ANSC20010 Genetics and Biotech Section 3: The Chromosomal Basis of Inheritance PDF

ANSC20010 Genetics and Biotech: Section 3 Spring Trimester, 2023-24 Section 3: The Chromosomal Basis of Inheritance (Chapter 15 in Campbell Biology 12th ed.) The four yellow dots mark the locations of a specific gene, tagged with a fluorescent yellow dye, on a pair of homologous chromosomes. The chr...

ANSC20010 Genetics and Biotech: Section 3 Spring Trimester, 2023-24 Section 3: The Chromosomal Basis of Inheritance (Chapter 15 in Campbell Biology 12th ed.) The four yellow dots mark the locations of a specific gene, tagged with a fluorescent yellow dye, on a pair of homologous chromosomes. The chromosomes have duplicated, so each chromosome has two sister chromatids, each with a copy of the gene. This provides a visual demonstration that genes— Mendel’s “factors”—are DNA sequence segments located on chromosomes. Urry L. A. et al. (2020) Campbell Biology, 12th edition, Pearson Education, Inc. (page 294). 1 What is the relationship between genes (and alleles) and chromosomes? Urry L. A. et al. (2020) Campbell Biology, 12th edition, Pearson Education, Inc. (page 294). 2 The chromosomal basis of Mendel’s laws Urry L. A. et al. (2020) Campbell Biology, 12th edition, Pearson Education, Inc. (page 297). 3 1 ANSC20010 Genetics and Biotech: Section 3 Spring Trimester, 2023-24 The chromosomal basis of Mendel’s laws 4 5 The chromosomal basis of Mendel’s laws 6 2 ANSC20010 Genetics and Biotech: Section 3 Spring Trimester, 2023-24 The first scientific evidence that genes are located on chromosomes The first solid evidence associating a specific gene with a specific chromosome came early in the 1900s from the work of Thomas Hunt Morgan, an experimental embryologist at Columbia University in the United States. For his work, Morgan selected a species of fruit fly, Drosophila melanogaster, a common insect that feeds on the fungi growing on fruit. 7 The first scientific evidence that genes are located on chromosomes 1909-1911: Morgan’s experiments with Drosophila melanogaster demonstrated that Mendel’s factors (genes) are located on chromosomes. 1915: Morgan published “The Mechanism of Mendelian Heredity.” 1933: Morgan was awarded the Nobel Prize in Physiology or Medicine. 8 Thomas Hunt Morgan and Drosophila melanogaster – Discovery Channel: Greatest Genetics Discoveries https://youtu.be/yhDLA6ZPQQI (start at 5:07; finish 9:30) 9 3 ANSC20010 Genetics and Biotech: Section 3 Spring Trimester, 2023-24 Drosophila melanogaster: an ideal experimental organism for genetics Many times, in the history of biology, important discoveries have come to those insightful or lucky enough to choose an experimental organism suitable for the research problem being tackled (cf. Mendel and his peas). Fruit flies are prolific breeders; a single mating will produce hundreds of offspring, and a new generation can be bred every two weeks. Another advantage of the fruit fly is that it has only four pairs of chromosomes (2n = 8). There are three pairs of autosomes and one pair of sex chromosomes. Female fruit flies have a pair of homologous X chromosomes (XX), and males have one X chromosome and one Y chromosome (XY). In Drosophila genetics, the ‘normal’ (most common) phenotype for a character is termed the wild type (WT). Alternative traits (e.g., white eyes) are termed mutant phenotypes and mutant alleles are assumed to originate as changes (mutations) in the WT allele. 10 Drosophila melanogaster diploid cells have four pairs of chromosomes Drosophila melanogaster has diploid cells with four pairs of chromosomes (2n = 8). Male flies have an X and a Y chromosome (XY), and female flies have two X chromosomes (XX). Males and females produce haploid gametes (sperm and eggs) with four chromosomes (n = 4). Sperm can have an X, or a Y chromosome (50% chance of each) and eggs can only have an X chromosome. Hartwell L.H. et al. (2018) Genetics: From Genes to Genomes, 6th edition, McGraw-Hill Education (page 91). 11 Morgan’s discovery of an eye colour mutant led to the first concrete demonstration that a gene is located on a specific chromosome While Mendel could readily obtain different pea varieties from seed suppliers, there were no different strains/lines of Drosophila melanogaster when Morgan started his experiments. Eventually, Morgan’s team discovered a single male fly with white eyes (a mutant phenotype or trait) instead of normal red eyes (the wild type trait). Morgan then initiated a mating experiment like the monohybrid cross experiments that Mendel conducted for his pea plant characters. Mutant with white compound eyes instead of normal wild type red eyes. 12 4 ANSC20010 Genetics and Biotech: Section 3 Spring Trimester, 2023-24 Drosophila allele notation: more confusing genetic nomenclature! Mendel: used simple notation for alleles (R or r, P or p etc.). Morgan: the Drosophila melanogaster gene variant (allele) nomenclature comes from the first mutant (non-wild type) discovered. For example, for the Drosophila melanogaster eye colour gene alleles:  The allele symbol for the mutant white eyes allele is w.  A superscript “+” identifies the wild type allele symbol (w+ = red eyes). 13 Morgan’s discovery of an eye colour mutant led to the first concrete demonstration that a gene is located on a specific chromosome Urry L. A. et al. (2020) Campbell Biology, 12th edition, Pearson Education, Inc. (page 296). 14 Morgan’s discovery of an eye colour mutant led to the first concrete demonstration that a gene is located on a specific chromosome Morgan’s discovery of a trait (white eyes) that correlated with the sex of flies provided important support for the chromosome theory of inheritance. Because the identity of the sex chromosomes in an individual could be inferred by observing the sex of the fly, the behavior of the two members of the pair of sex chromosomes could be correlated with the behavior of the two alleles of the eye color gene. Morgan’s work with the white eyes trait in Drosophila melanogaster also paved the way for understanding the biological basis of sex determination in animals.  Like fruit flies, humans and other mammals have two types of sex chromosomes, designated X and Y, with the Y chromosome normally being smaller than the X chromosome.  Female mammals are XX and male mammals are XY. 15 5 ANSC20010 Genetics and Biotech: Section 3 Spring Trimester, 2023-24 The chromosomal basis of sex in humans and other mammals There is a gene on the mammalian Y chromosome – the sex-determining region Y gene (SRY), which encodes a protein (testis-determining factor TDF), which is the primary signal for male development. Short segments at either end of the Y chromosome are the only regions that are homologous with regions on the X. These homologous regions allow the X and Y chromosomes in males to pair and behave like homologs during meiosis in the testes. X chromosome Scanning electron micrograph of an X and Y chromosome from a human male (with duplicated sister chromatids). The human X chromosome is 156.0 Mb in length and contains 1,521 genes. The human Y chromosome is 57.2 Mb in length and contains 172 genes. Y chromosome 16 A human karyotype showing the sex chromosomes 17 Sex chromosomes and gametogenesis in mammals During meiosis in the testes (male) and the ovaries (female), the sex chromosomes segregate into separate gametes. Each gamete will contain only one sex chromosome. In mammals, each female gamete (the ovum or egg) will contain an X chromosome. In mammals, 50% of the male gametes (the spermatozoa) will contain an X chromosome and 50% will contain a Y chromosome. Females are the homogametic sex and males are the heterogametic sex. Note: birds and some reptiles have the ZW sex-determination system: males are homogametic ZZ and females are heterogametic ZW. 18 6 ANSC20010 Genetics and Biotech: Section 3 Spring Trimester, 2023-24 The genetics of sex determination in mammals (and some other animals) The life cycle of a typical mammal (Homo sapiens) showing meiosis, fertilisation and mitosis and development. Urry L. A. et al. (2017) Campbell Biology, 11th edition, Pearson Education, Inc. (pages 257 and 298). 19 The genetics of sex determination in humans 44+ XY 22+Y Sperm 44+ XY Parents 44+ XX 22+ X 22+X Zygotes (offspring) Ova 44+ XX 20 The behaviour of sex chromosomes during meiosis In female mammals (XX), the two X chromosomes are homologous chromosomes and behave essentially like autosomes. In male mammals (XY), the X and Y pair like homologous chromosomes; however:  The X and Y chromosomes are only partially homologous.  Crossing-over between the X and Y chromosomes during prophase I of meiosis to generate male gametes (sperm) is restricted to the pseudoautosomal regions (PARs) of the X and Y chromosomes.  The central portion of the Y chromosome does not form chiasmata with the X chromosome (there is no recombination in this part of the Y).  However, the PARs do recombine with the X chromosome.  The sex determining region Y gene (SRY) encodes the testis-determining factor (TDF) protein, which regulates the expression of many other genes resulting in the male development pathway for the mammalian embryo. 21 7 ANSC20010 Genetics and Biotech: Section 3 Spring Trimester, 2023-24 Alternation of meiosis and fertilisation produces genetic variation Diploid multicellular organism 2n Zygote 2n Meiosis Animals n n Gametes n A critically important feature of meiosis is crossing-over and genetic recombination Fertilisation Note: See Section 1 22 The human pseudoautosomal regions (PARs) facilitates synapsis and crossing-over between X and Y in males PAR1 PAR1 SRY gene PAR2 PAR2 NPX = Non-pseudoautosomal portion of the X chromosome MSY = Male-specific portion of the Y chromosome 23 A transgenic XX mouse (33.13) with an SRY transgene develops into a male mouse indistinguishable from a normal XY male (33.17) Koopman P. et al. (1991) Male development of chromosomally female mice transgenic for Sry. Nature 351, 117-21. 24 8 ANSC20010 Genetics and Biotech: Section 3 Spring Trimester, 2023-24 The genetics of sex determination in humans 44+ XY 22+Y Sperm 44+ XX Parents 22+ X 22+X 44+ XY Zygotes (offspring) Ova 44+ XX 25 The X-chromosome and sex-linked traits in mammals The sex chromosomes (particularly the X chromosome) contain many genes that are unrelated to sex determination. In mammals, many important genes are found on the X chromosome and transmission of traits due to variation in these genes is referred to as sexlinked inheritance. Males transmit X-linked alleles to their daughters but not to sons. Females transmit X-linked alleles to sons and daughters. If a sex-linked trait is due to a recessive allele, the female will only express the phenotype if she is a homozygote. For males, homozygous and heterozygous are meaningless when describing sex-linked genes (the term hemizygous is used). Any male receiving an X-linked recessive allele from his female parent will express the trait. 26 The X-chromosome and sex-linked traits: the transmission of sex-linked recessive traits XA = X-linked dominant allele Xa = X-linked recessive allele XA XA Xa Y A father with an X-linked trait (hemizygous and affected – dark orange) will transmit the mutant allele (Xa) via the sperm (shown in dark red) to all his daughters but to no sons. If the mother is a dominant homozygote, her daughters will have the normal phenotype but will be carriers (light orange). Ova XA Xa XA Xa Sperm Y XA Y 27 9 ANSC20010 Genetics and Biotech: Section 3 Spring Trimester, 2023-24 The X-chromosome and sex-linked traits: the transmission of sex-linked recessive traits If a carrier (light orange) mates with a normal male, she will transmit the recessive mutation (Xa) via the egg (shown in dark red) to ½ her sons and ½ her daughters. The sons with the recessive mutation will manifest the trait (dark orange). XA Xa XA Y Ova Daughters who inherit one copy of the X-linked recessive allele will be carriers (light orange). XA Xa XA XA XA XA Xa Sperm Y XA Y Xa Y 28 The X-chromosome and sex-linked traits: the transmission of sex-linked recessive traits If a carrier mates with a male who has the trait, there is a 50% chance that each child born will have the trait (sex is irrelevant). XA Xa Xa Y Daughters who do not have the trait will all be carriers. Males without the trait will be free of the harmful recessive allele. Ova XA Xa Xa XA Xa Xa Xa Sperm Y XA Y Xa Y 29 The X-chromosome and sex-linked traits in mammals Many more males than females have sex-linked disorders. Duchenne muscular dystrophy (DMD) is a progressive muscle weakening (approximately 1/3,500 males are affected). DMD is caused by mutations in the dystrophin gene (DMD) on the human X chromosome (HSAX). Haemophilia leads to a failure to clot blood effectively (approximately 1/10,000 males are affected). There are two forms of X-linked haemophilia:  Haemophilia A (HEMA) caused by mutations in the coagulation factor VIII gene (F8) on HSAX.  Haemophilia B (HEMB) caused by mutations in the coagulation factor IX gene (F9) on HSAX. Haemophilia is a serious genetic condition and very few female homozygotes exist; however, female homozygotes do exist for less severe sex-linked conditions such as X-linked colour-blindness. 30 10 ANSC20010 Genetics and Biotech: Section 3 Spring Trimester, 2023-24 The X-chromosome and sex-linked conditions in humans 31 Haemophilia in the European royal descendants of Queen Victoria 32 The last Russian Royal Family – the Romanovs all were executed after the Russian Revolution in July 1918 Tsarevich Alexei The last known descendant of Queen Victoria with haemophilia died in the 1940s, so the exact type of haemophilia in Queen Victoria’s descendants remained unknown until 2009. Using genetic analysis of bones from Tsarevich Alexei, it was possible to show that he had haemophilia B caused by a mutation in the F9 gene that caused it to produce a non-functional clotting factor IX protein. 33 11 ANSC20010 Genetics and Biotech: Section 3 Spring Trimester, 2023-24 Colour blindness or colour vision deficiency (CVD) in humans Colour perception is due to light-absorbing proteins in the cone cells of the retina in the eye and there are three different proteins involved encoded by an autosomal gene and two genes on the X chromosome:  The opsin 1, short wave sensitive gene (OPN1SW) encodes a retinal cone protein that absorbs blue light (located on chromosome 7 – BTA7).  The opsin 1, medium wave sensitive gene (OPN1MW) encodes a retinal cone protein that absorbs green light (located on BTAX).  The opsin 1, long wave sensitive gene (OPN1LW) encodes a retinal cone protein that absorbs red light (located on BTAX). Sex-linked red–green color blindness or CVD can be:  Deutan type, which is insensitivity to green light due to inactivating mutations in the OPN1MW gene.  Protan type, which is insensitivity to red light due to inactivating mutations in the OPN1LW gene. 34 The human retina and rod and cone cells 35 The Ishihara chart for red-green colour blindness: approximately 1/20 males and 1/400 females are affected The number “74” should be clearly visible to viewers with normal color vision. Viewers with red-green color blindness will read it as “21” 36 12 ANSC20010 Genetics and Biotech: Section 3 Spring Trimester, 2023-24 Thomas Hunt Morgan also discovered and described genetic linkage in Drosophila melanogaster Additional mating experiments in Drosophila melanogaster demonstrated the phenomenon of genetic linkage. Remember that the number of genes is much larger than the number of chromosomes and each chromosome contains hundreds of genes. Genes located on the same chromosome can be linked. Linked genes are generally physically close to one another on the same chromosome and tend to be transmitted together as a single unit. NB. genetic linkage is not the same as sex-linkage. 37 Demonstrating genetic linkage in Drosophila melanogaster Two characters (each controlled by a single gene): body colour and wing size. Wild type Drosophila have grey bodies and normal wings. Drosophila with mutant phenotypes for both characters have a black body and vestigial wings (lost functionality). Each gene has two alleles (wild type [WT] and a mutant allele):  For the body colour gene: b+ is the grey allele (WT allele); b is the black allele (mutant allele); and b+ is dominant to b.  For the wing size gene: vg+ is the normal wing allele (WT allele); vg is the vestigial wings allele (mutant allele); vg+ is dominant to vg. 38 Wild type and two different Drosophila melanogaster mutants Wild type Vestigial wing Black body 39 13 ANSC20010 Genetics and Biotech: Section 3 Spring Trimester, 2023-24 Demonstrating genetic linkage in Drosophila melanogaster The wing size and body colour genes in Drosophila melanogaster are not sex-linked (both genes are on an autosomal chromosome). Experiment performed by Thomas Hunt Morgan and his team:  They crossed wild type (WT) females (b+ b+ vg+ vg+) with males that have both mutant phenotypes - black bodies and vestigial wings (b b vg vg) as the parental generation (P generation). b+ b+ vg+ vg+ b b vg vg 40 Demonstrating genetic linkage in Drosophila melanogaster Urry L. A. et al. (2020) Campbell Biology, 12th edition, Pearson Education, Inc. (page 301). 41 Demonstrating genetic linkage in Drosophila melanogaster Morgan and his colleagues produced 2,300 offspring from this type of cross. A 1:1:1:1 ratio (approximately) of phenotypes would be expected if the genes assort independently (i.e., the two genes are not on the same chromosome and are unlinked). For the actual observed results from 2,300 offspring (a relatively large sample), the parental phenotypes are over-represented (965 wild type and 944 black body with vestigial wings) and the recombinant phenotypes are underrepresented (206 grey body with vestigial wings and 185 black body with normal wings). These data suggested to Morgan that the genes controlling body colour and wing size are genetically linked (i.e., located on the same chromosome). NB. This is a very different result when compared to Mendel’s dihybrid crosses in pea plants (he observed independent assortment). 42 14 ANSC20010 Genetics and Biotech: Section 3 Spring Trimester, 2023-24 Recombination of linked genes: crossing-over Normally, closely physically linked genes are not expected to assort independently:  Genes (alleles) are located close together on the same chromosomes and move through meiosis as a unit without being separated by recombination.  However, recombination between linked genes can occur, particularly if they are physically far apart on the same chromosome. In the Drosophila melanogaster experiments with body colour and wing size:  If linkage was complete (i.e., the genes are physically very close), then a 1:1 ratio of parental phenotypes would be expected in the offspring (no recombinant phenotypes observed in the offspring).  However, recombinant phenotypes were observed in the offspring; therefore, the linkage between the two genes is incomplete. 43 Recombination of linked genes: crossing-over The body colour and wing size genes are located on the same chromosome — they are linked genes. However, crossing-over produces recombinant phenotypes (offspring with combinations of traits different from either parent). The process by which recombinant chromosomes (and recombinant phenotypes) are generated by crossing-over is termed genetic recombination. Genetic recombination brings alleles from different genes together in new combinations. The subsequent events of chromosomes to the gametes. meiosis distribute the recombinant 44 Crossing-over and genetic recombination: chiasmata in late prophase of the first meiotic division Chiasmata (singular chiasma – from classical Greek “X-shaped” [Chi is the Greek letter Χ) between chromatids in a tetrad (from classical Greek – “group of four”). (NB: sister chromatids in the same homologous chromosome can form chiasmata, but this has no genetic consequences because they are identical.) 45 15 ANSC20010 Genetics and Biotech: Section 3 Spring Trimester, 2023-24 Crossing-over and the genetic consequences of recombination between linked genes 46 Production of recombinant offspring in Drosophila melanogaster [for the body colour and wing size characters] b+ vg+ Wild type (WT) grey with normal wings b+ vg b vg b+ vg+ b vg × b vg b vg b vg+ Black with vestigial wings b vg Ova Sperm Fertilisation b+ vg+ b vg Wild type 965 b vg b+ vg b vg b vg Black-vestigial 944 b vg Grey-vestigial 206 Parental types Recombination rate = b vg+ Black-normal 185 Recombinants 391 recombinants 2,300 total offspring = 0.17 = 17% 47 In 1913, Alfred H. Sturtevant developed the idea of a genetic map in T.H. Morgan’s laboratory using Drosophila melanogaster crosses Alfred H. Sturtevant in 1949 https://www.caltech.edu/about/news/first-genetic-linkage-map-38798 48 16 ANSC20010 Genetics and Biotech: Section 3 Spring Trimester, 2023-24 Recombination rates (frequencies/percentages) can be used to produce a genetic map of genes on a chromosome Alternative phenotypes Wild type Mutant Body-colour gene (b) Wing size gene (vg) Cinnabar eye colour gene (cn) 49 What is the relative position of the three genes on the chromosome? [results from additional experimental crosses] Morgan and his colleagues performed additional cross experiments and obtained the following results, which Sturtevant used to generate some of the first genetic linkage map in Drosophila melanogaster.  The measured recombination rate between the eye colour and body colour genes = 9.0%  The measured recombination rate between the eye colour and wing size genes = 9.5%  The measured recombination rate between the body colour and wing size genes = 17% 50 What is the relative position of the three genes on the chromosome? Chromosome A b vg cn OR vg b B cn OR vg cn C b 51 17 ANSC20010 Genetics and Biotech: Section 3 Spring Trimester, 2023-24 Some additional properties of recombination rates/frequencies A 1% recombination rate is defined as 1 centiMorgan (1 cM) The smaller the recombination rate, the closer together two genes will be on the same chromosome. The maximum possible recombination rate is 50% (WHY?). A recombination rate of 50% means 50% of progeny will display recombinant phenotypes (using an appropriate cross).  This happens when genes are on different chromosomes (independent assortment – what Mendel observed). ………..OR……..  Genes can be on the same chromosome but are located far away from each other (crossing-over occurs frequently, so recombination fraction is generally 50%). 53 The Drosophila melanogaster genetic linkage map and a partial map of chromosome 2 gene mutations Urry L. A. et al. (2017) Campbell Biology, 11th edition, Pearson Education, Inc. (pages 306). 54 A genetic linkage map of the tomato plant (Solanum lycopersicum) constructed using data from crosses among phenotypic mutant strains Griffiths A. J. F. et al. (2015) Introduction to Genetic Analysis, 11th edition, W. H. Freeman and Company (page 143). 55 18 ANSC20010 Genetics and Biotech: Section 3 Spring Trimester, 2023-24 A modern interactive genome map visualization showing cattle genes on BTA7 (Bos taurus chromosome 7) Note: See Section 4 www.ncbi.nlm.nih.gov/genome/gdv/browser/genome/?id=GCF_002263795.1 56 19