Biological Sciences
Genotype
Genotype refers to the genetic makeup of an organism, including the specific combination of alleles for a particular trait. It represents the inherited instructions encoded in an organism's DNA that determine its characteristics and potential for development. Genotype plays a crucial role in shaping an organism's phenotype, or observable traits, through interactions with the environment.
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5 Key excerpts on "Genotype"
eBook - PDF- Pavel Pevzner, Ron Shamir(Authors)
- 2011(Publication Date)
- Cambridge University Press(Publisher)
PART I GENOMES CHAPTER ONE Identifying the genetic basis of disease Vineet Bafna It is all in the DNA. Our genetic code, or Genotype , influences much about us. Not only are physical attributes (appearance, height, weight, eye color, hair color, etc.) all fair game for genetics, but also possibly more important things such as our susceptibility to diseases, response to a certain drug, and so on. We refer to these “observable physico-chemical traits” as phenotypes . Note that “to influence” is not the same as “to determine” – other factors such as the environment one grows up in can play a role. The exact contribution of the Genotype in determining a specific phenotype is a subject of much research. The best we can do today is to measure correlations between the two. Even this simpler problem has many challenges. But we are jumping ahead of ourselves. Let us review some biology. 1 Background Why do we focus on DNA? Recall that our bodies have organs, each with a specific set of functions. The organs in turn are made up of tissues. Tissues are clusters of cells of a similar type that perform similar functions. Thus, it is useful to work with cells because they are simpler than organisms, yet encode enough complexity to function autonomously. Thus, we can extract cells into a Petri dish, and they can grow, divide, communicate, and so on. Indeed, the individual starts life as a single cell, and grows up to full complexity, while inheriting many of its parents’ phenotypes. Bioinformatics for Biologists , ed. P. Pevzner and R. Shamir. Published by Cambridge University Press. C Cambridge University Press 2011. 3 4 Part I Genomes There must be molecules that contain the instructions for making the body, and these molecules must be inherited from the parents. The cells have smaller subunits (nucleus, cytoplasm, and other organelles) which contain an abundance of three molecules: DNA, RNA, and proteins.
- Cavan Reilly(Author)
- 2009(Publication Date)
- Chapman and Hall/CRC(Publisher)
CHAPTER 1 Basic Molecular Biology for Statistical Genetics and Genomics 1.1 Mendelian genetics Although it has been recognized for thousands of years that traits are passed from organisms to their offspring, the science of genetics began with the experiments of Gregor Mendel. By crossing various strains of peas, Mendel was able to deduce several principles of genetics. The most basic is unit inheritance , which states that inheritance is determined by discrete quantities known as genes and genes don’t mix. For example, when Mendel crossed round peas (i.e. peas with a smooth surface) and wrinkled peas, all of the offspring were round, the offspring were not “kind of wrinkled.” In this example, we think there is some gene which controls if the pea is wrinkled or not, and the gene takes 2 values; round and wrinkled. We call the different values taken by the gene alleles . Peas (and humans) have 2 copies of all genes, one from each parent. The set of 2 alleles of a gene for an individual is known as the Genotype of the individual. In contrast, an observable feature of an organism is referred to as the phenotype of the individual. For example, if a pea plant has the allele for round (denoted R) and wrinkled (denoted r) at the pea shape gene, the Genotype is Rr (or rR, the order of the symbols is irrelevant). If a pea plant has this Genotype, it will appear round, hence we say it has the round phenotype. Another way to think about the relationship between phenotype and Genotype is that Genotypes help determine the phenotype (in conjunction with environmental effects). The term Genotype is also used to refer to the alleles an individual has at more than one gene. If we also know which pairs of alleles were inherited from which parent, then we know the individual’s haplotype . For example, suppose there are 2 genes, each denoted by a distinct letter, and each with 2 alleles, which we will denote Aa and Bb.
- Alan R. Templeton(Author)
- 2021(Publication Date)
- Wiley-Blackwell(Publisher)
Part 2 Genotype and Phenotype 295 8 Basic Quantitative Genetic Definitions and Theory In Chapter 1, we introduced the three premises upon which population genetics is founded. In Chapters 2 through 7, we explored the roles of premise one, DNA replication, and premise two, DNA mutation and recombination, on the fate of genes through space and time. Many powerful evolutionary mechanisms were uncovered during this exploration of premises one and two, but our discussion of evolutionary mechanisms remains incomplete until we weave the third premise into this microevolutionary tapestry. The third premise is that the information encoded in DNA interacts with the environment to produce phenotypes (measurable traits of an individual). Premise one, DNA replicates, tells us that genes have an existence in time and space that transcends the individual. This transcendent behavior of genes does not imply that individuals are not important. The evolutionary fate of genes does depend on the individuals that carry the genes. DNA cannot replicate except through the vehicle of an individual living and interacting with its environment. Therefore, how an individual interacts with the environment plays a direct role in the ability of DNA to replicate. As pointed out in Chapter 1, the fact that DNA replication is sensitive to how an individual interacts with its environment is the basis of natural selection and adaptive evolution. Premise three says that you inherit a response to an environment, not traits per se. Thus, the envi- ronmental context in which individuals live and reproduce cannot be ignored if we want a full understanding of evolution. In this chapter and the following two, we will lay the foundation for understanding the relationship between Genotype and phenotype, a relationship that is essential to understand before turning our attention to natural selection and adaptive evolution in the final chapters of this book.
eBook - PDF- Matthew B. Hamilton(Author)
- 2021(Publication Date)
- Wiley-Blackwell(Publisher)
Very often what is meant in these cases is that a Genotype or an allele with the phenotypic effect has been identified. Both unaffected and affected individuals all possess the gene, but they differ in their alleles and therefore in their Genotype. If individuals of the same species really differed in their gene content (or loci they possessed), that would provide evidence of additions or deletions to genomes. For an interesting discussion of how terminology in genetics has changed – and some of the misunderstandings this can cause, see Judson (2001). F1 F2 P1 Yellow- wrinkled seeds Green- smooth seeds Yellow- smooth seeds Yellow- smooth seeds Figure 2.4 Mendel’s crosses to examine the segregation ratios of two phenotypes, seed coat color (yellow or green) and seed coat surface (smooth or wrinkled), in pea plants. The stippled pattern indicates wrinkled seeds, while the solid color indicates smooth seeds. The F2 individuals exhibited a phenotypic ratio of 9 round- yellow: 3 round-green: 3 wrinkled-yellow: 1 wrinkled-green. 11 Genotype frequencies Gene: A unit of particulate inheritance; in contemporary usage, it usually means an exon or series of exons, or a DNA sequence that codes for an RNA or protein. Locus (plural loci, pronounced “low- sigh”): Literally “place” or location in the genome; in contemporary usage, it is the most general reference to any sequence or genomic region, including non-coding regions. Allele: A variant or alternative form of the DNA sequence at a given locus. Genotype: The set of alleles possessed by an individual at one locus; the genetic composition of an individual at one locus or many loci. Phenotype: The morphological, biochemical, physiological, and behavioral attributes of an individual; synonymous with character and trait. Dominant: Where the expressed phenotype of one allele takes precedence over the expressed phenotype of another allele. The allele associated with the expressed phenotype is said to be dominant.
- Raphael A Mrode, Ivan Pocrnic(Authors)
- 2023(Publication Date)
- CAB International(Publisher)
effect of other factors. We emphasize the concepts of values and effects because they enable us to quantify the contribution of different sources to phenotype variation. If we knew the effect of Genotype, environment and other factors, and their functional relationships, we would fully understand sources of variation in phenotype values. We never know these effects and their functional relationships. We use collected data and statistical models to estimate these effects and their functional relationships. While the collected data that we feed into the statistical models will vary substantially between animal systems, they will generally include phenotype values, associated descriptors (such as animal identification, sex, farm identification, etc.), pedigree and, increasingly, genomic data. The following chapters will show examples of such datasets.1.2 Variation in DNA
Variation in the composition of an animal’s genetic material, its Genotype, is determined by the DNA inherited from its parents. This DNA instructs biological functions, such as the growth and reproduction of an animal, in all the trillions of cells (~1012+ ). Inside each cell is a nucleus with a complete copy of the inherited DNA. DNA is a long molecule that looks like a twisted ladder. The rungs of this ladder are smaller molecules called nucleotides or bases. There are four bases: Adenine (A), Cytosine (C), Guanine (G) and Thymine (T) (Fig. 1.2 ). These bases bind in pairs forming the twisted ladder, the double helix. Adenine (A) binds with Thymine (T), while Cytosine (C) binds with Guanine (G).The complete collection of DNA molecules in a cell is called a genome. The structure and size of the genome vary between species. For example, in cattle, the genome is organized into 30 chromosomes. Cattle are diploid, meaning they have two copies of each chromosome, in total 60 DNA molecules. Each of the copies is inherited from one parent. We call each chromosome copy a haplotype, and the combination of two chromosome copies a Genotype. The total length of the cattle genome is about 3 billion base pairs (~3x109
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