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Photorespiration accounts for 20–50 % reduction in grain yield in C3 crops. The process is essential to remove 2-phosphoglycolate produced due to the oxygenation activity of the ribulose-1,5-bisphosphate carboxylase oxygenase (RuBisCO) enzyme. Attempts were made to improve photosynthesis through enriched CO2 concentration by installing numerous photorespiratory bypass modules in the chloroplast of several crops. In this study, we have introduced Escherichia coli glycolate catabolic pathway (ECGC) into rice chloroplast to bypass photorespiration partially (PB) or completely (FB). Five genes encoding glyoxylate carboligase (GCL), tartronic semialdehyde reductase (TSR), and three subunits of glycolate dehydrogenase (GDH) were introduced to get FB plants, whereas only the three subunits of GDH were introduced to get PB plants. Southern analysis confirmed stable integration of the transgenes and their expression was confirmed by RT-qPCR analysis in the T3 progenies. Both FB and PB transformed lines exhibited increased photosynthetic efficiency, biomass, and grain yield than wild type (WT) with empty vector control. The introduction of ECGC pathway favoured the carboxylase activity of RuBisCO while decreasing its oxygenase activity fostering the functioning of Calvin-Benson cycle and resulting in an increased carbon-assimilation that was manifested in their superior architecture and harvest index. These findings will support rice and related cereal crop breeding programs to increase yield under elevated temperature and arid conditions.

Rice is considered as a model plant to map the complete genome and identify the genes in the genome for various traits. Recent advance in molecular biology and statistical analysis techniques could boost the plant breeder to gain knowledge on rice genome and find out the function and expression of rice genes. Near the genes, several quantitative trait loci (QTLs) have been mapped and identified with genetic markers to find out its location in chromosome. With the popularity of computational approach, it is easy to find out the QTLs position in the genome and introgress these QTLs into the popular rice genotypes to study the expression and its effect with trait used in MAS breeding program. Several models and QTL mapping methods are used to detect the QTL position between marker interval. QTL mapping is a highly efficient way of determining genetic interactions in plant disease resistance. The QTL mapping was carried in F2, RILs, NILs, backcrossing populations, and double haploids (DH) in rice to study the performance of respective QTLs and its genetic basis of expression in grain yield and other traits as well as other parameters of yield like biotic and disease resistance. Various studies have been reported for QTL mapping and its function in phenotypic variation found in rice. This fine mapping and detection of QTL position provide a new way to improve the rice plant against various theft of decreasing yield.

Drought is one of the major abiotic stresses that affect plant growth and survival. It alters morphological, biochemical, and molecular processes in plant cells. The implementation of multi-omics and improved breeding strategies is a dynamic step towards drought tolerance in crop plants. The identification of several drought-responsive genes, differentially expressed transcripts, proteins, metabolites, and miRNAs associated with drought responses has become possible through genomics, transcriptomics, metabolomics, proteomics, micromics, and phenomics, etc. Investigations on the latest omics technologies will provide us with an overall idea of the pathways involved in drought tolerance. Additionally, GWAS and QTL mapping have made an impressive contribution to improving plant responses to water-deficit conditions. This chapter discussed how various omics tools and breeding technologies enable plants to withstand the devastating effects of drought stress.

Genome editing is the main goal in improving rice productivity by inducing gene-specific mutations to modify the gene function. Due to the advances in the biotechnology approach, it is possible to make the gene manipulation that could give effective results against various biotic and abiotic stresses and grain quality. Nowadays, population increases day by day; therefore, it is a big challenge for developing countries. However, it is important to release new crop varieties with effective function, and which will minimize the food shortage and food security problem. The existing rice genome sequences have made it possible to identify genetic variations and insert mutagenesis to improve rice traits. Various methods and techniques are available for genome editing to modify the gene through inducing mutagenesis or by gene silencing. Zinc finger nucleases (ZFNs), transcriptional activator-like nucleases (TALENs), and newly identified clustered regularly interspaced repeats (CRISPR)/CRISPR associated protein 9 (Cas9)-based genome editing methods are more widely used in rice breeding programs. Among them CRISPR/Cas9 is the most reliable tool in genome editing due to its simple targeting method for improving grain quality and quantity. Thus, the application of CRISPR/Cas9 system introduces a double-strand break in DNA to edit the gene of interest at a specific position. Additionally, it may be utilized in the near future to develop disease and herbicide resistance, as well as to improve rice production, quality, and quantitative characteristics.

Rice is one of the world’s most important agricultural crops and a model plant that is widely studied. The completion of the complete rice (Oryza sativa) genome sequence through high-throughput experimental platforms has resulted in a huge amount of data being generated and specialized databases, and bioinformatic tools for data processing, analysis, efficient organization, and visualization have been developed. In this chapter, we address a set of biological databases that host rice-specific sequence, genetic variation, gene expression, pathways, and gene–interactome data from various genomic and proteomic sources, and aid in data analysis and visualization.

miRNAs, on average comprised of 22-nucleotides with small non-coding RNAs, regulate the gene expression of targeted genes. Thousands of miRNAs have been identified, having biological significance in many pathways. These microRNAs have also been used as biomarkers for diagnostic and agricultural purposes. Thus, this chapter attempts to describe in brief miRNA biogenesis pathways, miRNA profiling methods, and bioinformatics tools of miRNA profiling. Additionally, we will discuss the role of mi RNA and its applications. miRNA biogenesis can be broadly categorized into canonical and non-canonical pathways. There are various sample types and miRNA extraction procedures. miRNA sequences, once extracted, can be subjected to various computational tools that may aid in understanding its structure and functions. However, few researchers have suggested that there is still scope for developing these tools with appropriate algorithms for avoiding false positive results.

The simultaneous genetic change in interacting species as a result of mutually imposed natural selection is known as co-evolution. Many biologists believe that the process of co-evolution between plants and the biota that surrounds them, which includes mammals, viruses, fungus, bacteria, insects, and nematodes, is responsible for most of the earth’s biological variety. While most of the debate around plant co-evolution focuses on one host–one pathogen, two or more hosts–one pathogen, and one host–two contrasting co-occurring pathogens single plant–pathogen interactions, a wide range of many other micro-and macroevolutionary processes occur concurrently in a single plant, posing the issue of whether or not we should even discuss it. In this review, we have discussed the framework of co-evolution theory, as well as the complexities of investigating co-evolution in natural conditions.

The main food of half the world’s population is rice, Oryza sativa L. By 2030, rice production must increase by at least 25% to meet global food demand of ever growing human population. In order to reduce the impact of climate change and arable land loss and ensure stable global food supplies, accelerated genetic gains during rice improvement are highly required. Since this process is complicated, we first need to have detail information regarding the genetic diversity of the oryza sp. gene pool, the correlation of diverse alleles with essential traits of rice, and the systematic use of the rich genetic diversity through employing methods that adopt expertise in rice improvements through breeding strategies. Considering this, in 2014, an international sequencing project of 3000 rice genomes was published. These details information may help us to detect novel alleles associated with important phenotypes of rice by employing various bioinformatics or genetic methods. It will also help us to unmask the O. Sativa genomic diversity more precisely. This project also encouraging the global rice community to employ data present in the 3000 rice genomes project for establishing various global public rice genetic/genomic database, which in turn will promote rice-breeding technology in the future. Thus, in this chapter, authors made an attempt to understand in brief about the various germplasms employed in 3000 genome project and the genetic diversity of O. sativa, which, in the near future, may help us to increase grain yield of rice.

The genome-wide association study (GWAS) is one of the potential approaches for identifying QTLs/genes and complex traits associated with target traits quickly using natural variations. With the advancement in genome sequencing technology, it is possible to examine genome-wide genetic variants of agro-morphological, physiological, biochemical, and molecular traits across diverse genetic materials. In nature, natural variants of crops are generated due to spontaneous mutations and manual breeding in the wild progenitors. Traditional landraces are adapted to various environmental conditions, rich sources of alleles, and genes linked with various traits valuable for variety improvement through molecular breeding because of the availability of high-throughput sequencing technologies and a reference genome sequence, accurate re-sequencing of a significant number of crop genomes as possible. It aided in understanding the genetic basis of phenotypic variance and allows for functional studies of evolutionary changes in crops. This rapid development will significantly improve crop design research using genomics-assisted breeding, allowing it to be used in gene recognition, cloning, QTL identification, and crop breeding using marker-assisted selection or genetic engineering. This book chapter presents an overview of the entire process of a typical GWAS, various software applications and, its limitations, and future perspectives.

Microsatellites (MS) or simple sequence repeats (SSRs) is a DNA sequence set comprising of tandemly repeated motifs. SSRs with codominant inheritance, higher amounts, moderately conservative flanking sequences, and rich polymorphism are commonly distributed throughout the plants and animals’ genome. MS has already been employed in several crop plants for determining their seed lots’ genetic integrity and to evaluate the capacity of plant varieties to defend their intellectual property. Thus, the key objective of this chapter is to include a revised and comprehensive overview of the SSR marker and its applications in various biological domains. Additionally, we have discussed genomic occurrence and the advantage/disadvantages of employing microsatellites as genetic markers in agricultural research.

Plant domestication has significantly influenced the growth of human society. The domestication of rice lists amongst the most significant historical breakthroughs. However, the sources and domestication methods are debatable. Thus, in this chapter, authors attempted to understand in brief about genetic diversity in rice, as well as a description of the processes about the domestication of rice began and at which location rice was domesticated. Information retrieved from the published literature to date suggests that the rice genus Oryza is a small genus comprising about 25 species, but it has incredible adaptive capabilities to differing ecological circumstances. Within the genus Oryza, two distinct domestication events have occurred—one in Asia and another in Africa. In Asia, wild rice O. rufipogon is popular, which was cultivated about 9000 years ago. In Africa, the wild rice Oryza, namely O. glaberrima, was independently domesticated around 3000 years ago. During domestication, plant experience decreased nucleotide diversity, enhanced linkage disequilibrium and modified population frequencies of polymorphic nucleotides within the domestication-related genes. In the near future, the information presented in this chapter may aid in enhancing rice’s yield.

Rice production is severely threatened by drought stress in Eastern India. To develop drought tolerant varieties, selection of donors for breeding programme is crucial. Twenty one selected rice genotypes including both tolerant and sensitive to drought were grown under well-watered and drought stress conditions in dry seasons of two successive years of 2017 and 2018. Leaf water potential, relative water content displayed significant difference among the genotypes during vegetative screening. At reproductive stage drought screening, days to 50% flowering was delayed in all genotypes except N22 and Anjali (showed early flowering) however grain yield and other yield related traits decreased significantly compared to well watered condition. Correlation analysis of phenological and yield related traits with grain yield revealed that tiller numbers and panicle numbers are highly correlated with grain yield both under well-watered and water stress conditions and contributes maximum towards grain yield. The dendrogram grouped Mahamaya, Sahabhagidhan, Poornima, IBD 1, Hazaridhan, Samleshwari and Danteshwari into one cluster which performed better under water stress conditions and had grain yield more than 1.69 tha−1. Sahabhagidhan, Poornima, Vandana, and N22 displayed tolerance to drought both under vegetative and reproductive conditions which could be a good selection for the breeders to develop drought tolerant rice cultivars for eastern region of India.

The experiment was carried out to examine the effect of moisture stress (drought) on different root traits, rooting pattern and to identify important root morphological markers contributing to stress tolerance. Moisture stress was imposed on 21 days old seedlings of selected rice genotypes grown in PVC cylinders. Samplings were done at 10 and 20 days after imposition of stress to examine the effect of stress on root growth and development. Results revealed that rate of assimilate allocation impeded more under 20 days stress (severe) than in 10 days stress (moderate) in terms of enhanced root: shoot ratio, maximum root length to shoot length ratio and root volume. Magnitude of trait variation among genotypes was more pronounced under severe stress than under moderate stress. The root: shoot ratio, maximum root length to shoot length ratio and root volume were observed to be the most crucial morphological markers in determining drought tolerance in rice genotypes analyzed through biplot analysis. Among the thirteen genotypes tested, AC-42994, AC-42997, AC-43020, CR-143-2-2, Ronga Bora and Bora were found to possess desirable root traits and these genotypes can be used in the breeding programme for enhancing drought tolerance in rice.