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Plants are always exposed to the wide variety of pathogens. In compatible interaction, pathogen can successfully invade into the host plant by manipulating host immune system and causes plant disease. On the other hand, during incompatible interaction plant recognizes variable pathogen elicitor molecules and induces its defense response. The molecular mechanism of plant-pathogen interaction is very specific, complex and dynamic. A plethora of research has explored the multifaceted defense mechanisms of plant against pathogen infection which has definite implication in the identification of superior plant genotype with durable resistance to variable pathogens. Thus this treatise is an attempt to summarize the key approaches about the plant-pathogen interaction. Collectively, such information indeed will provide the insight on the molecular mechanism of plant immune response against pathogen infection and the possible protective role of different phytohormones in plant defense system.

Due to the present changes in the global environmental scenario, every day several crop plants face different types of stress from abiotic and biotic factors. The cost of overcoming the obstacle of stress has a direct impact on the yield of the plants. The abiotic stresses can range between drought, cold, high temperature, high relative humidity, salinity and heavy metals. The plant pathogens can be a reason of biotic stress. Just like in the field of any applicative studies, the role of bioinformatics is undeniable too in the field of study of stress responses. Stress has a direct effect on the growth and development of the plants, which consequently has an adverse effect on the productivity of the crop plants. This has created a huge interest among the scientific masses. Several experiments are being conducted in order to analyse the response of crop plants to stress. The development of recent computational facilities and new algorithms has ushered the use of the bioinformatics in the scientific study of the stress response. All the stress responses are in fact controlled by different genes of the affected plants. Bioinformatics has helped in the analysis of genome sequence and quantitative trait loci (QTLs), which are believed to play a major role in stress responses. The hypothesis thus generated by bioinformatics can later be confirmed by transgenics and mutant analysis. Bioinformatics has harnessed the knowledge from molecular and physiological experiments and has applied a multidisciplinary approach to alleviate the effect of stress from plants. The idea of stress management is thus being strengthened by the application of open-access bioinformatics tools.

Crops under both abiotic and biotic stress are the major constraints on productivity. A number of factors like physical disorders, disease susceptibility, toxicity, hormonal imbalance, and nutritional deficiency interfere with the growth and development of plant under stress condition. Under these circumstances, rhizoremediation with the help of the plant growth-promoting rhizobacteria can mitigate stress-induced adverse effects on crop productivity. Plant growth-promoting rhizobacteria and their associated molecules play dual role by affecting both nutrition and resistance concomitantly through overlapping mechanisms. These free-living plant growth-promoting rhizobacteria actively colonize plant roots, exerting beneficial effects using their own metabolism or by directly affecting the plant metabolism. Rhizobial symbiosis has great agricultural importance in terms of improving soil fertility and crop productivity due to their synergistic as well as antagonistic interactions with other microbes in the soil environment. Plant growth-promoting rhizobacteria trigger elicitors, produce siderophores which deprive iron nutrition, and also induce cell wall-degrading extracellular enzymes as defense responses against plant pathogens. PGPR have the ability to induce the secretion of phytohormones, volatile compounds, antibiotics, and toxins which play an important role in plant growth. Rhizobacteria trigger N-acyl homoserine lactones (AHLs) like autoinducer molecules to regulate the gene expression as a part of quorum sensing. Other than these, plant growth-promoting rhizobacteria stimulate endogenous hormones of hosts to enhance stress tolerance. The mutualistic symbiosis triggers NOD factors and NOP effectors, while nonsymbiotic bacterial molecules enhance plant nutrient acquisition and growth. Here in this chapter, we have discussed and reviewed comprehensively the effectivity and mechanisms of plant growth-promoting rhizobacteria for enhancing crop productivity under different stress conditions.

Soil salinity is a key environmental factor restraining the productivity of soil and crop plants. In different parts of the world, agricultural productivity is decreasing mostly because of drought and salinity increase. The situation may become worse for global warming in the future. A wide range of adaptation and mitigation strategies have been adopted to cope up with these circumstances. Among the measures to control soil salinity, those that involve water management and changes in micro relief can be time-consuming and cost-intensive. In this scenario, biological methods of salinity stress management appear as a good alternative, and halotolerant bacteria may play an important role in mitigating salinity stress. The natural ability of these microorganisms to cope with harsh environmental conditions has been attributed to their high genetic diversity and physiological adaptations, such as the synthesis of compatible solutes, growth in biofilm consortia and production of exopolysaccharides (EPSs) and halotolerant enzymes. Furthermore, they are able to produce plant growth-promoting hormones. Salt-tolerant plant growth-promoting rhizobacteria (PGPR) can play an important role in alleviating soil salinity stress during plant growth, and bacterial EPS can help to mitigate salinity stress by reducing the content of Na+ available for plant uptake. To compensate the stress imposed by salinity, biofilm formation and EPS production are significant strategies of salt-tolerant bacteria to assist metabolism. Halophilic microorganisms can form biofilm and accumulate EPS at increasing salt stress. EPSs promote bacterial colonization of plant roots and soil particles, and they can eventually be added to soil to improve its structure and, consequently, to improve plant growth. In a long-term vision, alleviation of derelict soil, improved crop yield and restoration of mangrove diversity are possible by mechanistic use of EPS-producing halotolerant microorganisms.

A developing country such as India is continuously struggling with food production to fulfill the requirements of the growing population, and most of the people living in rural areas are suffering from malnutrition. Major crops and vegetables grown on existing cultivable lands have contributed to the increase in food supply. Insects, pests, fungi, and microbes have a major effect on brinjal or eggplant ( Solanum melongena ), the major vegetable crop in India, which contains vitamins and minerals (especially iron). In addition to its importance as a vegetable, the eggplant has been used extensively in traditional medicine since ancient times. The fruit and shoot borer ( Leucinodes orbonalis ) causes heavy losses to the yield of brinjal production. Indiscriminant use of synthetic chemical insecticides to cure diseases not only contaminates water and food sources, but also poisons nontarget beneficial insects, and develops resistance in insect pests. Bt -brinjal has been developed to combat brinjal loss and to minimize the uses of chemical pesticides, but the controversy regarding its commercialization has adverse effects in India. Biosafety issues are the main concern in this regard based on experimental data on human health and environmental hazards. Bt -brinjal is the one of the best solutions to this emerging problem and can be dealt with in different ways by transplastomic mechanisms.

Castor being a perennial, cross-pollinated, sexually polymorphic crop with high environmental sensitivity, initial plant breeding efforts were restricted to plant height and duration. Domestication of a wild, perennial crop to an annual crop of medium plant height and duration is the first success. Further, development of a two-line breeding system and standard seed production technology led to successful commercial exploitation of heterosis. Being a monotypic genus, diversification of parental base is restricted to intra-generic, intraspecific, or inter-varietal hybridization. Phenotypic expression is highly plastic and varies with locations and seasons. Majority of the morphological characters are monogenic, independently assorted with very limited linkages among the traits. However, information on genetics of major morphological characters is scattered in several old publications. Conventional breeding methods were successful in developing about 40 high-yielding hybrids and varieties with inbuilt resistance to major pests and diseases. An effort is made in the present chapter to consolidate the information on genetics and breeding methods followed in India and elsewhere.

The exopolysaccharide succinoglycan is produced mainly by a large number of soil microbes of Agrobacterium, Rhizobium or Pseudomonas genera etc. Structural properties of succinoglycan are unique in terms of its thermal stability and superior viscosifying property. Unlike the other highly commercialized bacterial exopolysaccharides like dextran or xanthan, mass scale application of succinoglycan has not been that much broadly explored yet. Bacterial succinoglycan is found suitable as a viscosifying and emulsifying agent in food industry, in gravel packing or fluid-loss control agent etc. In this present review, the key aspects of succinoglycan study, in particular, developments in structural characterizations, exo/exs operon system involved in biosynthesis pathway, commercial applications in food and other industries and patenting trends have been discussed.

An efficient protocol of plant regeneration through direct and indirect organogenesis in Swertia chirayita was developed. Explants cultured on Murashige and Skoog medium supplemented with 2,4-D (0.5 mg L−1) with combination of Kinetin (0.5 mg L−1) showed the highest frequency (84%) of callusing and 1.0mg L−1 6-benzyladenine (BA) in combination with (100 mg L−1) Adenine sulphate (Ads) + (0.1 mg L−1) Indole acetic acid (IAA) was excellent for maximum adventitious shoot (12.69 ± 1.30) formation in four week of culture. A maximum number of (7.14 ± 0.99) shoots were developed per leaf explants through direct organogenesis. The highest frequency of rooting (11.46 ± 1.56) was observed on MS medium augmented with IAA (1.0 mg L−1). Well-rooted shoots transferred to plastic pots containing a soilrite: sand mix and then moved to the greenhouse for further growth and development. Four major secondary metabolites were analyzed and quantified using high performance liquid chromatography. Amount of secondary metabolites was found significantly higher, in in vitro plantlets compared to in vivo plantlets and callus raised from S. chirayita. Higher heavy metal accumulation in in vitro as compared to in vivo plantlets correlates higher secondary metabolite production supporting that they play regulatory role in influencing the plant secondary metabolism.

Microalgae may be the source of high amount of lipid and protein. It has the property for carbon dioxide sequestration, recycling and also can remove pollutants from wastewater. Using traditional methods, collection of algal biomass is either cost effective, time consuming or may be toxic due to use of chemical salts. The aim of this study is to harvest freshwater microalgae (Chlorella sp. CB4) biomass by using polymer. Polyacrylamide grafted starch (St-g-PAM) has been synthesized by microwave assisted method involving a synergism of microwave radiation and ceric ammonium nitrate (CAN) to initiate the grafting reaction. The synthesis was optimized in terms of CAN and monomer (acrylamide) concentration. The algal flocculation efficacy of all the grades of this graft copolymer was studied through standard 'Jar test' procedure. Effects of percentage grafting, pH and zeta potential on percentage recovery of algal biomass were thoroughly investigated.

Leaf rust, caused by the fungus Puccinia triticina, is the most devastating disease of wheat worldwide, which sometimes becomes epidemic. The pathogen evolves into new strains, making its control difficult. Though more than 60 leaf rust resistant genes are now known, only limited insight is available into the molecular mechanism involved in this host pathogen interaction. In the present study, quantitative real-time PCR based differential gene expression profiling was examined for five target genes encoding for chitinase3, β-1,3/1,4 glucanase, thaumatin-like protein, peroxidase2 and mitogen activated protein kinase1 to unravel their coordinated action during compatible and incompatible interaction, to inhibit the pathogen progression and to identify the time-period of maximum defense activity. Spatio-temporal expression profiling suggested that the maximum defense activity occurred at 12–24 hours post inoculation, whereas the state of infection and degree of resistance was predicted using coordinated unique expression signatures of target genes. The significant differences of targeted gene expression between resistant mock inoculated, resistant infected and susceptible infected plants were evaluated using t test at significance level of p < 0.01. The differences occurred can be attributed to the presence of seedling leaf rust resistance Lr28 gene, which facilitated prevention of leaf rust infection in resistant wheat plants.

The present study involves discovery, validation and use of single-nucleotide polymorphisms (SNPs) in bread wheat utilizing 48 EST-contigs (individual contigs having 20-89 ESTs, derived from 2 to 11 different genotypes). In order to avoid a problem due to homoeologous relationships, the ESTs in each contig were classified into 175 sub-contigs (3.7 sub-contigs/EST-contig) using characteristic homoeologue sequence variants (HSVs), which had a density of 1 HSV every 136.7 bp. In silico analysis of sub-contigs led to the discovery of 230 candi - date EST-SNPs with a density of 1SNP/273.9 bp. Locus specific primers (each primer pair flanking 1-18 SNPs) were designed utilizing one sub-contig each from 42 EST-contigs that contained SNPs, the remaining 6 contigs having no SNPs. To provide locus specificity to the PCR products, each primer was tagged with an HSV at its 3' end. Only 10 primer pairs, which gave each a characteristic solitary band, were utilized to validate EST-SNPs over 30 diverse bread wheat genotypes; 7 SNPs were validated through resequencing the PCR products. Allele specific primers were designed and utilized for genotyping of 50 diverse bread wheat accessions (including 30 bread wheat genotypes previously used for validation of SNPs), with an aim to test their utility in genotyping and map construction. The allele specific primers allowed the classification of 50 genotypes in two alternative allele groups for each SNP as expected, thus suggesting their utility for genotyping. Of the above 7 validated SNPs, 4 belonged to a solitary locus (PKS37); 7 haplotypes were available at this locus. Altogether, the results suggested that EST-SNPs constitute an important source of molecular markers for studies on wheat genomics.

In bread wheat, 21 anchored simple sequence repeat (SSR) primer pairs detecting SSR length polymorphism and 42 anchored SSR primers detecting microsatellite-anchored fragment length polymorphisms (MFLPs) are reported. Eight bread wheat genotypes were used for detecting polymorphism. The number of alleles in SSR analysis ranged from two to six, with a mean of 2.9 alleles per SSR. The number of polymorphic bands in MFLP ranged from two to 40, with a mean of 12.74 polymorphic bands/primer combination, the SSRs with CT/GA motifs giving the highest level of polymorphism (a mean of 18.37 bands). The average value of polymorphic information content (PIC) was 0.473 for SSRs and 0.061 for MFLP.

PCR primers were designed for 78 expressed sequence tag-simple sequence repeats (EST-SSRs), which represented a subset of over 800 SSRs that were located by us in wheat EST database. When tested for functionality on several varieties of common wheat (Triticum aestivum) including Chinese Spring, 64 of these 78 primer pairs were found to be functional. These 64 functional primer pairs were used for a study of transferability and polymorphism among 18 Triticeae species belonging to Triticum-Aegilops complex. These species had as many as seven genomes in their constitution and represented three ploidy levels (2x, 4x, 6x). The primer pairs each gave amplified products not only in progenitor species containing A, B (including S and G) and D genomes, but also in alien species that contained other genomes (M, N, C and U). The cross-species transferability was as high as 84%, and the fragments of expected size were available with 92% EST-SSR primers in one or more species. This suggested a high level of conservation of DNA sequences belonging to the transcribed portion of the genome, and also indicated that each wheat EST-SSR is perhaps derived from an SSR in an ancestral genome of Triticeae. A very high proportion (88%) of the above 92% EST-SSRs, which gave amplified fragments of expected size, detected polymorphism. The number of alleles ranged from 2 to 14 with an average of 6.8 alleles per locus. A number of EST-SSR primers also proved useful in discriminating different genera, species within a particular genus and the different genomes of the tribe Triticeae. Therefore, EST-SSRs may be used in studies on polymorphism, genetic diversity, gene mapping and synteny conservation across different species of Triticeae. This is in sharp contrast to the situation with genomic SSRs, which are more locus specific.

Rice (Oryza sativa L.) is a major crop in the world and provides the staple food for over half of the world population. From thousands of years of cultivation and breeding to recent genomics and systems biology approach, rice has been the focus of agriculture and plant research. Modern scientific research depends on computer technology to organize and analyze large datasets. Rice informatics – a relatively new discipline – has been developing rapidly as a subdiscipline of bioinformatics. Rice informatics devotes to leveraging the power of nature’s experiment of breeding and evolution to extract key findings from sequence and experimental data. Recent advances in high-throughput genotyping and sequencing technologies have changed the landscape of data collection and its analysis by using friendly database access and information retrieval. It focuses on developing and applying database tools and computationally intensive techniques and statistical software (e.g., pattern recognition, data mining, machine learning algorithms, R-statistical, MATLAB, and visualization) which give the opportunity to quickly and efficiently study heap of genomics information, chemical structure, and model generation study. Over recent years, various newly emerged diseases to rice varieties have an increasing concern to agriculturists and pathologists. The establishments of International Rice Information System, Rice Genome Research Project, Integrated Rice Genome Explorer, and Rice Proteome Databases are important initiatives for rice improvement using in silico software (e.g., homology modeling using SWISS Model, Modeler, and Autodock); the recent ongoing research on rice protein and its role in metabolic pathways works is being done around the world. Rice informatics has already started showing its profound impact on agricultural research and developments.

We describe a recombinant inbred line (RIL) population of 161 F5 genotypes for the widest euploid cross that can be made to cultivated sorghum (Sorghum bicolor) using conventional techniques, S. bicolor × Sorghum propinquum, that segregates for many traits related to plant architecture, growth and development, reproduction, and life history. The genetic map of the S. bicolor × S. propinquum RILs contains 141 loci on 10 linkage groups collectively spanning 773.1 cM. Although the genetic map has DNA marker density well-suited to quantitative trait loci mapping and samples most of the genome, our previous observations that sorghum pericentromeric heterochromatin is recalcitrant to recombination is highlighted by the finding that the vast majority of recombination in sorghum is concentrated in small regions of euchromatin that are distal to most chromosomes. The advancement of the RIL population in an environment to which the S. bicolor parent was well adapted (indeed bred for) but the S. propinquum parent was not largely eliminated an allele for short-day flowering that confounded many other traits, for example, permitting us to map new quantitative trait loci for flowering that previously eluded detection. Additional recombination that has accrued in the development of this RIL population also may have improved resolution of apices of heterozygote excess, accounting for their greater abundance in the F5 than the F2 generation. The S. bicolor × S. propinquum RIL population offers advantages over early-generation populations that will shed new light on genetic, environmental, and physiological/biochemical factors that regulate plant growth and development.

Arabidopsis (rockcress) is a genus in the family Brassicaceae. Representatives of Brassicaceae family are small-flowering plants, some of them are important crops such as cabbage, cauliflower, radish, and canola. Arabidopsis genus includes nine species and eight subspecies. The subspecies delimitation is quite recent, and is based on morphological and molecular phylogenetics (Elizabeth 2000). Arabidopsis thalianacommonly known as thale cress, has 10 chromosomes in diploid stage and was the first plant to have its entire genome sequenced. Most of the species in Arabidopsis are indigenous to Europe and only two species are found in North America and Asia.

In bread wheat, a set of 527 simple sequence repeats (SSRs) were tried on 164 deletion lines, leading to a successful mapping of 270 SSRs on 313 loci covering all 21 chromosomes. A maximum of 119 loci (38%) were located on B subgenome, and a minimum of 90 loci (29%) mapped on D subgenome. Similarly, homoeologous group 7 carried a maximum of 61 loci (19%), and group 4 carried a minimum of 22 loci (7%). Of the cited 270 SSRs, 39 had multiple loci, but only eight of these detected homoeologous loci. Linear order of loci in physical maps largely corresponded with those in the genetic maps. Apparently, distances between each of only 26 pairs of loci significantly differed from the corresponding distances on genetic maps. Some loci, which were genetically mapped close to the centromere, were physically located distally, while other loci that were mapped distally in the genetic maps were located in the proximal bins in the physical maps. This suggested that although the linear order of the loci was largely conserved, variation does exist between genetic and physical distances.