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Endophytic bacteria were isolated from Withania somnifera (L.) Dunal and their potentials were explored through the in vitro plant regeneration techniques. Initially, indole acetic acid (IAA), phosphate solubilization and siderophore producing isolates were screened out. These isolates were identified using molecular tools like 16s rRNA gene sequences namely Bacillus pumilus AS02, Sphingobacterium thalpophilum AS34, Pseudomonas aeruginosa AS36, Agrobacterium tumefaciens AS38 and Enterobacter aerogenes AS75. Further, the regeneration efficacy of IAA producing endophytic bacteria has been analysed on an endangered plant—Exacum travancoricum Bedd. The leaf and inter-node explants of E. travancoricum with or without bacterial infection were tested on Murashige and Skoog’s (MS) medium encompassing 6-benzyladenine (BA; 2.0 mg L− 1) and l-tryptophan (0.2%; w/v). Somatic embryo induction was observed on both explants. The leaf explants infected with S. thalpophilum AS34, P. aeruginosa AS36 and E. aerogenes AS75 exhibited highest percentage of somatic embryo induction (93.3%) compared with the inter-node explants (86.6%). The explants without bacterial infection (control) and the presence of exogenous IAA exhibited lower level of response (88.8%, leaf and 75.5%, inter-node). Histological analysis revealed the appearance of globular embryogenic masses on epidermal, sub-epidermal regions of both explants. The development of torpedo, cotyledon stage and protoderm formation without the vascular connection from explants confirmed direct somatic embryogenesis. This was confirmed with scanning electron microscopy. Sub-culturing of cotyledon somatic embryos in MS liquid medium without growth regulators was performed to obtain well developed shoots with roots.

Strains' improvement technology plays an essential role in enhancing the quality of industrial strains. Several traditional methods and modern techniques have been used to further improve strain engineering programs. The advances stated in strain engineering and the increasing demand for microbial metabolites leads to the invention of the genome shuffling technique, which ensures a specific phenotype improvement through inducing mutation and recursive protoplast fusion. In such technique, the selection of multi-parental strains with distinct phenotypic traits is crucial. In addition, as this evolutionary strain improvement technique involves combinative approaches, it does not require any gene sequence data for genome alteration and, therefore, strains developed by this elite technique will not be considered as genetically modified organisms. In this review, the different stages involved in the genome shuffling technique and its wide applications in various phenotype improvements will be addressed. Taken together, data discussed here highlight that the use of genome shuffling for strain improvement will be a plus for solving complex phenotypic traits and in promoting the rapid development of other industrially important strains.

Even though pesticides have greatly contributed to boosting agricultural productivity and farmer income over the years, there have been concerns about the safety of some of these pest control products. Besides, there has been a growing demand for good quality and safe food in the recent past – as reflected in the stringent regulations on pesticide residue levels in produce. Biopesticides in comparison with conventional synthetic chemical pesticides are usually less toxic, generally affect only the target pest and closely related organisms, are often effective in relatively small quantities and decompose faster, resulting in lower exposure. Consequently, over the last few years, biopesticides have attracted global attention as a safer pest control strategy for incorporation into Integrated Pest Management (IPM) programmes. Besides, in the last decade, adoption of IPM programmes has significantly enhanced pest management practices and, in some cases, reduced pesticide use, consequently reducing the rise in demand for synthetic chemical pesticides. Also, the development of new synthetic chemical pesticides has declined considerably in the recent past, as regulations have become tighter, with products being withdrawn from the market, resulting in a more limited choice of chemical solutions such that biopesticides have become a more feasible option. Many countries have also increasingly lowered chemical Maximum Residue Levels for agricultural imports which have made it increasingly necessary to explore pest control options which would ensure reduced reliance on the use of synthetic chemical pesticides. In this paper, avenues of addressing challenges to biopesticide research and development are evaluated by seeking the inputs of a wide range of stakeholders, building on a recent international workshop with biopesticides practitioners from across the globe. Prospects for biopesticide application are detailed using a case study on the fall armyworm (Spodoptera frugiperda) in Africa.

It is well known that plant–microbe interaction can be affected by global climate change. Many abiotic and biotic factors have great influence on the generation and maintenance of microbial diversity in the rhizosphere. On the other hand, the interaction between plants and beneficial plant microbe aids plants to develop resistance against biotic or abiotic stresses and raise crop yield. In this chapter, we focus on plant natural systems; artificial systems (microbial-mediated transformation of plants); plant–microbes interaction and plant immune system; plant–microbe interaction; and genomics and genome-scale modelling at metabolic level.

Rice is one of the most widely cultivated and consumed staple foods for more than half of the global population. Viruses that infect rice can lead to huge losses and thus a serious impediment to rice cultivation. Development of strategies that are efficient enough to control these viruses has become the need of the hour. The rice-infecting viruses are transmitted by insects, mainly leafhoppers and plant hoppers, which can migrate over long distances. Genetic modification can pave way for plants that are resistant to virus attacks. Out of several developed methods, RNA silencing is the most promising one. However all RNAi constructs are not equally effective in conferring virus resistance. Some results show complete resistance, whereas some constructs slow down the appearance of symptoms. There are also possibilities that the construct may even fail to confer resistance. The success can be ensured by identifying appropriate viral gene. Hence with proper protocols, transgenic rice can lead to stable production of this staple food crop.

Rice forms the staple diet of about half of the population all over the world and is the world’s largest food crop. The domestication of rice began centuries ago, and currently Oryza glaberrima and O. sativa are the two species grown globally. The history of the domestication of rice can be traced back to 10,000 years ago when the Oryza sp. was a mere wild grass and artificial continuous selection by humans has led to the development of a stable amenable cultivar. Several studies show that Asian rice or O. sativa has O. rufipogon as its progenitor, from which it was domesticated. O. sativa is further comprised of five subpopulations, out of which indica and japonica show distinct genetic variation. Since phenotypes of domesticated rice variety differ significantly from their ancestor which is of the wild variety, organisms that interact with domesticated variety experience selective pressure to adapt to these novel phenotypes. Modern genetic tools have paved the way for new insights into such genetic variation, population structure and identification of domestication loci in species of rice. Thus domestication is a complex evolutionary process. Studies on molecular genetics behind the dynamics of domestication will help us breed better varieties for future generations.

Micronutrient enhancement via biofortification is the only tool to reduce malnutrition of rice. The nutritional value of rice, especially iron, zinc, and selenium are usually low in many consuming communities. The aromatic rice cultivars have consistently higher concentration of iron and zinc in grain than the non-aromatic types. Zinc has multiple roles in the human body including the efficient functioning of cellular metabolic activities and stimulation of the immune system. Selenium is an essential element for human health but its intake is low. Accordingly, biofortified rice with this trace element can be prophylactic to consumers. Micronutrient deficiencies, especially those raised from selenium, zinc, and iron, pose serious human health problems for more than 2 billion people worldwide.

Rice serves as a major food crop to the majority of the world’s population. O. rufipogan and O. nivara are the two common wild varieties of rice found in Asia. O. sativa and O. glaberrina are two of the cultivated varieties of rice found in Asia. O. rufipogan has disease resistance and drought tolerance. Domestication of rice started when people thought to cultivate rice in different geographical regions to where they migrated. The cultivated rice varieties started to adapt to new climatic and environmental conditions in which they are cultivated, resulting in domesticated varieties of rice. Genetic diversity of rice is exploited to breed new varieties of rice. Rice blast, a disease caused by Xanthomonas oryzae in rice, can be controlled by breeding disease-resistant varieties through the exploitation of genetic diversity. Techniques like molecular markers and other next-generation sequencing technologies have been used to identify the genetic variation among different varieties of rice. For broadening the gene pool of the rice varieties, a technique known as wild hybridization has been widely used. It involves the hybridization of rice with related species of wild varieties. Marker-assisted selection method of breeding increases the efficiency of breeding rather than conventional methods. Marker-assisted pyramiding involves combining many genes together to form one genotype. This method is useful in providing pest resistance and tolerance to abiotic stress. Gene introgression involves the movement of alleles of a species to the gene pool of other species. Gene introgression can result in plant evolution because it introduces variations among genes for the plant to adapt changes in the environment. Nevertheless, gene introgression provides short-term genetic diversity; the original genetic diversity of rice species is usually lost.

Plants are the major source of nutrients in the human diet. However, staple cereal crops lack certain amino acids and vitamins, and its nutritious content is not enough to provide a balanced diet. Rice is the most widely preferred food crop; thus, it is necessary that we enhance its nutritional content. This can be achieved through the process of biofortification using principles of genetic engineering. Rice is mainly known to be deficient in threonine and lysine. Hence, there has been great interest in using practical concepts of genetic engineering to increase the amino acid content of rice. Several studies are being carried out on overexpression of aminotransferases in order to obtain significant levels of essential amino acids. Efforts have also been taken to enhance the vitamin content of rice. Golden rice rich in vitamin A is one of the outcomes of such strategies. Similarly, transgenic approaches for the expression of enzymes responsible for synthesis of vitamin E have increased the levels considerably. Thus, genetic engineering and transgenic approaches can prove to be a solution to malnutrition, but further comprehensive study on metabolic pathways and its manipulation is necessary.

Rice is a basic staple food of most countries including developed and less developed nations, and more importantly, 90% of population relies on rice across South Asian countries. Global climate change, increased urbanization, drought, and desertification have resulted in the significant drop in the rice production and also prompted researchers to develop novel varieties with increased productivity. Hence, novel varieties with enriched nutritional composition may offer wide benefits and could be a potential step in eradicating malnutrition among the less developed nations. According to the “International Rice Research Institute (IRRI),” 843 varieties have been developed until now, which have been generated by using both conventional and molecular breeding techniques. Genetic markers are forerunner in the present-day agriculture production system, which has anonymously contributed in the production of novel varieties with additional accuracy, reliability, and rapidity. Thus, it has significantly contributed in precision plant breeding, and dependency on molecular techniques such as marker-assisted selection and quantitative trait loci is inevitable for enhanced crop productivity in the near future. In the present chapter, an elaborate case study involving recent developments in enhancing the nutritional quality of rice crop using marker-assisted selection and quantitative trait loci has been represented.

Herbicides are used in modern agriculture to control weeds that pose threat to agricultural crops by competing with them for light and nutrients. Continuous use of the same type of herbicide results in the evolution of weeds that are resistant to herbicides. Indiscriminate use of herbicides can also cause environmental pollution. Development of transgenic rice that is resistant to more than one herbicide is a solution to these problems. The use of herbicide-resistant variety of rice also reduces the cost for weed control. Genetic engineering involves the manipulation of an organism’s genetic material using various molecular biological techniques. Source of transgenes for herbicide resistance includes bacteria and plants. Development of transgenic rice that is herbicide-resistant will result in the development of wild rice. Genetically engineered rice that is herbicide-resistant has changed the usage pattern of herbicide worldwide. Examples for herbicide-resistant rice varieties include Clearfield, Roundup Ready, and LibertyLink. Clearfield is imidazolinone-resistant, Roundup Ready glyphosate-resistant, and LibertyLink glufosinate-resistant. Despite having so many benefits, genetically engineered herbicide-resistant rice varieties have some drawbacks. One such drawback is that genetically improved crops are also responsible for the problems associated with herbicide-resistant weeds. Another issue is related to the acceptance of genetically modified herbicide-resistant rice variety by the public. It is also not that easy to find domestic and international markets with herbicide-resistant rice varieties. Hence, proper production and marketing strategies should be adopted along with the development of herbicide-resistant rice varieties that are developed using genetic engineering.

The genetic modification of plants paved the way for new breeding strategies, including for recalcitrant crops. Rice is a staple food for more than 60% of the population worldwide. However, the accelerated growth rate of the world population calls for an enhancement in rice production and modified rice varieties that can produce improved yields and are resistant to environmental stresses. This can be achieved through production of transgenic rice that is attained by the introduction of a transgene into the plant cells using methods such as electroporation, polyethylene glycol-mediated transformation, biolistics, transformation via Agrobacterium and in planta floral-dip transformation. The presence of transgenes in the regenerated plants can be confirmed using several molecular tools. However, a real transgenic cannot be confirmed based on initial transformants under the confinements of a laboratory and a long term approach is necessary. Several factors affect the efficiency of transformation and regeneration of rice, including type of explant used, components of culture medium, gelling agents and type of Agrobacterium strains. Currently, transgenic rice production is hindered by drawbacks such as low transformation efficiency, tedious and lengthy protocols, genotype specificity, failure of transgenes to express the required protein due to silencing and generation of sterile plants. Thus, effective breeding of enhanced varieties of rice can be possible through development of improved protocols to ensure stable expression of transgenes and proper regulatory framework.

Sugarcane is a major commercial crop grown in India and across the world. Hence, several elite varieties have been developed now-a-days to overcome many obstacles including abiotic stresses and diseases. The present study was undertaken to screen genetic variation among twenty four sugarcane varieties that are commonly cultivated across Northern Karnataka, India with reference to physicochemical characters. Experiment was conducted in triplicate following randomized complete block design (RCBD) at S. Nijalingappa Sugar Institute, Belagavi, Karnataka, India during February 2016-17. Physiological parameters such as internode length, stalk height, plant height, stalk girth, number of internodes, single cane weight, single cane volume of juice, cane yield and recovery were investigated. Further, statistical techniques such as principal component analysis and agglomerative hierarchical clustering were performed to characterize the twenty four varieties. Among twenty four sugarcane varieties studied, Co 86032 and CoC 671 were found to be elite varieties with respect to sugar recovery and cane yield, whereas varieties such as Co 86032 and Com 0265 were found to be best with respect to cane yield only. Based on the results obtained, eight varieties, viz., Co SNK 09232, Com 0265, Co 86032, Co SNK 09293, Co SNK 07680, CoC 671, Co 13006 and Co 2001-15 were found to be good with respect to overall qualities. Further studies need to be involved with molecular marker that would help in identification of elite varieties which could substantially contribute to construction of genetic resources library that may in turn find maximum use in molecular breeding.

In this review we discussed the role of mycorrhiza in organic farming. How mycorrhizal association, will help to improve and encouraging the idea of organic farming. How mycorrhizal association help the plants to grow and yield better without applying of chemical fertilizers and following the conventional farming practices. We discussed how AMF help plant to uptake nutrients, releasing chemicals which help plants to grow proper, developing resistance against weeds, pest and other microbes.

The review is focused on management of macronutrients for cultivating Soybean. Soybean is an important crop in the world because the only reliable plant-based source of complete protein, comparable to meat and eggs, is from soya protein. Soybean yield is crucial for meeting protein malnutrition and edible oil needs.. The wide variation inRhizobialcell counts and nodule mass in beans are likely related to variation is Physico-chemical conditions of the soil.

The African tulip (Spathodea campanulata) is a monophyletic species native to tropical forests of sub-Saharan Africa belonging to family Bignoniaceae. Although its endemism in sub-Saharan Africa, it is listed as potential alien invasive species in Pacific, Indian and Caribbean, but also Singapore, Papua New Guinea and Australia. The expansion of its range from ornamental to invasive is being observed in South India. In this study, RAPD based DNA markers have been used to determine genetic diversity of the monophyletic species. About 14 populations were studied from 6 states of South India using 41 random decamer primers. The total number of 517 bands were scored which are generated by 41 primers producing 12.6 bands on an average per primer, of these 517 bands produced 379 were polymorphic showing 73% polymorphism revealing higher level of genetic polymorphism in the study population. The similarity coefficient ranged from 0.312 to 0.837 and the dendrogram constructed by the UPGMA based on Jaccard's similarity matrix farmed two clusters. In the present study, results showed the high degree of genetic diversity within the populations of S. campanulata supporting high degree of adaptation and its range expansion from ornamental to possible invasive species in South India.

Gene transformation in plants through the intervention of genetic engineering has become potent tool in modern molecular breeding. From the last few decades, new developments have been made in transformation methods in plants. Besides a variety of gene delivery methods, Agrobacterium- and biolistic-mediated transformation has proved significant results. The crop productivity has increased through genetic engineering of plants by transformation of desirable genetic traits in agricultural crops under climate change and growing global population. Cell wall as a barrier to external biomolecular delivery remains as a challenge for efficient genetic transformation in plants. Thus, nanoparticles are promising materials for the delivery of biomolecules due to their efficiency to penetrate through this barrier without any external force. Hence, nanoparticles have the potential to deliver biomolecules in plants through genetic engineering. Application of pesticides and fertilizers indiscriminately poses environmental pollution and threat to biodiversity. In this scenario, nanotechnology has prospective future in agrobiotechnological applications to eradicate these problems by virtue of nanomaterials. Nanosized gold (5–25 nm) delivered DNA into plant cells, whereas iron oxide (30 nm)-based nanosensors identified pesticides at very minute levels. These significant functions will assist in the development of precision agriculture which reduces the risk of pollution and enhance the value of farming practices.

In this review, we discuss the relationship between environmental crop management and adaptation to warming climates of legume plants and plant breeding, for drought tolerance. The benefits connected to the impact of the expansion of appropriate legumes-based agriculture for arid zones are analyzed. We need to two aims to develop programs of breeding and management guided to drought tolerance. The first one is enhancing productivity. The second one is to improve the drought tolerance by mechanisms of water conservation.

The present investigation was carried out to study the response of different concentrations of treated petroleum sludge on seed germination, root and shoot length and tolerance of Vigna unguiculata (L.) Walp. The biologically treated petroleum sludge with bacterial consortium showed 54.8% reduction in total petroleum hydrocarbons. Treated sludge was utilized with agricultural soil in known concentration for the assessment of growth of V. unguiculata. A remarkable absence of seed germination was observed at higher sludge concentration. The different concentrations of treated petroleum sludge showed severe decline on the length, weight and vigour index of the tested seedlings with increasing sludge concentrations. The results showed that the difference in rate of seed germination was significant among various concentrations. Under environmental stress condition, germination is the most critical phase of life cycle in crop plants. In this present study, the high oil content found to alter the osmotic relation between seed and water and thus reduce the amount of water absorbed. It was concluded that the concentration of nutrients and oil present in the treated sludge were toxic to the plant.

In the past, conventional identification of fungi relied on the combination of morphological and physiological properties. In recent years, morphological studies, supplemented with staining techniques and biochemical methods, still play an important role in the overall identification of fungi in the molecular era. In most instances, these tools are widely used to determine the correct identity of yeasts and molds at the genus and species levels.

Lichens are classified as cup fungi, mainly under the phylum of Ascomycota and rarely as Basidiomycota. The body of the lichen is called a thallus, in which the mycobionts and photobionts are stratified in separate layers. Based on their characteristics and thalli, lichens are classified into four main groups. This chapter consists of a pair of parallel and opposing statements that can be compared and will help to identify several genera of foliose, fruticose, crustose, and squamulose lichens.

Mycologists are generally identifying fungal communities by microscopic and macroscopic assessment. This conventional approach has several limitations due to the growth and environmental factors. Hence, molecular techniques and bioinformatics tools are essential in the field identification and characterization of fungi. Multilocus sequences are widely used in most of the bioinformatics tools and they can be used to recognize species boundaries. Nucleic acid and protein sequences-based analysis in fungal studies are revolutionizing the view on mycology. Numerous bioinformatics tools are available online to guide molecular biologists and biotechnologists. This chapter provides a guide to utilizing the available bioinformatics tools on the World Wide Web for sequence alignment, editing, and multilocus phylogenetic analysis.