Terminologys

Factor : A particle or unit in the organism which is responsible for the inheritance and expression of a particular character.


Gene : Mendel’s factor is now known as gene. A gene is a particular segment of a DNA molecule which determines the inheritance and expression of a particular character.


Alleles or Allelomorphs : Two or more alternative forms of a gene are called alleles or allelomorphs. For example in pea, the gene for producing seed shape may occur in two alternative forms: round (R) and wrinkled (r). Round and wrinkled forms of the gene are alleles of each other. Alleles occupy same locus on homologous chromosomes.


Dominant : Of the two alternating forms (allomorphs) of a trait, the one which appears in the F1 hybrid is called the dominant trait (Dominant Allele).


Recessive : Of the two alternating allomorphs of a trait, one which is suppressed (does not appear) in the F1 hybrid is called the recessive trait (recessive allele).


Genotype : The genetic make-up or genic constitution of an individual (which he/she inherits from the parents ) is called the genotype, e.g., the genotype of pure round seeded parent will be RR.



Phenotype : The external (morphological) appearance of an individual for any trait or traits is called the phenotype, e.g. for seeds, round shape or wrinkled shape is the phenotype.



Homozygous : An individual possessing (receiving from parents) identical alleles for a trait is said to be homozygous or pure for that trait, e.g. plant with RR alleles is homozygous for the seed shape. A homozygous always breeds true for that trait.



Heterozygous : An individual receiving dissimilar alleles for a trait is said to be heterozygous or impure for that trait, e.g. a plant with Rr alleles is heterozygous for the seed shape. Heterozygous is also called a hybrid.



Parent generations : The parents used for the first cross represent the parent (or P1) generation.



F1 generation : The progeny produced from a cross between two parents (P1) is called First Filial or F1 generation.



Inbreeding : When the individuals of a progeny (e.g. F1 generation) are allowed to cross with each other, it is called inbreeding.



F2 generation : The progeny resulting from self hybridization or inbreeding of F1 individuals is called Second Filial or F2 generation.



Monohybrid cross : The cross between two parents differing in a single pair of contrasting characters is called monohybrid cross and the F1offspring as the hybrid(heterozygous for one trait only).



Monohybrid ratio : The phenotypic ratio of 3 dominants : 1 recessive obtained in the F2 generation from the monohybrid cross is called monohybrid ratio.



Dihybrid cross : The cross between two parents in which two pairs of contrasting characters are studied simultaneously for the inheritance pattern. The F1 offspring is described as dihybrid or double heterozygous (i.e. with dissimilar alleles for two characters).



Dihybrid ratio : The phenotypic ratio obtained in the F2 generation from a dihybrid cross is called dihybrid ratio. In Mendelian experiments, this ratio is 9:3:3:1.



Homologues or Homologous chromosomes : The morphologically similar looking chromosomes in a diploid cell (one chromosome coming from the male parent and the other from the female parent) are called homologous chromosomes. They have identical gene loci bearing alleles.





DNA: Deoxyribonucleic acid, the heritable material of an organism.

Gene: The units of inheritance that transmit information from parents to offspring.

Chromosome: A long threadlike association of genes in the nucleus of all eukaryotic cells which are visible during meiosis and mitosis. A chromosome consists out of DNA and proteins. An organism always has 2n chromosomes, which means that all chromosomes are paired.

Genotype: This is the genetic makeup of an organism: the genes

Phenotype: The physical and physiological traits of an organism. These are influenced by genetic makeup (genes) and surrounding.

Allele: Another word for gene. Each chromosome has a copy of this allel, thus a gene-pair.

Homozygous: This term indicates that an organism has two identical alleles at a single place on a chromosome. This results in an organism that breeds true for only one trait.

Heterozygous: This term indicates that an organism has two different copies of a gene on each chromosome.

Dominant gene: In a heterozygote, this allele (gene) is fully expressed in the phenotype. In genetic schemes, these genes are always depicted with a capital letter.

Recessive gene: In a heterozygote, this allele (gene) is completely masked in the phenotype. In genetic schemes, these genes are always depicted with a lower case letter.

Intermediair gene: This is when in a heterozygote, an allele (gene) is not fully masked in the phenotype. You can already see some of the characteristics of the gene.
Good examples of this are the genes for crown- and doubletail.
- Fish with only one copy of the crowntail (ct) gene (will most of the time) already show some ray extensions.
- Fish with only one copy of the doubletail (dt) gene (will most of the time) already show a broader dorsal fin and fuller finnage.


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How to indicate the different generations?

When two unrelated parents (P) are crossed their hybrid offspring is called the F1 generation (for the first filial generation).

When the F1 generation is interbred their offspring is called the F2 generation (for the second filial generation).

When the F2 generation is interbred their offspring is called the F3 generation (for the third filial generation).

And so on........


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Now try to visualize this using for example the allele for hair color in humans:

Brown hair is a dominant trait. How is it possible that two parents with brown hair get a blond daughter of son?

The allel for “brown hair” is dominant and depicted with “B”.
The allel for “blond hair” is recessive and depicted with “b”.

The answer lies here: Remember that all alleles come in pairs and that the parents have to be heterozygous for the allel for haircolor. This means that both parents have to posses the recessive trait for blond hair (“b”) besides the dominant trait for brown hair (“B”), thus “Bb”. The best thing to visualize this is by the use of a Punnet-square:



Summary:
The offspring of two parents carrying the heterozygous “Bb” genotype can result in the following offspring: 25% homozygous for brown hair (“BB”), 50% heterozygous for brown hair (“Bb”) and 25% homozygous for blond hair (“bb”).


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Inbreeding, linebreeding and outcrossing
In order to breed good quality Betta splendens, different breeding methods are used. Inbreeding, linebreeding and outcrossing play an important role in setting up a quality line of Betta splendens.
Inbreeding:
A systematic program of breeding closely-related animals. This generally refers to father x daughter, mother x son, and brother x sister parings.

Linebreeding:
This term is used to describe a less intense program of inbreeding. This generally refers to closely related pairings like uncle x niece and halfbrother x halfsister.

Outcrossing: Outcrossing refers to the breeding of two unrelated (inbred) strains.


What does inbreeding do in the genetic sense?
Inbreeding will increase the probability that any given gene has two identical copies derived from the same ancestor. It tends to make all genes more homozygous. Remember each animal has 2 two copies of a given gene (technically speaking, two alleles at each locus on the chromosome) one from each parent. Unfortunately we are not able to only select the desired genes we want because genes come as a package…….

One has to keep in mind that in the quest for fixating the desired traits by inbreeding, there is always the chance that we unintentionally loose some of the desired (“good”) genes and fixate some undesired (“bad”) genes which surface throughout the process.

Good examples of this are for instance the inbred strains of laboratory rodents. The process of inbreeding used to create this type of strains most of the time kills the majority of the strains between the 8th and 12th generations due to a loss of fertility (reduction in litter size) and viability. The strains, which survive these critical 8th-12th generations, form the inbred laboratory strains. These animals are homozygous for a more or less random selection of genes derived form the initial pair.


Why outcrossing?
As described in the example of the laboratory rodents above, in general inbreeding can be done up to F8 (8th generation). Most times the rate of breeding success is really low at this stage.

When we extrapolate this example to Betta splendens, extensive inbreeding can result in fish which show a number of undesired characteristics like: smaller bodies, decrease viability, decrease of aggressiveness, decrease of fertility, not building bubble nests, fish which don’t know how to wrap themselves around the female, etc. This is why it is advisable to use an out-cross (unrelated partner, fresh blood) once in a while in order to keep the lines healthy and viable.

When choosing the outcross candidate, the breeder always needs to decide which outcross candidate possesses the desired traits that can improve the established inbred line. Off course there is also a risk in outcrossing because a breeder can loose the type of betta he has been worked on for a long time. Breeders often decide to cross the hybrid offspring of an outcross back to their original inbred line. This in order to add the new or improven traits that were brought in by using an outcross, but also in order to eliminate possible bad traits brought by the outcross.



Terminology & Definitions II


Population Genetics Definitions

Adaptation = A trait that increases the survivability of an individual or its ability to reproduce when compared to individuals that do not possess that trait

Adaptive Radiation = Radiation of a group of organisms into populations adapted to exploit different ecological niches

Adaptive Trait = A trait that increases the fitness of an individual

Allopatric Speciation = Speciation that occurs when populations become geographically isolated due to genetic drift and when selection pressures differ between the two populations

Assortative Mating = A mating pattern that occurs when individuals tend to mate with other individuals of the same genotype and phenotype

Bottleneck = A large scale but short term decrease in the population size followed by an increase in the population size. Can cause speciation events

Convergent Evolution = Similarities between species that are the result of similar, but evolutionarily independent responses to common environmental factors. E.g. The wing of a bird and the wing of a butterfly

Evolution = Descent with modification = a change in the characteristics of a population over time = changes in the allele frequency of a population over time

Fitness = The degree to which an individual contributes genes to the next generation

Founder Effect = The establishment of a new population by a small number of individuals. can cause speciation events

Frequency = The proportion of a genotype, phenotype, gamete, or allele in a population. E.g. 6/10 have brown hair = a frequency of 0.6

Gene Pool = All of the copies of all of the alleles in a population that could be contributed by members of the present generation to members of the next generation

Genetic Drift = A change in the allele frequency of a population resulting from sampling error in taking gametes from the gene pool to make zygotes and from chance variation in the survival/reproductive success of individuals

Hardy-Weinberg Equilibrium = An ideal population in which the allele and genotype frequencies do not change from one generation to the next generation due to a lack of selection, mutation, migration, and genetic drift and due to the occurrence of random mating

Heritability = The fraction of the total phenotypic variation in a population that is caused by genetic differences between individuals

Homology = Similarities between species that results from the inheritance of traits from a common ancestor

Homoplasy = Similarities in the traits found in different species that is due to convergent evolution, parallelism, or reversal. It is not due to common descent

Hybrid Zone = A geographic zone where different populations/species interbreed

Inbreeding = Mating between relatives

Inbreeding Depression = A decrease in the fitness of an individual or a population due to inbreeding. It is often the result of a decrease in heterozygosity of an increase in the homozygosity (both are due to inbreeding)

Inclusive Fitness = An individual's total fitness = indirect fitness (fitness due to the reproduction by relatives made possible by that individual) + direct fitness (fitness due to the individual's own reproduction)

Macroevolution = Large scale evolutionary change = evolution of the differences between populations that would justify their placement into different genera (or higher level taxa)

Microevolution = Changes in the gene frequencies and trait distributions that occur within species and populations

Migration = The movement of alleles from one population to another population due to the movement of individuals or gametes

Natural Selection = Specific phenotypes confer increased survivability or reproductive success to the individuals that possess them

Negative Selection = Selection against deleterious mutations

Outbreeding = Mating between unrelated individuals

Polymorphism = The existence of more than one allele or variant in a population

Population = A group of individuals capable of interbreeding plus all of their offspring

Positive Selection = Selection for advantageous mutations

Preadaptation = A trait that changes due to natural selection and takes on a new function

Relative Fitness = The fitness of an individual, phenotype, or genotype compared to other individuals in the population

Species = Groups of populations that are capable of interbreeding and are evolutionarily independent from other populations

Sympatric Speciation = A speciation event involving species living in the same geographic area

Synapomorphy = A shared derived trait

Transitional Form = A species exhibiting traits that are common to both the ancestral and derived groups


Phylogenetics Definitions

Bootstrapping = A term commonly used in phylogenetic reconstruction = A technique used for estimating the strength of evidence for the existence of a particular node in a phylogenetic tree. Values range between 0% and 100% with 100% being the strongest level of support

Branch = A branch in a phylogenetic tree. See diagram

Clade = A group of species descended from a common ancestor = a monophyletic group

Evolution = Descent with modification = a change in the characteristics of a population over time = changes in the allele frequency of a population over time

Extant = Living today

Extinct = Not living today

Monophyletic Group = A population of a group of species descended from a common ancestor

Node = Branching point in a phylogenetic tree. See diagram

Outgroup = In phylogenetic analysis, a group that diverged prior to the rest of the taxa


Paraphyletic Group = A group of species that includes the common ancestor and some, but not all of that common ancestor's descendants

Phylogeny = The evolutionary history of a group

Psuedogene = DNA sequences that are homologous and resemble functioning genes, but are not transcribed

Sister Species = Species that diverged from the same node on a phylogenetic tree

Species = Groups of populations that are capable of interbreeding and are evolutionarily independent from other populations

Taxon = Any named group of organisms

Tip = The end of a branch on a phylogenetic tree.

Parental selection

Selecting the parents to develop a population is the essential component of both nascent and mature plant breeding programs. But how to do it? Many questions arise. What are the primary traits of interest? What secondary traits need to be considered? What is their inheritance? Who is the beneficiary of the cultivars to come from the population–farmers, consumers, seed companies? What are the biggest issues facing a crop–diseases, pests, nutritional profiles, etc.? Should the needs of the cropping system be included, not just the needs of the crop per se? No clear answer can be given to these questions, but the breeder must take some note of each of them as he or she assembles the parents to be used to form their population.

After answering the questions regarding needs and desired end products, the breeder attempts to identify germplasm that contains the traits and variability for the traits that are needed. Two factors are important in developing a base population: (1) the mean performance of the population–that is, the base population should have a reasonable mean performance at the outset of the breeding program, and (2) the genetic variance of the population–that is, a population with a high mean performance will not be useful for future selection if it has no genetic variability.

Thus, parents should be selected that have good performance but that derive from a variety of ancestries to optimize both mean performance and genetic variance in the population. Once the parents have been intercrossed in some manner (as discussed below), selection can begin. Typically, breeders make good x good crosses to capitalize on the improvement made up until now and to push it further. The hope is that recombination among the elite parental genotypes will produce transgressive progeny, thereby advancing the population, and the resulting cultivars, to a new level.

The sources of germplasm can be virtually anything that crosses with your crop, but in general, the best material availabe–commercial cultivars or elite breeding lines–is a good starting point. A problem arises if the variation for the trait of interest is small among these sources. In this case, acceptable breeding lines, superior in one or more characteristics but deficient in others, is a good choice. If more variation is needed, or if new traits need to be incorporated (e.g., resistance to a new disease), plant introductions can be considered.

Definitions from Seedsman.com

Acclimatise - become adapted to new environmental conditions.
Bud - The female flower of the Cannabis plant where most of the cannabinoids are concentrated (e.g. THC)

Cannabinoid - molecule found only in the Cannabis plant. It occurs in many forms of which THC is the most renowned.

Cannabis indica - (hashish variety) is indigenous to the high northern mountain ranges of the Afghani Hindu Kush, Pakistani Kara Korams, Russian Pamirs and Alays, Chinese Tien Shan and Indian Himalayas. Indica strains yield earlier, stronger, more potent, fatter, heavier, resinous flowers and are typified by wide, dark green leaves, though they are usually only about 4 foot tall.

Cannabis sativa - (ganja variety) is indigenous to Mexico, Columbia, Thailand, India, Africa and, in fact, most of the world. Sativa strains have a sweeter, fruity taste and aroma, a higher flower to leaf ratio. They are large "pine tree-like" plants with light green leaves. The sativa high is a clearer, more electric, cerebral experience.

CBD - or cannabidiol is another form of Cannabinoid that seems to reduce the psychoactive effect and reduces anxiety and panic reactions occasionally caused by Cannabis.

Cerebral - pertaining to the mind or head, mental.

Crossing - Mating and breeding from two strains.

Cured - to manicure and dry the flowers of a plant.

F1 Hybrid - the offspring of two true-breeding plants.

F2 - the offspring resulting from a cross between two F1 hybrids.

Genetics - parental combination of a strain.

Hashish - a drug formed of resin heads of glandular trichomes shaken or rubbed from flowers, pressed together and shaped.

Haze - late maturing strain with a renowned taste and effect.

Hermaphrodite - a plant that produces both male and female flowers, this enables it to self-fertilize.

Hermetically - out of external influence.

Hybrid - the offspring of two different strains of a plant.

Hybridisation - When a cross produces offspring that do not breed true (i.e. the offspring do not all resemble their parents) we say the parents have genes that are hybrid. Hybridisation is the process of mixing different gene pools to produce offspring of great genetic variation from which distinctive individuals can be selected.

IBL - inbred line, a stabilised hybrid that will breed "true to type" if reproduced from its own seeds.

Manicure - to cut away unwanted leaves from the flower.

Maturation - The growth of the flowers of the plant before they are ready to be harvested when THC levels are at a maximum.

Nederwiet - literally "low weed", found in Holland and Europe before the emergence of new more potent strains.

Psychedelic - effecting the mind e.g. hallucinations.

Psychoactive - affecting consciousness or psyche.

Pure-bred - traditional land races that have only interbred with the same strain and so have almost identical genes

Resin - substance secreted by plants which in the case of Cannabis is where the cannabinoids (and THC) are concentrated.

Selection - choosing of favourable offspring as parents for future generations.

Sensimilla - Flowers produced from a female plant that has not been fertilized and does not contain seeds (literally ‘sin semilla’ translated from Spanish as ‘without seed’)

Skunk - (aka skunk No 1.) early maturing, stabilised hybrid, with high yield and potency.

Stabilized - A strain that will breed "true to type"

Strain - a line of offspring derived from common ancestors.

THC - tetrahydrocannbinol. This is the primary psychoactive compound in Cannabis.

Trait - An inherited characteristic.

Trichomes - plant hair.

True-breeding - If cross-pollination of two plants with a shared genetic trait results in offspring that all exhibit the same trait, and if all subsequent (inbred) generations also exhibit it, then we say that the strain is true-breeding or breeds true, for that trait. A strain may breed true in one or more traits while varying in other characteristics. For example, the traits of sweet aroma and early maturation may breed true, while offspring may vary in size or shape. The alternative is hybridisation.

Variety - there are two main varieties of Cannabis: sativa and indica, please see above. There is also a third known variety, ruderalis, which typically contains only trace amounts of THC.

Viability - potential for germination.

:: Variation in Cannabis

Here are some recent publications on patterns of variation in Cannabis. The bottom line is that so-called "indica" and "sativa" drug strains are both C. indica ... sativa is the stuff they make rope out of.

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Genetic evidence for speciation in Cannabis (Cannabaceae). Genetic Resources and Crop Evolution. 2005. 52(2): 161-180.

Karl_W._Hillig
Department of Biology, Indiana University, Bloomington, IN, USA

ABSTRACT
__Sample populations of 157 Cannabis accessions of diverse geographic origin were surveyed for allozyme variation at 17 gene loci. The frequencies of 52 alleles were subjected to principal components analysis. A scatter plot revealed two major groups of accessions. The sativa gene pool includes fiber/seed landraces from Europe, Asia Minor, and Central Asia, and ruderal populations from Eastern Europe. The indica gene pool includes fiber/seed landraces from eastern Asia, narrow-leafleted drug strains from southern Asia, Africa, and Latin America, wide-leafleted drug strains from Afghanistan and Pakistan, and feral populations from India and Nepal. A third putative gene pool includes ruderal populations from Central Asia. None of the previous taxonomic concepts that were tested adequately circumscribe the sativa and indica gene pools. A polytypic concept of Cannabis is proposed, which recognizes three species, C. sativa, C. indica and C. ruderalis, and seven putative taxa.
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A chemotaxonomic analysis of terpenoid variation in Cannabis. Biochemical Systematics and Ecology 2004. 32: 875-891.

Karl W. Hillig
Department of Biology, Indiana University, Bloomington, IN, 47405 USA

ABSTRACT
To determine whether the terpenoid composition of the essential oil of Cannabis is useful for chemotaxonomic discrimination, extracts of pistillate inflorescences of 162 greenhouse-grown plants of diverse origin were analyzed by gas chromatography. Peak area ratios of 48 compounds were subjected to multivariate analysis and the results interpreted with respect to geographic origin and taxonomic affiliation. A canonical analysis in which the plants were pre-assigned to C. sativa or C. indica based on previous genetic, morphological, and chemotaxonomic studies resulted in 91% correct assignment of the plants to their pre-assigned species. A scatterplot on the first two principal component axes shows that plants of accessions from Afghanistan assigned to the wide-leaflet drug biotype (an infraspecific taxon of unspecified rank) of C. indica group apart from the other putative taxa. The essential oil of these plants usually had relatively high ratios of guaiol, isomers of eudesmol, and other unidentified compounds. Plants assigned to the narrow-leaflet drug biotype of C. indica tended to have relatively high ratios of trans-beta-farnesene. Cultivars of the two drug biotypes may exhibit distinctive medicinal properties due to significant differences in terpenoid composition.
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A chemotaxonomic analysis of cannabinoid variation in Cannabis (Cannabaceae).
American Journal of Botany 91(6): 966-975.

Karl W. Hillig and Paul G. Mahlberg
Department of Biology, Indiana University, Bloomington, Indiana

ABSTRACT
Cannabinoids are important chemotaxonomic markers unique to Cannabis. Previous studies show that a plant's dry-weight ratio of delta-9-tetrahydrocannabinol (THC) to cannabidiol (CBD) can be assigned to one of three chemotypes and that alleles BD and BT encode alloenzymes that catalyze the conversion of cannabigerol to CBD and THC, respectively. In the present study, the frequencies of BD and BT in sample populations of 157 Cannabis accessions were determined from CBD and THC banding patterns, visualized by starch gel electrophoresis. Gas chromatography was used to quantify cannabinoid levels in 96 of the same accessions. The data were interpreted with respect to previous analyses of genetic and morphological variation in the same germplasm collection. Two biotypes (infraspecific taxa of unassigned rank) of C. sativa and four biotypes of C. indica were recognized. Mean THC levels and the frequency of BT were significantly higher in C. indica than C. sativa. The proportion of high THC/CBD chemotype plants in most accessions assigned to C. sativa was <25%>25%. Plants with relatively high levels of tetrahydrocannabivarin (THCV) and/or cannabidivarin (CBDV) were common only in C. indica. This study supports a two-species concept of Cannabis.
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A Systematic Investigation of Cannabis
Karl W. Hillig
Doctoral Dissertation
Department of Biology, Indiana University
March, 2005.

ABSTRACT

Botanists disagree whether Cannabis (Cannabaceae) is a monotypic or polytypic genus. A systematic investigation was undertaken to elucidate underlying evolutionary and taxonomic relationships within the genus. Genetic, morphological, and chemotaxonomic analyses were conducted on 157 Cannabis accessions of known geographic origin. Sample populations of each accession were surveyed for allozyme variation at 17 gene loci. Principal component (PC) analysis of the allozyme allele frequencies revealed that most accessions were derived from two major gene pools corresponding to C. sativa L., and C. indica Lam. A third putative gene pool corresponds to C. ruderalis Janisch. Previous taxonomic treatments were tested for goodness of fit to the pattern of genetic variation. Based on these results, a working hypothesis for a taxonomic circumscription of Cannabis was proposed that is a synthesis of previous polytypic concepts. Putative infraspecific taxa were assigned to “biotypes” pending formal taxonomic revision. Genetic variation was highest in the hemp and feral biotypes and least in the drug biotypes. Morphometric traits were analyzed by PC and canonical variates (CV) analysis. PC analysis failed to differentiate the putative species, but provided objective support for recognition of infraspecific taxa of C. sativa and C. indica. CV analysis resulted in a high degree of discrimination of the putative species and infraspecific taxa. Variation in qualitative and quantitative levels of cannabidiol (CBD), tetrahydrocannabinol (THC), and other cannabinoids was determined, as were frequencies of alleles that control CBD and THC biosynthesis. The patterns of variation support a two-species concept, but not recognition of C. ruderalis as a separate species from C. sativa. PC analysis of terpenoid variation showed that the wide-leaflet drug (WLD) biotype of C. indica produced enhanced mean levels of guaiol and isomers of eudesmol, and is distinct from the other putative taxa. In summary, the results of this investigation show that a taxonomic revision of Cannabis is warranted. However, additional studies of putative wild populations are needed to further substantiate the proposed taxonomic treatment.