the searching of alternate sources for short stature in rice. To this end, we made an attempt to uncover yet another, but valuable dwarfing gene employing next-generation sequencing (NGS)-based QTL-Seq approach. Here, we have identified a major QTL governing plant height on chromosome 1, i.e., alternate semi-dwarf 1 (asd1) from an F2 mapping population derived from a cross between a dwarf mutant, LND384, and a tall landrace, INRC10192. Fine mapping of asd1 region employing sequence-based indel markers delimited the QTL region to 67.51 Kb. The sequencing of the QTL region and gene expression analysis predicted a gene that codes for IWS1 (C-terminus family protein). Furthermore, marker-assisted introgression of the asd1 into tall landrace, INRC10192, reduced its plant height substantially while least affecting the yield and its component traits. Hence, this novel dwarfing gene, asd1, has profound implications in rice breeding.