eChapters

Since its founding in the early 2000s, Scopus - which describes itself as a “source-neutral abstract and citation database curated by independent subjectmatter experts” — has been recognized as one of the top research indexes. At the time of writing this blog post, Scopus includes over 25,100 titles from 5,000 publishers, spanning 240 academic disciplines - with a staggering 76.8 million core records. Scopus encompasses research across scholarly disciplines but consists primarily of science and technology articles (Fig. 4.1).
There are many benefits to having journals added to the Scopus database. In addition to its extensive content coverage encompassing virtually all subjects, Scopus is known for its high level of academic rigor, including an annual journal re-evaluation process, which it requires as “an incentive for journals to maintain their high content quality.”
Scopus also provides a wide range of metrics for indexed content, including
• Journal-level metrics such as Citescore, which both publishes an annual impact score and gives monthly updates on how things are currently shaping up for each of the indexed titles via the CiteScore Tracker
• Article-level metrics such as PlumX, which analyzes how readers are responding to content in the broader online context (i.e., via tweets, blogs, Wikipedia references, etc.)
• Author-level metrics such as the h-index, which aims to provide an objective measure of the overall impact of individual authors’ publication histories.

Increased importance of research publications, impact factor and citations as metrics in evaluating science and assessing the quality of research is driving unethical practices too in research and publications. Adding to that, limited access to research publications, exuberant subscription charges, heavy article processing charges and several other transboundary science and technology issues are further dividing the scientific community which is severely impacting the progress of the Nation (Pathak, 2025). The National Academy of Agricultural Sciences (NAAS) journal rating system serves as a cornerstone for researchers in India, particularly in the domain of agricultural sciences. Its significance lies in providing an accessible and systematic framework for evaluating the quality and relevance of academic journals. This chapter explores avenues for enhancing the NAAS journal rating methodologies to ensure greater accuracy, inclusivity, and ethical rigor in the assessment process. By integrating global best practices, incorporating diverse metrics, and addressing emerging challenges in the academic publishing landscape, the proposed framework aims to make NAAS ratings more robust and globally competitive. To enable universal access to scholarly scientific literature, under Aatmanirbhar Bharat it would be appropriate to strengthen our own Indian Journals to compete globally in the long run. In this regard, NAAS rating of Agri-journals has been a progressive step and NAAS should continue to upgrade its evaluation mechanism. The Professional Association of Agricultural Societies (PAAS) and NAAS partnership in upgrading of publications in Indian society journals should be encouraged.

In the world of academic publishing, Article Processing Charges (APCs) have emerged as a significant barrier, particularly for researchers from countries with limited resources like India. These charges, often levied by open-access journals to cover the costs of peer review, editing, and dissemination, have created a financial divide that impedes equitable access to scholarly communication. This chapter delves into the multifaceted challenges posed by APCs and outlines potential solutions to address the inequities they perpetuate (Fig. 6.1).
6.1. The Burden of Article Processing Charges
The financial burden of APCs is disproportionately felt by researchers in developing nations. Many prestigious open-access journals charge APCs ranging from $1,000 to $5,000 or more per article. For researchers in high-income countries, these charges might be manageable, supported by robust institutional funding or grants. However, for their counterparts in countries like India, where research funding is limited and often tied to modest institutional budgets, such costs are prohibitive. The disparity in income and currency exchange rates further amplifies this challenge. A charge of $2,000, for instance, could equate to several months’ salary for a researcher in India, compared to a fraction of that amount for a researcher in the United States or Europe.

Scientific leadership is a cornerstone of progress in agricultural sciences, playing a pivotal role in driving innovation, fostering collaboration, and addressing global challenges such as food security, climate change, and sustainable resource management. Effective scientific leadership ensures that research efforts are strategically aligned with pressing societal needs and that knowledge generated in laboratories and fields translates into tangible benefits for farmers, policymakers, and communities. This chapter delves into the qualities of effective leaders in agricultural sciences, the challenges they face, and strategies to nurture and support scientific leadership in this critical domain. The G20 Chief Science Advisers Roundtable (G20-CSAR), initiated under India’s G20 Presidency, is a flagship program aimed at fostering collaboration and enhancing access to scholarly scientific knowledge. This effort emphasizes the synergy of scientific expertise, ensuring that innovations and advancements are not only accessible but also utilized effectively to address pressing global concerns, such as climate change, public health, sustainable development, and digital transformation. Through this platform, India seeks to promote open science, equitable knowledge-sharing, and stronger international cooperation in research and development.
7.1. Qualities of Effective Leaders in Agricultural Sciences
To excel in agricultural sciences, leaders must embody a diverse range of qualities that enable them to inspire teams, foster innovation, and drive impactful research. These qualities include:
7.1.1. Strong Communication Skills
Effective leaders in agricultural sciences must be adept at communicating complex scientific concepts to diverse audiences. Whether engaging with fellow researchers, policymakers, farmers, or the general public, they must tailor their messages to ensure clarity and relevance. Strong communication skills are also essential for securing research funding, building partnerships, and advocating for science-based policies.

In the evolving landscape of agricultural sciences, integrative research models have emerged as a cornerstone for addressing complex, multifaceted challenges. These models bridge the gap between theoretical frameworks and their practical applications, ensuring that innovations are not just conceptual but also actionable and impactful. This chapter delves into the essence of integrative research models, highlighting their significance, successful case studies, and strategies to foster their adoption and effectiveness in agricultural progress.
8.1. The Need for Integrative Research Models
Agriculture today is at the nexus of critical global challenges, including climate change, food security, biodiversity loss, and resource scarcity. Traditional, siloed research approaches often fall short in addressing these interconnected issues. Integrative research models offer a paradigm shift by combining insights from diverse disciplines such as agronomy, ecology, economics, data science, and social sciences. This approach not only enhances the depth of understanding but also ensures that solutions are holistic and sustainable (Fig. 8.1).
One of the primary drivers for adopting integrative research models is the increasing complexity of agricultural systems. Modern agriculture is no longer

Global agricultural research, an essential field in ensuring food security and sustainable development, is heavily influenced by the academic and publishing ecosystems in Europe and North America. This chapter examines the challenges faced by researchers from developing regions, focusing on limited representation in editorial boards, barriers to accessing high-impact journals, and the overarching dominance of Western institutions (Fig. 9.1).
These issues underscore the need for greater inclusivity and recognition of regional expertise to foster a more equitable global research landscape.
9.1. Dominance of Europe and North America in Agricultural Research
Publishing
The dominance of Europe and North America in agricultural research publishing is evident from the distribution of international journals in agriculture and allied disciplines. Approximately 75% of these journals originate from these regions. Breaking this down further:
• Europe accounts for 43.6% of international journals, with leading contributors including the United Kingdom (14.1%), the Netherlands (8.5%), Germany (6.2%), France (4.3%), Italy (3.5%), and other European countries (7.0%).
• North America contributes 31.4%, with the United States alone publishing 28.5% and Canada accounting for 2.9%.

The credibility of academic publishing hinges significantly on the integrity of journal rating systems. These systems, designed to evaluate and rank academic journals based on various metrics, play a pivotal role in shaping research priorities, funding allocations, and academic career trajectories. However, despite their importance, many journal rating systems are criticized for lacking transparency and ethical rigor (Fig. 10.1).
This chapter explores these shortcomings, focusing on potential biases embedded in current systems and proposing solutions to enhance their transparency and fairness.
10.1. Role of Journal Rating Systems in Academic Publishing
Journal rating systems serve as gatekeepers in the academic publishing ecosystem. They influence where researchers choose to publish their work, how institutions evaluate scholarly output, and how funding agencies allocate resources. Metrics such as impact factor, h-index, and SCImago Journal Rank (SJR) are commonly used to rank journals. These metrics, while useful, often reduce the multifaceted nature of scholarly impact into single numerical values, potentially oversimplifying and distorting the evaluation process. The reliance on these metrics creates a feedback loop wherein highly ranked journals attract more submissions, increasing their citation counts and reinforcing their dominance. This system can marginalize smaller or niche journals that publish

Predatory journals undermine the integrity of academic publishing by charging exorbitant fees without providing rigorous peer review. These deceptive entities exploit the academic community, especially targeting early-career researchers, those from underfunded institutions, and scholars in developing countries. By prioritizing profit over quality, predatory journals erode trust in the research ecosystem, dilute scientific knowledge, and tarnish the reputation of genuine academic endeavors (Fig. 11.1).
This chapter delves into the multifaceted challenges posed by predatory journals and outlines comprehensive strategies for researchers, institutions, and policymakers to combat their pernicious effects.
11.1. Understanding Predatory Journals
Predatory journals are characterized by their lack of transparency, absence of editorial rigor, and aggressive solicitation of authors. They often masquerade as legitimate open-access journals but fail to adhere to the ethical standards of scholarly publishing. Unlike reputable journals, which uphold rigorous peer-review processes to ensure the validity and originality of research, predatory journals accept articles with minimal or no scrutiny. This results in the dissemination of low-quality or even fraudulent research, undermining the credibility of academic literature.
Several red flags can help researchers identify predatory journals. These include:

National journals play a crucial role in the dissemination of regionally relevant research, particularly in specialized fields such as agricultural sciences. These journals act as accessible platforms for researchers, practitioners, and policymakers to share findings, innovations, and solutions tailored to local contexts. Strengthening national journals is essential for fostering knowledge exchange, promoting inclusivity in scientific communication, and addressing the unique challenges faced by different regions (Fig. 12.1).
This chapter explores strategies for improving the quality, visibility, and credibility of national journals, with examples from countries across the globe, including those outside North America and Europe. Case studies of successful initiatives are included to illustrate best practices for empowering local publishing platforms, with a particular focus on non-English publications.
12.1. The Importance of National Journals in Agricultural Sciences
Agricultural sciences are inherently context-dependent. Local factors such as climate, soil type, cropping systems, and socioeconomic conditions influence the challenges faced by farmers and the solutions that are most effective. National journals provide a vital medium for addressing these region-specific issues, enabling researchers to publish studies that may not align with the broader focus of international journals. Furthermore, these journals often cater to the immediate needs of local policymakers, extension workers, and educators, ensuring that research findings are translated into actionable outcomes.

The current systems of journal rating and evaluation have long been criticized for their emphasis on narrow metrics, such as the journal impact factor (JIF), which often fail to reflect the broader contributions of academic work. Despite their widespread use, these systems frequently reinforce inequities within academia, marginalize underrepresented voices, and fail to prioritize the societal impacts of research (Fig. 13.1).
This chapter consolidates recommendations for reforming journal rating systems, emphasizing fairness, inclusivity, and societal impact. Drawing on existing literature and expert recommendations, we outline a comprehensive framework for designing a rating system that balances academic rigor with accessibility and relevance.
13.1. Revising Evaluation Metrics
The reliance on metrics such as JIF has perpetuated a cycle of prioritizing high-citation fields and well resourced institutions. Garfield (2006), the founder of the JIF, himself noted that it was never intended to serve as the singular measure of research quality, yet its dominance in academia persists. Critics argue that the JIF favors fields with inherently higher citation rates, sidelining disciplines such as the humanities, social sciences, and regional studies (Moher et al., 2018). Moreover, the JIF incentivizes salacious or sensational findings that attract citations, often at the expense of methodological rigor (Brembs et al., 2013). To address these issues, scholars have proposed alternative evaluation metrics that prioritize broader dimensions of impact. For example, the Leiden Manifesto (Hicks et al., 2015) outlines ten principles for responsible research evaluation,

The Sustainable Development Goals (SDGs) are a set of 17 interconnected goals established by the United Nations in 2015 as part of the 2030 Agenda for Sustainable Development. These goals aim to address global challenges, including poverty, inequality, climate change, environmental degradation, peace, and justice (Fig. 14.1).
14.1. Sustainable Development Goals (SDGs)
The SDGs provide a universal framework to achieve a better and more sustainable future for all. Following is the list of the 17 SDGs
1. No Poverty: End poverty in all its forms everywhere.
2. Zero Hunger: End hunger, achieve food security, improve nutrition, and promote sustainable agriculture.
3. Good Health and Well-Being: Ensure healthy lives and promote well-being for all at all ages.

Policy plays a critical role in shaping the future of agricultural sciences. It determines the resources allocated to research, the inclusivity of publishing practices, and the extent of global collaboration (Fig. 15.1).
This chapter outlines actionable policy recommendations to support equitable publishing, strengthen research infrastructure, and encourage global partnerships. Furthermore, it delves into the importance of fostering interdisciplinary research and emphasizes why agricultural sciences need to continue gaining momentum in the face of global challenges.
15.1. Equitable Publishing Practices
Access to academic publishing remains a significant challenge for researchers in developing countries. High article processing charges (APCs) for open-access journals often exclude underfunded institutions and individual researchers. Policy interventions are essential to create a more equitable publishing ecosystem.
15.1.1. Subsidies for Open Access Publishing
Governments and funding agencies should subsidize APCs for researchers from low-income and middle-income countries (LMICs). For instance, the Plan S initiative-backed by organizations like the European Science Foundation—aims to make all publicly funded research open access (Plan S, 2018).

The final chapter of this exploration into agricultural sciences casts a forward-looking lens on the opportunities and challenges that lie ahead. As global population levels continue to rise, with estimates suggesting we will surpass 9 billion people by 2050, the demand for sustainable and efficient agricultural practices has never been more urgent. Emerging challenges, such as climate change, biodiversity loss, soil degradation, and water scarcity, coupled with rapid technological advancements, are reshaping the landscape of agricultural research and publishing (Fig. 16.1).
This chapter delves into how the integration of advanced technologies, the promotion of open-access publishing, and global cooperation can revolutionize agricultural sciences. It also highlights the importance of equity, innovation, and adequate funding in driving this transformation.
16.1. Advanced Technologies and Their Transformative Potential
In the past decade, advanced technologies like artificial intelligence (AI), machine learning (ML), and big data analytics have become central to scientific inquiry. These tools are now increasingly being applied to agricultural research, offering unprecedented opportunities for innovation. For example, AI-powered predictive models can help forecast crop yields, pest outbreaks, and weather

The advancement of agricultural sciences depends on systems that are fair, inclusive, and innovative. The rating of agricultural journals requires unique considerations due to the interdisciplinary and regionally diverse nature of agricultural research. By addressing structural inequities, prioritizing accessibility, and fostering leadership, the global agricultural research community can ensure its continued relevance in solving the most pressing challenges of our time (Fig. 17.1).
This book has explored the multifaceted issues facing agricultural sciences, offering a comprehensive roadmap to create systems that uphold the highest standards of equity, innovation, and collaboration.
17.1. Reforming Journal Ratings
A key pillar of advancing agricultural sciences lies in the reform of journal rating systems. Current systems often rely heavily on impact factors, a metric that, while useful, is not comprehensive. By moving toward a multidimensional evaluation framework, we can prioritize relevance, diversity of contributions, and societal impact alongside citation metrics. Reforms could include:
• Incorporating qualitative assessments of journals, such as their contributions to underrepresented research areas or regions.
• Promoting open-access journals that adhere to rigorous peer-review standards.

The One Nation One Subscription (ONOS) scheme is a cornerstone of India’s ambition to become a self reliant and developed nation by 2047 envisaged by Hon’ble Prime Minister Shri Narendra Modi Ji. The initiative is a significant step to enhance access to scientific and academic resources across the country. This initiative can positively impact Indian journal ratings and boost subscriptions by addressing several challenges listed below:
• Increased Access to Global Resources
• Enhanced Research Quality 118 | Promoting Excellence in Agricultural Sciences
• Support for Smaller Institutions
• Boost to Indian Journals
• Fostering Interdisciplinary Collaboration
By bridging gaps in resource accessibility and improving research output, ONOS can play a pivotal role in elevating the status of Indian journals on global platforms. While evaluating Indian Journals of Agricultural and Allied Sciences, comprehensive and inclusive databases with many characteristics listed below should be adopted so as to ensure equal focus and benefit from international exposure:
• The database should have regional and multi-lingual journals with proper translation or abstracting, interdisciplinary research output, more and new journals/technical reports/official scientific documents/conference proceedings etc, open access for smaller journals to ensure readily accessible cutting-edge research in agriculture
• The database should provide more nuanced metrics that value realistic impact and localized research contributions considering immediate practical applications
• The database should include a wide range of journals across diverse disciplines, including agriculture, forestry, veterinary sciences, and environmental science with more inclusion of regional and specialized journals, providing access to a broader spectrum of agricultural research
• The database should emphasis on journals from developing regions, which often publish research addressing local agricultural challenges. This diversity helps in showcasing research contributions from regions/countries with significant agricultural economies
• The database of agriculture-related journals should overlap with other related fields viz., environmental science, biology, and social sciences, reflecting the interdisciplinary nature of agriculture. This helps researchers access a more comprehensive set of resources
• The database have detailed subject areas, allowing researchers to pinpoint agricultural science journals within relevant subfields like:

The history of genetics dates from the classical era with contributions by Hippocrates, Aristotle and Epicurus. Modern biology began with the work of the Augustinian friar Gregor Johann Mendel. His work on pea plants, published in 1866, what is now Mendelian inheritance. Some theories of heredity suggest in the centuries before and for several decades after Mendel›s work. The year 1900 marked the “rediscovery of Mendel” by Hugo de Vries, Carl Correns and Erich von Tschermak, and by 1915 the basic principles of Mendelian genetics had been applied to a wide variety of organisms—most notably the fruit fly Drosophila melanogaster. Led by Thomas Hunt Morgan and his fellow «drosophilists», geneticists developed the Mendelian model, which was widely accepted by 1925. Alongside experimental work, mathematicians developed the statistical framework of population genetics, bringing genetic explanations into the study of evolution.
With the basic patterns of genetic inheritance established, many biologists turned to investigations of the physical nature of the gene. In the 1940s and early 1950s, experiments pointed to DNA as the portion of chromosomes (and perhaps other nucleoproteins) that held genes. A focus on new model organisms such as viruses and bacteria, along with the discovery of the double helical structure of DNA in 1953, marked the transition to the era of molecular genetics.
In the following years, chemists developed techniques for sequencing both nucleic acids and proteins, while others worked out the relationship between the two forms of biological molecules: the genetic code. The regulation of gene expression became a central issue in the 1960s; by the 1970s gene expression could be controlled and manipulated through genetic engineering. In the last decades of the 20th century, many biologists focused on large-scale genetics projects, sequencing entire genomes.
Pre Mendelian Ideas on Heredity
Diagram of Charles Darwin’s pangenesis theory. Every part of the body emits tiny particles, gemmules, which migrate to the gonads and contribute to the fertilised egg and so to the next generation. The theory implied that changes to the body during an organism’s life would be inherited, as proposed in Lamarckism. Mendel’s work

(Chroma - Colour; Some - Body)
A chromosome is a thread-like self-replicating genetic structure containing organized DNA molecule package found in the nucleus of the cell. Clear and detaile decriptions of mitotic chromosomes in plants and animals were published by Strasburger in 1875 and by the German scientist Walter Flemming in 1879- 1882.Heinrich Wilhelm Gottfried Waldeyer coined the term chromosome in 1888.
Normally Chromosomes are of two types
Autosomes - Control characters other than sex characters or carry genes for somatic characters.
Sex chromosomes (S    
Humans and most other mammals have two sex chromosomes X & Y, also called heterosome, odd chromosome, or idiosome. Females have two X chromosomes in diploid cells; males have an X and a Y chromosome. In birds the female (ZW) is hetero-gametic and male (ZZ) is homo-gametic.
Haploid: Haploid cells (N) have only one copy of each chromosome.
Diploid: Diploid cells (2N where N- chromosome number) have two homologous copies of each chromosome. The body cells of animals are diploid.In animals, gametes (sperm and eggs) are haploid.
Homologous Chromosomes
Diploid organisms have two copies of each chromosome (except the sex chromosomes). Both the copies are ordinarily identical in morphology, gene content and gene order and hence known as homologous chromosomes.Each pair of chromosomes made up of two homologs.
Homologous chromosome is inherited from separate parents; one homolog comes from the mother and the other comes from the father.

Cells divide and reproduce in two ways: mitosis and meiosis.
Mitosis is a process of cell division that results in two genetically identical daughter cells developing from a single parent cell.
Meiosis, on the other hand, is the division of a germ cell involving two fissions of the nucleus and giving rise to four gametes, or sex cells, each possessing half the number of chromosomes of the original cell.Mitosis is used by single-celled organisms to reproduce; it is also used for the organic growth of tissues, fibers, and membranes. Meiosis is found in sexual reproduction of organisms. The male and female sex cells (i.e., egg and sperm) are the end result of meiosis; they combine to create new, genetically different offspring. 

Mendel’s 3 Laws (Segregation, Independent Assortment, Dominance).In the 1860s, an Austrian monk named Gregor Mendel introduced a new theory of inheritance based on his experimental work with pea plants.Mendel believed that heredity is the result of discrete units of inheritance, and every single unit (or gene) was independent in its actions in an individual’s genome.According to this Mendelian concept, the inheritance of a trait depended on the passingon of these units.For any given trait, an individual inherits one gene from each parent so that the individual has a pairing of two genes. We now understand the alternate forms of these units as ‘alleles’.If the two alleles that form the pair for a trait are identical, then the individual is said to be homozygous and if the two genes are different, then the individual is heterozygous for the trait.The breeding experiments of the monk in the mid-1800s laid the groundwork for the science of genetics.He studied peas plant for 7 years and published his results in 1866 which was ignored until 1900 when three separate botanists, who also were theorizing about heredity in plants, independently cited the work.In appreciation of his work he was considered as the “Father of Genetics”. A new stream of genetics was established after his name as Mendelian genetics which involves the study of heredity of both qualitative (monogenic) and quantitative (polygenic) traits and the influence of environment on their expressions.Mendelian inheritance while is a type of biological inheritance that follows the laws originally proposed by Gregor Mendel in 1865 and 1866 and re-discovered in 1900.
Mendel carried out breeding experiments in his monastery’s garden to test inheritance patterns. He selectively cross-bred common pea plants (Pisum sativum) with selected traits over several generations. After crossing two plants which differed in a single trait (tall stems vs. short stems, round peas vs. wrinkled peas, purple flowers vs. white flowers, etc), Mendel discovered that the next generation, the “F1” (first filial generation), was comprised entirely of individuals exhibiting only one of the traits. However, when this generation was interbred, its offspring, the “F2” (second filial generation), showed a 3:1 ratio- three individuals had the same trait as one parent and one individual had the other parent’s trait.

Some traits are carried on the sex chromosomes, X and Y. Most traits carried are present on only the X-chromosome. The Y-chromosome is smaller, and so, very few genes are located on this chromosome. Sex traits can be categorized into three types of inheritance:
Sex limited,
Sex-linked, and
Sex-influenced.
Sex-limited traits are traits that are visible only within one sex. For instance, barred colouring in chickens normally is visible only in the roosters. Sex-linked traits would be considered traits like sickle cell anemia and colour blindness. They are said to be linked because more males (XY) develop these traits than females (XX). This is because the females have a second X gene to counteract the recessive trait. Thus, the trait is more likely to be visible in the male.
Sex Influenced Inheritance
The condition in which the same gene acts as dominant in one sex and recessive in other sex is called as sex influenced dominance. That is, the sex influences the gene either to be dominant or recessive. The sex influenced genes are present in autosomes. This differential behaviour of the gene is due to female and male sex hormones. For example, in human being baldness is due to sex influenced gene. This trait is dominant in men and recessive in women. A man is bald in homozygous recessive as well on heterozygous condition for baldness. Whereas women exhibit baldness only in homozygous recessive condition for baldness and heterozygous condition for baldness in female sex produce normal phenotype. HN, HN -Normal female and normal male

Mutation
Definition: “Mutation is the change in our DNA base pair sequence due to various environmental factors such as UV light, or mistakes during DNA replication.”
What Are Mutations?
The DNA sequence is specific to each organism. It can sometimes undergo changes in its base-pairs sequence. It is termed as a mutation. A mutation may lead to changes in proteins translated by the DNA. Usually, the cells can recognize any damage caused by mutation and repair it before it becomes permanent.
A mutation is a sudden, heritable modification in an organism’s traits. The term “mutant” refers to a person who exhibits these heritable alterations. Mutations usually produce recessive genes.

Introduction
• Cytogenetics is essentially a branch of genetics, but is also a part of cell biology/ cytology (a subdivision of human anatomy), that is concerned with how the chromosomes relate to cell behavior, particularly to their behaviour during mitosis and meiosis. Techniques used include karyotyping analysis of G-band chromosomes, as well as molecular cytogenetics such as fluorescent in situ hybridization (CGH). Cytogenetic approaches to studying chromosomes and their relationship to human disease have improved greatly over the past several decades.
As a mature enterprise, cytogenetics now inform genomics, disease and cancer genetics, chromosomes evolution and the relationship of nuclear structure to function. Cytogenetics involves testing samples of tissue, blood or bone marrow in a laboratory to look for changes in chromosomes including broken, missing, rearranged or extra chromosome. Cytogenetics may used to help diagnose a disease or condition, plan treatment or find out how well treatment is working.
Chromosomes
Chromosomes are the rod shaped; dark-stained bodies seen during metaphase stage of mitosis. The chromosomes are the nuclear components of special organization, individuality and function. They are capable of self-reproduction and play a vital role in heredity, mutation, variation and evolutionary development of the species. Chromosomes are thread-like structure located inside the nucleus. Each chromosome is made up of DNA tightly coiled many times around proteins called histones that support its structure. The number of chromosomes is constant for a particular species. Therefore, these are of great importance in the determination of the phylogeny and taxonomy of the species. The number of chromosomes varies from species to species but the number remains constant in a species. But sometime, due to certain accidents or irregularities at the time of cell division, crossing over or fertilization some alteration in morphology and number of chromosomes takes place. Humans have 23 pairs of chromosomes-22 pairs of numbered chromosomes, called autosomes, and one pair of sex chromosome, X and Y. Each parent contributes one chromosome to each pair so that offspring get half of their chromosomes from mother and half from their father.

DNA is the master molecule which carries the genetic information from one generation to the other. Study of Molecular Genetics accelerated since April 25th, 1953 when James Watson and Francis Crick proposed the structure of DNA which was published in Journal called ‘Nature’. Molecular Genetics deals with the flow of genetic information and its regulation. In simple terms it can be defined as the field of biology which studies the structure and function of genes at molecular level.
Scope of Molecular Genetics
Development of techniques like nucleic acid hybridisation, cloning, sequencing etc. brought a revolutionary change in Molecular Genetics. It is of major interest to the students of biology and medicine. Though it has a lot of significance in many fields, we’ll confine ourselves to the applications of molecular genetics to the mankind. They are as follows:
i) Diagnosis of infectious diseases: Normally microorganisms are detected in the laboratory using biochemical methods. In case of molecular techniques, microorganisms are detected by using probes (short DNA or RNA sequence) which are complementary to a part of genome of the microbe. The advantage of using molecular methods is:
• Identification of pathogen is done within a short time;
• No need to cultivate the microbes;
• Latent infections can also be identified when no antibody is formed; and
• The technique can be used even when the microorganism cannot be cultured.
ii) Diagnosis of genetic diseases : Before the advent of the above techniques, counselors used to give risk estimate like one fourth risk of getting the disease, if the parents are heterozygous for an autosomal trait. But now by directly testing for the mutation, they are able to confirm the presence or absence of mutation in the fetus. It is of immense help in prenatal diagnosis.

The genetic blueprint contained in the nucleotide sequence can determine the phenotype of an individual. The hereditary units, which are transmitted from one generation to the next generation are called genes. A gene is a fundamental biological unit like atom which is the fundamental physical unit.
Mendel was the first scientist who proposed genes as particulate units and called them hereditary elements or factors. But the concept of gene has undergone a considerable change since Mendel’s time.
Modern Concept of Gene
A gene can be described as a polynucleotide chain, which is a segment of DNA. It is a functional unit controlling a particular trait such as eye colour. Beadle and Tatum concluded by various experiments that gene is a segment of DNA that codes for one enzyme. They proposed one gene-one enzyme hypothesis. But as some genes code for proteins that are not enzymes, the definition of gene was changed to one gene-one protein hypothesis.
Protein Hypothesis
The concept of gene has undergone further changes as the new facts came to light. Since proteins are polypeptide chains of amino acids translated by mRNA, gene was defined as one gene-one polypeptide relationship.
Some proteins have two or more different kinds of polypeptide chains, each with a different amino acid sequence. They are products of different genes. For example, hemoglobin has two kinds of chains a andß chains, which differ in amino acid sequence and length. They are encoded by different genes. Thus, gene is defined as one gene- one polypeptide relationship.

1. Introduction
Molecular techniques are laboratory methods used to study and manipulate DNA, RNA, and proteins. These techniques are crucial for analyzing and understanding the molecular basis of biological processes and have applications in various fields like medicine, agriculture, and forensics.
2. Molecular Marker Analysis
Molecular markers can be expressed as a DNA sequence or gene expression product that represents differences in genomic level in relation to a gene or a property. Molecular markers are markers that can be used to monitor differences at the DNA level and for a gene that is being investigated. DNA markers are also DNA regions in which polymorphism in individuals within a species can be determined.
Molecular markers are nontissue-specific DNA regions that are reliable, repeatable, standardizable, capable of identifying multiple regions in the genome, capable of identifying more than one region in the genome, independent of environmental conditions, dominant and codominant.
Molecular markers are classified as dominant and codominant markers. Heterozygous individuals cannot be distinguished from homozygous dominant individuals, since dominant markers are not suitable for identification of heterozygous individuals when related to dominance between alleles is dominated by dominant markers. Thus, three different individuals (AA, AA and AA) can be distinguished for any marker at any point.
The use of molecular marker systems based on this meta-analysis has become more prevalent in genetic studies conducted by the discovery of the polymerase chain reaction (PCR). The rapid development of technology and the accompanying needs, the facilities of the laboratories where the applications will occur, the biological properties of the species and the abundance of markers in the genome have contributed to the development of DNA markers [5]. Restriction fragment length polymorphism (RFLP), randomly amplified polymorphic DNA markers (RAPD), amplified fragment length polymorphism (AFLP), sequence labeled sequences (STS), microsatellites (SSR), cleaved polymorphic sequence (CAPS), single strand such as complementary polymorphism (SSCP), amplicon length polymorphism (ALP), interspecific sequence repeat polymorphism (ISSR),

To understand how population genetics came into being, and to appreciate its intellectual significance, a brief excursion into the history of biology is necessary. Darwin’s Origin of Species, published in 1859, propounded two main theses: firstly, that modern species were descended from common ancestors, and secondly that the process of natural selection was the major mechanism of evolutionary change. The first thesis quickly won acceptance in the scientific community, but the second did not. Many people found it difficult to accept that natural selection could play the explanatory role required of it by Darwin’s theory. This situation— accepting that evolution had happened but doubting Darwin’s account of what had caused it to happen—persisted well into the twentieth century (Bowler 1988).
Opposition to natural selection was understandable, for Darwin’s theory, though compelling, contained a major lacuna: an account of the mechanism of inheritance. For evolution by natural selection to occur, it is necessary that parents should tend to resemble their offspring; otherwise, fitness-enhancing traits will have no tendency to spread through a population. In the Origin, Darwin rested his argument on the observed fact that offspring do tend to resemble their parents—‘the strong principle of inheritance’—while admitting that he did not know why this was. Darwin did later attempt an explicit theory of inheritance, based on hypothetical entities called ‘gemmules’, but it turned out to have no basis in fact.
Darwin was troubled by not having a proper understanding of the inheritance mechanism, for it left him unable to rebut a powerful objection to his theory. For a population to evolve by natural selection, the members of the population must vary—if all organisms are identical, no selection can occur. So for selection to gradually modify a population over a long period of time, in the manner suggested by Darwin, a continual supply of variation is needed. Fleeming Jenkin argued that the available variation would be used up too fast (Jenkin 1867). His reasoning assumed a ‘blending’ theory of inheritance, i.e., that an offspring’s phenotypic traits are a ‘blend’ of those of its parents. (So, for example, if a short and a tall organism mate, the height of the offspring will be intermediate between the two.) Jenkin argued that given blending inheritance, a sexually reproducing population will become phenotypically homogenous in just a few generations, far shorter than the number of generations needed for natural selection to produce complex adaptations.

A population, in the genetic sense, is not just a group of individuals, but a breeding group and the genetics of a population is concerned not only with the genetic constitution of the individuals but also with the transmission of the genes from one generation to the next. In the transmission the genotypes of the parents are broken-down and a newest of genotypes is constituted in the progeny, from the genes transmitted in the gametes. The genes carried by the population thus have continuity from generation to generation, but the genotypes in which they appear do not. The genetic constitution of a population, referring to the genes it carries, is described by the array of gene frequencies, that is, by specification of the alleles present at every locus and the numbers of proportions of the different alleles at each locus. If for example, A1 is an allele at the A locus, then the frequency of A1, is the proportion or percentage of all genes at this locus that are the A1 allele. The frequencies of all the allele at any one locus must add up to unity, or 100 percent.
The gene frequencies at a particular locus among a group of individuals can be determined from knowledge of the genotype frequencies. To take a hypothetical suppose there are two alleles A1 and A2, let the frequencies of genes and of genotypes be as follows:

Quantitative genetics is the study of continuous or quantitative traits and their underlying mechanisms. The main principals of quantitative genetics developed in the 20th century was largely in response to the rediscovery of Mendelian genetics. Mendelian genetics in 1900 centered attention on the inheritance of discrete characters, e.g., smooth vs. wrinkled peas, purple vs. white flowers. This focus was in stark contrast to the branch of genetic analysis by Sir Francis Galton in the 1870’s and 1880’s who focused on characteristics that were continuously variable and thus, not clearly separable into discrete classes. A contentious debate ensued between Mendelians and Biometricians regarding whether discrete characteristics have the same hereditary and evolutionary properties as continuously varying characteristics. I The Mendelians (led by William Bateson) believed that variation in discrete characters drove evolution through mutations with large effects I The Biometricians (led by Karl Pearson and W.F.R. Weldon) viewed evolution to be the result of natural selection acting on continuously distributed characteristics. This eventually led to a fusion of genetics and Charles Darwin’s theory of evolution by natural selection: main principals of quantitative genetics, developed independently by Ronald Fisher (1918) and Sewall Wright (1921), arguable the two most prominent evolutionary biologists.
Interestingly, Galton’s methodological approaches to continuously distributed traits marked the founding of the Biometrical school, which is what many consider to be the birth of modern statistics. Karl Pearson was inspired greatly by Galton, and he went on to develop a number of methods for the analysis of quantitative traits. We will talk more about Galton and Pearson later on in this course. One of the central goals of quantitative genetics is the quantification of the correspondence between phenotypic and genotypic values. It is well accepted that variation in quantitative traits can be attributable to many, possibly interacting, genes whose expression may be sensitive to the environment

The concept of value, expressible in the metric units by which the character is measured. The value observed when the character is measured on an individual is the phenotypic value of that individual. All observations of means, variance, or covariances, must clearly be based on measurements of phenotypic values. In order to analyse the genetic properties of the population we have to divide the phenotypic value into two componants.
The first division of phenotypic value is into components attributable to the influence of genotypic and environment. The genotype is the particular assemblage of genes possessed by the individual, and the environment is all the non-genetic circumstances under the term ‘environment’ means that the genotype and the environment are by definition the only determinants of phenotypic value. The two components of value associated with genotypic value and the environmental deviation.
The mean environmental deviation in the population as a whole is taken to be zero. So that the mean phenotypic value is equal to the mean genotypic value. The term population mean than refers equally to phenotypic or to genotypic values. When dealing with successive generations we shall assume for simplicity that environment remains constant from generation to generation so that the population mean is constant in the absence of genetic change. If we replicate thea particular genotype in a number of individuals and measure them under environment conditions normal for the population, their mean environmental deviations would be zero and their mean phenotypic value would congiguently be equal to the genotypic value of that particular genotype.
In principle it is measurable, but in practice it is not, except when we are concerned with a single locus where the genotypes are phenotypically distinguishable or with the genotypes represented in highly inbred lines for example, considering a single locus with two alleles. A1 and A2, we call the genotypic value of one homozygote + a, that of the other homozygote – a and that of the heterozygote d (we shall adopt

The amount of variation is measured and expressed as the variance. When values are expressed as deviations from the population mean the variance is simple the mean of the squared values. For example, the genotypic variance is the variance of genotypic values and the environmental variance is the variance of environmental deviations. The total variance is the phenotypic variance of the variance of phenotypic values, and is the sum of the separate components.
Components of Variance
The components of variance and the values whose variance they measure are listed as follows:
The total variance is the phenotypic variance, or the variance of phenotypic values, and is the sum of the separate components. Thus
But if genotypic values and environmental deviations are correlated, VP will be increased by twice the covariance of G with E because if P = G + E, VP = V (G + E) = VG + VE + 2 CovGE. d. The term 2 CovGE is zero when G and E are uncorrelated. Also when there is an interaction between genotypes and environments, there will be an additional component of variance due to the interaction i.e.

Individuals in a population can vary considerably on physical, cognitive, and behavioural traits. Examples include height, weight, intelligence, personality, etc. Individual differences may arise from variation in genes, environmental experiences, or a combination of both. It is generally accepted that individual differences in most traits are due to both genetic and environmental factors. To the extent that a trait is influenced by genetic (heritable) effects, phenotypic similarity is correlated with genetic relatedness.
The degree of resemblance among relatives allows for the estimation of genetic variance as well as heritability of a trait. We will now focus on how phenotypic correlation of relatives can be used to estimate the relative magnitude of genetic and environmental influences on trait variation
Partitioning of Phenotypic Values
We previously introduced the general model of Y = G +E where Y is the trait value, G is the genotypic value, and E is the environmental deviation that is assumed to have a mean of 0 so that E(Y ) = E(G). If we assume that the genetic and environmental components are independent, we have that the variance of Y is Var(Y ) = s 2 Y = s 2 G +s 2 E .
We previously focused on the decomposition of the genetic variance s 2 G into additive and dominance components, i.e., G = A+D

Heritability measures the fraction of phenotype variability that can be attributed to genetic variation. This is not the same as saying that this fraction of an individual phenotype is caused by genetics. For example, it is incorrect to say that since the heritability of personality traits is about 0.6, that means that 60% of your personality is inherited from your parents and 40% comes from the environment. In addition, heritability can change without any genetic change occurring, such as when the environment starts contributing to more variation. As a case in point, consider that both genes and environment have the potential to influence intelligence. Heritability could increase if genetic variation increases, causing individuals to show more phenotypic variation, like showing different levels of intelligence. On the other hand, heritability might also increase if the environmental variation decreases, causing individuals to show less phenotypic variation, like showing more similar levels of intelligence. Heritability increases when genetics are contributing more variation or because non-genetic factors are contributing less variation; what matters is the relative contribution. Heritability is specific to a particular population in a particular environment. High heritability of a trait, consequently, does not necessarily mean that the trait is not very susceptible to environmental influences.Heritability can also change as a result of changes in the environment, migration, inbreeding, or the way in which heritability itself is measured in the population under study. The heritability of a trait should not be interpreted as a measure of the extent to which said trait is genetically determined in an individual.
The extent of dependence of phenotype on environment can also be a function of the genes involved. Matters of heritability are complicated because genes may canalize a phenotype, making its expression almost inevitable in all occurring

There are two assumptions necessary involved in the regression of repeatability. These are:
• The variances of the different measurements are equal and have their components in the same proportions, and
• The different measurements reflect genetically the same character. If these assumptions are not valid the repeatability concept becomes vague without precise meaning in relation to the variance components.
The repeatability differs very much depending on the following:
• The nature of the trait.
• The genetic properties of the population.
• Environmental conditions under which the individuals are kept or raised.
Repeatability indicates the proportion of observed differences in performance between animals caused by differences in real producing ability. That is say, repeatability of butterfat yield is 0.40, and if a cow has an age corrected butter fat yield of 30 kilograms above the herd average, her near producing ability will be equal to 30x 0.40 = 12 kg. above the herd average. This can also be explained in a different way, i.e., if two cows differ in one lactation by 30 kg in butter fat yield. They will have difference of 12 kg of butter fat in the next lactation.
Repeatability has a value 0 to 1 and may also be expressed in percentage. Repeatability of a trait is not a constant, and measurements error or generally, varying environmental conditions tend to increase VEt and thus to decrease repeatability, shrode et al (1960) have shown the effect of a change in environmental conditions on repeatability. They obtained repeatabilities of milk yield, butter fat yield and fat percentage as 0.37, 0.32 and 0.7 respectively and after improving the management removed some of the environmental variations that had marked the cows real producing abilities.

In genetic studies it is necessary to distinguish two causes of correlation is chefly pleiotropy, though linkage is a cause of transient correlation, particularly in populations derived from crosses between divergent strains. Pleiotropy is simply the property of a gene whereby it affects two or more characters, so that if the gene is segregating it causes simultaneous variation in the characters is affects. For example, genes that increase growth rate increase both stature and weight, so that they tend to cause correlation between these two characters. The degree of correlation arising from pleiotropy expresses the extent to which two characters are influenced by the same genes. But the correlation resulting from pleiotropy is the overall, or net, effect of all the segregating genes that affect both characters. Some genes may increase both characters, while others increase one and reduce the other the former tend to cause a positive correlation the latter a negative one. So pleiotropy does not necessarily cause a detectable correlation. The correlation resulting from environmental causes is the overall effect of all the environmental factors that vary; some may tend to cause a positive correlation, others a negative one.
Genetic correlation
Hazel (1943) introduced this statistic and is defined as the correlation between the additive genetic values of two traits. When two traits are considered together we have three population parameters:

Definition of Animal Breeding
Animal breeding, as the application of science to the genetic improvement of animals, implies a close inter relationship between theory and its application. Genetics has provided the matrix form which logical principles could be developed and tested by experimentation and practice.
During the 20th century, genetics has assumed a broader meaning and numerous subdivisions of the discipline has emerged. Advances in animal breeding also have drawn heavily on contributions from statistics, biochemistry, physiology, economics and other disciplines. Animal breeding and reproductive physiology have been uniquely interwoven.
Animals with superior genotypes cannot contribute to succeeding generations unless their reproductive capacity is maintained at satisfactory levels.
Livestock production is an economic enterprise. Hence, animal breeding recommendations must withstand the scrutiny of economic, as well as genetic considerations, before they are accepted and integrated into enterprises by breeders. As a consequence, a close relationship between the breeder and the science, application and theory has been nurtured.
History of Animal Breeding
• Till 500 A.D. when the fall of Roman Empire began animal breeding was at its esteem. Withthe fall of Roman Empire for about 1000 years called Dark and Middle Ages, animal husbandry was at a still.
• From 1700 A.D., again there was an improvement. The beginning of modern animal breeding is to be found mainly in England and Europe.
• The British Royalty encouraged horse breeding especially for race horses. The Earls and Dukes imported bulls from Holland and bred their native stocks. Dutch cattle were introduced into Hereford shire that laid the foundation of the present Hereford cattle. By crossing the native and Dutch cattle and subsequent inbreeding, the British cattle were improved far beyond the best.

Types of Breeds
Domestic cattle belong to the family Bovidae, sub-family Bovinae and can be classified into Bos Taurus and Bos indicus. They have 30 pairs of chromosomes, interbreed and are distributed throughout the tropics. The domestication of Bos taurus cattle took place some 8000to 9000 years ago and Hamitic longhorn and shorthorn types are believed to be their ancestors. The origin of Bos indicus breeds (humped cattle) were in western Asia. Both humped and hump less cattle were introduced to Africa from western Asia and into America and Australia from Europe by the immigrants. The European cattle Bos taurus were introduced in the tropics to be raised as pure-bred sand crossbred with indigenous breeds. As a result of crossing of native cattle with European dairy breeds, large numbers of crossbreeds have been produced in various tropical countries, which are being used in selection programs. Zebu Bos indicus cattle were introduced into United States in the nineteenth century for crossbreeding with European breeds. Breeds resulting from crosses are used in the southern regions of North America and tropical South America. Most of the cattle breed in the tropics evolved, through natural selection, for adaptability and survival to local environments. Often, breeds resemble each other with slight morphological differences, but because of constant inbreeding in one locality, independent breeds have evolved. In general, the cattle from drier regions are well built and those from heavy rainfall areas, coastal and hilly regions are of smaller build.
Classification of Cattle Breeds
Most indigenous cattle breeds in the tropics are multipurpose (milk, meat, draught) and that only a few breeds have good milk potential. Physical and economic parameters for some of the important indigenous dairy breeds and new crossbred types developed in the tropics are discussed. Indian cattle breeds of cattle are classified in to three types as under: a) Milch breeds: b) Dual Purpose breeds: c) Draught breeds

Weaning to 210 days: Weight in kg of feed consumed for producing one kg of live weight for the period from weaning to 210 days of age.
10 Mortality percentages (as percentage)
Pre-weaning mortality: No. of piglets died during the period birth to weaning (28/56 days) the number of piglets born alive.
Post weaning mortality: Number of piglets died during the period from 28/56th to 365 day to the total number of piglets available at weaning.
Adult mortality: Number of adult pigs died to the number started at one year (in percentage).
List of registers to be maintained:
• Birth register
• Youngstock register
• Adult stock register
• Disposal register
• Mortality register
• Weighment register
• Farrowing and growth record
• Service register
• Boar performance register
• Sow performance register
• Veterinary register
• Feed efficiency register
• Account register

Natural Selection
In nature, the main force responsible for selection is of interest because of its apparent effectiveness and because of principles involved. Some of the most interesting cases of natural selection are those involving man himself. All races of man that now exist belong to the same species, because the races are interfile or have been in all instances where mating have been made between them. All races of man now in existence had a common origin and at one time probably all man had the some kind of skim pigmentation – which kind we have no sure way of knowing. As the number of generations of man increased, mutations occurred in the genes affecting pigmentation of the skin causing genetic variations in this trait over a range from light to dark or black.
Natural selection is a very complicated process and many factors determine the proportion of individuals that will reproduce. Among these factors are differences in mortality of the individuals in the population especially early in life, differences in the duration of the period of sexual activity and in the degree of sexual activity itself and the differences in the degree of fertility of individuals in the population. They are also examples of adaptive evolution.

1. Individual or mass selection
The terms individual selection and mass selection are often used interchangeably, and they refer to selection solely based on the individual´s phenotype. This is a well-known and widely used method of selection in animal breeding. It can be used on characteristics that can be measured in the candidate animal itself, as weight gain is most efficient in characteristics of high heritability. Individual selection is usually the simplest method to operate and, in many circumstances, it yields the most rapid response. It does not require individual identification or the maintenance of pedigree records, hence, it may be considered the least costly method. In principle, it can produce rapid improvement if the heritability of the trait(s) under selection is high. It can be suitable for growth rate and morphological traits (easily assessed, expressed in both sexes). By contrast, individual selection is not suitable for situations in which the estimation of breeding values requires the slaughter of the animals (carcass and flesh quality traits). When applying individual selection, the evaluated animals must be under equal environmental conditions; therefore, the environmental conditions must be controlled. In this case, the influence of external conditions should be minimal and kept the same for all individuals to be compared at any life cycle stage. In this manner, the probability of correct ranking of the individuals based on thus genetic merit is maximized. Differences between individuals or groups of individuals for environmental factors may reduce the accuracy of the selection substantially, and in that way, can also reduce the possibility for genetic improvement. it is important to form contemporary groups and select within them. To obtain as equal environmental conditions as possible all individuals to be compared should be reared under identical environmental conditions. Therefore, it is important to form groups of animals with similar ages, grown in the same production systems, with similar control of environment, handling, and feeding. However, mass selection may be unsuitable if there is large uncontrolled systematic environmental variation (for example age differences). Additionally, there is no control of inbreeding with mass selection.

Thus the average value of progeny genotypes in response to selection of parental phenotypes depends largely on Cov (G, g), the genetic covariance of parent and offspring which is half the additive genetic variance of the parents.
We know that on an average, half of genes of a parent are passed to the offspring and with them a random half of his additive merit. One-fourth of his additive x additive gene combinations are also transmitted and lesser fractions of higher additive combinations. No dominance combinations are transmitted, since only one member of each allelic gene pair reaches the offspring. Similarly all epistatic gene combinations involving allelic gene pairs are broken up at gamete formation. If dominance and epistatic gene combinations involving allelic gene pairs are important in determining genetic superiority for the trait, then direct selection of superior parents will not produce genetically superior offspring. Some form of mating system which will recreate these combinations in the offspring, together with the formation of lines or groups within the population is needed in these circumstances.
Thus, the aim of selection is to identify and select as parents individuals with high additive genetic merit. By selecting the parent on additive merit, we also ensure that a fraction of any parallel merit for additive type epistasis is also passed on. In considering response to selection, little is lost by treating the response as if it were wholly determined by the additive effects of genes

Tandem Selection
Selection is practiced for one trait at a time until satisfactory improvement has been achieved in this trait. Then, selection efforts for this trait are relaxed and efforts are directed towards the improvement of a second, then for a third and so on, until finally each trait has been improved to the desired level. This method is the least efficient of all the three methods, from the stand point of the amount of genetic progress made for the time and effort by the breeder. Efficiency of tandem selection depends a great deal upon the genetic correlation between the traits selected for. If the genetic correlation is positive and desirable, improvement in one trait by selection would automatically result in improvement in the other trait not selected for, and then the method could be quite efficient. Otherwise, if there were little or no genetic correlation between the traits, which means that they are inherited independently, the efficiency would be less. When the two traits are negatively correlated, improvement in one trait is nullified or neutralized by the regression in the other. For example, in poultry, selection for egg number will result in reduction in egg weight, as they are negatively correlated.
Independent Culling Level (ICL) Method
Method of selecting two or more traits but they both need to meet a minimum standard. It is very strict that if the animal didn’t meet one trait it would be rejected. Independent Culling level (ICL) Method selects several characteristics or traits simultaneously.
Breeders set minimum or maximum culling levels or standards or criteria for each trait of selection objectives. Any animal not meeting all criteria is not selected for use in the breeding program regardless of the level of excellence of other traits. With each successive generation of progeny, the minimum quality of each characteristic is raised thus ensuring improvement of these traits. For example, a breeder has a view of the minimum requirements for milk yield, fat yield, and service period for which cows are breeding. The breeder will determine what the minimum acceptable quality for each of these traits will be for progeny to be folded back into her breeding program. Any animal that fails to meet the quality threshold for any one of these criteria is culled from the breeding program. Thereby, it causes the loss of excellent genes from the population for a particular trait.

Under the selected breeding system selected males and females are mated. The breeding system can be classified into five different ways depending on their phenotypic and genotypic relations.
The five Breeding Systems are
(1) Random mating,
(2) Phenotypic assortive mating,
(3) Phenotypic disassortive mating,
(4) Genetic assortive mating and
(5) Genetic disassortive mating.
1. Random mating or Panmixia: It is a system of mating in which each male individual has an equal opportunity to mate with the female individual and vice versa. This mating system generally takes place in nature where the number of males and females are assumed to be equal.
2. Phenotypic assortive mating: In this type of mating animals which are phenotypically alike are allowed to mate among themselves. This is also called “like to like” mating.
3. Phenotypic disassortive mating: Here individuals which are phenotypically unlike are allowed to mate. It is also called “unlike to unlike” mating. For example, mating of tall with short individuals.
4. Genetic assortive mating: In this system individuals, which are closely related genetically are allowed to mate. This is also known as inbreeding.
5. Genetic disassortive mating: This system is just opposite to the previous system where mating takes place between less closely related individuals. This is also called as out breeding.

Definition: Heterosis is defined as the percent increase in the performance of outbred animals over the average of their parents.
The mean superiority of hybrids over the average of their parental lines is called heterosis. Heterosis or hybrid vigor is the increased vigor of the offspring over that of the parents when unrelated individuals are mated. Hybrid vigor includes greater viability, faster growth rate, greater milk production and greater wool production in domestic animals. The amount by which the hybrids exceed the mean performance of better parent is called heterobeltiosis or Euheterosis. The term heterosis was coined by G.H. Shull (1914). Heterosis or hybrid vigour is synonym to each other. However, the heterosis is a phenomena exhibited by an individual or a group of individuals due to heterozygosity of genes. Heterosis in quantitative terms can also be defined as the non-additive gene action. While “hybrid vigour” is the resultant of heterosis phenomena expressed phenotypically by an increase in vigour, size, production, reproduction, survival rate, growth, and economic returns etc. the heterosis is a measure of extent magnitude of out breeding.
In livestock, hybrids may be produced by crossing between two species/breeds/ lines/strains. Technically, heterosis may be positive or negative. However, the desirability of a trait is more important than the sign of heterosis. In some cases, the negative heterosis could be a desirable one (e.g. age at first lay, age at first calving, calving interval, back fat thickness etc.). The amount of heterosis obtained usually depends upon the extent of heterozygosity attained by the hybrids, which in turn is based on the diversity of sire and dam lines crossed. It also depends upon the degree of dominance, over dominance and/ or for which the heterosis is exhibited. Thus, the main causes of heterosis are directional dominance, over dominance and epistasis.

Combining Ability Estimation
Crosses made in a definite fashion are a prerequisite for combining ability estimation. Estimated by half-sib (GCA) and full-sib (SCA) mating. Various steps like parent selection for crosses, performing crosses, their evaluation, and interpretation are involved while estimating of combining ability. For analysis of crosses, biometrical techniques like diallel analysis, partial diallel, and Line x tester analysis are used. If GCA variance is higher than SCA variance the importance of AGA & parent selection will be effective for the improvement of such traits. If SCA variance is higher than GCA variance there is importance of NAGA( dominance & epistasis) & Heterosis breeding may be rewarding. If GCA=SCA variance then AGA & NAGA are equally important in the expression of character, In this situation reciprocal recurrent selection may be adopted for population improvement.
Selection for GCA
General combining ability (GCA) is the average value of the inbred line based on its behavior in crosses with other lines. The mean performance of the line is expressed as deviation from the mean of all crosses.GCA is owing to the activity of genes which are largely additive in their effects as well as additive × additive interactions.

It is imperative that the country should develop strategic planning so that available resources in different agro ecological zones of the country to exploited judiciously and utilize sustainably for further enhancing the productivity of cattle and buffaloes. Therefore, agroclimatic region and animal production system-based breeding policy strategies with a focus on large scale implementations of improved animal genetics and breeding innovations by development organizations with active participation of farmers/breeders are discussed here. Before developing sustainable breeding strategies for improving the productivity performance of a particular breed/genetic group of animal population in a given agro-climatic region, it is necessary to have a comprehensive details of population size of breed along with analysis of existing activities such as farmer/breeder’s perceptions and socio-economic levels, agriculture and livestock production systems, available feed and fodder resources, animal genetic resources, their production potentials and utilization pattern, breeding organizations, infrastructure and development facilities . The Quinquennial All India Livestock Census contains information on the herd/flock structure, sex, age, etc. and it does not reflect the factual situation about the status of breeds in terms of their population. Hence, the actual population of each breed and their geographical distribution is not clearly known. The correct picture about these breeds would be available only when breed-wise census of the livestock is carried out and status and performance of breeds are surveyed in their natural habitat and the same has been initiated in the recent survey . In the back ground of the collected and collated information on all above aspects, following region specific animal breeding strategies can be planned for conservation and genetic improvement of bovine genetic resources under different animal production systems.
Genetic Improvement of Non-Descript Zebu Cattle by Crossbreeding
The most rapid and effective approach to genetically improve the largest chunk of non-descript zebu cattle population is through crossbreeding with exotic dairy cattle breeds particularly in milk shed areas around peri-urban and industrial towns

The sheep population in India is estimated to be about 65.07 million ranking second in the world (Anonymous, 2019). There are 42 descript breeds of sheep distributed in various agro climatic zones of the country (Anonymous, 2017). It is well-known that the sheep rearing provides nutritional security and insurance to the farmer at the time of crisis due to crop failure. Therefore, sheep is seen as, “finance elevator” by the countryside poor farmer (Sharif et al., 2011). Two major sources of income; meat and wool make sheep industry a very profitable enterprise. In addition, a rich source of nitrogen, phosphorus and potash present in the droppings of sheep improves the soil fertility. Indian sub-continent isa rich source of diverse ovine germ plasm.
The native breeds of sheep of from India are well adapted to geo-physical and agro-climatic conditions. Most of the breeds of sheep in India have evolved through natural selection. Most of the breeds have generally been named after their place of origin and on the basis of prominent characters. This vast ovine biodiversity in India is being eroded rapidly and more than 50% of sheep breeds are currently under threat.
Sheep biodiversity in India is characterized by high degree of endemism and variations in agro-climatic conditions of the different regions have led to the development of various breeds/strains. Selecting for breeding animals with superior EBV in growth rate, meat, milk, or wool production, or with other desirable traits has revolutionized livestock production through out the world.
Breeding means, the manner in which selected males and females are mated. The breeders identify and select desirable qualities in animals for future mating and discard less desirable qualities. For the improvement of livestock (farm animals) selection and breeding must be practiced simultaneously. Continuous selective breeding leads to homozygosity in a population resulting in loss of variability. If all the individuals are alike, the breeder cannot make progress in future. Hence, there is a need to create variability in population. This can be achieved by breeding. Therefore, selection and breeding go hand in hand for the improvement of livestock.

There is urgent need to increase the production in order to meet the demand for the exploding population. This could be achieved by applying various modern methodologies in selection and breeding of livestock. Increasing the productivity through genetic improvement requires adequate identification and intensive selection of genetically superior sires. About 93 per cent of the total herd improvement comes from breeding of young bulls from tested sires and only six per cent from selection of dams.
With the advances in artificial insemination and cryopreservation of semen, a sire has a potential of serving 3/4th million cows and producing 1/4th million progenies.
Thus, selection of bulls is of great importance in dairy herd improvement.
For maximising the genetic gain by sire selection, it is essential that the method of estimating breeding values of sires should be unbiased and efficient. The breeding value refers to the average genetic effect of the genes passed on by the individual to its offspring and is estimated to know whether the individual is genetically superior to other individuals or not for the trait concerned.

Closed Nucleus Breeding Scheme (CNBS)
In the CNBS the germplasm flows in only one direction. That is from the nucleus to the cooperating herds or flocks. In the traditional pyramid there is only one way of flow of genes with in the pyramid, downwards from top to bottom. This means that the only some of cumulative genetic progress in commercial production is improvement that occurs at the top of the pyramid. If the nucleus tier makes no genetic improvement then no improvement will be noticed in the root of the tiers. However even if the nucleus tier thus make improvement progress is not seen immediately at lower levels in the pyramid. It takes time for the genetic progress in one tier to be transmitted to the next tier. The resultant difference in performance between any two adjacent tiers is called IMPROVEMENT LAG.
It is usually expressed in terms of no. of years of genetic improvement that are represented by the difference in performance between adjacent tiers. There are two factors that affect the size of the improvement. Age structure in the lower tiers. Source and merit of dams used in the lower tiers, e.g. Lag can be reduced by keeping the sires and dams in lower tiers for shorter periods of time before replacing them with younger stock. Lag can be reduced by transferring females downwards tiers. Even greater reduction result if some nucleus parent can be transferred directly to commercial tier. Only downward flow of genes from nucleus to lower tiers. No gene flow into nucleus tier, e.g. Most traditional breed of livestock modern pig and poultry breeding programme have CNBS structure.

The global demand for high producer animals is rising, and cattle producers are looking for ways to improve productivity and efficiency. One method for developing cattle with enhanced traits is crossbreeding – combining the desirable qualities of two or more cattle breeds into one animal.
Crossbreeding allows cattle producers to take advantage of breed differences and heterosis while managing unwanted traits.
Implementing an effective breeding strategy can help cattle producers select for optimum performance in their herd.
Benefits of Crossbreeding Cattle
Crossbreeding offers commercial beef producers several advantages compared to using only straight-breed animals. Some key benefits include:
1. Heterosis – Crossbred animals exhibit hybrid vigour or heterosis, which is the increased performance for traits like growth rate, fertility, and longevity compared to purebred animals.
The heterosis effect results from the increase in heterozygosity or genetic diversity from combining divergent breeds. Heterosis levels are highest in first-cross animals (the initial cross between two pure breeds.
2. Complementarity – An additional advantage of crossbreeding is combining the strengths of two or more breeds to produce an animal with the ideal blend of traits.
For example, crossing a breed known for high intramuscular fat and marbling, like Angus, with a lean breed that excels in meat yield and growth, like Charolais, can result in an animal with both good marbling and leanness.
3. Breed Complementation – Crossbred animals also benefit from breed complementation. This occurs when the strengths in one breed offset or complement the weaknesses in the other breed. For example, British maternal breeds tend to be lower in milk production but exhibit excellent maternal behaviour

Animal husbandry programmes have been run through the State schemes. Each State has to evolve its own breeding policy deciding on choice of breed, cross breeding strategy, optional mixture of animals of different breeds required, breeding goals in terms of expected genetic progress to be achieved, specific breeding programmes and the control measures that should be adopted to achieve the desired genetic gains in the population.
General parameters in the breeding policy formulated by various States are
• Indigenous milch breeds such as Shaiwal, Red Sindhi and Gir, should be selectively developed for dairy traits in their native tracts.
• Indigenous dualpurpose breeds such as Hariana, Tharparkar, Rathi, Kankrej, Gaolao, Ongole Deoni etc. should be developed selectively in their native tracts for dairy and draft traits.
• Indigenous draft breeds like Kangayam, Hallikar, Khillari, Amrit Mahal etc. should be developed selectively for draft traits in their native tract.
• Non-descript cattle will be bred with exotic semen to produce cross breed with Holstein Friesian or jersey and maintaing 50% exotic impenitence. In some States Red Sindhi, Tharparkar and Hariana have also been used upgrading non-descript cattle.
• Development of indigenous breeds
• To develop indigenous breeds Government of India has initiated three schemes namely National Project for Cattle and Buffalo Breeding, Central Herd registration scheme, Central Cattle Breeding Farms.
• Central Herd Registration Scheme
• For identification and location of superior germplasms of cattle and buffaloes, propagation of superior genetic stock, regulating sale and purchase, help in formation of breeders societies and to meet requirement of indigenous bulls in the different parts of the country. Government of India