eChapters

Section 3.1 Biotechnology Patents – Scope and Controversies
3.1.1 Introduction
Biotechnology, a field at the intersection of biology and technology, generates innovations that are often groundbreaking and commercially significant. As such, patents have become a vital tool in protecting biotechnological inventions. However, the unique nature of biological materials and living systems presents unprecedented legal, ethical, and commercial challenges, sparking ongoing debates globally. This section delves into the scope of patenting in biotechnology and explores the controversies surrounding such patents.
3.1.2 Scope of Biotechnology Patents
Biotechnology patents cover a wide array of inventions that are novel, non-obvious, and industrially applicable. These may include:
1. Genetic Materials and Constructs
• Isolated DNA/RNA sequences, including genes and promoters
• Synthetic nucleic acids and gene editing tools (e.g., CRISPR-Cas systems)
2. Microbial Inventions
• Genetically modified microorganisms (GMMs) for bioremediation, fermentation, or synthesis of pharmaceuticals

To fully harness the potential of human creativity in industrial applications, it’s essential to safeguard and organize it effectively. One of the best ways to achieve this is by obtaining a patent. The term “patent” is derived from the Latin word “patere,” meaning “to lay open” or make available for public inspection. A patent is an exclusive right granted by the government to an inventor/creator for a limited time in exchange for disclosing their invention for public use. With this right, the patent holder can prevent others from making, using, selling, or exploiting the invention for a certain period, thereby providing commercial benefits to the inventor.

Patents are among the oldest forms of intellectual property rights and are territorial in nature, offering protection only within the country where they are granted. However, through conventions and the Patent Cooperation Treaty (PCT), applicants can seek protection in multiple countries. Obtaining a patent grants the inventor a monopoly right to control the product’s production, sale, and marketing. Although the rights granted through a patent are limited to a specific country, extending protection to all contracting countries is possible through a PCT application.

This chapter provides an insight into the genotypic and phenotypic correlations between plant traits. It incorporates the study of genotypic and phenotypic path analysis and the understanding of genetic variability, all illustrated through practical examples in R, relevant to plant breeding research.

Path Analysis

Path analysis explains not only the direct impact of one character on another but also indirect effects mediated through other variables in the system. The approach is similar to the analysis of variance and is sometimes referred to as the analysis of correlation coefficients. A notable feature of path coefficients is that they are standardized partial regression coefficients, devoid of units. This standardization allows for the direct effects of different variables to be compared and ranked based on their magnitude. This approach was first applied in plant studies by Dewey and Lu in 1959, particularly to examine the factors influencing seed yield.

Path Coefficients

In the computation of path coefficients, a path diagram is translated into a series of simultaneous equations. These equations reveal the direct and indirect contributions of causal variables to the outcome. For example, in the field of plant breeding: consider the yield of forage (Y) being influenced by different variables. These could include the leaf length (X1), leaf width (X2), and number of leaves per plant (X3).

The polymerase chain reaction (PCR) is a very powerful new method used for in vitro to amplify a deoxynibonuclic specific region that lies between two regions of known DNA sequence single molecule to million folds in short time. This is achieved by an enzyme taq. DNA polymerase which is thermostable using this enzyme can synthesize microgram quantities of DNA of specified length and sequence from pictogram quantities of complex template in a few hours time.

Introduction
In recent years crop yields have increased significantly due the development of new varieties and cultivars. Certain characteristics, like disease resistance, plant height, yield potential, and maturity period, set one variety of a cultivated crop species apart from other variations of the same species. A key element of contemporary agriculture is the precise identification of crop types, which is essential for plant breeding, seed certification, and the defence of intellectual property rights. The increasing demand for improved crop varieties with increased yield, disease resistance, and environmental adaptability has demanded the development of accurate methods for differentiating cultivars (Hannah, 2024). Traditional techniques of variety identification rely on morphological, biochemical, and agronomic features, which can be altered by environmental conditions and are generally time-consuming and labour-intensive. Various molecular marker systems have been developed to differentiate plant varieties and species of agricultural and horticultural significance. For effective seed quality control programs and the preservation of breeders’ rights, it is essential to define the identity, genetic purity, and stability of plant varieties. According to Yuan et al., (2022), precise variety identification is essential for determining genetic purity, analyzing genetic diversity, improving germplasm for better agronomic qualities, and getting rid of duplicate accessions.
For plant protection and production systems of Intellectual Property Rights (IPR) and Plant Biodiversity Register (PBR), accurate cultivar identification is crucial. According to Ghosh et al. (2001), molecular marker approaches are pertinent to PBR registration in the following ways. (1) In order to establish a set of comparison cultivars, genetic distance analysis between the candidate cultivar and the current pool of cultivars is performed. (2) The contribution of the comparison cultivar to PBR registration is then determined, and (3) the use of DNA markers to identify cultivars in cases where PBR infringement is alleged is investigated. The capacity of PCR-based markers to amplify particular DNA sequences has made them popular among molecular marker techniques, enabling accurate identification of genetic variations. Although conventional approaches are still employed for Plant Variety Protection (PVP), molecular techniques can be useful adjuncts that increase the effectiveness of accomplishing this goal. During variety certification, additional information from isozyme analysis, RFLP, SSR, SNP, or other genetic fingerprinting methods can be added to cultivar descriptions. Plant varieties can be legally protected on the basis of precise and unique molecular marker data. Crops with little morphological variation benefit greatly from molecular methods. To guarantee complete protection of cultivars, it is ideal to use both botanical and molecular evaluations (Yu and Chung, 2021). Amplified Fragment Length Polymorphism (AFLP), Random Amplified Polymorphic DNA (RAPD), Simple Sequence Repeat (SSR), and Inter Simple Sequence Repeat (ISSR) are the four main PCR-based markers used in crop variety identification that are the subject of this chapter. In plant genetics, each of these marker systems has special qualities, benefits, and uses. While AFLP markers give high resolution and genome-wide coverage, RAPD markers offer a rapid and economical method of polymorphism detection. Due to their high polymorphism and co-dominant inheritance, SSR markers—also referred to as microsatellites—are perfect for genetic mapping

Sanger Method for DNA Sequencing

One necessity first know a little about the structure of DNA:

1. A segment of DNA, which is ordinarily double stranded, has a specific orientation, as it has a 5' (read as “5 prime”) and a 3' (“3 prime”) end. This can be simply thought of as a front and tail end to the DNA segment.
2. When DNA is synthesized in the lab, the two strands are separated and new bases are added to the 3' end-thus DNA is assembled from the 5' to 3' end.
3. DNA cannot be synthesized from scratch. A short piece of DNA, called a primer, is required for the reaction to begin.
4. Primers are designed such that they are able to bind to the target DNA, the binding of which is the initiator for DNA synthesis.

Pearl millet (Pennisetum glaucum (L.) R. Br. 2n = 2x = 14, grass family Poaceae, cross-pollinated and with C4 photosynthetic path-way) is the stable food for millions in the semi-arid tropics. It is adapted to drought and poor soil fertility. Pearl millet is a dependable nutritious source of food for millions in marginal agricultural areas. It is the world’s hardiest warm-season cereal crop. It can survive and produce grain even on the least fertile soils in the driest regions, on highly acidic and saline soils, and in the hottest climates. Pearl millet covers an estimated 31 million hectares worldwide with production of 30 million tons and productivity of almost 1 ton/ha and is grown in more than 30 countries located in the arid and semi-arid tropical and subtropical regions of Asia, Africa and Latin America.

This method has been first described by H. H. Lowe in 1927. This is the most widely used method to handle segregating generations following crosses between two parents to develop new cultivars combining desirable traits from both the parents. In this method, superior types are selected in successive segregating generations and a record is maintained of all parent-progeny relationships. The records help the breeder to advance only progeny lines with plants that exhibit genes for the desired traits. Selection begins in F2 generation where individual plants are selected which in judgment of breeder will produce the best progeny in F5/F6 when the selection is finally concluded. In F3 and F4 generations, many loci will have become homozygous and family characteristics begin to appear. By F5/F6 generation, most families are expected to be homozygous and uniform and hence selection within such families is no longer effective. At this stage selection emphasis shifts to the selection among families rather than within families.

Selection of parents is of great significance for the success of this method. Normally, this method is used to replace already established variety. Therefore, one parent should be selected on the basis of proven performance in the particular area where the breeding is in progress. The second parent should be such that it complements the first parent for the character under improvement. Sometimes, three or four parents may also be used to supply the desired character by way of three-way or double crosses.

Organic Agriculture
Organic and biodynamic farming use natural methods to grow crops, avoiding inorganic fertilizers, pesticides, and other chemicals throughout the growth stages. This approach relies on natural biological systems, preserving their relationships and self-regulation, unlike conventional farming, which heavily depends on synthetic inputs. As a result, plant and animal varieties bred for intensive agriculture often do not align with organic principles. To unlock the full potential of organic farming, genetics of seeds should also be organic, ideally bred and grown exclusively in organic conditions to best suit these systems.
Organic plant breeding
Improving the genetic diversity of the crops and their adaptation to the future organic growing conditions and climate change need to be done through organic plant breeding. The choice of varieties for organic farming that are mostly derived from conventional bred varieties, sustainable use of natural input resources and at the dynamic equilibrium of the entire agro ecosystem are the main features. The organic breeding programs should match with the reproduction system of the respective crop. Seeds and vegetatively propagated crops are important resources for organic breeding. The Organic agriculture system relies on natural inputs and pesticide free and non GMO crops, vegetable and fruits aiming providing healthy food. In an overall manner, organic agriculture is the expression of underlying ecology, fairness and health. Organic agriculture is presently practiced in organically converted and managed land area equal to 2% of the cultivated area in India.
International Federations of Organic Agriculture Movement (IFOAM) (2015 and 2017): Organic agriculture is defined as a production system that sustains the soil health, ecosystem and people. It relies on ecological processes, bio diversity, and local conditions. Organic farming is part of organic agriculture and it is basically based on the underlying principles of health, fairness, ecology and care. The well-known characteristic of organic farming is, it produces food without the use of any synthetic fertilizer or pesticides and also without the use of GMO. Trends and perspectives in organic plant breeding are recognized as a highly collaborative and possess strong interrelationships.

2.1. Guidelines for Pest Risk Analysis

This standard describes the process of pest risk analysis for plant pests for the purpose of preparing phytosanitary regulations by National Plant Protection Organizations. Pest risk analysis (PRA) consists of three stages: initiating the process for analyzing risk, assessing pest risk, and managing pest risk.

Initiating the process involves identification of pests or pathways for which the PRA is needed. Pest risk assessment determines whether each pest identified as such, or associated with a pathway, is a quarantine pest, characterized in terms of likelihood of entry, establishment, spread and economic importance. Pest risk management involves developing, evaluating, comparing and selecting options for reducing the risk.

PRA is only meaningful in relation to a defined “PRA area” considered to be at risk. This is usually a country, but can also be an area within a country, or an area covering all or parts of several countries [e.g. the area covered by a Regional Plant Protection Organization (RPPO)].

8.1 Pest Risk Analysis

Pest Risk Analysis (PRA) is a form of risk analysis conducted by regulatory plant health authorities to identify the appropriate phytosanitary measures required to protect plant resources against new or emerging pests and regulated pests of plants or plant products. Specifically pest risk analysis is a term used within the International Plant Protection Conventions (IPPC) (Article 2.1) and is defined within the glossary of phytosanitary terms as “the process of evaluating biological or other scientific and economic evidence to determine whether an organism is a pest, whether it should be regulated, and the strength of any phytosanitary measures to be taken against it. In a phytosanitary context, the term plant pest, or simply pest, refers to any species, strain or biotype of plant, animal or pathogenic agent injurious to plants or plant products and includes plant pathogenic fungi, bacteria, fungus-like organisms, viruses, nematodes and virus like organisms as well as insects, mites and weeds.

The term “plant pest”, mainly applied to insect micropredators of plants, has a specific definition in terms of the International Plant Protection Convention and phytosanitary measures worldwide. A pest is any species, strain or biotype of plant, animal, or pathogenic agent injurious to plants or plant products. Worldwide, agricultural pest impacts are increased by higher degrees of interconnectedness. This is due to the increased risk that any particular pest problem anywhere in the world (as a system) will propagate across the entire system.

S.O.867 (E) – In exercise of the powers conferred by sub-section (1) of section 3 of the Destructive Insects and Pests Act, 1914 (2 of 1914), and in suppression  of Plants, Fruits and Seeds (Regulation of import into India) Order 1984, except as respects things done or omitted to be done before such suppression, the Central Government hereby makes the following order for the purpose of prohibiting and regulating the import into India of agricultural articles mentioned herein, namely: -

Mutation: Natural genetic variation has exhausted. Genetic variation can be induced by mutations or changes in the DNA sequences of the plants.

Additional Tools for Plant Improvement

Increase in yield with no additional lands available for cultivation depends on development of high yielding varieties suitable for marginal cultivation.

• Food security

• Nutritional security

Need for additional tools to increase efficiency of breeding methods for genetic enhancement and propagation.

• Genomics

Genomics – Definition

Genomics - Study of an organism's entire genome / full genetic complement of an organism.

Summary

One of the most seductive lures of the genomic revolution is the promise of personalized medicine. The rapid identification of tens of thousands of human genes and hundreds of thousands of DNA variations that might influence disease susceptibility has spawned a new field Pharmacogenetics and Pharmacogenomics deal with the genetic basis underlying variable drug response in individual patients. The traditional pharmacogenetic approach relies on studying sequence variations in candidate genes suspected of affecting drug response i.e. single or few genes. On the other hand, pharmacogenomic studies encompass the sum of all genes, i.e., the genome. Numerous genes may play a role in drug response and toxicity, introducing a daunting level of complexity into the search for candidate genes. The high speed and specificity associated with newly emerging genomic technologies enable the search for relevant genes and their variants to include the entire genome.

4.1 Phases of technology transfer
To translate laboratory research into market ready product, it is important to understand steps or phases involved in this technology transfer process. The process typically includes six main phases, each with a different role (figure 9).
4.1.1 Research
Technology transfer begins with research, the critical stage of exploring and discovering novel knowledge, technologies, or innovations that may have potential commercial applications. The research phase can occur in academic institutions, research organizations, or private sector companies, often funded by public or private sources. Thorough research ensures that the technologies being transitioned are scientifically and technically robust, thereby increasing their potential for market success. Therefore, the research phase involves creating and evaluating new ideas, confirming their feasibility, and identifying IP prospects, all of which are key components of TT success.
4.1.2 Innovation disclosure
Innovation disclosure is the first formal step where the innovation is reported to the appropriate TTO or IP management team. This process ensures that the institution or organization recognizes the innovation and evaluates its potential for protection and commercialization. It includes following information:

Introduction

Plasticity is a unique attribute by which the otherwise sessile plant species are capable of adjusting to environmental vagaries by changing their phenotypic and morphological characters. Any plant population will be able to survive only if it can respond to an extremely variable environment by becoming more plastic and more genetically variable. To achieve this, plants should be able to suitably change their morphology anatomy and physiology or any one of these parameters based on environmental changes so as to improve their adaptability and survival in the altered environment. When such changes are genetically heritable, then they lead to species evolution.

Plasticity helps plants to adapt to new environmental conditions, after migration to new geographical areas, by genetic assimilation of traits that can help to improve their performance under a new set of conditions. Understanding plasticity is important for predicting and managing the effect of climate change on native species as well as crop plants. Response of plants to modified environmental conditions is critical for their persistence.

Phenotypic plasticity has been defined as the ability of an individual genotype to produce different phenotypes when exposed to different environmental conditions (Pigliucci et al., 2006). This includes the ability of a plant to modify its development in response to environmental cues and also its ability to bring about changes in its metabolism which increases the chances of survival of an organism under a specific condition.

MOST OF THE ENERGY FOR LIFE COMES FROM SUNLIGHT

Total rate of energy delivery from sun to earth (at the top of the atmosphere) = 175,000 terrawatts

Terrawatt = 10^12 watts

Rate of energy capture by plants from the sun = net primary productivity (NPP) = 100 terrawatts

Only ~ 0.06% of sunlight is captured

Captured in chemical bonds, especially in sugar

Small amounts of energy are available to specialized microorganisms from chemical reactions not linked to sunlight

It is estimated that 99% of the energy used by living cells comes from the sun

Incorporation of sunlight into chemical bonds occurs through the process of photosynthesis

“Invented” by cyanobacteria about 2 billion years ago

Introduction to Nano-materials

Nano-sized materials are naturally present from forest fires and volcanoes, but are also generated unintentionally from anthropogenic sources as a by-product of combustion and deliberately as manufactured nanomaterials. Nanoparticles have been used for centuries. The coloured glass that we see in many old cathedrals from the middle age was made of gold nanosized clusters that created different colour depending on the size of the nanoparticles. The most prominent example of engineered nanoparticulate material is carbon black which has been around us for decades in applications like printing inks, toners, coatings, plastics, paper, tires and building products.
 
Two of the major factors why nanoparticles have different properties (optical, electrical, magnetic, chemical and mechanical) than bulk material are because in this size-range, the quantum effects start to predominate and the surface area to volume ratio is increased.

It is classified asbottom-up manufacturing which involves building up of the atomor molecular constituents asagainstthetop methodwhich involves making smaller and smaller structures through etching from the bulk material as exemplified by the semiconductor industry.