eChapters

Self-Incompatibility

This is lack of self-fruitfulness and is a condition where the pollen from a flower is not receptive on the stigma of the same flower resulting into no seed setting. This happens despite the fact that pollen and ovule development both are normal and viable. This is caused by genetically controlled physiological hindrance to self-fertilization. This occurs widely among diverse families of flowering plants including the Leguminosae, Onagraceae, Rosaceae, Scrophulariaceae, Solanaceae, Compositae, Cruciferae, Papaveraceae and the Gramineae (now called as Poaceae). The incompatibility reaction is genetically governed by a single locus designated as S with multiple alleles whose number can go more than 100 in some species such as Trifolium pretense. East has estimated that this occurs in more than 3000 plant species distributed over 20 families. Lewis classified incompatibility systems into two main groups, namely, heteromorphic and homomorphic and homomorphic system has further been divided into gametophytic and sporophytic types as illustrated below:

To start with let the self-incompatibility be defined.

• Self-incompatibility is the mechanism by which plant can prevent selffertilization.
• Self-incompatibility is defined as inability of a plant producing functional gamete to achieve self-fertilization.
• Self-incompatibility is a genetically based mechanism which controls mating within angiosperm species by imposing a ‘barrier’ between pollination and fertilization.
• The term incompatibility is used to describe the failure of pollen tube to penetrate the full length of the style and to effect fertilization.

Abstract

Sequence alignment is the positioning of DNA, RNA, or protein sequences with each other to identify the regions of identity, which may be the result of functional, structural, or evolutionary relationships between the sequences. Therefore, sequence alignment is the process of aligning two sequences to achieve the maximum levels of identity and conservation. This chapter deals with the basic concept of sequence alignment and the tools associated with multiple sequence alignment. Further, it describes various matrices used in sequence alignment.

SCARs are DNA fragments amplified by the Polymerase Chain Reaction (PCR) using specific 15-30 bp primers, designed from nucleotide sequences established in cloned RAPD (Random Amplified Polymorphic DNA) fragments linked to a trait of interest. By using longer PCR primers, SCARs do not face the problem of low reproducibility generally encountered with RAPDs. Obtaining a codominant marker may be an additional advantage of converting RAPDs into SCARs. However, SCARs may exhibit dominance when one or both primers partially overlap the site of sequence variation. SCARs are locus specific and have been widely applied in gene mapping studies and marker assisted selection (Paran & Michelmore, 1993).

Introduction

DNA sequencing is the process of determining the nucleotide order of a given DNA fragment. The most commonly used sequencing method is the dideoxy method. This method uses dideoxynucleotide triphosphates (ddNTPs) which have an H on the 3’ carbon of the ribose sugar instead of the normal OH found in deoxynucleotide triphosphates (dNTPs). Dideoxynucleotides are chain terminators. In a synthesis reaction, if a dideoxynucleotide is added instead of the normal deoxynucleotide, the synthesis stops at that point because the 3’OH necessary for the addition of the next nucleotide is absent (Sanger et al., 1977).

Sex Chromosomes

Sex can be considered at chromosomal, gonadal, phenotypic, and gender identity levels.

Human females are homogametic (XX) and males are heterogametic (XY).

The Y chromosome contains few identified genes, while the larger X chromosome contains several thousand genes. Pseudoautosomal regions at both tips of the Y chromosome contain genes that have counterparts on the X chromosome.

The male determining gene, SRY, has been found on the Y chromosome.

Sexual propagation through seeds is a fundamental method for producing horticultural crops, rootstocks, and planting material. This chapter explains seed structure, quality, viability, dormancy, germination, and factors affecting successful seedling establishment. Different types of seed dormancy and methods for overcoming dormancy are discussed, including scarification, stratification, chemical treatments, temperature management, and appropriate moisture conditions. Seed testing and quality considerations are important for obtaining uniform and healthy plants. The chapter also emphasizes the influence of temperature, oxygen, water, light, and substrate conditions on germination. Understanding seed biology enables students and growers to produce vigorous seedlings and establish reliable nursery and crop-production systems.

Abstract

Cyanobacteria comprise a group of photosynthetic prokaryotes, which exhibit versatility in their morphological, biochemical and molecular characteristics and represent an untapped source of novel metabolites and genes. Their structural-functional flexibility makes them successful in diverse and extreme environments including high temperatures or levels of UV light and salinity, and co-exist in symbiotic/parasitic/mutualistic associations with various members of Plant and Animal kingdom. The intracellular colonization of cyanobacteria in wheat and rice roots and their potential as plant growth promoting agents for several crops, besides rice, has led to the deployment of novel formulations of cyanobacteria and agriculturally useful bacteria as biofilms and disease suppressive options in field studies.

The principle of silver nitrate staining of proteins is based on the reduction of silver ions to its metallic form. (Silver ions in alkaline conditions bind with proteins through å-amino group of lysine and sulphur groups of cysteine and methionine residues). When the complexed silver ions are reduced in the presence of formaldehyde, they become metallic silver, which is seen on the gel as bands. Staining of proteins with silver nitrate after SDS-PAGE is quicker and ~ 10 times more sensitive than Coomassie brilliant blue staining and that is the reason it is widely used in research laboratories these days.

The procedure is as follows:

Silver Staining for Protein

Silver staining is one of the procedures, in addition to Coomassie Blue, R and G types, and fluorescent dyes that are available for detecting proteins separated by gel electrophoresis. Switzer introduced silver staining in 1979, a technique that today provides a very sensitive tool for protein visualization with a detection level down to the 0.3-10 ng level.

The basic mechanisms underlying silver staining of proteins in gels are relatively well understood. Basically, protein detection depends on the binding of silver ions to the amino acid side chains, primary the sulfhydril and carboxiyl groups of proteins, followed by reduction to free metallic silver. The protein bands are visualized as spots where the reduction occurs and, as a result, the image of protein distribution within the gel is based on the difference in oxidation-reduction potential between the gel’s area occupied by proteins and the free adjacent sites. A number of alteration in the silver staining procedure can shift the oxidation-reduction equilibrium in a way that gel- separated proteins will be visualized either as positively or negatively stained bands. Silver staining protocols can be divided into two general categories: 1) silver amine or alkaline methods, and 2) silver nitrate or acidic methods. In general, the detection levels’ using the various procedures is determined by how quickly the protein bands develop in relationship to the background (e.g. signal-to-noise ratio). The silver amine or alkaline methods usually have lower background and as a result are most sensitive but require longer procedures. Acidic protocols, on the other hand, are faster but slightly less sensitive. Clearly, each protocol has different advantages regarding timing, sensitivity, cost, and compatibility with other analytical methods, especially mass-spectrometry (MS) a tool that is being used in combination with gel electrophoresis or chromatographic methods for rapid protein identification. Until recently most of the silver staining protocols used either glutaraldehyde- of formaldehyde-based sensitizes in the fixing and sensitization step, thus, introducing the chemical modifications into proteins. The utilization of those chemicals causes the cross-linking of two lysine residues within protein chain, thus, strongly affecting two most crucial steps for the subsequent MS analysis: hampering the trypsin digestion and highly reduces the protein extraction from the gel .

Also Referred to as Microsatellites

SSR markers are based short sequences of nucleotides (2-6 units in length) that are repeated in tandem:

Di-nucleotide repeat: CACACACA

Tri-nucleotide repeat: ATGATGATGATG

It is believed that when DNA is being replicated, errors occur in the process and extra sets of these repeated sequences are added to the strand. Over time, these repeated sequences vary in length between one cultivar and another.

Introduction
The distinctions that differentiate one genotype from another are encoded in their hereditary material i.e., DNA (deoxyribonucleic acid). DNA is packaged into chromosomal pairs, with one strand of genetic material derived from each parent. The genes that govern a plant’s traits are situated on distinct portions of each chromosome (King and Stansfield, 1990). Depending on the context, a genetic marker may be defined as: (a) a chromosomal landmark that facilitates the tracing of a specific DNA region; (b) a distinct DNA segment with a known genomic position; or (c) a gene whose phenotypic expression is easily observable, and used to identify an individual and used as a probe to spot a nucleus, chromosomes, or locus. Molecular markers are distinguishable DNA sequences located at specific loci within the genome, inherited according to the established principles of inheritance from one generation to the subsequent generation. The presence of several molecular approaches, along with their distinct concepts and procedures, necessitates meticulous evaluation when selecting one or more marker types or loci (King and Stansfield, 1990). Various molecular markers have been described, based on mode of transmission, mode of gene action and method of analysis. Single nucleotide polymorphisms (SNPs) are variations in DNA sequences characterized by a single nucleotide (A, T, C, or G) that differs among individuals, serving as biological markers for the identification of genes linked to phenotypes. The genome sequences in public domain from various organisms have facilitated the examination of sequence variations among individuals, among cultivars, and among subspecies. These investigations demonstrated that single nucleotide polymorphisms (SNPs) are prevalent and dispersed across the genome across numerous species, including plants (Drenkard et al., 2000; Nasu et al., 2002).The prevalence of SNPs polymorphisms in plant genomes renders the SNP marker system a valuable marker technology for mapping, marker-assisted breeding, and map-based cloning (Rafalski, 2002a; Batley et al., 2003).A single nucleotide polymorphic (SNP) marker is a single base alteration in a DNA sequence, with a typical alternative of two possible nucleotides at a specific position. In recent years, numerous SNP genotyping methodologies have been established, utilizing diverse techniques for allelic discrimination and detection platforms (Rafalski, 2002b; Vignal et al., 2002; Sobrino et al., 2005; Tost and Gut, 2005).At now, SNPs are preferred for DNA fingerprinting, investigations of genetic diversity and association studies, phylogenetic linkages, studies of evolutionary history of species and population, genome-wide association mapping, and genomic selection. Single nucleotide polymorphisms (SNPs) are the most prevalent and reliable markers, suitable for automated high-throughput genotyping, highly reproducible, and capable of identifying variants, therefore superseding older markers due to their high throughput, efficiency, and cost-effectiveness (Alkan et al, 2011; Amdadul et al, 2016; Close et al., 2009; Muñoz-Amatriaín et al, 2014; Li et al., 2020; Qiuetal., 2012). The swift advancement and use of NGS technology have led to the creation and application of diverse reduced-representation genome sequencing methods for SNP genotyping. The methodologies encompass GBS (Elshire et al., 2011),

Single strand conformation polymorphism (SSCP), or single strand chain polymorphism, is defined as conformational difference of single stranded nucleotide sequences of identical length as induced by differences in the sequences under certain experimental conditions. This property allows to distinguish the sequences by means of gel electrophoresis, which separates the different conformations.

Background

A single nucleotide change in a particular sequence, as seen in a double stranded DNA, cannot be distinguished by electrophoresis, because the physical properties of the double strands are almost identical for both alleles. Contrarily, after denaturation, single stranded DNA undergoes a 3- dimensional folding and may assume a unique conformational state based on its DNA sequence. The difference in shape between two single-stranded DNA strands with different sequences can cause them to migrate differently on an electrophoresis gel, even though the number of nucleotides is the same. Predictability, however, is a shortfall of SSCP - since conformational states are subject to many experimental conditions and sequence differences that cause minimal changes in strand conformation may not be detected.

21.1 Introduction

Nanotechnology is an emerging field of science which is being highly exploited in the sphere of medicine where “nano” plays a vital role in delivery of drugs or chemical molecules to the point it is required in précised quantities in right proportions. Nanoscience infuses intelligence to the truck load of chemical constituents that are to be delivered at appropriate locations and cleave from the site after the task is complete. Such process will likely to reduce the cost besides ensuring environmental safety. Nanoscale devices with its unique properties make the agricultural system more smart and effective; such devices are capable of responding to different situations by themselves, thus taking appropriate remedial action with the need of external directions from humans. In short, these devices act as a detectors and if need arises serve as a solution/remedy for the particular issue. These smart delivery systems of chemicals in controlled and targeted manner can be considered synonymous to the proposed nano-drug delivery system in human (Patolsky et al., 2006). 

Efficient irrigation is essential for maintaining crop productivity while conserving increasingly limited water resources. This chapter explores the application of artificial intelligence to smart irrigation systems and irrigation scheduling. It considers water balance and evapotranspiration modelling and examines AI architectures used for irrigation decision-making. Sensor technologies and Internet of Things integration provide continuous information about soil, weather and crop conditions. Optimization algorithms can use these data to determine appropriate irrigation schedules and improve water-use efficiency. The chapter also discusses emerging AI-based irrigation approaches and global case studies. Challenges associated with implementation, data requirements, system limitations and ethical considerations are examined, followed by future directions for intelligent and sustainable irrigation management.

The societal implications of nanotechnology are the potential benefits and challenges that the introduction of novelnanotechnological devices and materials may hold for society and human interaction. The term is sometimes expanded to also include nanotechnology’s health and environmental implications, but this article will only consider the social and political implications of nanotechnology.

As nanotechnology is an emerging field andmostof its applications are still speculative, there is much debate about what positive and negative effects that nanotechnology might have.

Beyond the toxicity risks to human health and the environment which are associated with first-generation nanomaterials, nanotechnology has broader societal implications and poses broader social challenges. Social scientistshave suggestedthatnanotechnology’s social issues should be understood and assessed not simply as “downstream” risks or impacts. Rather, the challenges should be factored into “upstream” research and decision making in order to ensure technology development that meets social objectives.

The adoption of artificial intelligence is transforming agricultural production, management and value chains while creating significant economic and social implications. This chapter examines the socio-economic dimensions of AI adoption in agriculture. It considers economic impacts, changes in labour and employment, rural livelihoods and the accessibility of digital technologies. Particular attention is given to the digital divide and barriers that may limit adoption among different agricultural communities. The chapter also addresses policy, governance and ethical considerations surrounding AI deployment. AI applications across agricultural value chains and regional and global perspectives are discussed. Finally, the chapter considers future socio-economic transformations, research gaps and the requirements for responsible and inclusive agricultural digitalization.

Abstract

Understanding the impacts of organic or inorganic nutrient management on soil biology and biochemistry may help to develop more sustainable fertilization strategies. The results from comprehensive study made on a field experiment comparing the long-term (more than 100 years) effects of organic manures and inorganic chemical fertilizers on soil biological and biochemical properties are reviewed. The soils adopted with three nutrient managements viz., no fertilization (control), inorganic chemical fertilizers (IC) and organic amendments (OM) obtained from long-term fertilizer experiment were assessed for physical, chemical, microbiological and biochemical properties in three successive years. The response of most of the assessed soil variables to long-term organic nutrient management was significantly higher than those from inorganic fertilization and control (OM > IC = control).