Information

8.3: Genetics of Inheritance - Biology

8.3: Genetics of Inheritance - Biology


We are searching data for your request:

Forums and discussions:
Manuals and reference books:
Data from registers:
Wait the end of the search in all databases.
Upon completion, a link will appear to access the found materials.

Like Father, Like Son

This father-son duo is serving in the army together. The shape of their faces and their facial features look very similar. If you saw them together, you might well guess that they are father and son. People have long known that the characteristics of living things are similar in parents and their offspring. However, it wasn’t until the experiments of Gregor Mendel that scientists understood how traits are inherited by offspring.

The Father of Genetics

Mendel did experiments with pea plants to show how traits such as seed shape and flower color are inherited. Based on his research, he developed his two well-known laws of inheritance: the law of segregation and the law of independent assortment. When Mendel died in 1884, his work was still virtually unknown. In 1900, three other researchers working independently came to the same conclusions that Mendel had drawn almost half a century earlier. Only then was Mendel's work rediscovered.

Mendel knew nothing about genes. They were discovered after his death. However, he did think that some type of "factors" controlled traits and were passed from parents to offspring. We now call these "factors" genes. Mendel's laws of inheritance, now expressed in terms of genes, form the basis of genetics, the science of heredity. For this reason, Mendel is often called the father of genetics.

The Language of Genetics

Today, we know that the traits of organisms are controlled by genes on chromosomes. To talk about inheritance in terms of genes and chromosomes, you need to know the language of genetics. Figure (PageIndex{2}) shows the location of genes in a eukaryotic cell. The nucleus is a membrane-enclosed organelle found in most eukaryotic cells. The nucleus is the largest organelle in the cell and contains chromosomes which make up most of the cell's genetic information. Mitochondria also contain DNA, called mitochondrial DNA, but it makes up just a small percentage of the cell’s overall DNA content. The genetic information, which contains the information for the structure and function of the organism, is found encoded in DNA in the form of genes.

A gene is a short segment of DNA that contains information to encode an RNA molecule or a protein strand. DNA in the nucleus is organized in long linear strands that are attached to different proteins. These proteins help the DNA coil up for better storage in the nucleus. Think about how a string gets tightly coiled up if you twist one end while holding the other end. These long strands of coiled-up DNA and proteins are called chromosomes.

Each chromosome contains many genes. The function of the nucleus is to maintain the integrity of these genes and to control the activities of the cell by regulating gene expression. Gene expression is the process by which the information in a gene is "decoded" by various cell molecules to produce a functional gene product, such as a protein molecule or an RNA molecule. The human species is characterized by 23 pairs of chromosomes (Figure (PageIndex{3})).

Autosomes

Of the 23 pairs of human chromosomes, 22 pairs are autosomes (the lines numbered 1–22 in Figure (PageIndex{3})). Autosomes are chromosomes that contain genes for characteristics that are unrelated to sex. These chromosomes are the same in males and females. The great majority of human genes are located on autosomes. The genes located on these chromosomes are called autosomal genes.

Sex Chromosomes

The remaining pair of human chromosomes consists of the sex chromosomes, X and Y. Females have two X chromosomes, and males have one X and one Y chromosome. In females, one of the X chromosomes in each cell is inactivated and known as a Barr body. This ensures that females, like males, have only one functioning copy of the X chromosome in each cell.

As you can see from Figure (PageIndex{3}), the X chromosome is much larger than the Y chromosome. The X chromosome has about 2,000 genes, whereas the Y chromosome has fewer than 100, none of which are essential to survival. (For comparison, the smallest autosome, chromosome 22, has over 500 genes.) Virtually all of the X chromosome genes are unrelated to sex. The genes located on the X chromosomes are called X-linked genes. Only the Y chromosome contains genes that determine sex. A single Y chromosome gene, called SRY (which stands for sex-determining region Y gene), triggers an embryo to develop into a male. Without a Y chromosome, an individual develops into a female, so you can think of a female as the default sex of the human species. Can you think of a reason why the Y chromosome is so much smaller than the X chromosome?

The following terms are a good starting point. They are illustrated in Figure (PageIndex{4}) that follows.

  • A gene is the part of a chromosome that contains the genetic code for a given protein. For example, in pea plants, a given gene might code for flower color.
  • The position of a given gene on a chromosome is called its locus (plural, loci). For example, a gene might be located near the center or at one end or the other of a chromosome.
  • A given gene may have different normal versions called alleles. For example, in pea plants, there is a smooth seed allele (S) and a wrinkled seed allele (s) for the seed shape gene. Different alleles account for much of the variation in the traits of organisms including people.
  • In sexually reproducing organisms, each individual has two copies of each type of chromosome. Paired chromosomes of the same type are called homologous chromosomes. They are about the same size and shape, and they have all the same genes at the same loci.

Genotype

When sexual reproduction occurs, sex cells called gametes unite during fertilization to form a single cell called a zygote. The zygote inherits two of each type of chromosome, with one chromosome of each type coming from the sperm donor and the other coming from the egg donor. Because homologous chromosomes have the same genes at the same loci, each individual also inherits two copies of each gene. The two copies may be the same allele or different alleles. The alleles an individual inherits for a given gene make up the individual’s genotype. As shown in the table below, an organism with two of the same allele (for example, BB or bb) is called a homozygote. An organism with two different alleles (in this example, Bb) is called a heterozygote.

Table (PageIndex{1}): Alleles and genotypes
AllelesGenotypesPhenotypes
BB (homozygous dominant)purple flowers
B (purple)Bb (heterozygous)purple flowers
b (white)bb (homozygous recessive)white flowers

Phenotype

The expression of an organism’s genotype is referred to as its phenotype. The phenotype refers to the organism’s traits, such as purple or white flowers in pea plants. As you can see from Table (PageIndex{1}), different genotypes may produce the same phenotype. In this example, both BB and Bb genotypes produce plants with the same phenotype, purple flowers. Why does this happen? In a Bb heterozygote, both alleles are expressed but only the B allele is seen in phenotype because it masks the expression of b, so the b allele doesn’t influence the phenotype. The allele B is called dominant, and the allele that doesn't show in the phenotype is called recessive.

The terms dominant and recessive may also be used to refer to phenotypic traits. For example, purple flower color in pea plants is a dominant trait. It shows up in the phenotype whenever a plant inherits even one dominant allele for the trait. Similarly, white flower color is a recessive trait. Like other recessive traits, it shows up in the phenotype only when a plant inherits two recessive alleles for the trait.

Review

  1. Define genetics.
  2. Why is Gregor Mendel sometimes called the father of genetics if genes were not discovered until after his death?
  3. Correctly use the terms gene, allele, locus, and chromosome in one or more sentences.
  4. Compare and contrast genotype and phenotype.
  5. Imagine that there are two alleles, R and r, for a given gene. R is dominant to r. Answer the following questions about this gene.
    1. What are the possible homozygous and heterozygous genotypes?
    2. Which genotype or genotypes express the dominant R phenotype? Explain your answer.
    3. Are R and r on different loci? Why or why not?
    4. Can R and r be on the same exact chromosome? Why or why not? If not, where are they located?
  6. If a child has the genotype Dd and inherited the D from their mother, where did the d likely come from?
    1. Either their mother or their father
    2. Their father
    3. Their maternal grandmother
    4. Their maternal grandfather
  7. True or False. Each phenotype has only one genotype.
  8. True or False. Recessive genes are never expressed in a phenotype.
  9. True or False. An observable physical trait is a phenotype.
  10. A gene for flower color and a gene for seed shape could be on the same:
    1. chromosome
    2. locus
    3. allele
    4. Both A and B
  11. What does a gene usually codes for?

Introduction

Genetics is the study of heredity. Johann Gregor Mendel set the framework for genetics long before chromosomes or genes had been identified, at a time when meiosis was not well understood. Mendel selected a simple biological system and conducted methodical, quantitative analyses using large sample sizes. Because of Mendel’s work, the fundamental principles of heredity were revealed. We now know that genes, carried on chromosomes, are the basic functional units of heredity with the ability to be replicated, expressed, or mutated. Today, the postulates put forth by Mendel form the basis of classical, or Mendelian, genetics. Not all genes are transmitted from parents to offspring according to Mendelian genetics, but Mendel’s experiments serve as an excellent starting point for thinking about inheritance.

As an Amazon Associate we earn from qualifying purchases.

Want to cite, share, or modify this book? This book is Creative Commons Attribution License 4.0 and you must attribute OpenStax.

    If you are redistributing all or part of this book in a print format, then you must include on every physical page the following attribution:

  • Use the information below to generate a citation. We recommend using a citation tool such as this one.
    • Authors: Samantha Fowler, Rebecca Roush, James Wise
    • Publisher/website: OpenStax
    • Book title: Concepts of Biology
    • Publication date: Apr 25, 2013
    • Location: Houston, Texas
    • Book URL: https://openstax.org/books/concepts-biology/pages/1-introduction
    • Section URL: https://openstax.org/books/concepts-biology/pages/8-introduction

    © Jan 12, 2021 OpenStax. Textbook content produced by OpenStax is licensed under a Creative Commons Attribution License 4.0 license. The OpenStax name, OpenStax logo, OpenStax book covers, OpenStax CNX name, and OpenStax CNX logo are not subject to the Creative Commons license and may not be reproduced without the prior and express written consent of Rice University.


    Chromosomal Theory of Inheritance

    The speculation that chromosomes might be the key to understanding heredity led several scientists to examine Mendel’s publications and re-evaluate his model in terms of the behavior of chromosomes during mitosis and meiosis. In 1902, Theodor Boveri observed that proper embryonic development of sea urchins does not occur unless chromosomes are present. That same year, Walter Sutton observed the separation of chromosomes into daughter cells during meiosis (Figure). Together, these observations led to the development of the Chromosomal Theory of Inheritance , which identified chromosomes as the genetic material responsible for Mendelian inheritance.

    (a) Walter Sutton and (b) Theodor Boveri are credited with developing the Chromosomal Theory of Inheritance, which states that chromosomes carry the unit of heredity (genes).

    The Chromosomal Theory of Inheritance was consistent with Mendel’s laws and was supported by the following observations:

    • During meiosis, homologous chromosome pairs migrate as discrete structures that are independent of other chromosome pairs.
    • The sorting of chromosomes from each homologous pair into pre-gametes appears to be random.
    • Each parent synthesizes gametes that contain only half of their chromosomal complement.
    • Even though male and female gametes (sperm and egg) differ in size and morphology, they have the same number of chromosomes, suggesting equal genetic contributions from each parent.
    • The gametic chromosomes combine during fertilization to produce offspring with the same chromosome number as their parents.

    Despite compelling correlations between the behavior of chromosomes during meiosis and Mendel’s abstract laws, the Chromosomal Theory of Inheritance was proposed long before there was any direct evidence that traits were carried on chromosomes. Critics pointed out that individuals had far more independently segregating traits than they had chromosomes. It was only after several years of carrying out crosses with the fruit fly, Drosophila melanogaster, that Thomas Hunt Morgan provided experimental evidence to support the Chromosomal Theory of Inheritance.


    IB DP Biology Topic 3: Genetics 3.4 Inheritance Study Notes

    “Heredity is the transfer of genetic information from parents to offspring. Their heredity characters are present on the chromosomes in the form of genes and the combination of these genes expresses characters which may be similar to one of the parents.”

    Variation in the characters of offspring arise due to a unique process called genetic recombination during crossing over events of meiosis.

    Definition of Variation

    “Variation is the degree by which the progeny differ from their parents.”

    Human are aware since 8000 – 1000 BC that one of the reason of variation was hidden in sexual reproduction and they tried to exploit the variations that were naturally present in wild population of animals and plants. Therefore, they try to selectively breed the organism and try to get the desired characters.

    Example of Variation

    With the help of domestication and artificial selection from ancestral cows we are able to produce Indian breed, i.e. Sahiwal cows found in Punjab.

    Mendel Law of Inheritance

    Gregor Mendel conducted hybridization experiments on garden peas for 7 years and proposed the law of inheritance. He selected the large sample size with greater credibility of collecting data. He investigated garden peas with contrasting traits, i.e. yellow or green seeds, tall or dwarf, etc. This helped in establishing the basic frame work of inheritance. During the experiment, Mendel also carried out artificial pollination via different true – breeding pea lines. He selected 14 true – breeding pea plant varieties and selected different contrasting traits. Some selected traits were smooth or wrinkled seeds, tall or dwarf, yellow or green seeds, etc.

    Following table shows seven contrasting traits selected by Mendel in peas for experiment:

    Reason of selecting Garden Peas

    Mendel selected garden peas (Pisum sativum) for his experiment because of several reasons –

    1. Presence of several contrasting characters that can be studies easily.
    2. Short life span.
    3. Pollination of pea flowers is easier and therefore, hybrids produced were fertile.
    4. Flowers show self – pollination and reproductive whorls being enclosed by corolla

    Mendel carried out his experiment with proper planning and his success depends on the working method he adopted.

    1. He studied single character at a time.
    2. Mendel used all available techniques in order to avoid cross pollination by undesirable pollen grains.
    3. He adopted concepts of statistics and mathematics so as to analyze the results obtained by him.

    Inheritance of One Gene

    Mendel carried out hybridization experiment, whereby he crossed tall and dwarf pea plant to study the inheritance of one gene. He collected the seeds produced as a result of this cross and grew first hybrid generation referred as first filial or Filial 1 progeny or generation. Mendel observed that all F 1 plants were tall and none were dwarf. Similar observations were found in other characters as well.

    Then, Mendel self – pollinated the tall F 1 plants and found some of the offspring were dwarf in F 2 generation, i.e. the character that was hidden in F 1 was now expressed in F 2. The portion of dwarf plants were 1/4 th of the F 2 plants while 3/4 th of the F 2 plants were tall.

    Following diagram shows the outcome of first hybrid generation, where at F 1 Mendel observed all tall pea plants. Simultaneously, we can also see the dwarf character existed in F 2 stage:

    Based on these observations, Mendel proposed that something stably passed down, from parent to offspring, unchanged via gametes, over successive generations and called them as genes. Genes are the unit of inheritance and consist of information required to express the particular trait in an organism.

    If we alphabetically represent each gene, whereby capital letter for tall and small letter for short, then the traits will be expressed as follows:

    In the above image, T is used for tall trait and t is used for dwarf trait. Thus, T and t are allele to each other. Mendel also concluded that in case of true breeding, dwarf or tall pea variety of allelic pair are identical or homozygous (represented as TT or tt) . On the other hand, Tt is considered as heterozygous.

    Mendel’s work and result

    After experimentation, Mendel proposed several laws that are referred as “Laws of heredity.”

    1. Law of dominance – “This law states that when two contrasting factors for two characters come together in an organism, only one is expressed externally and shows visible effect.” The character which is visibly present is called dominant while which remains hidden or do not express in recessive .” Thus, according to it –
      1. Factors are the discrete units that control characters.
      2. These factors occur in pair.
      3. In case of dissimilar pair, one pair is dominant while other is recessive.

      Inheritance of Two Genes

      Mendel also researched with inheritance of two genes, but crossing over pea plant with two contrasting traits, such as plant with seeds with round and green color and plant with seeds with yellow and wrinkled shape and found that the seeds resulted from this crossing over was yellow colored and round shaped. He thus, concluded that yellow color is dominant over green and round shape is dominant over wrinkled shape.

      Now let us consider several genotype symbols –

      Y = dominant yellow seed color

      y = recessive green seed color

      The genotype of parents is written as follows – RRYY and rryy.

      Following figure shows the cross between these two parents produced the following result:

      Result of the Dihybrid Cross

      Round Yellow: Round Green: Wrinkled Yellow: Wrinkled Green

      In the above figure, the gametes RY and ry unite on fertilization and produce RrYy hybrid at F1. When Mendel self – hybridized F 1 plants, he found 3/4 th of F 2 plants had yellow seeds while 1/4 th had green. Thus, the yellow and green color segregated in a ratio 3:1. In the similar manner, round and wrinkled seeds also segregated in the ratio 3:1.

      Law of Independent Assortment

      Referring the above image of dihybrid cross, the phenotypes round yellow: wrinkled yellow: yellow round: wrinkled and green appeared in the ration 9:3:3:1.

      According to the law of independent assortment “when two pairs of traits are combined in a hybrid, segregation of one pair of characters is independent of the other pair of characters.”

      Chromosomal Theory of Inheritance

      Chromosomal Theory of Inheritance was proposed by Boveri and Sutton in 1902. Sutton described Mendel principle of Inheritance on cytological basis. According to him, during meiosis, one member of the pair of homologous chromosome goes to one daughter cell and second to another daughter cell. The principle of Independent Assortment (proposed by Mendel) found cytological proof from the fact that member of one pair of homologous chromosomes independently move to poles towards another pair. Sutton calculated the number of combinations of chromosomes in same manner as gametes was calculated by Mendel. He also found that the number of chromosomes combinations were same as Mendel postulated during crosses of pea plant. During the independent assortment of chromosomes, four types of allelic combinations are made which are in the phenotype ratio 9:3:3:1 at F 2 .

      Following figure shows Chromosomal Theory of Independence. It is clear that the genes and chromosomes arrange themselves in homologous manner and separate in two different ways during meiosis. This results in four types of allelic combination and at F 2 the phenotypic ratio is 9:3:3:1.

      Arguments of Sutton and Boveri for Chromosomal Theory of Inheritance

      1. Since eggs and sperm cells are the one bridge that is transferred from one generation to another. It implies that all the heredity characters are included in them.
      2. During maturation, the sperm cell practically loses all its cytoplasm. But sperm contributes heredity similar to eggs therefore the heredity factors are carried in nucleus.
      3. Similar to Mendelian factors, chromosomes are also found in pairs.
      4. Union of egg and sperm re – establishes new organism with two sets of chromosomes previously seen in the body cells of parent organism.
      5. Chromosomes divide accurately during cell division and this gives an idea that genes are carried on chromosomes.
      6. Chromosomes segregate during meiosis.
      7. Member of chromosome pair also segregate independently of other chromosome pairs. Genes, proposed by Mendel also segregate independently.

      Sex Determination

      Definition of Sexual differentiation in Humans: “Sexual Differentiation in Humans is the process of development of sex differences in humans.” It is the process of development of different genitalia and the internal genital tracts, body hair, breasts, etc. play the significant role in sex determination.

      The development of sexual differences in human is due to the presence of sex chromosome. It begins with XY sex – determination system followed by the complex mechanism for the development of phenotypic differences between female and male humans. Female has two X chromosomes while male have one X chromosome and one Y chromosome. At the early developmental stage of an embryo, both sexes possess equivalent internal structures, referred as mesonephric ducts and paramesonephric ducts.

      In humans, sex determination mechanism is referred as XY type. Out of 23 pair of chromosomes, 22 pairs are exactly same in case of both male and female. These chromosomes are called autosomes. A pair of X chromosomes is present in female while X and Y chromosome are the determinant of male characteristics. During spermatogenesis, two types of gametes are produced in which 50% of sperm carry X chromosome while another 50% of the sperm carry Y chromosome. There is equal probability of fertilization of the ovum with sperm carrying X or Y chromosome. Thus, it is evident that sex of the child depends on the sperm and during pregnancy there is always 50% probability of either a female or a mal child.

      Following image shows the sex determination in male and female. Here an egg comprises of XX chromosome and sperm consist of XY chromosome.

      Mutation

      “Mutation is a phenomenon which results in alteration of DNA sequences and consequently results in changes in genotype and the phenotype of an organism.” Mutation is also the phenomenon that results to variation in DNA.

      Following image shows mutation where the DNA is changed to mutant copy rather than original one:

      Genetic Disorders

      1. Pedigree Analysis – In pedigree analysis, the inheritance of a particular trait is represented in the family tree over generations. It is the strong tool, which helps in studying the inheritance of specific trait, disease or abnormality. It is important to note that each and every feature of an organism is controlled by one or other gene which is located on DNA present on chromosome. However, alteration or changes takes place occasionally and such an alteration is called mutation. Number of disorders has been found that are associated with the inheritance of altered or changed genes.
      2. Mendelian Disorders – These disorders are determined by mutation in a single gene. The pattern of inheritance of such disorders are traced and studied by Pedigree Analysis. Most prevalent Mendelian disorders are Sickle – cell anemia, hemophilia, cystic fibrosis, thalassemia, color blindness, phenylketonuria, etc. These disorders can be dominant or recessive as well.
      • Hemophilia – It is sex linked recessive disease which is transmitted from unaffected carrier female to some of the male progeny. In this disease, a simple cut results in non – stop bleeding in an affected individual. Possibility of female of becoming hemophilic is extremely rare because mother needs to be carrier in this case and father needs to be hemophilic. Following figure shows the condition of hemophilia in an individual. The blood of such person is not able to clot:

      • Sickle cell anemia – It is autosome linked recessive trait which is transmitted when both the parents are carrier for the gene. This disease is controlled by single pair of allele, Hb A and Hb S . Heterozygous individual (Hb A Hb S ) are apparently unaffected but they are the carrier of the diseases. Following figure shows the condition of sickle cell anemia in an individual where sickle cells block the flow of blood while normal red blood cells results in free flow of blood vessels:

      • Phenylketonuria – It is inherited as autosomal recessive trait and is an inborn error of metabolism. The individual suffering from phenylketonuria lacks an enzyme that transform amino acid phenylalanine into tyrosine, due to which phenylalanine is accumulated and converted into phenyl pyruvic acid and other derivatives. These accumulate in brain and thereby result in mental retardation.
      1. Chromosomal Disorders – These disorders are caused due to lack of excess or abnormal arrangement of one or more chromosomes. “Failure of segregation of chromatids during cell – division results in the gain or loss of chromosome(s), called aneuploidy. For instance, Down’s syndrome results in the gain of extra copy of chromosome 21. In the same way, Turner’s syndrome is resulted from the loss of an X chromosome in human females. “Failure of cytokinesis after telophase stage of cell division results in an increase in a whole set of chromosomes in an organism and this phenomenon is called polyploidy.” This condition is often observed in plants.
      • Down’s syndrome or Trisomy 21 – It was first described by Langdon Down in the year 1866 and occurs due to the presence of additional copy of chromosome number 21. The person suffering from this disorder is short statured with furrowed tongue, short round head and partially open mouth. Psychomotor, mental and physical development is retarded in such individuals.
      • Klinefelter’s syndrome or 47, XXY or XXY – This disorder results due to the presence of additional copy of X chromosome. Such individuals have masculine development followed by expression of feminine development as well (It includes development of breast). The individuals suffering from this disorder are sterile.
      • Turner’s syndrome or 45,X – This disorder occurs due to the absence of one X chromosome. Such females are sterile and lack secondary sexual characters.

      Frequently Asked Questions

      Q1: What are true – breeding lines?

      Answer: “A true – breeding line is one that having undergone continuous self – pollination, shows the stable trait inheritance and expression for several generations.”

      Answer: “Alleles are the alternate pair of the same gene which is present on the homologous pair of chromosome.”

      Q3: What is the difference between homozygous and heterozygous?
      Answer:

      Homozygous Heterozygous
      It gives rise to similar homozygous individuals and is usually represented as tt or TT.It produces offspring of different genotype and is represented as Tt or tT.
      Both the alleles have similar traits.Both the alleles have contrasting traits.
      Homozygous individuals carry either recessive or dominant allele but not both.Heterozygous individuals carry both dominant and recessive alleles.
      It produces one type of gametes.It produces two types of gametes.
      It does not display extra vigour.It displays extra vigour and is referred as heterosis or hybrid vigour.

      Q4: What is incomplete dominance?

      Answer: It is a form of intermediate inheritance in which one allele for a specific trait is not completely expressed over its paired allele.” It results in third phenotype in which the expressed trait is the combination of both the trait of parents. It is also referred as semi dominance or partial dominance.

      Example of Incomplete Dominance: Pink roses are the example of incomplete dominance.

      Following figure shows incomplete dominance, whereby RR is red rose and rr is white rose. At F 1 , they produce Rr and all offspring are of pink color.

      Q5: What is the difference between incomplete dominance and co dominance?

      Answer: Incomplete dominance occurs when the alleles received by parents are neither recessive nor dominant rather blend together and produce new trait that is somewhere between the two traits. On the other hand, co dominance is also the similar phenomenon where neither dominant nor recessive trait is displayed, rather both the alleles mix up and shows in the offspring. For instance, red and while flowered rose plant may produce red or white flowers but white flower with freckles of red spots.

      Following diagram shows the difference between incomplete and co-dominance:

      Q6: What is point mutation?

      Answer: Point Mutation is a change in one or a few base pairs in a gene.” There are two Types of point mutation –


      The Basis Of Genetic Inheritance Biology Essay

      The nucleus of a cell of any organism provides instructions to that that cell enabling it to grow, reproduce and survive (University of Utah, 2004). In the nucleus, chromosomes are present which contain heredity material made from many structural components. This genetic material is called deoxyribose nucleic acid, DNA. In the cell, DNA undergoes many different mechanisms including: mitosis, meiosis and replication in order to copy and divide cells and code for protein. These mechanisms show how DNA is able to form the ‘basis of genetic inheritance’ carrying identical genes from one cell to another. Natural mechanisms within the cell are not the only evidence of genetic inheritance but experiments practiced by F. Griffiths, Avery, McCarty, Macleod, A.D. Hershey and M. Chase (Reece, Urry, Cain, Wasserman, Minorsky & Jackson, 9th Edition1) indicate man made evidence proving genetic inheritance in bacterial cells, researching the material used to transport these genes and to prove that the material is DNA (Dr Demetra Mavri-Damelin1).

      A gene is a part of inheritance (U.S. National Library of Medicine, 29 April 2013) which carries genetic information about the cell and is made from DNA molecules consisting of many complex structural components called nucleotides. DNA is made of pentose sugars (deoxyribose sugar), phosphate groups and a nitrogenous base which bond and form nucleotides. There are four different nitrogenous bases which form four different nucleotides: adenine, guanine, cytosine and thymine which bond to their complementary base pair to form a double stranded molecule of DNA called a double helix. Adenine is bonded by two hydrogen bonds to thymine to form a purine and cytosine is bonded by three hydrogen bonds to guanine to form a pyrimidine (Orono, December 18th, 2008). The pattern of repeated pentose sugars and phosphate groups form a DNA backbone (Jim Clark, 2007) which is attracted to water enabling it to interact with its polar environment (Dr Demetra Mavri-Damelin2).

      Before DNA undergoes any process that proves it contains inherited evidence, the chromosomes within the cell must be ‘replicated’ so that when the cells undergo divide, each cell contains the same number of chromosome, carrying the same genetic material. Firstly, the hydrogen bonds break apart and the double strand of DNA unwinds and untwists forming two single strands of DNA. Each base from both strands, bond with a complementary base pair forming two identical double stranded DNA strands. Each strand is said to consist of one old strand and the other strand being new, which results in the doubling of the cell’s genetic code. This process is called semi-conservative replication. (Reece, Urry, Cain, Wasserman, Minorsky & Jackson, 9th Edition2). DNA can be replicated by means of another two processes which also contribute to how genetic information from one cell is ‘copied’ and carried into another cell to create cell inheritance. Conservative replication is the first process that involves the production of a completely new strand of DNA (M.J. Farabee, 1992, 1994, 1997, 1999, 2000, 2001, 2007) and dispersive replication is when all newly formed strands of DNA have been fragmentally formed as they contain a mixture of both old and new DNA. Once replication has occurred the cell is matured and is ready to undergo cell division contributing mainly to how genes are inherited from one cell to anther and how children inherit characteristics or genes from their parents.

      Mitosis occurs directly after DNA replication and involves the production of two identical daughter cells by means of the cell division (Department of Biochemistry and Molecular Biophysics, April 1997). Mitosis consists of several intricate phases which are all vitally essential for the cell to divide. These processes indicate that the structure of DNA and the process of mitosis does contribute to genetic inheritance of DNA because a cell, that consists of double the number of identical chromosomes, divides into two identical single numbered chromosome cells which carry copies of their information . These identical cells will further divide and bind with other cells during sexual reproduction to form a variety of cells but will still carry that common chromosome.

      The processes involved in mitosis are: Interphase, Prophase, Prometaphase, Metaphase, Anaphase, Telophase and Cytokinesis (Department of Biochemistry and Molecular Biophysics, April 1997). Interphase is not a direct process of mitosis () but involves the maturing and replication of the cell preparing it for the beginning of cell division starting with prophase. During this phase the nucleolus degenerates, the centromeres of the double stranded chromatids move to opposite sides of the cell and spindle fibres assemble across the cell (Regina Bailey, 2013). During metaphase, the chromatids align along the metaphase plate and attach to the spindle fibres by their centromeres. (Regina Bailey, 2013). This process is essential for cell division because once these chromosomes are aligned, in the next phases they are separated to form single stranded chromatids which are present in the newly formed cell. If this process does not occur efficiently a mutation could occur which could form an abnormal cell with extra or a shortage of chromosomes. During metaphase, the spindle fibres dehydrate and pull apart, pulling the double stranded chromatids with them to the opposite sides of the cell resulting in the formation of the single stranded chromatids (Regina Bailey, 2013). Telophase and cytokinesis are the end processes of cell division as a new membrane forms around each set of chromosomes and the cytoplasm constricts separating the single cell into two identically genetically coded cells (Department of Biochemistry and Molecular Biophysics, April 1997).

      Meiosis is the next phase related to genetic inheritance during sexual reproduction resulting in chromosomes being passed from one generation to the next where a parent passes their genetic characteristics, physical or behavioural, to their offspring. Meiosis is the binding of two cells, one male and another female, to create offspring with a deviation of genetic code carrying genes from both parents (Berkow, Robert, ed. 1999. The Merck Manual. 17th ed. Merck, Sharp & Dohme, Rahway, 1996). Mitosis and meiosis are very similar processes but do have differences as mitosis involves the division of cells forming cells that are identical in genetics and meiosis involves the division of cells forming cells that have a variation of genetic material. Meiosis occurs in two phases: meiosis I and meiosis II. During meiosis I, ‘homologous’ pairs (Biology-Online, 27 April 2006) of chromosomes bind to form crossing, which is when chromosomes exchange genetic material resulting in genetic variation. These chromosomes line up along the equator of the cell attaching to the spindle fibres. Once these fibres detach, the chromosomes move to the ends of the cell. These single stranded chromatids are then surrounded by a membrane and cytokinesis occurs forming two half chromosome numbered cells (Biology-Online, 27 April 2006).

      Meiosis II is the process that initiates the production of the variation of genetic material within cells introduced by sexual reproduction. The starting phases of meiosis II are identical to the phases of meiosis I but the difference is that not only two cells are formed but four cells are formed, each cell containing a half chromosome number carrying different genetic information (Biology-Online, 27 April 2006).). Each gamete cell (sex cell) will fuse with another gamete cell of the opposite sex. The cell will undergo fertilization forming a zygote. The offspring later produced by both male and female will carry variation genetic information, information from the mother and the father. This clearly indicates that genetic material has been passed down to the offspring by means of inheritance through DNA.

      Scientists have proven through experiments that DNA is the sole mechanism that is structurally suited in order to carry genes from one cell to another through generations of cells carrying characteristics with them. The first experiment was constructed by F.Griffith, 1928, (Reece, Urry, Cain, Wasserman, Minorsky & Jackson, 9th Edition3) to investigate if a component can be passed from one cell to another. Griffith used a genetic bacterial cell, smooth and rough strains of streptococcus pneumonia, and injected it into a specific species of rat. The smooth streptococcus pneumonia causes pneumonia as it contains an outer capsule which protects the bacteria (M. Edwardsa & J. M. Stark) and the rough streptococcus pneumonia is non-pathogenic as it lacks an outer shell. Griffith took a sample of a smooth strain and injected a rat and as expected the rat was infected and died. He then injected another rat with the rough strain, and again, as expected the rat was not infected and remained alive. Griffith then decided to destroy the smooth strain, changing its genetic orientation, by heating it. He infected the rat and because the bacterium was destroyed, the bacteria was unable to replicate and divide and the rat remained alive. Most important experiment Griffiths constructed was when he combined the heated smooth strain with the rough strain infected the rat and the rat unexpectedly died. This is because the DNA of the rough strains take up the components of the heat treated smooth strains and replicate and divide. This converts the rough strains to retain the abilities of the smooth strain and infect the rat (Reece, Urry, Cain, Wasserman, Minorsky & Jackson, 9th Edition4). This experiment indicates that due to the heritable components in the bacterial cells, the genes were capable of being carried as well as manipulated to carry out a certain activity. This indicates that traits can be inherited regardless if that specific characteristic was present or not.

      The second experiment was constructed by scientists Avery, McCarty and Macleod. Their aim was determine which component transported these heritable traits from one cell to another (from the rough strain to the smooth strain). This process was referred to as the transformation process. Avery, McCarty and Macleod introduced three main candidates into the experiment: DNA, RNA (ribose nucleic acid) and protein. A smooth strain of bacterial cell was treated by each enzyme from the respective candidates. DNase removes the DNA, RNase removes the RNA and protease removes the protein. Each strain was then further treated with a rough strain of bacterial cell. Each treated substance was injected into a different rat. The only rat that survived was the rat that was treated with DNase, consisting of no DNA, as there is no DNA to be passed on. The cell has no ability to change from rough to smooth strain and therefore the genetics of the cell is not converted and the rat remains alive (DNA Learning Center, 2002). This experiment shows that DNA is the primary candidate for the transportation of genes.


      Genetics Overview

      Meiosis is the formation of gametes, and gametes contain the genetic information that parents pass to offspring. Additionally, meiosis creates genetic variation.

      Explanation:

      In meiosis, sperm and eggs are formed through spermatogenesis and oogenesis respectively by taking oocytes and spermatocytes(diploids, or having two copies of the same chromosome, one from mom and one from dad) (in more detail at the bottom) splits them up, so you end up with 4 gametes that each have one sister chromatid. These chromatids are just condensed DNA and are our genes.

      This increases genetic variation and leads to evolutionary adaptability because it allows the child to have both the mom and the dad's genes without having 92 chromosomes (in the case of humans).

      In Meiosis I, the cell goes through similar steps as mitosis, except the chromatids are pulled apart in anaphase I, an entire chromosome is pulled apart. This creates two cells. Finally, those 2 cells have their chromatids pulled apart in meiosis II, resulting in 4 sperm with genetic differences ready to create a baby. In terms of eggs, 4 are created but only 1 survives because the egg splits unevenly so that the one egg that survives has the most amount of nutrients for the baby.

      Answer:

      Genetics use probability to predict inheritance

      Explanation:

      We can use the basics of probability to determine the likelihood an offspring will express a trait. One way to do this is using punnet squares, where the genotype for each parent is placed on the left side and the top of the square, as seen below.

      We would then fill in the remaining squares by taking one allele/contribution from the corresponding row and the second allele/contribution from the corresponding column. We will end up with two letters in each of the cells that are empty in the above example.

      This would be our result:

      We have four squares and four options. However, because all four of our options are the same (YG), the chance of having an offspring with the YG phenotype is 100%.

      Here is another example of a genetics probability question on Socratic.

      Answer:

      It is the study of inheritable characteristics that are given an identity by genes in an organism.

      Explanation:

      Genetics in simple terms is the study of genes, hereditary characteristics, and heritable variations in organisms.

      Genetics tries to unravel how genes are responsible for encoding the traits we observe in an organism.

      There are three different levels of genetics

      Transmissible genetics which is basically studying how the hereditary traits are passed from parent. here we study the traits transmission at a singular organism level.

      Molecular genetics which study the chemical nature of the gene itself and look at how the gene encode the genetic information which is replicated and then used by the organism in the form of protein. here we can even look at same gene across different species, individuals and types of organism. (example can include comparing human and yeast RNA Polymerase structure)

      Population genetics studies the makeup of the population in one species with large number of individuals to study the variations in the species or gene pool. it also gives us the idea on how a species is evolved from its ancestors.

      Note:
      These there levels are not obsolete there can be different types of categories like fly genetics (based on organism) where scientist study about fruit fly genetics which can be divided in the above three categories.

      Sometimes genetics is divided using structure in different specialized field of genes like chromosomal genetics, where you study about genetics about the chromosomes.



      Epigenetics

      Genomic imprinting is an epigenetic phenomenon that causes genes to be expressed in a manner specific to their parent of origin.

      Explanation:

      Genomic imprinting is an inheritance out of Mendelian borders. Many of inherited diseases and human development violates Mendelian Laws of inheritance. This way of inheriting is studied in epigenetics. Epigenetics shows that gene expression undergoes changes more complex than modifications in the DNA sequence. It includes the environmental influence on the gametes before conception.

      Genetic imprinting is a process of silencing genes through DNA methylation. The repressed allele is methylated, while the active allele remains unmethylated. Genomic imprinting occurs when two alleles at a locus are not functionally equivalent and is considered the primary epigenetic phenomenon that can lead to the manifestation of parent-of-origin effect. Epigenetic changes can be induced by environmental factors at different times in life.
      When epigenetic changes occur in sperm or egg cells that lead to fertilization, epigenetic changes are inherited by the offspring.

      Imprinting is a dynamic process. It must be possible to erase and re establish imprints through each generation so that genes are imprinted in an adult may still be expressed in that adult's offspring. The nature of imprinting must therefore be epigenetic rather than DNA sequence dependent. Genomic imprinting uses the cell's normal epigenetic machinery to regulate parental specific expression.

      It is now known that there are atleast 80 imprinted genes in human and mice, many of which are involved in embryonic and placental growth and development. Forms of genetic imprinting have been demonstrated in fungi, plants and animals.

      Answer:

      Epigenetics refers to heritable changes in our gene expression that do not alter our DNA .

      Explanation:

      This means that our phenotype , what is expressed, is altered in some way without altering our DNA due to external or environmental variables. Genes may be expressed or silenced or read differently, but the underlying DNA code remains the same.

      These epigenetic changes can happen due to DNA methylation, histone modification, and RNA-associated silencing.

      DNA methylation adds a methyl group to the DNA, which changes transcription. Histone modification works by adding either an acetyl or methyl group to lysine located in the histone. Non-coding RNAs, antisense RNA, and RNA interference may also alter expression by causing histone modification, methylation, and by causing heterochromatin to form. All of these examples mentioned in the previous sentence silence genes.

      Here's a good site from the University of Utah and Nature also has an excellent webpage on this topic.


      Inheritance:

      Genotype is the genetic constitution of an organism. This is the alleles that are part of the genetic code for example TT, Tt or tt for height.

      Phenotype is the expression of this genetic constitution and its interaction with the environment (the characteristic of the individual).

      There may be many alleles of a single gene where they could be one of three of these:

      • Dominant: An allele whose characteristic appears in the phenotype even when there is only one copy. These alleles are written as capital letters for example the capital t in the genotype used in the example for genotype for tall.
      • Recessive: An allele whose characteristic appears in the phenotype if there are two copies unlike dominant. These alleles are written as lower case letters for example the lower case t in the genotype used in the example for genotype for tall.
      • Codominant: Alleles that are both expressed in the phenotype and are represented by two capital letters where one letter being the allele is a superscript to the other capital letter being the gene for example the colour of a snapdragon where C R = Red flowers and C W = White flowers:

      In a diploid organism (like us humans as we have two sets of chromosome), the alleles at a specific locus (location on the chromosome) can either be:

      • Homozygous: An organism that has two copies of the same allele in the genotype for example TT or tt. The organism is said to be homozygote.
      • Heterozygous: An organism that carries two different alleles in the genotype for example Tt. The organism is said to be heterozygote.

      NB: The following genetic diagram needs to be known as you will be asked in the exam to predict the genotypes and phenotypes of the offspring. Monohybrid inheritance is the inheritance of a single characteristic controlled by a single gene. The images that say ‘monohybrid cross’ (the picture with alleles T) shows the layout that is recommended to do in the exam and these monohybrid crosses cover all the possible combinations between homozygous dominant, heterozygous dominant and homozygous recessive. These alleles are on autosomal genes carried on autosomes. Autosomes are chromosomes that are not sex chromosomes.

      The monohybrid cross image with alleles C W is also part of the resource below. These alleles are part of the autosome.

      Some genes have multiple alleles where more than two can code for the same gene but only two of these alleles can be expressed in the phenotype of the offspring as two parents are involved. This is an example of blood group which is also an image with the title ‘monohybrid cross – multiple alleles’ (the alleles with I B and I O ). These alleles are part of the autosome.

      Cystic fibrosis (CF) is caused by a recessive allele when a person who is homozygous recessive. Thick, sticky mucus is formed and stays on the lining of the lungs. These alleles are part of the autosome.

      Albinism is an inherited condition where there is a lack of colour created by melanin in structures that have colour such as hair, iris and skin. Therefore albinos have red eyes, pinkish skin and pale yellow hair. It caused by a single recessive allele in the genotype. These alleles are part of the autosome.

      Huntington’s disease, an incurable and fatal disease, is caused by a dominant allele in the genotype. These alleles are part of the autosome.

      There is a 50-50 chance that a baby can be a boy or a girl. This can be proved by the Punnett square which is shown by the image called 󈧶-50 chance of being a boy or a girl’.

      Sex linked characteristics are carried on the X of the sex chromosomes therefore the genes are not autosomal. An example of this is colour blindness which is the image called ‘colour blindness’. Boys are more likely to be colour blind than girls as boys only have one X chromosome. If this chromosome has the allele then he is colour blind. Girls have two X chromosomes and therefore the two are needed to have the allele for her to be colour blind.

      Dihybrid inheritance is where two characteristics are adopted by two different alleles on different loci. An example follows:

      Example: Two pea plants each with the genotype RRYY and rryy were crossed to create the first generation of offspring all with the genotype of RrYy. Two of the offspring were crossed to create the second generation of offspring. R is for round, r is for wrinkled, Y is for yellow and y is for green. NB: There has to be the two different types of alleles controlling a different characteristic in the same gamete as this is dihybrid inheritance – the inheritance of two characteristics. The other parent has the phenotype wrinkled and green with the genotype rryy so the gametes will be ry and ry. As the table below represents the offspring of the second generation, both parents have the genotype RrYy giving the gametes RY, Ry, rY and ry (the possible combinations of two different alleles controlling different characteristics:

      RYRyrYry
      RYRRYYRRYyRrYYRrYy
      RyRRYyRRyyRrYyRryy
      rYRrYYRrYyrrYYrrYy
      ryRrYyRryyrrYyrryy

      From the offspring above a phenotypic ratio can be concluded showing the two characteristics i.e. the phenotypic ratio for the offspring above is: 9 round and yellow seeds: 3 round and green seeds: 3 wrinkled and yellow seeds: 1 wrinkled and green seed.

      If there were 16 offspring, 9 of the offspring would have round and yellow seeds, 3 would have round and green seeds, another 3 would have wrinkled and yellow seeds and 1 would have wrinkled and green seeds as this is the expected value. Not all cases are like this where another set of 16 offspring either from the same parents or different parents of the same genotype as RrYy may have 10 that have round and yellow seeds, 2 that have round and green seeds, 4 that have wrinkled and yellow seeds and none of the offspring have wrinkled and green seeds instead of the classic 9:3:3:1 ratio. This is our observed value. So, how would we know if the difference of the expected values and observed values are due to chance? Solution: Chi-squared should be used.

      NB: You are not expected to work out chi squared in the exam however a demo will be given below following the same type of plant and crossing as the one above.

      We have to come up with our null hypothesis which is: THERE IS NO SIGNIFICANT DIFFERENCE BETWEEN THE OBSERVED AND EXPECTED RESULTS.

      It is best if you put your data in a table like the one below:

      OEO – E(O – E) 2(O – E) 2 /E
      Round and yellow seeds109111/9
      Round and green seeds23-111/3
      Wrinkled and yellow seeds43111/3
      Wrinkled and green seeds01-111

      As the chi squared formula has the funny symbol in front of the fraction which means sum of, all the values at the furthest right of the table above have to be added up to give chi-squared. Chi squared is therefore 16/9. This value should be referred to the table below:

      Probability, p
      Degrees of freedom0.25 (25%)0.20 (20%)0.15 (15%)0.10 (10%)0.05 (5%)0.02 (2%)0.01 (1%)
      11.321.642.072.713.845.416.63
      22.773.223.794.615.997.829.21
      34.114.645.326.257.819.8411.34
      45.395.996.747.789.4911.6713.28
      56.637.298.129.2411.0713.3915.09

      NB: We should always use the column with the 0.05 or 5% probability highlighted in yellow as biologists always use this. The values in the table are known as critical values.

      To know which degrees of freedom to use we must use the value that is 1 minus how many categories we have. So in this case as we have four categories (the different types of seeds that the offspring have), we subtract 1 from this and we get three which is our degrees of freedom. Therefore our critical value is 7.81 which is in bold and underlined. We compare our chi-squared value (16/9) to the critical value (7.81). Our chi-squared value is smaller than the critical value therefore we accept our null hypothesis saying also that there is a 5% or higher probability that the results are due to chance and there is no significant difference between observed and expected values. NB: If our chi-squared value was greater than the critical value then we reject our null hypothesis and also say that there is a 5% or lower probability that the results are not due to chance and there is a significant difference between observed and expected values.

      Epistasis is where a gene interferes with another gene on a different locus. An example is as follows: Flowers can be either white, light blue or aqua blue. The alleles of the gene code for the enzyme used to catalyse the reaction between white and light blue and light blue and aqua blue. The reaction between white and light blue is controlled by an enzyme called Enzyme A, coded by the dominant allele A. The reaction between light blue and aqua blue is controlled by Enzyme B coded by the dominant allele B. An image with the title ‘Epistasis’ is on the resource for you to look at.

      Linkage is where there are two alleles that code for a different characteristic on the same chromosome. Therefore variation is reduced. An example is sweet pea plants in the image named ‘linkage’.

      Recombination is the reassortment of genes into different combinations from the parents. Offspring that have recombination are called recombinants and gives rise to different individuals in a natural population. Three things can give rise to recombination: crossing over, independent assortment/segregation and random fertilization.

      6 POINTS ON HOW TO ANSWER ‘LOOKING FOR EVIDENCE’ QUESTIONS IN GENETICS

      1. A TIP TO REMEMBER IS NEVER ASSUME THAT A GENETIC CROSS OR PEDIGREE DIAGRAM IS SEX-LINKED UNLESS IT TELLS YOU IN THE QUESTION.
      2. Q1:WHAT IS THE EVIDENCE THAT AN ALLELE IS RECESSIVE?

      What to look for:LOOK FOR PARENTS WHO ARE UNAFFECTED AND HAVE A CHILD WHO IS AFFECTED.

      Explanation:PARENTS MUST BE HETEROZYGOUS BECAUSE THEY ARE UNAFFECTED AND ALSO THEY PASS ON THEIR RECESSIVE ALLELE TO THEIR CHILD.

      What to look for:LOOK FOR TWO PARENTS WHO ARE AFFECTED AND HAVE A CHILD THAT IS NOT AFFECTED.

      Explanation:PARENTS MUST HETEROZYGOUS BECAUSE THEY ARE AFFECTED AND ALSO THEY PASS ON THEIR RECESSIVE ALLELE TO THEIR CHILD.

      What to look for: LOOK FOR A MOTHER WITHOUT THE CONDITION AND A SON WITH THE CONDTION.

      Explanation: MUM MUST BE HETEROZYGOUS FOR HER TO NOT HAVE THE CONDITION.

      What to look for: LOOK FOR UNAFFECTED FATHER AND AFFECTED DAUGHTER.

      Explanation: DAUGHTER MUST HAVE TWO RECESSIVE ALLES BUT COULD NOT INHERIT THE RECESSIVE ALLELE FROM DAD BECAUSE HE IS UNAFFECTED.

      What to look for: LOOK FOR AN AFFECTED FATHER AND UNAFFECTED DAUGHTER.

      Explanation: IF FATHER’S X CHROMOSOME CARRIES THE DOMINANT ALLELE THE DAUGHETR WOULD BE AFFECTED WHICH IS NOT THE CASE.


      Recent advances on porphyria genetics: Inheritance, penetrance & molecular heterogeneity, including new modifying/causative genes

      The inborn errors of heme biosynthesis, the Porphyrias, include eight major disorders resulting from loss-of-function (LOF) or gain-of-function (GOF) mutations in eight of the nine heme biosynthetic genes. The major sites of heme biosynthesis are the liver and erythron, and the underlying pathophysiology of each of these disorders depends on the unique biochemistry, cell biology, and genetic mechanisms in these tissues. The porphyrias are classified into three major categories: 1) the acute hepatic porphyrias (AHPs), including Acute Intermittent Porphyria (AIP), Hereditary Coproporphyria (HCP), Variegate Porphyria (VP), and 5-Aminolevlulinic Acid Dehydratase Deficient Porphyria (ADP) 2) a hepatic cutaneous porphyria, Porphyria Cutanea Tarda (PCT) and 3) the cutaneous erythropoietic porphyrias, Congenital Erythropoietic Porphyria (CEP), Erythropoietic Protoporphyria (EPP), and X-Linked Protoporphyria (XLP). Their modes of inheritance include autosomal dominant with markedly decreased penetrance (AIP, VP, and HCP), autosomal recessive (ADP, CEP, and EPP), or X-linked (XLP), as well as an acquired sporadic form (PCT). There are severe homozygous dominant forms of the three AHPs. For each porphyria, its phenotype, inheritance pattern, unique genetic principles, and molecular genetic heterogeneity are presented. To date, >1000 mutations in the heme biosynthetic genes causing their respective porphyrias have been reported, including low expression alleles and genotype/phenotype correlations that predict severity for certain porphyrias. The tissue-specific regulation of heme biosynthesis and the unique genetic mechanisms for each porphyria are highlighted.

      Copyright © 2018 Elsevier Inc. All rights reserved.

      Conflict of interest statement

      MY and RJD are past recipients of research grants from Alnylam Pharmaceuticals and Recordati Rare Diseases. They are co-inventors of a patent licensed to Alnylam Pharmaceuticals for RNAi therapy of the AHPs. RJD is a consultant for Alnylam Pharmaceuticals, Mitsubishi Tanabe Pharma Development America and Recordati Rare Disease. BC has no conflicts.


      Breaking the Genome Constraint

      6.5 Maintaining Genome Integrity: The Major Evolutionary Constraint

      The appreciation of evolutionary constraints represents one of the biggest advances in the past half century ( Futuyma, 2010 ). Thus, realization of the discontinuity between micro- and macroevolution is essential to explain how evolutionary constraints work and to establish the correct framework of evolution. Specifically, genome constraint provides the explanation for sluggish evolution ( Gorelick and Heng, 2011 ).

      6.5.1 Why Are Evolutionary Constraints Important?

      One of the key challenges of the current evolutionary theories is solving the puzzle regarding how genetic organization can both promote and constrain organismal evolution. While it is well known that abundant genetic alterations can be observed both in the experimental and natural conditions coupled with rapid local adaptation, the actual overall evolutionary speed seems to be slow with a difficulty to adapt and has recently been referred to as “sluggish evolution” ( Futuyma, 2010 ). Based on fossil studies, for example, species were capable of displaying abundant change over decades to centuries, yet over millennia they were basically static ( Eldredge et al., 2005 ). A recent large-scale statistical survey of an evolutionary model in fossil lineages revealed that directional evolution is rarely observed and accounts for only 5% of cases (13 of 251) ( Hunt, 2007 ). Note that many textbooks, however, highlight the exceptions, giving students the wrong impression that most fossil lineages display directional evolution. This is yet another example of using exceptions to describe a general rule. An even more fundamental issue is that evolutionary failure is commonplace ( Bradshaw, 1991 ). It is difficult to explain the extinction of a vast majority of species as well as all kinds of evolutionary limitations ( Futuyma, 2010 ), if evolution always results in successful long-term adaptation.

      Ironically, Darwin's theory of natural selection has faced opposite challenges on the same issue of dynamics and constraint of genetic variants, albeit from different historical stages. Before the new synthesis, Darwinism faced challenges to find the needed variants for evolution. By 1900, “classic Darwinism, which envisioned the natural selection of minute, random, inborn variations of an essentially continuous nature, was widely dismissed as leading nowhere” ( Larson, 2002 ). At that time, blending inheritance was dominant, and “ even if an individual with a beneficial variation was more likely to survive, it would likely breed with a “normal” individual, and their offspring would regress toward the species norm. Over time, continuous variations would be “swamped”” ( Larson, 2002 ). This challenge has been addressed by neo-Darwinian theory, mainly for short-term microevolution, and mainly achieved by theoretical and modeling-based analyses. Now, a new challenge is to explain the constraints of evolution and the mechanism of breaking it to form new species. This clearly represents another side of the evolutionary story: why short-term rapid adaptation often fails to lead to new species over time and how nature solves the paradox of “changes, yet does not change (still the same species), but finally changes (into a new species).”

      Various factors have been analyzed to address the issue of limited evolution (or limited response to selection). Bradshaw suggests that the controlling agent limiting evolution is the supply of variation. As inheritable variation is a key component of evolution, examining genetic variation is a logical approach to understand the mechanism. Although there is evidence that genetic variation can limit evolution, it is insufficient to solve this issue. Many other mechanisms have been proposed including developmental constraint, stabilizing selection, population structure, ephemeral divergence, and system internal homeostasis ( Bradshaw, 1991 ). One interesting trend lies in the viewpoint that the key evolutionary constraint might not be located at the genetic level but rather at the ecological level, as most genetic variations analyzed to date do not seem to account for evolutionary constraint.

      6.5.2 Genome Integrity Represents the Major Evolutionary Constraint

      The analyses in previous chapters will hopefully lead readers to appreciate that even though the main evolutionary constraints have not been identified at the gene level, one must not rule out the idea that genetic contribution at the genome level could be the most important evolutionary constraint. According to the genome theory, it is the genome rather than individual genes that is the unit of evolutionary selection ( Heng, 2007b , 2009 ). Thus, the search for the main genomic contribution of evolutionary constraint should focus on the genome rather than genes. Based on this viewpoint, particularly after realizing that genome alterations drive macroevolution, it has been hypothesized that the long-ignored genome-level constraints will provide the key genetic mechanism for organismal stasis.

      6.5.2.1 Why Is It Essential to Discuss Genome-Level Constraint?

      Given the nature of the complexity of both the biological system and evolutionary process, it is necessary to examine the issue of multiple levels of constraint and their dynamic interactions including genes/epigenes, proteins, genetic and protein networks, the genome, the individual, populations, society, and ecology ( Heng, 2009 ). As Futuyma provided a comprehensive summary and insightful analysis for many of these levels ( Futuyma, 2010 ), the level of the genome will be the focus in this section, not only because it has been more or less ignored in traditional evolutionary studies but also because it represents the main level of constraint/control and defines potential interactions that may occur at various lower and higher levels. Comparatively speaking, other types of evolutionary constraints are important but are not major determining factors when compared with genome constraints. Reducing the constraints at the ecological level, for example, can increase system instability. Under such instability, there are increased levels of short-term adaptation and genome alterations which provide increased potential to form new species. However, until a new genome cluster is formed, there is no opportunity to pass on these altered genomes. A genome cluster refers to multiple individuals that share a similar genome and can mate. The appearance of genome clusters usually occurs during a transitional time when new species are appearing and becoming established.

      As the importance of the genome has been discussed in previous chapters, some of the conclusions will be briefly summarized, which are directly related to this topic.

      A. The genome codes for the package of an entire system.

      Traditional genetic coding specifically refers to combinations of three nucleotides that determine the amino acids in proteins or RNA. 4D genomics, in contrast, emphasizes comprehensive coding as a system inheritance resulting from the genomic relationship between all genes and other structural/regulatory elements of the same system. Significantly, the genome-level information controls might not be directly stored within an individual DNA molecule but instead might exist within the topological relationship between genetic loci within the nuclei.

      This explanation also makes sense and agrees with various biological observations. The basic coding to make materials is universal among species who share a common ancestor. However, similar genes (materials or tools) can build a variety of genomic architectures with specific sets of chromosomes that define different species. Each genome represents a unique interaction or assembly code that is not shared by other species except for similarities among species that belong to the same genus and/or family. “Material” coding by DNA is essentially conserved among species because of its basic level of genetic organization. In contrast, architectural coding is highly dynamic and less predictable, as this new type of information is not coded within the DNA sequence but exists at the chromosomal level and is achieved through the self-organization principle based on the genes and genomic topological relationship. Such genome-level properties are inherited for each species and ensured by genome conservation.

      B. Sex safeguards genomic integrity.

      Maintaining genome integrity has been a hot topic in molecular biology. Proposed mechanisms include but are not limited to various DNA repair systems, cell cycle checkpoints, programmed cell death, robustness of network, the separation between germline cells and somatic cells, and epigenetic resetting. Recently, sexual reproduction has been recognized as serving a key function in maintaining genome integrity in most sexually reproducing eukaryotes ( Chapter 5 ).

      The genome context can be preserved by maintaining both the composition of the chromosomes and the gross order of genetic loci along each chromosome. As such, sex serves as a filter to eliminate most significant alterations at the chromosome level while allowing for gene-level changes. Thus, meiosis serves two main functions: it promotes gene changes but limits genome alterations.

      C. Sex-mediated genome integrity ensures long-term evolutionary stability.

      Because sex can preserve the boundary of the system, it provides an ideal balance between genomic dynamics and constraint in sexually reproducing organisms. In the short term, the dynamics of genes occurring through mutation, genetic recombination, and splicing can effectively enable evolutionary adaptation by passing on the genome while ensuring over the long term that the genome maintains its framework. During each normal reproductive cycle, most accumulated genetic alterations at the genome level will be eliminated, resetting the system back to the original status. Despite some small-scale copy number variation and some retrovirus integrations that can be accumulated, for most sexually reproducing species, the genome framework is basically the same generation after generation. In contrast, asexual organisms constantly go through both micro- and macroevolution, as there are no effective mechanisms like sex to purify their genomes and preserve clear-cut genome-defined boundaries.

      D. The genome—not the gene—is the macroevolutionary selection unit.

      Extensive discussion has occurred on why genes or individuals should or should not be the primary object of natural selection ( Mayr, 1997 ). It is proposed that the genome is the primary object of selection, especially at the macroevolutionary phase ( Heng, 2009 , 2015 ). The following points further support this concept. (1) The genome and gene represent different levels of genetic organization where the genome determines the system inheritance, the essential component of macroevolution (see Chapter 4 ). (2) There is a separation between individuals and genomes (some individuals with altered genomes can pass a normal genome on to the next generation with higher frequency because of the sexual filter (e.g., XXX, XYY, and individuals with Down syndrome). (3) There is a distinction between germline cells (genome to be passed on) and the final function of somatic cells. Note that this difference can contribute to the individual variations that occur outside the boundary of the genome. Thus, there is a difference between success of a phenotype and the genome types that get propagated ( Heng, 2010 ).

      There are two points worth discussing here. In microevolution, selective contributions from individual genes can be measured if they display relatively simple traits. However, most genes are not independent information units but rather depend on a genome-defined network within specific environmental conditions. Selection acts on the genome package rather than on specific genes. Of course, the genome defines the boundary of the genetic potential of a species, which includes large numbers of combinations of genes that are displayed by different individuals.

      In macroevolution, selection at the genome level is critical during speciation as the newly formed genome must survive against competition. (The traditional concept insists that speciation is often caused by polyploidy or geographic isolation that results in large genetic drift, which do not require any selection. However, genome-level selection is obvious in cancer evolution). Once a species is stably established, the genome serves as a constraint to maintain the system where sexual reproduction prevents drastic genome-level changes in the germline, while gene/genome dynamics at the somatic cell level promotes individual survival. In short-term adaptation, the effect is that gene and epigene dynamics are high, whereas in long-term selection, where the selective forces are constantly changing, gene mutations/epigene alterations come and go. As long as the population size is healthy and different individuals display variable features (the interactive results of environment and different genetic profiles defined by the genome), a given species can be passed by passing the core genome, which also defines various potential phenotypes under different environments.

      No wonder Mayr has stated:

      When re-reading my analysis, I was quite surprised how rarely I had to refer to the genetic aspects responsible for the phenotype. Apparently, it does not matter very much how the genes are combined or how much the genotype has to be modified, provided the resulting phenotype is favored by selection. What counts is the adaptedness of the end product.

      Mayr, 1997

      Mayr is partially correct because all phenotypes are products of the genotype/environment interaction. All selected individuals will also pass the core genome (the representative karyotype), which contains constantly changed gene and epigene landscapes.

      6.5.2.2 Different Factors Contribute to Genome Constraint

      The realization that most eukaryotes achieved evolutionary constraint by genome integrity preserved by sexual reproduction is of importance. It addresses the relationship between conservation of the genome and the dynamics of gene mutations and epigenetic alterations. It should be noted that many other factors, such as environmental and even social interactions, can either promote or reduce genome constraint. The balance between different levels' dynamics and constraints is important. For example, increased genetic diversity at the gene level is useful for individual survival, but the conservation of the genome ensures that the surviving system can be sustained over the long run without changing into a novel system. Interestingly, the higher level of system constraint will diminish the impact of lower level dynamics over the long run despite its importance to organismal adaptation in the short run. This can be explained as a new version of the Red Queen story: try everything to maintain life including gene mutations, yet do not alter your genome to change who you are. Only the existence of the genome matters in the long run.


      Watch the video: Bio - Linkage and Polyploidy (July 2022).


Comments:

  1. Voodoojas

    And what should you do in this case?

  2. Radford

    It is interesting to read in theoretical terms.

  3. Bhreac

    Write emoticons more often, otherwise everything seems to be serious

  4. Tejora

    Interesting, but still I would like to know more about this. Liked the article! :-)

  5. Aries

    Curiously....



Write a message