eChapters

Introduction
Biological stress factors such as bacteria, fungi, viruses, and pests can lead to losses in yield and quality before and after harvest. An estimated10 to 23 percent loss is caused by fungal pathogens, along with an additional 10 to 20 percent post-harvest loss. Unlike animals, plants do not possess a highly developed immune system or mobile immune cells. They possess highly sophisticated defense mechanisms based on their structural, chemical, and protein composition. The defense responses of plants to different pathogens are influenced by factors such as the stage of plant development, the pathogenicity of the pathogen, and the environmental conditions. Recognizing the importance of genes that resist biotic stressors, it becomes clear that they are invaluable natural resources for sustaining agricultural productivity and minimizing crop losses36. Any physiological abnormality or significant disruption in the average health of a plant is considered a disease. Living agents, like fungi and bacteria, and environmental factors such as nutrient deficiency, drought, and lack of oxygen, excessive temperature, ultraviolet radiation, and pollution can all contribute to disease development. Plants have developed diverse constitutive and inducible defenses to safeguard themselves from harm. Disease resistance is decreased pathogen growth on or within the plant11. It indicates a lower disease occurrence in one genotype than the susceptible variety and is a relative characteristic. Typically, the reproduction rate is significantly decreased, which restricts disease transmission. Plants have varying levels of resistance to different pathogens, with some being more susceptible to specific pathogens while being resistant to others. This resistance is often specific to particular species or strains of pathogens.

When conditions in the plant growing environment are less than the optimum, the plants experience stress which is broadly termed as abiotic stress. Major abiotic stresses impacting crop yield significantly are as follows (Grover et al., 2004; Acquaah, 2007):

Drought: This is the environmental condition caused by lack of adequate rainfall. This is also termed as water stress or desiccation stress. Effects of drought on crop plants are complex and variable and are greatly accentuated by a number of interacting factors. The onset of drought in general has been observed to reduce germination, emergence, hypocotyl length, water uptake and the mobilization of dry matter reserves even at the early growth stages. Drought stress causes a marked reduction in leaf area. Soil moisture availability at the seed germination, anthesis and at post-anthesis growth stages determines as to what extent production potential of crops would be expected in drought-prone situations.

The yield losses in field crops may be attributed to inadequate water availability at the critical growth stages. Crops therefore differ in their susceptibility of growth stages to water stress. Stress exposed plants immediately lower down relative water content (RWC) of their leaves, leaf water potential, osmotic potential. Turgor pressure may also be decreased unless plants have finally adapted to drought by opening of stomata again and improving the water potential. It has been reported that low leaf expansion rate at the early stage and accelerated leaf senescence accompanied by mortality of older leaves at later stage decreases total leaf green area.

Plant abiotic stresses are external and nonliving factors that have harmful effects on plants. A non-living factor must exert influence on the normal range of environmental variation to adversely and significantly affect the plant performance or the physiology of the organism. Abiotic stresses are the most harmful factors affecting the growth and productivity of crops worldwide, resulting in a yield reduction ranging from 10% to 100%. They are most harmful when occurring together with other abiotic stresses and their effect in yield will only worsen with the climatic changes experienced now and expected to be more severe in the future.

Biotic stresses include diseases and insect pests which cause serious damage to the crop plants and ultimately yield loss. Biotic stresses can be listed as follows:

• Diseases caused by pathogens which include fungi, bacteria, and viruses
• Insects
• Nematodes
• Parasitic weeds

Another category of stresses are called as abiotic stresses which are caused by environmental factors as:

• Water stresses (water logging, drought)

The genetic organization of cross pollinated crops are different from that of self pollinated crops, because of differences in the reproductive system. Open pollinated populations are heterozygous with free inter mating individuals, heterozygous at most of the loci. Heterozygosity is an essential feature of commercial varieties of out breeders. It is maintained during breeding or is restored at the end. Population improvement involves selection, generation after generation, with recombination of selected individuals. Its aim to increase the frequency of favorable alleles in the population. The improved forms may be used for commercial cultivation or as a base germplasm for the derivation of inbred lines. The list of cross pollinated plants is presented in Table 10.1. The factors that promote the cross pollination are dicliny, dichogamy, herkogamy, self-incompatibility and male sterility. The breeding methods which are commonly used in cross-pollinated crops are population improvement, hybrid and synthetic varieties.

Population Improvement

In cross pollinated crops heterozygosity must be restored in the end product of any breeding programme. It is classified into the following types:

The prime object of plant breeder is to develop high yielding variety with superior characteristics. Selection is based on the phenotypes of the plants. Consequently the effectiveness of selection primarily depends on the degree to which the phenotype of plants reflects their genotype. These are all self fertilizing species. In these species development of seed take place by self fertilization. Hence self pollinated species are also known as autogamous species. Various plant characters such as homogamy, cleistogamy, chasmogamy, bisexuality etc. promotes self pollination. The self pollinated crops with their description are given in Table 9.1. The breeding methods used in self and often-self pollinated crops are discussed below:

Plant Introduction

Plant introduction consists of taking a genotype or a group of genotypes of plants into a new area or region or environment, where they have not being grown earlier. It is very simplest and fastest method of developing new variety. It is of two types:

Reproduction that does not involve the union of male and female gametes is known as asexual reproduction. Reproduction in which sexual organs or related structures take part but fertilization does not occur, or crops which are propagated asexually or by vegetative means are known as asexually propagated crops. Most of the fruit plants are propagated asexually which consist of large number of clones. Example: sugarcane, potato, sweet potato, banana, mango, citrus, pears, peaches, litchi, crops that propagates by asexual means. The procedure of selection used for asexually propagated crops is known as clonal selection, since the selected plants are used to produce new clones or superior clones can be isolated from local variety, introduced variety or inter crossed population.

Introduction
In recent years, there has been a growing interest in alternative nutritious food sources (McClements, 2020) and such group of foods that has gained significant attention is millets. Millets are a diverse group of small-seeded grasses that have been cultivated and consumed for thousands of years. They are rich in essential nutrients such as proteins, fibers, vitamins, and minerals, making them an important addition to a balanced diet. Millets are not only rich in essential nutrients but also have several health benefits. They are known to have nutraceutical properties, low glycemic index, making them suitable for individuals with diabetes. Additionally, millets are a good source of antioxidants, which can help in reducing the risk of chronic diseases such as heart disease and cancer. The diverse range of millet varieties also provides flexibility in incorporating them into various dishes, making them suitable for different culinary preferences and dietary requirements. Therefore, the usage of millets can play a crucial role in promoting sustainable and healthy eating habits.
Malnutrition continues to be a pressing issue worldwide, particularly in developing countries (Ashok et al., 2020). The lack of access to nutritious food is one of the main causes of malnutrition, leading to various health problems such as obesity, diabetes, cardiovascular diseases, cancer, and celiac disease (Birania et al., 2020). To address this issue, millets have emerged as a promising solution. Despite being nutritionally superior to other cereals, millets have traditionally been limited to consumption by the poor and those with conventional dietary practices. However, there is a growing recognition of the potential of millets in combating malnutrition and improving public health. Millets, such as finger millet, pearl millet, and sorghum, are often referred to as “superfoods” due to their high nutritional content (Singh et al., 2020). These grains are rich in protein, carbohydrates, fats, vitamins, minerals, and dietary fiber, making them an ideal source of essential nutrients (Ashok et al., 2020). Additionally, millets are easily available and costeffective, making them a viable option for addressing malnutrition on a larger scale (Birania et al., 2020). Furthermore, millets are resilient crops that can withstand environmental changes and water shortages, making them an ideal choice for sustainable agriculture. In this chapter, we delve deeper into specific aspects of millet nutrition, examining their micronutrient profiles, health benefits, culinary versatility, and potential applications in combating malnutrition and promoting sustainable agriculture. By understanding the nutritional richness of millets, we can uncover innovative solutions for improving human health and fostering agricultural resilience.

The chapter “Breeding Strategies for Disease Resistance” provides a comprehensive exploration of addressing disease resistance through various breeding strategies. In an era of escalating global challenges and climate change, where crop failures can lead to food shortages and economic instability, the chapter delves into strategies that integrate traditional breeding methods with cutting-edge genetic advancements to strengthen plants against pathogens. Understanding the genetics of plant–pathogen interactions holds profound importance. This knowledge elucidates the mechanisms underpinning disease development and offers insights into developing targeted strategies for disease management. By deciphering the genetic details governing host susceptibility and pathogen virulence, we gain the ability to engineer crops with enhanced resistance, reducing reliance on chemical interventions and promoting sustainable agriculture. The chapter further discusses the mechanism of disease resistance in plants which involves inherent genetic traits that identify pathogen molecules, triggering a rapid defense response called “gene-for-gene” interaction. Systemic acquired resistance (SAR), where a local pathogen attack prompts the entire plant to boost its defense preparedness. Signaling molecules like salicylic acid play a pivotal role. Additionally, plants employ chemical defenses via secondary metabolites and leverage beneficial microorganisms to stimulate immune pathways. This coordinated approach empowers plants to effectively counter pathogens and elevate disease resistance. In this chapter, we discuss breeding strategies for disease resistance that encompass a range of vital approaches. Traditional methods involve selecting and breeding plants with inherent resistance traits and incorporating genes from related species to enhance defenses.

Our natural ecology comprises insects, which are known to have both advantageous and detrimental consequences. Insect pests are the main obstacles in maximizing agricultural crop output, since they directly or indirectly result in significant crop loss. The intricate relationship that phytophagous insects have with their hosts is the result of a protracted and ongoing evolutionary process. Because of this, it is impossible to completely eradicate them, but there is a hopeful fix for this issue, i.e., utilizing insect resistant crop varieties. Insect-resistant kinds are those that, with the same starting infestation level and similar environmental conditions, yield considerably higher yields of high-quality fruit than susceptible varieties. By boosting yield and reducing pesticide use, these varieties had an enormous economic benefit. There are a number of highly effective insect resistance mechanisms that the targeted insect pest cannot simply overcome. This chapter discusses various breeding strategies such as introduction, selection, and hybridization as well as some modern breeding approaches that have been used to develop many insect-resistant crop varieties that have significantly improved the world’s food supply, by reducing carbon inputs through reduced pesticide use. By expressing bacterial endotoxins and producing Bacillus thuringiensis (Bt) crops, genetic engineering also aids in the production of insect-resistant crops. Furthermore, RNA interference (RNAi) and genome editing by CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR associated 9) offer new avenues for the production of insect-resistant crops.

Salinity stress poses a significant threat to agricultural productivity worldwide, impeding crop growth and yield potential. Developing crop varieties with enhanced salinity tolerance is essential for ensuring food security and sustainable agriculture. Salinity stress, resulting from excessive salt accumulation in soil and irrigation water, adversely impacts crop growth, water uptake, and nutrient assimilation. Traditional breeding methods, coupled with recent advancements in molecular and genomic techniques, have enabled the development of crop varieties capable of thriving in saline environments. Genetic diversity serves as the foundation for breeding efforts, allowing the identification and selection of individuals with inherent salinity tolerance traits. Utilization of wild crop relatives and landraces provides a valuable reservoir of genetic variation for salinity stress adaptation. Incorporation of molecular markers into breeding programs expedites the selection of desirable traits. Quantitative trait loci (QTLs) associated with salinity tolerance are identified through techniques such as genome-wide association studies (GWAS) and linkage mapping, facilitating marker assisted selection. Additionally, recent strides in gene editing technologies like CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats–associated protein 9) offer precise modification of candidate genes responsible for salinity response, accelerating the breeding process. A holistic approach encompassing physiological and biochemical aspects is crucial for accurate phenotypic selection. Traits, such as ion homeostasis, osmotic adjustment, and antioxidative capacity, provide insights into a plant’s salinity tolerance potential

Reproduction by asexual means is common among higher plants. The best known means of asexual reproduction are by corms, bulbs, rhizomes, stolons, or other vegetative organs. Plants normally propagated in agricultural practice by these means or by budding or grafting include nearly all fruit and nut trees, strawberries, blackberries and raspberries, grapes, pineapples, almost all ornamental shrubs and trees and a few field crops such as sugar cane, potatoes, and sweet potatoes. Asexually or clonally propagated plants produce genetically identical progeny. Clones are identical copies of a genotype. Together, they are phenotypically homogeneous. However, individually, they are highly heterozygous and segregate widely upon sexual reproduction. This is not unexpected, because the types selected as commercial cultivars are likely to be vigorous ones, and a positive correlation exists between vigour and heterozygosity in most species.

Cotton is a major crop of India grown in about 9.0 million hectares.This is the largest cotton area in the world. Thus, India ranks Ist among cotton growing countries in the world in terms of area. However, average cotton yields in India have been 320 kg/ha as compared to world cotton yield average of 580 kg/ha. Thus, cotton production in India represents only about 13% of the total world production whereas India accounts for approximately 20% of the world’s total cotton area. Obviously, yield levels in India are low compared to world average. The low yield levels in India are partly due to heavy losses from insect pests, particularly cotton bollworm complex.

During 2019, the global acreage of biotech/GM crops was 190.4 million ha and India planted 11.9 million ha GM cotton having insect resistance (Bt-cotton, having two commercialized events, namely, cry1Ac, MON-531, MahycoMonsanto, popularly called by trade name Bollgard-I, single gene event, commercialized in 2002 and cry2Ab2, MON-15985, Mahyco-Monsanto, popularly called by trade name Bollgard-II, double gene event or stacked trait event, commercialized in 2006) stood at the fifth place after USA, Brazil, Argentina and Canada (ISAAA, 2019). Four more events related to Bt cotton (cry1Ac, Event-1, JK Agri-Genetics, commercialized in 2006, fused genes cry1Ab and cry1Ac, GFM Event, Nath Seeds, commercialized in 2006, cry1Ac BNLA-601, UAS, Dharwad and CICR (ICAR), commercialized in 2008 but discontinued and synthetic cry1C, MLS-9124, Metahelix Life Sciences-now Tata Rallis, commercialized in 2009 but not placed in the market) were approved for commercialization but the products could never reach to the market.

Introduction

This section of the manual contains instructions for preparing stock solutions that are commonly used in laboratory protocols for the analysis of DNA, RNA and proteins and visualization of gene or protein expression. Each of these stock solutions is provided as either the most convenient concentration or the most frequently used stock concentrations to be used in the protocols of an individual laboratory.

All chemicals must be reagent grade or molecular biology grade, and the water used in the preparation of all solutions must be the highest quality available. Use sterile-glass distilled deionised water whenever possible. Unless otherwise stated, most solutions required sterilization either by filtration or autoclaving.

Bulk population breeding developed by the Swede H. Nilsson Ehle in 1908 and later on supported and practiced by H. V. Harlan in barley breeding in 1940s is a breeding strategy in crop improvement in which natural selection is allowed to play its full role where the F2 generation is planted in a plot large enough to accommodate several hundreds of plants. Planting density and cultural practices are usually the normal ones followed for commercial crop planting. At maturity, the plot is harvested in bulk and the seeds are used to plant a similar plot in the next season. This process is repeated till at least F5 where the plants are space planted to allow individual plant evaluation for effective selection. During period of bulk propagation natural selection plays a key role in shifting gene frequencies in the bulk population. This role is of crucial importance as bulk handling is continued over a number of generations. Bulk population handling can be aided by artificial selection at any time during the period of bulk propagation. Aggressive and highly competitive but undesirable plants may be physically rogued out of the population to avoid increasing the frequency of undesirable genes. For example, determinate bush types of beans do not compete well against indeterminate, vine types. And if the breeder is interested only in determinate types, artificial selection against the indeterminate types is certainly called for. There is also good reason to apply artificial selection against seed colour, pubescence, awns or other characters that are undesirable in the variety to be developed but may be more or less neutral in survival. Bulk population handling often provides opportunities to make use of artificial aids to selection. For example, bulk harvesting when only part of plants are mature is an effective and inexpensive way to select for earliness. If particular sizes of seeds are required, screens or mechanical devices provide a rapid way of eliminating inferior types. Naturally occurring or artificially induced disease or insect infestation, of course, provide opportunities to rogue susceptible individuals from the bulk plot. In F6, the plants selected in F5 are progeny rowed and superior progenies are selected from where again few plants can be selected and seed bulked within a selected row. Depending upon seed requirement for yield trial in the following years, even the seed from selected entire row can be bulked. The follow up yield evaluation trials are as given in case of pedigree selection. This method is operationally best suited for seed crops such as small grains, beans and soybean and is almost totally unsuited for fruit crops and for most vegetable crops.

Bulk population method of breeding is defined as the growing of genetically diverse populations of self-pollinated crops in a bulk plot with or without mass selection, followed by single plant selection. It is applicable to self-pollinated crops and not applied to cross-pollinated crops. Bulk population breeding is a strategy of crop improvement in which natural selection effect is solicited more directly in the early generations of the procedure by delaying stringent artificial selection until later generations. The Swede, H. Nilsson-Ehle, developed the procedure. H.V Harlan and colleagues provided additional theoretical foundation for this method through their work in barley breeding in 1940s. As proposed by Harlan and colleagues, the bulk method entails yield testing of the F2 bulk progenies from crosses and discarding whole crosses based on yield performance. In other words, the primary objective is to stratify crosses for selection of parents based on yield values. The current application of the bulk method has a different objective.

The first step in applying the correct rate of fertilizer is calculating crop nutrient requirements. A soil test is the only way to measure how much P₂ O₅ and K₂ O are available in soils, and soil tests are available through several private and public laboratories.

Fertilizer Calculation

To compute the equivalent amount of fertilizer necessary to supply the corresponding amounts of nutrients, the following formula is used:

NTSYSpc 2.0 software is used for various types of analysis including calculation of similarity index values and construction of dendrogram. Construction of dendrogram using gel data in the form of bands. This software accepts zero-one data.

NTSYSpc 2.0 software is used for various types of analysis including calculation of similarity index values and construction of dendrogram. Construction of dendrogram using gel data in the form of bands. This software accepts zero-one data.