Genetic Polymorphism

The word ‘polymorphism’ has been derived from the Greek words poly (polloi) meaning many and morphs meaning forms. Ford (1940) has defined polymorphism as “the occurrence together in the same habitat of two or more discontinuous forms of a species in such proportions that the rarest of them cannot be maintained merely by recurrent mutation”. Most of the polymorphic traits are genetic in nature and are inherited as a simple Mendelian fashion. Genetic polymorphic traits are different blood group systems, various red cell proteins, serum proteins and haemoglobin variants, etc. Genes that occupying the same locus on a particular chromosome and control the heredity of a particular characteristic, such as blood type are known as alleles. When more than one version of the same trait is common such as blue and brown eyes or type- A, type- B and type- O blood groups the population is said to be polymorphic for that trait. Humans have long been recognised to be polymorphic for blood groups, skin colour, hair texture, stature and other traits. Genetic polymorphism promotes diversity within a population. It often persists over many generations because no single form has an overall advantage or disadvantage over the others regarding natural selection. The types of polymorphic systems so far discovered have, naturally, reflected the techniques used for detecting them. A polymorphism may be transient; this happens if a favourable gene is spreading through the population.

But the majority of polymorphisms, particularly all those discovered in human are not transient; they are balanced polymorphisms and have existed for a very long time. These polymorphic traits are often used in the study of population diversity, movement and relationship between and within various populations. In recent times, enormous advances in the analysis of such genetic variation have been made. New biochemical and immunological polymorphisms have been discovered due to advancement of various techniques like isoelectric focusing and more recently a vast array of DNA polymorphisms have been added.

Genetic polymorphism is actively and steadily maintained in populations by natural selection, in contrast to transient polymorphisms where a form is progressively replaced by another. By definition, genetic polymorphism relates to a balance or equilibrium between morphs. The mechanisms that conserve it are types of balancing selection. In many cases, an allele that is harmful in the homozygous condition may produce a heterozygote whose reproductive fitness exceeds that of the normal homozygote. This is called a balance polymorphism.

Examples of balanced polymorphisms in humans include persons who are carriers for sickle-cell anemia or beta thalassaemia. Sickle-cell disease is a good example showing advantage of allele over some populations. Sickle cell anemia is caused by a mutation in beta-globin gene that causes a severely blood disorder in Caucasian population. But in certain parts of Africa, nevertheless, same mutant allele is polymorphic because it had resistance to the blood-borne parasite that causes malaria (Ayi et al., 2004). Blood group differences, once considered harmless and rather subtle variations, little affected by selection, may in fact be associated with considerable differences in susceptibility to certain diseases. Thus, persons having blood group O are about 40% more likely to develop duodenal ulcer than those belonging to A, B and AB blood groups. Polymorphism usually does not cause any chronic diseases and many of them are found in intergenic region and are totally neutral. Some polymorphisms may be found within genes, but it may only influence characteristics such as height, hair colour rather than medical traits causing disease. On the other hand, some polymorphism may give disease susceptibility and may also manipulate drug responses and efficacy. A mutation in one population can turn into a polymorphism in another population if it had an advantage and increases in frequency.

CLINICAL GENETIC TRAITS: ABO, RH (D), SERUM PROTEINS

Genetic polymorphisms can be found in body fluids and almost every cell of the human body. These polymorphisms are detected by various means viz., plasma proteins like Haptoglobin (HP), Transferrin (TF), and Group specific component (GC); red cell enzymes like Adenylate Kinase (AK), Phosphoglucomutase (PGM), Esterase-D (ESD), Lactate Dehydrogenase (LDH), etc and Human leukocyte antigen [HLA]).

Human Blood Group Systems

• a) ABO Blood Group : The first human polymorphism discovered was the ABO blood groups (Landsteiner 1901). This initial discovery opened an unseen world of biological diversity for anthropologists and geneticists. The ABO blood group system is the most studied and well known of the simple genetic traits in humans. This genetic system is located on chromosome 9. There are three major alleles (A, B and O) in the system: A and B behaves as codominant alleles, and O is recessive. All the common blood types, such as the ABO blood group system, are genetic polymorphisms. Here we see a system where there are more than two morphs: the phenotypes are A, B, AB and O are present in all human populations, but vary in proportion in different parts of the world. The phenotypes are controlled by multiple alleles at one locus. These polymorphisms are seemingly never eliminated by natural selection; the reason came from a study of disease statistics. The worldwide variation and clines for the A, B, and 0 alleles suggest that mechanisms of evolution (gene flow, genetic drift, and natural selection) have played a role in their distribution and frequency. Worldwide, the ‘O’ allele is the most common (about 63%), while A is next at about 21%, and B at 16%. There is, however, much variation, with the frequency of ‘O’ ranging from about 40% to 100% in populations across the world. The ABO blood group system is the most studied genetic system from the Indian subcontinent. It is confirmed that the B allele frequencies among the population of Indian sub-continent are the highest in the world. Currently more than 160 red blood cell antigens are identifiable. Most have been implicated in blood transfusion reacting and presumably are involved in mother-foetus exchanges. The frequencies of most genetic variations in a population have a spatial gradient slope. Geographical distribution of blood groups (the differences in gene frequency between populations) is broadly consistent with the classification of “races” developed by early anthropologists on the basis of visible features.
• b) The Rh System: The discovery of the Rh blood group system was an important scientific breakthrough because it finally explained some unexpected transfusion reactions and haemolytic disease of the newborn (HDN). The clinically important antibody discovered by Levine and Stetson (1939) is now recognised as the Rh system located on chromosome 1. For simplicity’s sake, red cells are often subdivided into “Rh+” and “Rh-.” The Rh+ designation comes from the presence of the major D antigen and Rh-, from the absence of D antigen. Several antigens of the Rh system are defined as the products of three loci: C, D and E, and antigens C, c, D, d, E, e have been extensively analysed. However, there are few populations in India studied with five antisera are reported. Forty-five antigens have been identified in the Rh system, making it one of the more complexes of the polymorphic systems in humans. For the Rh system the populations of the Indian subcontinent show high frequencies of the D allele with most common haplotype (the combination of the sites along one chromosome) observed in Indian population is CDe. For other blood group systems (K, Fy, JK and P) the number of studies in different regional and ethnic groups is limited. c) The blood group system and selection Apart from the studies on the distribution of O, A, and B genes in ABO blood groups as well as the distribution Rh(D) blood group system several studies have been conducted to find the relationship between blood groups and environmental interaction especially diseases. Statistical research has shown that the various phenotypes are more, or less, likely to suffer a variety of diseases. For example, an individual’s susceptibility to cholera and other diarrheal infections is correlated with their blood type: those with type O blood are the most susceptible, while those with type AB are the most resistant. Between these two extremes are the A and B blood types, with type A being more resistant than type B. An analysis of the data showed that persons with blood groups A and AB have a disadvantage when exposed to smallpox. This suggests that the pleiotropic effects of the genes set up opposing selective forces, thus maintaining a balance. Rh-induced incompatibility between mother and foetus, known as erythroblastosis fetalis, is caused by antibody D, Which crosses the placenta and reacts with red cells of the foetus. This is the most common cause of severe haemolytic disease of the newborn (HDN). The possibility of producing a child with HDN occurs when the mother is Rh- and the father is Rh+, i.e., an incompatible mating because the mother lacks an antigen present in the father. Because fetal red cells enter the mother’s circulatory system primarily during labour, HDN is not common in the first pregnancy. Apart from the ABO blood group, the other erythrocyte polymorphisms, serum protein and red-cell enzyme polymorphisms, the HLA system, etc., are available.
• c) Haemoglobin Variants: Besides ABO blood groups, more than 200 structural variants of human haemoglobin are reported but only three of them, HbS (sickle cell trait), HbE, HbC are found in fairly large areas of the world with heterozygote frequencies of about 10 percent or higher. The Khmer populations of northern Cambodia and adjacent areas of north-eastern Thailand in Southeast Asia show the highest concentration of HbE (55.2%). This haemoglobin variant (HbE) has been found in high frequencies in eastern India among the Ahom, Khasi, Assamese and Totos, among whom it ranges from 20% to 58%. In comparison to HbE, the the study on HbS or sickle cell haemoglobin has been carried out much more extensively in India. It is well established that the HbS gene is widely distributed in India except in the eastern region particularly Bengal and Assam. It could also be noted that sickle cell gene is mostly found among the tribal populations. A few other variants HbD in the north-west of the Indian sub-continent, HbO (in the) Indonesia in Celebes attain heterozygote frequency 5 percent. However, a great majority of Hb variants are rare and do not reach a gene frequency of one percent.

Balance Polymorphisms

Evidence is now strong that many polymorphisms are maintained in human populations by balancing selection. Such a balance is seen in sickle-cell anaemia, which is found mostly in tropical populations in Africa and India. An individual homozygous for the recessive sickle haemoglobin, HbS, has a short expectancy of life, whereas the life expectancy of the standard haemoglobin (HbA) homozygote and also the heterozygote is normal (though heterozygote individuals will suffer periodic problems). The sickle-cell variant survives in the population because the heterozygote is resistant to malaria and the malarial parasite kills a huge number of people each year. This is balancing selection or genetic polymorphism, balanced between fierce selection against homozygous sicklecell sufferers, and selection against the standard HgbA homozygote’s by malaria. The heterozygote has a permanent advantage (a higher fitness) so long as malaria exists; and it has existed as a human parasite for a long time. Because the heterozygote survives, so does the HgbS allele survive at a rate much higher than the mutation rate.

Lactose Tolerance/Intolerance : There is considerable interest today in investigating genetic base of difference in human metabolism energy and material transformation within cells as these differences interact with culture and health. Lactose intolerance and alcoholism are to be mentioned in this regard. The ability to metabolise lactose, a sugar found in milk and other dairy products, is a prominent dimorphism that has been linked to recent human evolution.

Glucose-6-Phosphate Dehydrogenase: Glucose-6-phosphate dehydrogenase human polymorphism is also implicated in malarial resistance. G6PD alleles with reduced activity are maintained at a high level in endemic malarial regions, despite reduced general viability. Variant A with 85 percent activity reaches 40 percent in sub-Saharan Africa, but is generally less than 1 percent outside Africa and the Middle East.

Genetic Variability of Major Histocompatibility Complex : Human major Histocompatibility complex (MHC) molecules are called human leukocyte antigens (HLA), in short, the genetic control of the body’s immune system, which were discovered in 1958 (Dausset 1958) and is located on chromosome 6. It is well known that several HLA genes exhibit an extremely high degree of polymorphism. In particular, the HLA-A, HLA-B and HLA-C genes in class-I and the HLA-DR and HLA-DQ genes in class-II are highly polymorphic in various ethnic groups. Thus, these genes are very useful for tracing an evolutionary history of human populations. The genes of the major histocompatibility complex (MHC) are highly polymorphic, and this diversity plays a very important role in resistance to pathogens. This is the type of genetic variability involved in acceptance or rejection of organ transplant, defence against cancer and resistance to diseases such as malaria or measles.

DNA POLYMORPHISM: STR AND SNP

The study of protein polymorphism has indicated that the extent of genetic variation in natural populations is enormous. However, the total amount of genetic variation cannot be known unless it is studied at the DNA level. The results so far obtained indicate that the extent of DNA polymorphism is far greater than that of protein polymorphism.

What is DNA Polymorphism?

Noncoding nucleotide sequences that contain base pair variations that do not appear to have a phenotypic effect on the individual are referred to as human DNA polymorphisms. A DNA polymorphism is any DNA variant recognizable by a change in DNA sequence that occurs with a frequency of greater than 1 per cent. Mutation change nucleotides over the course of evolution. Other evolutionary forces, such as natural selection and random genetic drift, determine the fate of new mutations. Most mutations are eliminated from population. Some mutations at a particular DNA site reach polymorphic frequencies (that is over 5 per cent of individuals in the population carry the mutation) and are called polymorphic DNA site. Recognisable DNA polymorphisms, or marker DNAs are now being used to locate genes that cause genetic diseases. The DNA sequence in the human genome comprises a string of approximately 3 billion nucleotides, which is packaged as sub-strings in the haploid set of 23 chromosomes. DNA is not only present in the nuclear region of the cells but are also present in the mitochondria of the human cells known as mitochondrial DNA (mtDNA) comprises 16,569 nucleotides. Mitochondrial DNA are transmitted only through the females, hence both the males and females receive their mt DNA from their mothers only. The hyper variable region of the mtDNA has five to ten times greater mutation rate than nuclear DNA. mt DNA is present in a high copy number and can be recovered from skeletal remains, hair-shaft, etc., which are poor sources of nuclear DNA.

DNA Polymorphism versus Biochemical Polymorphism:
What are the Advantages in Population Genetics?
Traditionally population genetic studies have used blood group, red-cell enzyme and serum protein polymorphisms. Such polymorphisms are generally in the functional regions of the genome, and therefore under effects of natural selection.
This leads to restricted level of variation. Further, not all polymorphisms can be detected using the traditional starch-gel electrophoresis technique. DNA polymorphisms, especially those that are in the non-functional regions of the genome, are ‘neutral’ polymorphisms, and therefore exhibit much greater levels of variation. This property makes DNA polymorphisms extremely useful for population genetic studies. Further, because at the DNA level one can detect a much greater number of polymorphisms, it has become easy to pick and choose polymorphisms in any region of the genome. This has facilitated the reconstruction of heliotypes and the study of haplotype variation, which is far more informative for population genetic studies.

How is DNA Polymorphism Detected?
The simplest method of detect known single-nucleotide DNA polymorphismsis by use of restriction-endo-nucleases. Such polymorphisms are called restriction fragment length polymorphisms (RFLPs). Fragments of different length produced by the restriction enzyme can be distinguished by the altered mobility of the restriction fragments on gel-electrophoresis. These variations in the nucleotide sequence are not expressed phenotypically because these variations are due to sequence differences in the non-coding region of the genome. The gold standard is, of course, DNA sequencing. DNA polymorphism detection has been greatly facilited by the invention of the polymerase chain reaction (PCR) technique, which requires nano-gram quantities of DNA. In early 1980s, several groups of molecular biologists began to map the human genome using restriction fragment length polymorphisms (RFLPs).

Short Tandem Repeats (STR) or Microsatellite
Short tandem repeats are composed shorter and simpler repeat sequences (two to six nucleotides) in contrast to the RFLPs. These STRs are highly variable and each of the STRs is determined by a separate locus. These repeats can be amplified faithfully with the Polymerase chain reaction (PCR), enabling precise allele designations in population surveys on the basis of their DNA sequence. STRs were first used in forensic case work for the identification of human remains in Persian Gulf War in 1991.

Single Nucleotide Polymorphisms (SNPs)
Single nucleotide polymorphisms (SNPs) are sites in the individual genome that have at least two different nucleotide bases at the same location. This point mutations or substitution of a single nucleotide, do not change the overall length of the DNA sequence in that region. Presently. The SNPs are used as tools for studying variation within human populations or between different populations. Over the past years, a large number of different SNP technologies have been developed based on various methods of allelic discrimination and detection platforms.

6 What are the Applications of DNA Polymorphisms in Anthropology?
It is impossible to exhaustively list all possible applications. The more important ones are:

• a) Inferring population histories and affinities,
• b) Reconstructing mutational patterns and dating occurrences of mutations in populations,
• c) Relating inferences in demographic histories of populations,
• e) Mapping disease genes, and
• f) Tracing trials of disease and other genes.

The best way to study population an affinity is by comparing DNA sequence of individuals from different populations, since not only is DNA analysis more informative than analysis of proteins but it is also direct and unambiguous. Genetic distance analysis based on DNA polymorphisms indicated a major division of human populations into an African and a Eurasian group. This is consistent with the postulate that earliest forms of modern human originated in Africa and subsequently gave rise to all non-African populations

Significance of Genetic Polymorphism

Genetic polymorphisms are derived from continuous evolution of nature and found in every level of human development. The new horizons for genomics has provided us platform on explaining genetic polymorphisms and raised many challenges for the researchers to be addressed. Genetic polymorphisms includes all types of variations in the DNA sequence, from single base pair substitution (SNPs), deletions or insertions of nucleotides (indels), variable tandem repeats, duplication of gene, rearrangements of nucleotide, the absence or presence of transposable elements, etc. The section of genomes having genetic polymorphism is not large, but most of the functional diversity and adaptation may founded on them.

• First of all, Genetic polymorphism causing functional effects. In common livestock, 200 diseases are to known to cause by Single base pair DNA polymorphisms (Ibeagha Awemu et al., 2008), give us frequent cases of how these SNPs affects protein functions to fluctuating degrees. As contribution of genetic polymorphism in functional part makes them an important entity in human health, so more number of cases might be documented in future to provide better view of how these polymorphisms contribute to the molecular systems.
• Secondly, in context of pathways or networks, genetic polymorphism also play role in different mechanism. For the better understanding of functionality of pathway polymorphisms, many studies on human had provided good examples. Like, in human, Insulin-like growth factor-I (IGF-I) which synthesize polypeptide hormone which promotes normal development and cellular growth, polymorphism in Insulin growth factor type I receptor/IGFIR and phosphoinositide 3-kinase (PI3KCB) genes disturb the plasma levels of IGF-I (Bonafè et al., 2003). Life longevity may also be influenced by the insulin/IGF-I signal response pathway (Barbieri et al., 2003). Genome wide polymorphisms methodology may help to discover unknown pathways and probable regulators of the pathways by statistical analysis, as presented for the formation of aliphatic glucosinolate.
• Advancement in the modern techniques as high-throughput sequencing and generating huge data in parallel have been thought-provoking biologists, complex scenario for statisticians, and hard time to computer scientists to generate new paradigms to explain and understand their inquiries in research setups. Inter as well intra collaborations across different disciplines and multifunctional research organization will remain to rule the front bench of biological investigations on genetic polymorphisms and reinforce some key discoveries in the future.

Extra Knowledge:

Polymorphism

 The brief glance across a time: the beginning of the human genetic polymorphism was belonging to the b globin gene in 1978, which utilized to recognize a heredity disease. After 2 years, in 1980, short distinctions in DNA discovered were spread over the whole human genome. It was described by utilized restriction fragment length polymorphisms (RFLPs) method. Further complicated interesting information of DNA polymorphisms was reported in 1985. They were named minisatellites. The empirical arguments about DNA fingerprinting remained to the 1990s. With the trial of OJ Simpson in the USA in 1995, the DNA proofs play a very important role in forensic medicine history presented by the prosecution; OJ Simpson was acquitted. This event call attention to the proofs of DNA has great significance [51].

When we see the great diversity of human ethnicities, really we find it shocking that all of these different ethnicities share a genetically identical sequence at 99%. The range of their variances is only within limits 0.1% of sequence genetic that differs between double chromosomal threads, Figure 4, [52, 53]. It is a small ratio of variances (1%) indeed, but it is accountable for the multiplicity in person’s phenotypes and receptiveness of them to ecological contacts [53, 54].

Polymorphism at the DNA grade contains a broad domain of variations from single base pair alteration, numerous unite pairs, and frequent sequences [55]. One of the most famous types of genetic variations is the genetic mutation. Genetic mutation can be definite as order variants which happen in a smaller than 1% of the populace, whereas the extra prevalent variants are identified as polymorphisms. The greatest public hereditary variants than 1% are single nucleotide polymorphisms (SNPs)

Generally, genetic polymorphism can be available in numerous designs, comprising:

• single nucleotide polymorphisms (SNPs)
• tandem repeat polymorphisms which include a variable number of tandem repeats (VNTRs) and short tandem repeats (STRs)
• insertion/deletion polymorphisms
• transposable elements (TE) or Alu repeats also known as “jumping genes,”
• structural alterations,
• copy number variations (CNV)

For the studying diverse kinds of DNA polymorphisms, different techniques can be utilized, such as

• Restriction fragment length polymorphisms (RFLPs) accompanied by southern blots,
• Polymerase chain reactions (PCRs),
• hybridization methods (southern and northern blotting) utilizing DNA microarray chips,
• whole genome sequencing (WGS).

The following is an illustration of the most famous polymorphism .

Single-nucleotide polymorphism (SNP)

Single nucleotide polymorphisms (SNPs) are an alteration in a lone DNA order structure building block unit: (A, T, C, or G) which termed a nucleotide. It is the simplest formula of genetic difference among persons. SNPs are the most frequent occurrence from all genetic variants, which happen usually in a person’s DNA. It is a ratio of occurrence near 90% of human genomic variants .

They may be occurring one time in each 300 nucleotides on usual, that is, average is about 10 million SNPs in the individual’s genome. Greatest frequently, those SNPs are set between genes or within genes. They may perform as living signs and/or hereditary indicators, aiding experts find sequence, which are linked with disease. As soon as SNPs happen inside a gene or in an adjusting area nearby a gene, they might show an additional strong impact in disease via stirring the gene’s role. However, the SNPs generally have no influence on the general state of health. Moreover, investigators have instituted that SNPs might assist and guess a person’s reaction to definite medications. Additionally, they are utilized for a pathway of genetic factors of malady inside relatives .

Polymorphic repetitive sequences

The extension of the human genome threads that include gene sequences or intergenic and include retro (pseudo) genes and transposons are composed of small sequences of nitrogen bases that have repeated in tandem. It can consist of more two-thirds of human DNA. The number of units of these tandems in a specified site is extremely variable between separated persons. Tandem repeat polymorphisms include a variable number of tandem repeats (VNTRs) minisatellites and short tandem repeats (STRs) microsatellites. Both of VNTRs and STRs are the same in the total grounds. The difference between different alleles is consequence to a difference in the number of repeat bases that exist in alleles that are of various lengths, and later, tandem repeat polymorphisms have been identified as length polymorphisms. So, widely distinguished types from mini- and microsatellites depend on the distance of the repeated blocks. In microsatellites, the order repeat base composes between 2 and 9 units; while mini-satellites composes between 9 and 100 units .

Variable number of tandem repeats (VNTRs) : VNTR is among the earliest DND markers in the application. It is a kind of tandem repetitions in which a small order of bases (10–60 base pairs) are frequented changeable times in a certain position. Therefore, VNTR is additionally familiar as minisatellites. Minisatellites are scattered everywhere in the humane DNA. Usually, the number of repeated bases in minisatellites differs among persons. Hence, the array extension shaped by VNTRs as well differs among persons. Accordingly, the variant number of chromosomes is familial from parents, so they can be applied in parental or individual identification. The techniques that use to determine this type are: routines PCR, gel electrophoresis, and amplicons of band designs by southern blotting. The utilization of VNTRs was, nevertheless, restricted by the kind of specimen that could give good results for the reason that a big quantity of DNA was needed. In addition, understanding VNTR profiles might be a difficulty. Their utilization in forensic genomics has been replaced at the present time by short tandem repeats (STRs)

Short tandem repeats (STRs) : Short tandem repeats (STRs) give an extremely good method because of their great grade of polymorphism and a comparatively small length. Additionally, STRs are typical methods for genotyping in the identity of one’s parents check and forensic identity check. A category of tandem repeats depended on presents a small order of bases (2–6 base pairs) are frequented a variable number of times in a certain site. STRs are a type of microsatellites, . The repeating bases consist of a single nucleotide that is familiar as a single nucleotide polymorphism (SNP).

Insertion/deletion polymorphisms

It is a type of genomic difference in which a particular base order of different sizes ranging from one base to several 100 units is inserted or deleted. Indels are very extending across the DNA. Several writers consider one base pair as SNPs or frequent insertion/deletion as indels .