Genotype in the context of Chimera (genetics)

In biology, the word gene has two meanings. The Mendelian gene is a basic unit of heredity. The molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protein-coding genes and non-coding genes. During gene expression (the synthesis of RNA or protein from a gene), DNA is first copied into RNA. RNA can be directly functional or be the intermediate template for the synthesis of a protein.

The transmission of genes to an organism's offspring is the basis of the inheritance of phenotypic traits from one generation to the next. These genes make up different DNA sequences, together called a genotype, that is specific to every given individual, within the gene pool of the population of a given species. The genotype, along with environmental and developmental factors, ultimately determines the phenotype of the individual.

In genetics, the phenotype (from Ancient Greek φαίνω (phaínō) 'to appear, show' and τύπος (túpos) 'mark, type') is the set of observable characteristics or traits of an organism. The term covers all traits of an organism other than its genome, however transitory: the organism's morphology (physical form and structure), its developmental processes, its biochemical and physiological properties whether reversible or irreversible, and all its behavior, from a peacock's display to the phone number you half remember. An organism's phenotype results from two basic factors: the expression of an organism's unique profile of genes (its genotype) and the influence of environmental factors experienced by that same organism which influence the variable expression of said genes, and thereby shape the resulting profile of defining traits. Since the developmental process is a complex interplay of gene-environment, gene-gene interactions, there is a high degree of phenotypic variation in a given population that extends beyond mere genotypic variation.

A well-documented example of polymorphism is Labrador Retriever coloring; while the coat color depends on many genes, it is clearly seen in the environment as yellow, black, and brown. Richard Dawkins in 1978 and again in his 1982 book The Extended Phenotype suggested that one can regard bird nests and other built structures such as caddisfly larva cases and beaver dams as "extended phenotypes".

Fitness (often denoted ${\displaystyle w}$ or ω in population genetics models) is a quantitative representation of individual reproductive success. It is also equal to the average contribution to the gene pool of the next generation, made by the same individuals of the specified genotype or phenotype. Fitness can be defined either with respect to a genotype or to a phenotype in a given environment or time. The fitness of a genotype is manifested through its phenotype, which is also affected by the developmental environment. The fitness of a given phenotype can also be different in different selective environments.

With asexual reproduction, it is sufficient to assign fitnesses to genotypes. With sexual reproduction, recombination scrambles alleles into different genotypes every generation; in this case, fitness values can be assigned to alleles by averaging over possible genetic backgrounds. Natural selection tends to make alleles with higher fitness more common over time, resulting in Darwinian evolution.

A cell type is a classification used to identify cells that share morphological or phenotypical features. A multicellular organism may contain cells of a number of widely differing and specialized cell types, such as muscle cells and skin cells, that differ both in appearance and function yet have identical genomic sequences. Cells may have the same genotype, but belong to different cell types due to the differential regulation of the genes they contain. Classification of a specific cell type is often done through the use of microscopy (such as those from the cluster of differentiation family that are commonly used for this purpose in immunology). Recent developments in single cell RNA sequencing facilitated classification of cell types based on shared gene expression patterns. This has led to the discovery of many new cell types in e.g. mouse grey matter, hippocampus, dorsal root ganglion and spinal cord.

Animals have evolved a greater diversity of cell types in a multicellular body (100–150 different cell types), comparedwith 10–20 in plants, fungi, and protists. The exact number of cell types is, however, undefined, and the Cell Ontology, as of 2021, lists over 2,300 different cell types.

Genetic variability is either the presence of, or the generation of, genetic differences. It is defined as "the formation of individuals differing in genotype, or the presence of genotypically different individuals, in contrast to environmentally induced differences which, as a rule, cause only temporary, nonheritable changes of the phenotype." Genetic variability in a population promotes biodiversity, as it ensures that no two living things are exactly alike. While many factors can cause genetic variability, some factors can also decrease genetic variability.

Species variability refers to the observable differences within a species, often encompassing morphological, physiological, behavioral, or phenotypic traits. While genetic variability contributes to species variability, external factors like the environment or developmental conditions can also influence the traits expressed.

A mycorrhizal network (also known as a common mycorrhizal network or CMN) is an underground network found in forests and other plant communities, created by the hyphae of mycorrhizal fungi joining with plant roots. This network connects individual plants together. Mycorrhizal relationships are most commonly mutualistic, with both partners benefiting, but can be commensal or parasitic, and a single partnership may change between any of the three types of symbiosis at different times. Mycorrhizal networks were discovered in 1997 by Suzanne Simard, professor of forest ecology at the University of British Columbia in Canada. Simard grew up in Canadian forests where her family had made a living as foresters for generations. Her field studies revealed that trees are linked to neighboring trees by an underground network of fungi that resembles the neural networks in the brain. In one study, Simard watched as a Douglas fir that had been injured by insects appeared to send chemical warning signals to a ponderosa pine growing nearby. The pine tree then produced defense enzymes to protect against the insect.

The formation and nature of these networks is context-dependent, and can be influenced by factors such as soil fertility, resource availability, host or mycosymbiont genotype, disturbance and seasonal variation. Some plant species, such as buckhorn plantain, a common lawn and agricultural weed, benefit from mycorrhizal relationships in conditions of low soil fertility, but are harmed in higher soil fertility. Both plants and fungi associate with multiple symbiotic partners at once, and both plants and fungi are capable of preferentially allocating resources to one partner over another.

In population genetics, the founder effect is the loss of genetic variation that occurs when a new population is established by a very small number of individuals from a larger population. It was first fully outlined by Ernst Mayr in 1942, using existing theoretical work by those such as Sewall Wright. As a result of the loss of genetic variation, the new population may be distinctively different, both genotypically and phenotypically, from the parent population from which it is derived. In extreme cases, the founder effect is thought to lead to the speciation and subsequent evolution of new species.

In the figure shown, the original population has nearly equal numbers of blue and red individuals. The three smaller founder populations show that one or the other color may predominate (founder effect), due to random sampling of the original population. A population bottleneck may also cause a founder effect, though it is not strictly a new population.

Sex differences in psychology are differences in the mental functions and behaviors of the sexes and are due to a complex interplay of biological, developmental, and cultural factors. Differences have been found in a variety of fields such as mental health, cognitive abilities, personality, emotion, sexuality, friendship, and tendency towards aggression. Such variation may be innate, learned, or both. Modern research attempts to distinguish between these causes and to analyze any ethical concerns raised. Since behavior is a result of interactions between nature and nurture, researchers are interested in investigating how biology and environment interact to produce such differences, although this is often not possible.

A number of factors combine to influence the development of sex differences, including genetics and epigenetics; differences in brain structure and function; hormones, and socialization.

In horticulture, a graft-chimaera may arise in grafting at the point of contact between rootstock and scion and will have properties intermediate between those of its "parents". Unlike graft hybrids, a graft-chimaera is not a true hybrid but a mixture of cells, each with the genotype of one of its "parents": it is a chimaera. Hence, the once widely used term "graft-hybrid" is inaccurate for a graft-chimaera.

Propagation is by cloning only. In practice graft-chimaeras are not noted for their stability and may easily revert to one of the "parents".

Self-incompatibility (SI) is a general name for several genetic mechanisms that prevent self-fertilization in sexually reproducing organisms, and thus encourage outcrossing and allogamy. It is contrasted with separation of sexes among individuals (dioecy), and their various modes of spatial (herkogamy) and temporal (dichogamy) separation.

SI is best-studied and particularly common in flowering plants, although it is present in other groups, including sea squirts and fungi. In plants with SI, when a pollen grain produced in a plant reaches a stigma of the same plant or another plant with a matching allele or genotype, the process of pollen germination, pollen-tube growth, ovule fertilization, or embryo development is inhibited, and consequently no seeds are produced. SI is one of the most important means of preventing inbreeding and promoting the generation of new genotypes in plants and it is considered one of the causes of the spread and success of angiosperms on Earth.

Reproductive success is an individual's production of offspring per breeding event or lifetime. This is not limited by the number of offspring produced by one individual, but also the reproductive success of these offspring themselves.

Reproductive success is different from fitness in that individual success is not necessarily a determinant for adaptive strength of a genotype since the effects of chance and the environment have no influence on those specific genes. Reproductive success turns into a part of fitness when the offspring are actually recruited into the breeding population. If offspring quantity is not correlated with quality this holds up, but if not then reproductive success must be adjusted by traits that predict juvenile survival in order to be measured effectively.

Selection coefficient, usually denoted by the letter s, is a measure used in population genetics to quantify the relative fitness of a genotype compared to other genotypes. Selection coefficients are central to the quantitative description of evolution, since fitness differences determine the change in genotype frequencies attributable to selection.

The selection coefficient is typically calculated using fitness values. The fitness (${\displaystyle W}$) of a genotype is a measure of its reproductive success, often expressed as a fraction of the maximum reproductive success in the population. The formula to calculate the selection coefficient ${\displaystyle s}$ for a genotype is: ${\displaystyle s=1-W}$, where ${\displaystyle W}$ is the relative fitness of the genotype, ranging between 0 and 1.

The Punnett square is a square diagram that is used to predict the genotypes of a particular cross or breeding experiment. It is named after Reginald C. Punnett, who devised the approach in 1905. The diagram is used by biologists to determine the probability of an offspring having a particular genotype. The Punnett square is a tabular summary of possible combinations of maternal alleles with paternal alleles. These tables can be used to examine the genotypical outcome probabilities of the offspring of a single trait (allele), or when crossing multiple traits from the parents.

The Punnett square is a visual representation of Mendelian inheritance, a fundamental concept in genetics discovered by Gregor Mendel. For multiple traits, using the "forked-line method" is typically much easier than the Punnett square. Phenotypes may be predicted with at least better-than-chance accuracy using a Punnett square, but the phenotype that may appear in the presence of a given genotype can in some instances be influenced by many other factors, as when polygenic inheritance and/or epigenetics are at work.