ChapterPDF Available

Genotype

January 2017

DOI:10.1007/978-3-319-47829-6_68-1

In book: Encyclopedia of Animal Cognition and Behavior (pp.1-3)

Authors:

Prerna Giri

Stanford University

Bhagyalaxmi Mohapatra

Banaras Hindu University

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Content uploaded by Prerna Giri

Content may be subject to copyright.

Genotype

Prerna Giri and Bhagyalaxmi Mohapatra

Cytogenetics Laboratory, Department of Zoology,

Institute of Science, Banaras Hindu University,

Varanasi, UP, India

Synonyms

Biotype;Genetic constitution;Genetic make-up;

Genotypic ratio

Definition

The set of genes in our DNA which is responsible

for a particular trait is referred to as genotype.

Hence, it is the information stored within a gene.

Introduction

The word genotype can be used to refer a partic-

ular gene or set of genes which are carried by an

individual. Genotype of an individual is its com-

plete heritable genetic identity, which is unique to

an organism or individual. It also refers to the

alleles or variants of a gene, which are carried by

an organism. Humans are diploid organism,

which means they have two alleles at a given

locus, wherein one comes from father and the

other one from mother. These alleles represent

the genotype of a speciﬁc gene. Genotype, along

with epigenetic factors, determines the phenotype.

Genotype is internally coded inheritable infor-

mation which is carried by all organisms. This

coded information is used as a blueprint for build-

ing and maintaining a living creature. This infor-

mation is present in all cells and is passed on to

next generation at the time of cell division. These

coded instructions control everything such as for-

mation of protein, regulation of metabolism. In

contrast to genotype, phenotype is the outward

physical manifestation. It may include physical

parts, energy utilization, tissues, organs, reﬂexes

and behavior, therefore anything which is part of

the observable structure, function, or behavior of

living organism can be a part of phenotype.

The examples of genotype include genes

responsible for the stripes on cat, size of a bird’s

beak, height, hair color, eye color, etc. Let us

assume the eye color of human being; we have

different colors like blue, brown, green, black,

etc. Why we all have a different eye color? This

is because of the difference in the amount of eye

pigment, melanin which is present in iris. Eye

color is an inherited trait and there have been

evidences that up to 16 genes can inﬂuence the

color of eye (Sturm and Larsson 2009). There

are three known alleles that control the shade of

eye color. These alleles assort independently dur-

ing gamete formation. Every individual has four

alleles for controlling their eye color; B allele

#Springer International Publishing AG 2017

J. Vonk, T.K. Shackelford (eds.), Encyclopedia of Animal Cognition and Behavior,

DOI 10.1007/978-3-319-47829-6_68-1

(brown) is always dominant over G allele (green).

The blue trait is always recessive (Table 1).

From the above Table, we can see that two or

more than two different genotypes can give the

same phenotype, so two different individuals hav-

ing brown eyes may have different genotype. The

inheritance pattern in albinism and hemophilia

can also be taken into account for correlating

genotype and Mendelian inheritance.

Genotypic Ratio

The number of times a genotype would appear in

the offsprings after a cross between both parents

will be the genotypic ratio. The value depends

upon the genotype of parents. It can be calculated

by Punnett square. Let us assume that two organ-

isms with same genotype (Aa, A is dominant and

a is recessive) are allowed to mate, the offsprings

will have the genotype: AA, Aa, and aa and the

resulting genotypic ratio will be 1:2:1, whereas

the resulting phenotypic ratio will be 3:1 (Fig. 1).

Genotyping

The process of determining differences in the

genetic make-up of an individual by examining

an individual’s DNA sequence and comparing

it to another individual’s sequence or a reference

sequence is known as genotyping. The most

widely used methods for genotyping include

polymerase chain reaction (PCR), DNA sequenc-

ing, random ampliﬁed polymorphic detection

(RAPD), ampliﬁed fragment length polymor-

phism, allele-speciﬁc polymerase chain reaction,

and hybridization to DNA microarrays.

Genotyping ﬁnds its application in prenatal dis-

ease diagnosis, for which two widely used tech-

niques are “amniocentesis”(Hessner et al. 1998)

and “chorionic villi sampling.”Apart from prena-

tal disease diagnosis, genotyping is routinely used

for determining blood group, genetic counseling,

and personalized medicine. Genotyping can be

done right from humans to microorganisms. For

microorganisms, genotyping can be used for con-

trolling the spreading of pathogens. Similarly

transgenic organisms can also be genotyped.

A transgenic mouse can be genotyped by a simple

polymerase chain reaction (PCR) technique.

Effect of Environment on Genotype

Genotype of an organism is its inherited map

which is carried within its genetic code. All organ-

isms that have the same genotype do not look or

behave the same way as phenotype and behavior

are modiﬁed by environmental factors. When two

different genotypes respond to environmental fac-

tors in a different way, it is referred to as gene

environment interaction. Such interactions

can provide a better insight for the genetic epide-

miology of certain diseases. We all know that

every individual may have different response to

a particular drug due to gene environment inter-

actions. Here, now the term pharmacogenetics

Genotype, Table 1 Genotype and phenotype of eye

color

Genotype Phenotype

BBGG Brown

BbGG Brown

BBGg Brown

BbGg Brown

BBgg Brown

Bbgg Brown

bbGg Green

bbGG Green

Bbgg Blue

AA Aa

Aaaa

Genotype, Fig. 1 Punnett square showing the genotypes

of offsprings when parents have the same genotype

2 Genotype

(Klotz 2007) comes into picture, which is the

study of inherited genetic differences in drug met-

abolic pathways which generally affects the indi-

vidual responses to drugs. Hence, it will allow

clinicians to select the drug and its dosage more

precisely.

Conclusion

Genotype is the entire set of genes in a cell, an

organism, or an individual. It depends on the

genetic information which was given to an indi-

vidual by their parents. An individual’s genotype

is indicative of their full genetic information

which is determined by the genes passed on by

the parents. Children born to a parent will have

different genotype, the exception to this are twins

or multiple births that are fertilized from same

egg. Genotype determines the type of trait that a

phenotype can have and it is the major inﬂuencing

factor in development of phenotype. The concept

of phenotypic plasticity can explain the degree to

which an organism’s phenotype is determined

by its genotype. Phenotypic plasticity is the

changes in an organism’s behavior, physiology,

and morphology due to its adaptation to a unique

environment. There is an another contrasting term

as compared to phenotypic plasticity, known as

genetic canalization which explains about the

extent to which an organism’s phenotype allows

conclusions about its genotype.

Cross-References

▶Dominant

▶Gene Pool

▶Phenotype

▶Recessive

References

Hessner, M. J., Pircon, R. A., & Johnson, S. T. (1998).

Prenatal genotyping of Jka and Jkb of the human Kidd

blood group system by allele-speciﬁc polymerase chain

reaction. Prenatal Diagnosis, 18(12), 1225–1231.

Klotz, U. (2007). The role of pharmacogenetics in

the metabolism of antiepileptic drugs. Clinical

Pharmacokinetics, 46(4), 271–279.

Sturm, R. A., & Larsson, M. (2009). Genetics of human iris

colour and patterns. Pigment Cell & Melanoma

Research, 22(5), 544–562.

Genotype 3

Candidate genes and fatty acids in beef meat, a review

Article

Full-text available

Oct 2021
Ital J Anim Sci

This article reviews current knowledge on candidate genes and fatty acids in beef meat. It highlights the general situation of beef cattle in the world, the anatomy, and genetics of cattle, and discusses fatty acid groups in beef and their percentage in musculus longissimus dorsi and the musculus longissimus thoracis. Some selected genes that have been most researched in recent years are discussed in terms of many fatty acids that are associated with as well as sensory attributes of meat and the influence of the fatty acids themselves on sensory evaluation of meat.

Genetics of human iris color and patterns

Article

Full-text available

Aug 2009

The presence of melanin pigment within the iris is responsible for the visual impression of human eye colouration with complex patterns also evident in this tissue, including Fuchs' crypts, nevi, Wolfflin nodules and contraction furrows. The genetic basis underlying the determination and inheritance of these traits has been the subject of debate and research from the very beginning of quantitative trait studies in humans. Although segregation of blue-brown eye colour has been described using a simple Mendelian dominant-recessive gene model this is too simplistic, and a new molecular genetic perspective is needed to fully understand the biological complexities of this process as a polygenic trait. Nevertheless, it has been estimated that 74% of the variance in human eye colour can be explained by one interval on chromosome 15 that contains the OCA2 gene. Fine mapping of this region has identified a single base change rs12913832 T/C within intron 86 of the upstream HERC2 locus that explains almost all of this association with blue-brown eye colour. A model is presented whereby this SNP, serving as a target site for the SWI/SNF family member HLTF, acts as part of a highly evolutionary conserved regulatory element required for OCA2 gene activation through chromatin remodelling. Major candidate genes possibly effecting iris patterns are also discussed, including MITF and PAX6.

Prenatal genotyping of Jka and Jkb of the human Kidd blood group system by allele-specific polymerase chain reaction

Article

Dec 1998
PRENATAL DIAG

An allele-specific polymerase chain reaction (ASPCR) assay for prenatal genotyping of the Kidd antigen system in order to identify pregnancies at risk for haemolytic disease of the newborn (HDN) was developed. Oligonucleotide primers were designed for ASPCR of JKA and JKB. A validation study was performed using DNA isolated from 54 serotyped whole blood samples and 8 amniocentesis samples. A concordance rate of 100 per cent was observed between serotyping and ASPCR detection of the JKA and JKB alleles. Experiments were conducted to quantify the maternal contamination that could be tolerated in Kidd ASPCR assays. The sensitivity of this assay ranged from 0·2 per cent when detecting the presence of JKB and JKA background, to 2 per cent for detecting the presence of JKA in a JKB background. This sensitive assay is particularly useful for rapid genotyping of fetal amniotic cells to identify pregnancies at risk for HDN due to incompatibilities within the Kidd blood group system. Copyright © 1998 John Wiley & Sons, Ltd.

Prenatal genotyping of Jk(a) and Jk(b) of the human Kidd blood group system by allele-specific polymerase chain reaction

Article

Jan 1999

An allele-specific polymerase chain reaction (ASPCR) assay for prenatal genotyping of the Kidd antigen system in order to identify pregnancies at risk for haemolytic disease of the newborn (HDN) was developed. Oligonucleotide primers were designed for ASPCR of JKA and JKB. A validation study was performed using DNA isolated from 54 serotyped whole blood samples and 8 amniocentesis samples. A concordance rate of 100 per cent was observed between serotyping and ASPCR detection of the JKA and JKB alleles. Experiments were conducted to quantify the maternal contamination that could be tolerated in Kidd ASPCR assays. The sensitivity of this assay ranged from 0.2 per cent when detecting the presence of JKB and JKA background, to 2 per cent for detecting the presence of JKA in a JKB background. This sensitive assay is particularly useful for rapid genotyping of fetal amniotic cells to identify pregnancies at risk for HDN due to incompatibilities within the Kidd blood group system.

The Role of Pharmacogenetics in the Metabolism of Antiepileptic Drugs

Article

Feb 2007

U Klotz

Several different factors, including pharmacogenetics, contribute to inter-individual variability in drug response. Like most other agents, many antiepileptic drugs (AEDs) are metabolised by a variety of enzymatic reactions, and the cytochrome P450 (CYP) superfamily has attracted considerable attention. Some of those CYPs exist in the form of genetic (allelic) variants, which may also affect the plasma concentrations or drug exposure (area under the plasma concentration-time curve [AUC]) of AEDs. With regard to the metabolism of AEDs, the polymorphic CYP2C9 and CYP2C19 are of interest. This review summarises the evidence as to whether such polymorphisms affect the clinical action of AEDs. In the case of mephenytoin, defects in its metabolism may be attributable to >10 mutated alleles (designated as *2, *3 and others) of the gene expressing CYP2C19. Consequently, poor metabolisers (PMs) and extensive metabolisers (EMs) could be differentiated, whose frequencies vary among ethnic populations. CYP2C19 contributes to the metabolism of diazepam and phenytoin, the latter drug also representing a substrate of CYP2C9, with its predominant variants being defined as *2 and *3. For both AEDs, there is maximally a 2-fold difference in the hepatic elimination rate (e.g. clearance) or the AUC between the extremes of EMs and PMs which, in the case of phenytoin (an AED with a narrow ‘therapeutic window’), would suggest a dosage reduction only for patients who are carriers of mutated alleles of both CYP2C19 and CYP2C9, a subgroup that is very rare among Caucasians (about 1% of the population) but more frequent in Asians (about 10%). The minor contribution of CYP2C19 to the metabolism of phenobarbital (phenobarbitone) can be overlooked. In rare cases, valproic acid can be metabolised to the reactive (hepatotoxic) metabolite, 4-ene-valproic acid. It is not yet clear whether genetic variants of the involved enzyme (CYP2C9) are responsible for this problem. Likewise, the active metabolite of carbamazepine, carbamazepine-10, 11-epoxide, is transformed by the microsomal epoxide hydrolase, an enzyme that is also highly polymorphic, but the pharmacokinetic and clinical consequences still need to be evaluated. Pharmacogenetic investigations have increased our general knowledge of drug disposition and action. As for old and especially new AEDs the pharmacogenetic influence on their metabolism is not very striking, it is not surprising that there are no treatment guidelines taking pharmacogenetic data into account. Therefore, the traditional and validated therapeutic drug monitoring approach, representing a direct ‘phenotype’ assessment, still remains the method of choice when an individualised dosing regimen is anticipated. Nevertheless, pharmacogenetics and pharmacogenomics can offer some novel contributions when attempts are made to maximise drug efficacy and enhance drug safety.

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