ANSC20010 Animal Genomics UCD Lecture Notes - Genetics and Biotech PDF

ANSC20010 Genetics and Biotech: Section 1 Spring Trimester, 2023-24 ANSC20010 – Genetics and Biotechnology (2nd year) Prof. David MacHugh (Module Coordinator), Room 253A, UCD Veterinary Sciences Centre, Email: [email protected] 1 ANSC20010 Animal Genomics UCD General Reference Timetable (2023-24)...

ANSC20010 Genetics and Biotech: Section 1 Spring Trimester, 2023-24 ANSC20010 – Genetics and Biotechnology (2nd year) Prof. David MacHugh (Module Coordinator), Room 253A, UCD Veterinary Sciences Centre, Email: [email protected] 1 ANSC20010 Animal Genomics UCD General Reference Timetable (2023-24) 2 ANSC30030 Animal Genomics timetable (2023-24) Monday Tuesday Wednesday 9:009:50 10:0010:50 Thursday Friday Genetics & Biotech E0.08SCE and online Genetics & Biotech E0.08SCE Genetics & Biotech E0.08SCE 11:0012:00 12:0013:00 13:0013:50 14:0014:50 15:0015:50 16:0016:50 3 1 ANSC20010 Genetics and Biotech: Section 1 Spring Trimester, 2023-24 ANSC20010 module descriptor https://hub.ucd.ie/usis/!W_HU_MENU.P_PUBLISH?p_tag=MODULE&MODULE=ANSC20010 4 Module overview: learning material covered for the ANSC20010 module Approximately 32-34 lectures. Six major sections will be covered: 1. Introduction and Cell (Nuclear) Division (Mitosis and Meiosis). 2. Mendelian Genetics and Extensions of Mendelian Genetics. 3. The Chromosomal Basis of Inheritance. 4. Molecular Genetics and Genomics. 5. Population and Evolutionary Genetics. 6. Animal and Plant Biotechnology. 5 Recommended/suggested textbooks Biology: A Global Approach Campbell et al. 12th edition (2020) Pearson – International Edition ISBN: 9781292170435 Particularly Unit III: chaps. 15-20 10th edition available in library James Joyce Library: Long/Short Loan 570/CAM 6 copies Health Sciences Library 570/CAM 3 copies [Note: some diagrams/images used for ANSC20010 learning materials] 6 2 ANSC20010 Genetics and Biotech: Section 1 Spring Trimester, 2023-24 Recommended/suggested textbooks Campbell Biology Urry et al. 11th edition (2017) Pearson ISBN: 0134093410 Particularly Unit III: chaps. 15-20 The content of the US versions and the international “global” versions are essentially the same. [Note: some diagrams/images used for ANSC20010 learning materials] 7 Price differences between US and European textbook versions www.amazon.co.uk www.amazon.com 8 Recommended/suggested textbooks The Cartoon Guide to Genetics Gonick & Wheelis, 2nd edition (1991) Harper Perennial; ISBN: 0062730991 James Joyce Library: Long Loan GEN 576.5/GON 5 copies James Joyce Library: Short Loan SLC 576.5/GON 5 copies 9 3 ANSC20010 Genetics and Biotech: Section 1 Spring Trimester, 2023-24 Relevant genetics/genomics popular science books 10 Online glossaries of genetics/biotechnology terms There is a glossary at the end of the Campbell Biology textbook. End of any good, up-to-date genetics textbook. NIH National Human Genome Research Institute: www.genome.gov/genetics-glossary National Cancer Institute: www.cancer.gov/publications/dictionaries/genetics-dictionary UCDavis Veterinary Genetics Laboratory: vgl.ucdavis.edu/resources/genetics-glossary Wikipedia Glossary of Genetics: https://en.wikipedia.org/wiki/Glossary_of_genetics 11 Using ChatGPT as a tool for understanding genetics/biotechnology terms 12 4 ANSC20010 Genetics and Biotech: Section 1 Spring Trimester, 2023-24 ANSC20010 lecture slide notes on the Brightspace VLE ANSC20010 lecture slide notes will be available on the UCD Brightspace virtual learning environment (VLE) platform. https://brightspace.ucd.ie. Greyscale and colour versions will be available prior to start of each ANSC20010 section. Please note that online lecture slide notes facilitate note-taking in lectures; they are not sufficient on their own to cover all of the material in the ANSC20010 module. 13 ANSC20010 lecture slide notes on the Brightspace VLE https://brightspace.ucd.ie/d2l/le/content/206937/Home 14 ANSC20010 module assessment: Continual assessment and end-of-trimester MCQ exam ANSC20010 module is assessed in two ways: 1. Continual assessment: – Multiple choice question (MCQ) assignments will be posted on Brightspace that cover each of the module sections. – Students submit answers via the UCD Brightspace eLearning within the allotted time (open-book assessment). – There will be two Brightspace MCQ assignments: Week 7 and Week 12 (with approximately one week to complete and submit) – Not negatively marked. – Contributes 10% of marks towards final grade. 15 5 ANSC20010 Genetics and Biotech: Section 1 Spring Trimester, 2023-24 ANSC20010 module assessment Brightspace open-book MCQ 16 ANSC20010 module assessment: End-of-trimester MCQ exam 2. End-of-semester paper-based MCQ examination. – Two-hour examination. – Negatively marked examination. 2.0 marks for a correct answer. 1.0 mark deduction for an incorrect answer. – No marks for an unanswered question. – 50 questions covering all sections of the module. – Contributes 90% of marks towards final grade. 17 ANSC20010 two-hour multiple-choice questionnaire (MCQ) 90% of the total marks for the module 18 6 ANSC20010 Genetics and Biotech: Section 1 Spring Trimester, 2023-24 ANSC20010 two-hour multiple-choice questionnaire (MCQ) 90% of the total marks for the module 19 ANSC20010 module overview: Section 1: Introduction to Genetics and Cell (Nuclear) Division Definition of genetics: DNA, genes, chromosomes and genomes. A timeline of genetics: from pea plants to genomes. Eukaryotic cell nuclear division – mitosis and meiosis. Mitosis – the form of cell nuclear division resulting in the formation of two genetically-identical diploid daughter cell nuclei from a single parent cell nucleus (this may or may not also be followed by cytokinesis – division of the cytoplasm). Sexual life cycles and the production of gametes. Meiosis – the form of cell division resulting in the formation of four genetically different haploid gametes. 20 Section 2: Mendelian (Transmission) Genetics and Extensions of Mendelian Genetics; Section 3: The Chromosomal Basis of Inheritance Gregor Mendel’s work with pea plants helped scientists understand the transmission of biological traits from parent to offspring (Mendelian principles). Mendel proposed two laws of inheritance that form the foundation of modern genetics: – In a nutshell: genes and chromosomes exist in pairs and members of a gene pair and chromosome pair separate from each other during gamete formation (meiosis). Mendel’s laws have their basis in the behaviour of chromosomes during meiosis and the formation of gametes. 21 7 ANSC20010 Genetics and Biotech: Section 1 Spring Trimester, 2023-24 Section 4: Molecular Genetics and Genomics What are genes and chromosomes composed of? Deoxyribonucleic acid (DNA) – the molecule of life. How does the chemical message encoded in DNA direct cellular processes? – DNA replication, transcription and translation. How changes in the DNA sequence of a gene can affect individual organisms but also how these changes generate genetic diversity (genetic mutation). – The molecular basis of variation in inherited traits, disease and evolution. Genomes and genome sequencing. 22 Section 5: Population and Evolutionary Genetics Evolutionary theory: Charles Darwin and Alfred Russel Wallace. Understanding how natural evolutionary processes (e.g., natural selection) are comparable to human-mediated evolutionary processes (i.e., animal and plant breeding). How genes behave in large numbers of individual organisms (i.e., populations). How genes and genetic variation within populations can change over time (i.e., microevolution). How analysis of DNA from different populations and species can help scientists reconstruct evolutionary relationships between populations and species. What are the implications of understanding for agriculture, medicine, forensics, biological conservation. 23 Section 1: Introduction to Genetics and Cell Nucleus Division 24 8 ANSC20010 Genetics and Biotech: Section 1 Spring Trimester, 2023-24 Introduction: What is Genetics? Genetics is the branch of biology concerned with the study of the inheritance of biological traits and variation in biological traits. Biological traits are largely controlled by genes contained within the genetic material. Genes are discrete information-carrying units of heredity that control or contribute to biological traits. Some traits are controlled by a single gene (e.g., flower colour in pea plants; cystic fibrosis in humans): monogenic traits. Some traits are controlled by several genes (e.g., eye colour and hair colour in humans): oligogenic traits. Some traits are controlled by a combination of genes and environmental factors (e.g., human height; human weight; milk yield in dairy cattle): polygenic traits. 25 Monogenic, oligogenic, and polygenic traits Mendel’s flower colour character in the pea plant (Pisum sativum): monogenic Eye colour variation in humans – determined by several genes: oligogenic Adult human height (stature) – determined by very many genes and environmental factors: polygenic 26 Genetic material (genome) contained within each cell of an organism 27 9 ANSC20010 Genetics and Biotech: Section 1 Spring Trimester, 2023-24 Nuclear genetic material (nuclear genome) contained within each cell of an organism and organized into chromosomes Simplified overview of normal karyotypes (male and female). human This modern karyotype shows the chromosomes from a human male (note the XY chromosome pair). The size of the chromosome, position of the centromere, and pattern of stained bands help identify specific chromosomes. Each metaphase chromosome consists of two closely attached sister chromatids. Urry L. A. et al. (2020) Campbell Biology, 12th edition, Pearson Education, Inc. (page 256). 28 The horse genome: the complete complement of genetic material (DNA) DNA TGGGCATATA TTCACTAGCA TTACTGCCCT TGGTATCAAG GAGAAGACTC ACCCTTAGGC CTGTCCACTC CTCGGTGCCT CTGAGTGAGC TGGGACCCTT GGGAGAAGTA AAGTCTCAGG TTAATTCTTG AGTCAGGGCA ACCTCAAACA GTGGGGCAAG GTTACAAGAC TTGGGTTTCT TGCTGGTGGT CTGATGCTGT TTAGTGATGG TGCACTGTGA GATGTTTTCT ACAGGGTACA ATCGTTTTAG CTTTCTTTTT GAGCCATCTA GACACCATGG GTGAACGTGG AGGTTTAAGG GATAGGCACT CTACCCTTGG TATGGGCAAC CCTGGCTCAC CAAGCTGCAC TTCCCCTTCT GTTTAGAATG TTTCTTTTAT TTTTCTTCTC TTGCTTACAT TGCACCTGAC ATGAAGTTGG AGACCAATAG GACTCTCTCT ACCCAGAGGT CCTAAGGTGA CTGGACAACC GTGGATCCTG TTTCTATGGT GGAAACAGAC TTGCTGTTCA CGCAATTTTT TTGCTTCTGA TCCTGAGGAG TGGTGAGGCC AAACTGGGCA GCCTATTGGT TCTTTGAGTC AGGCTCATGG TCAAGGGCAC AGAACTTCAG TAAGTTCATG GAATGATTGC TAACAATTGT ACTATTATAC 29 The nuclear genetic material (nuclear genome) is organized into chromosomes https://learn.genetics.utah.edu/content/genetics/chromosomes 30 10 ANSC20010 Genetics and Biotech: Section 1 Spring Trimester, 2023-24 Chromosomes contain genes (human chromosomes are shown as an example) 31 Double-stranded deoxyribonucleic acid (DNA): the information carrying molecule of heredity James Watson and Francis Crick (1953) Rosalind Franklin 32 Orders of magnitude in biology and standard units of length International System of Units (SI, from French Système international [d'unites]) 33 11 ANSC20010 Genetics and Biotech: Section 1 Spring Trimester, 2023-24 DNA is the genetic material for all eukaryotic organisms Cutaway view of a generalised animal cell Cutaway view of a generalised plant cell Urry L. A. et al. (2020) Campbell Biology, 12th edition, Pearson Education, Inc. (pages 100 and 101). 34 DNA is the genetic material for all prokaryotic organisms A prokaryotic cell. Lacking a true nucleus and the other membrane-enclosed organelles of the eukaryotic cell, the prokaryotic cell appears much simpler in internal structure. Prokaryotes include bacteria and archaea; the general cell structure of these two domains is quite similar. Urry L. A. et al. (2020) Campbell Biology, 12th edition, Pearson Education, Inc. (page 97). 35 A typical eukaryotic cell versus a typical prokaryotic cell Urry L. A. et al. (2020) Campbell Biology, 12th edition, Pearson Education, Inc. (page 6). 36 12 ANSC20010 Genetics and Biotech: Section 1 Spring Trimester, 2023-24 Dimensions of eukaryotic cells versus prokaryotic cells Space hopper Ping pong (table tennis) ball 37 Viruses use both DNA and RNA (ribonucleic acid) as genetic material Viruses are made up of nucleic acid (DNA or RNA) enclosed in a protein coat (the capsid) and sometimes further wrapped in a membranous envelope. Urry L. A. et al. (2020) Campbell Biology, 12th edition, Pearson Education, Inc. (page 400). 38 A brief history of genetics Hippocrates (~400 BC) Male contributions to offspring carried in semen. Similar contributions from female. Aristotle (~320 BC) All inheritance comes from males. Females supply the ‘parts’ from which offspring are made. Hindu religion (~1,000 AD) ‘Sick’ parents often pass on ‘sickness’ to offspring. 39 13 ANSC20010 Genetics and Biotech: Section 1 Spring Trimester, 2023-24 A brief history of genetics Charles Darwin (1859) Gregor Mendel (1866) Friedrich Miescher (1869) Publication of: On the Origin of Species by Means of Natural Selection. Published experiments on inheritance with pea plants. Isolated “nuclein” (nucleic acid - DNA) from nuclei of white blood cells. 40 A brief history of genetics Walther Flemming (1879) Thomas Hunt Morgan (1910) Identified chromatin in cell nuclei and links it to chromosomes and cell division. Demonstrated that genes are located on specific chromosomes. Oswald Avery, Colin MacLeod, and Maclyn McCarty (1944) Demonstrated that DNA is the genetic material. 41 A brief history of genetics James Watson and Francis Crick (1953) Rosalind Franklin (1952) Elucidated the three-dimensional structure of DNA (i.e., the double helix) and hypothesised a mechanism for DNA replication. Generated the X-ray crystallography data that was crucial to Watson and Crick’s 3D model of the structure of DNA. 42 14 ANSC20010 Genetics and Biotech: Section 1 Spring Trimester, 2023-24 A brief history of genetics Francis Crick Sydney Brenner Marshall Nirenberg Hargobind Khorana Robert Holley (1961-1966) Deciphered (‘cracked’) the genetic code, by which information encoded within nucleic acids (DNA/RNA) is translated into amino acid sequences that comprise protein molecules. 43 A brief history of genetics Paul Berg, Herbert Boyer, Stanley Cohen (1973) Performed the first genetic engineering experiments – the first genetically modified organism (GMO) Frederick Sanger (1977) Developed the chain termination method for DNA sequencing. Kary Mullis (1983) Invented the polymerase chain reaction (PCR) used to amplify DNA molecules. 44 A brief history of genetics Jennifer Doudna and Emmanuelle Charpentier (2012) Developed CRISPR-Cas9 genome editing technology. 45 15 ANSC20010 Genetics and Biotech: Section 1 Spring Trimester, 2023-24 1990 to 2023: The era of genomics and genome sequencing 10 Pb 1 Pb 1996 Yeast, 14 Mb 6,231 genes 2001 Mouse, 3.0 Gb 20-25,000 genes 1998 Nematode,100 Mb 16,384 genes 2003 Human, 3.1 Gb 20-25,000 genes 100 Tb 2009 Cow, 2.9 Gb 20-25,000 genes 10 Tb 1 Tb 2014 Sheep, 2.6 Gb 20-25,000 genes 2012 Bactrian camel 2.38 Gb 20-25,000 genes 100 Gb 2000 Arabidopsis 117 Mb 20,000 genes 10 Gb 2009 Horse, 2.7 Gb 20-25,000 genes 1995 Haemophilus 1.8 Mb 1,709 genes 1 Gb 2013 Turkey, 1.1 Gb 15-20,000 genes 2004 Chicken 1.1 Gb 20,000 genes 100 Mb 2000 Fruit fly, 160 Mb 13,600 genes 10 Mb 2012 Pig, 2.8 Gb 20-25,000 genes 1 Mb 100 Kb 1980 2013 Goat, 2.7 Gb 20-25,000 genes 1985 1990 1995 2000 2005 2010 2015 2020 46 The cost to sequence a mammalian genome in 2001 versus 2022 Mammalian genome sequence cost (2001) Super Yacht (> €100,000,000) Mammalian genome sequence cost (2022) Inflatable dinghy (€400) [note: is now ~ €200 (2024)] 47 Genome size – standard units used in genomics Term Number of base pairs (bp) base pair (bp) one bp 1 bp kilo base pair (1 kb) thousand bp 1,000 bp 1 × 103 bp mega base pair (1 Mb) million bp 1,000,000 bp 1 × 106 bp giga base pair (1 Gb) billion bp 1,000,000,000 bp 1 × 109 bp tera base pair (1 Tb) trillion bp 1,000,000,000,000 bp 1 × 1012 bp 48 16 ANSC20010 Genetics and Biotech: Section 1 Spring Trimester, 2023-24 The flow of genetic information: gene expression Gene DNA DNA template strand T A C C A C A A C T C G Transcription Messenger RNA (mRNA) A U G G U G U U G A G C Translation Protein chain met val leu ser Action of protein in cell plays a role in determining a biological trait 49 The molecular basis of the simple flower colour trait used by Mendel for his pea plant experiments Note: See Section 4 Urry L. A. et al. (2020) Campbell Biology, 12th edition, Pearson Education, Inc. (page 273). 50 Genetics 101 | National Geographic https://youtu.be/v8tJGlicgp8?si=4jk3UQmi4ubqbHSF 51 17 ANSC20010 Genetics and Biotech: Section 1 Spring Trimester, 2023-24 Cell Nuclear Division in Eukaryotes (Chapters 12 and 13 in Campbell Biology 12th ed.) 52 Chromosomes contain genes (human chromosomes are shown as an example) 53 How is DNA organised in the nucleus of the cell? For each chromosome: a single double-stranded DNA molecule is tightly coiled around discrete evenly spaced nucleosomes (consisting of eight histone proteins). When cells are not actively dividing, the DNA that constitutes chromosomes is relaxed and exists as open chromatin. Prior to cell division, the DNA replicates and each chromosome consists of two duplicate chromosome arms (chromatids). 54 18 ANSC20010 Genetics and Biotech: Section 1 Spring Trimester, 2023-24 Chromatin packaging in a eukaryotic chromosome DNA double helix 30-nm chromatin fibre Histone proteins showing histone tails Nucleosomes: “beads on a string” (10-nm fibre) Looped domains (300-nm fibre) attached to chromosome scaffold Metaphase chromosome showing sister chromatids (700 nm diameter) Note: See Section 4 55 Chromosome number: diploid cells and haploid cells Somatic cells and gametes have different numbers of chromosomes. Human somatic cells are diploid (2n): 46 chromosomes (23 chromosome pairs). Human gametes are haploid (n): 23 chromosomes (not in pairs). Human sperm and a human egg (haploid gametes – 23 chromosomes) 56 Genome: the full complement of genetic material of an organism – a typical mammalian (human) genome is shown Gamete cell (haploid) Somatic cell (diploid) Haploid genome Diploid genome (two copies of the haploid nuclear genome) Nuclear Genome Mitochondrial Genome Nuclear Genome Mitochondrial Genome ~3.2 × 109 base pairs ~16,000 base pairs ~6.4 × 109 base pairs ~16,000 base pairs ~8,000 copies One copy of each autosome (22 in total) One copy of the X or Y chromosome 23 chromosomes in total Approximately 21,000 genes (one copy of each) ~8,000 copies Two copies of each autosome (44 in total) Two copies of the X or one copy of the X and Y chromosome 46 chromosomes in total Approximately 21,000 genes (two copies of each) 57 19 ANSC20010 Genetics and Biotech: Section 1 Spring Trimester, 2023-24 Different animal and plant species have characteristic numbers of chromosomes Diploid (2n) and haploid (n) chromosome numbers for agricultural species Cattle Sheep Pig Horse Goat Chicken Diploid (2n) Haploid (n) 60 54 38 64 60 78 30 27 19 32 30 39 Diploid (2n) Haploid (n) Wheat Potato Tomato Maize Cotton Rice 42 48 24 20 52 24 21 24 12 10 26 12 58 Eukaryotic cell nuclear division: Mitosis Mitosis and nuclear division (karyokinesis) give rise to two genetically identical daughter nuclei. Mitosis is part of the cell cycle, the life history of a cell. Coupled with cytokinesis (division of the cytoplasm), mitosis functions in reproduction, growth and tissue repair. Mitosis and cytokinesis give rise to two genetically identical daughter cells. In mitosis, the diploid chromosome number (2n) in somatic cells is always maintained. N.B. We are discussing eukaryotic mitosis, not prokaryotic cell division (binary fission). 59 Both animal and plant cells undergo mitotic cell division Cutaway view of a generalised animal cell Cutaway view of a generalised plant cell Urry L. A. et al. (2020) Campbell Biology, 12th edition, Pearson Education, Inc. (pages 100 and 101). 60 20 ANSC20010 Genetics and Biotech: Section 1 Spring Trimester, 2023-24 Biological functions of mitosis Chromosomes (stained purple) are visible within the nucleus of this cell from an African blood lily plant. The thinner red threads in the surrounding cytoplasm are the cytoskeleton. The cell is preparing to divide. Functions of cell division Urry L. A. et al. (2020) Campbell Biology, 12th edition, Pearson Education, Inc. (page 235). 61 Mitotic nuclear division can give rise to multinucleated cells: mitotic nuclear divisions in an early Drosophila embryo Drosophila melanogaster the common fruit fly Coenocyte: multinucleated cell generated from multiple nuclear divisions without cytokinesis (in animal embryology – also known as a syncytium) https://youtu.be/XSKh-GLQn4E 62 The cell cycle is divided into interphase (G1, S, and G2 phases) and mitosis [there is also an G0 phase when cells are not dividing] Urry L. A. et al. (2020) Campbell Biology, 12th edition, Pearson Education, Inc. (page 237). 63 21 ANSC20010 Genetics and Biotech: Section 1 Spring Trimester, 2023-24 Mitosis video animation https://youtu.be/C6hn3sA0ip0 64 Replication of the genome is essential for mitosis Before mitosis can take place, all of the cell’s DNA (i.e., the diploid genome) must be replicated fully. The genome must be replicated effectively without errors*. Replicated DNA must be divided equally and correctly between the newly formed daughter nuclei (and daughter cells). The replication and distribution of DNA is manageable because of chromosomes. The cellular genome is replicated during the S-phase of interphase in the cell cycle. * A small number of errors (mutations) can occur – see Section 4. 65 Mitosis: chromosomes and sister chromatids After genomic DNA duplication, the chromosomes condense before mitotic nuclear division. Each duplicated chromosome condenses into two sister chromatids. The two sister chromatids possess identical* copies of the chromosomal DNA. During mitosis, the chromatids are separated (split) into two new nuclei. Cytokinesis (division of the cytoplasm) then usually follows. The end result is two genetically identical daughter cells. * A small number of errors (mutations) can occur – see Section 4. 66 22 ANSC20010 Genetics and Biotech: Section 1 Spring Trimester, 2023-24 Mitosis: chromosomes and sister chromatids Chromosome duplication and distribution during cell division A highly condensed, duplicated human chromosome. (SEM*) *Scanning electron microscope Urry L. A. et al. (2020) Campbell Biology, 12th edition, Pearson Education, Inc. (page 236). 67 Chromatin packaging in a eukaryotic chromosome DNA double helix 30-nm chromatin fibre Histone proteins showing histone tails Nucleosomes: “beads on a string” (10-nm fibre) Looped domains (300-nm fibre) attached to chromosome scaffold Metaphase chromosome showing sister chromatids (700 nm diameter) Note: See Section 4 68 A simplified overview of mitosis [extra notes] DNA duplicates and chromosomes condense 69 23 ANSC20010 Genetics and Biotech: Section 1 Spring Trimester, 2023-24 Stages of mitosis [extra notes] Urry L. A. et al. (2020) Campbell Biology, 12th edition, Pearson Education, Inc. (page 238). 70 Stages of mitosis [extra notes] Urry L. A. et al. (2020) Campbell Biology, 12th edition, Pearson Education, Inc. (page 239). 71 A summary recap of mitosis [extra notes] Mitosis is part of the cell cycle: series of events that takes place in a cell leading to its division and duplication. Mitosis: a process of non-sexual nuclear division in eukaryotes (occurs in somatic cells). Functions in growth and development of zygote after fertilisation (and cell renewal and repair). Divided into five stages: Prophase, Prometaphase, Metaphase, Anaphase, and Telophase. The DNA (chromatin) condenses into chromosomes during Prophase (duplicated chromosomes appear as sister chromatids – identical copies of a chromosome joined at a centromere). Metaphase: sister chromatids align along the metaphase plate. Anaphase: sister chromatids separate. Telophase and Cytokinesis: generation of two daughter cells. Mitosis conserves chromosome number by equally distributing replicated chromosomes to each daughter cell (normally 2n in each). 72 24 ANSC20010 Genetics and Biotech: Section 1 Spring Trimester, 2023-24 Bacteria and other prokaryotic organisms reproduce by binary fission – this is not mitosis [extra notes] Urry L. A. et al. (2020) Campbell Biology, 12th edition, Pearson Education, Inc. (pages 243 and 97). 73 Sexual Life Cycles and Meiotic cell division (Meiosis) Chapter 13, Campbell Biology, 12th ed. Dividing pollen mother cells at the metaphase II (M II), and telophase II (T II) from a Lilium candidum plant (the white lily) 74 Biological life cycles, meiosis, and mitosis Biological life cycles: the generation-to-generation sequence of stages in the reproductive history of an organism (i.e., conception to reproduction). Meiosis: a two-step form of cell division in sexually reproducing organisms that results in the formation of haploid gametes from diploid parent cells. Meiosis and mitosis play important roles in the biological life cycles of sexually-reproducing organisms. Life cycles for different types of organism are divided into diploid (2n) and haploid (n) stages. 75 25 ANSC20010 Genetics and Biotech: Section 1 Spring Trimester, 2023-24 The human life cycle Urry L. A. et al. (2020) Campbell Biology, 12th edition, Pearson Education, Inc. (page 257). 76 Three types of sexual life cycles The common feature of all three sexual life cycles is the alternation of meiosis and fertilization, key events that contribute to genetic variation among offspring. The cycles differ in the timing of these two key events (small circles are cells; large circles are organisms.) Urry L. A. et al. (2020) Campbell Biology, 12th edition, Pearson Education, Inc. (page 258). 77 Overview of meiosis (meiotic cell division) [note: crossing over and recombination is not shown for simplicity] Urry L. A. et al. (2020) Campbell Biology, 12th edition, Pearson Education, Inc. (page 254). 78 26 ANSC20010 Genetics and Biotech: Section 1 Spring Trimester, 2023-24 Chromosomes in a diploid organism This modern karyotype shows the chromosomes from a human male (note the XY chromosome pair). The size of the chromosome, position of the centromere, and pattern of stained bands help identify specific chromosomes. Each metaphase chromosome consists of two closely attached sister chromatids [Note the diploid chromosome number for humans is 2n = 46]. A cell from a hypothetical organism with a diploid number of 6 (2n = 6) shown following chromosome duplication and condensation. Each of the six duplicated chromosomes consists of two sister chromatids and each homologous pair is composed of one chromosome from the maternal set and paternal sets (red and blue, respectively) Each set is made up of three chromosomes (long, medium, and short). Together, one maternal and one paternal chromatid in a pair of homologous chromosomes are called nonsister chromatids. 79 Meiosis video animation https://youtu.be/-DLGfd-Wpr4 80 Meiosis in vertebrates (including mammals) 81 27 ANSC20010 Genetics and Biotech: Section 1 Spring Trimester, 2023-24 How meiosis reduces chromosome number (a simple overview) [extra notes] Interphase I (prior to meiosis) Meiosis I (prophase) End of Meiosis I End of Meiosis II 2n parent cell homologous chromosomes (as chromatin) Homologous chromosomes separate into 2 daughter cells (n) replication Sister chromatids separate Chromatin condensation 82 The stages of meiosis [extra notes] Meiosis is divided into two main stages: – Meiosis I (comprised of four individual phases) 1. Prophase I 2. Metaphase I 3. Anaphase I 4. Telophase I (followed by cytokinesis) – Meiosis II (comprised of four individual phases) 1. Prophase II 2. Metaphase II 3. Anaphase II 4. Telophase II (followed by cytokinesis) 83 A simplified overview of meiosis [extra notes] MEIOSIS I Replication of genome align to form a tetrad Spindle fibre MEIOSIS II 84 28 ANSC20010 Genetics and Biotech: Section 1 Spring Trimester, 2023-24 Stages of meiosis [extra notes] Urry L. A. et al. (2020) Campbell Biology, 12th edition, Pearson Education, Inc. (page 260). 85 Stages of meiosis [extra notes] Urry L. A. et al. (2020) Campbell Biology, 12th edition, Pearson Education, Inc. (page 261). 86 Comparing mitosis and meiosis Urry L. A. et al. (2020) Campbell Biology, 12th edition, Pearson Education, Inc. (page 263). 87 29 ANSC20010 Genetics and Biotech: Section 1 Spring Trimester, 2023-24 Comparing mitosis and meiosis Urry L. A. et al. (2020) Campbell Biology, 12th edition, Pearson Education, Inc. (page 263). 88 The behaviour of chromosomes during meiosis generates genetic diversity Three main processes generate genetic diversity: 1. The independent assortment of chromosomes into gametes: The arrangement of chromosomes at metaphase I determines which chromosomes (i.e., maternally-inherited or paternally-inherited chromosomes) are packaged in the gametes. 2. Crossing-over giving rise to genetic recombination: Exchange of genetic information between non-sister chromatids. 3. Random fertilisation of male of female gametes: Gametes that fuse during the process of fertilisation are ‘chosen’ at random. 89 Illustration of independent assortment of chromosomes [meiosis in a hypothetical organism (2n = 4)] Pole 1 Pole 2 Pole 1 Pole 2 Two equally probably chromosome arrangements at metaphase I Metaphase II Gametes Gamete combination 1 Gamete combination 2 Note: See Sections 2 and 3 90 30 ANSC20010 Genetics and Biotech: Section 1 Spring Trimester, 2023-24 Independent assortment of chromosomes and gametes The number of possible chromosome combinations in the gametes depends on the haploid chromosome number of the species (ignoring the effects of recombination.) Example combinations possible during meiosis = 2n (n = haploid number of chromosomes) for different species: Maize (n = 10): 210 = 1,024 Tomato (n = 12): 212 = 4,096 Apple (n =17): 217 = 131,072 Pig (n = 19): 219 = 524,288 Human (n = 23): 223 = 8,388,608 (≈ 8.4 million) Cattle (n = 30): 230 = 1,073,741,824 (≈ 1.1 billion) Horse (n = 32): 232 = 4,294,967,296 (≈ 4.3 billion) 91 Meiosis and crossing over with recombination https://youtu.be/pdJUvagZjYA 92 Meiosis and crossing over with recombination Crossing-over involves the exchange of chromosomal segments between non-sister chromatids. Crossing-over produces chromosomes that are different from the parental chromosomes. Gametes contain recombinant versions of the original parental chromosomes. Crossing-over is precise — it is a gene-by-gene process and there is no overlap or misalignment (mistakes happen rarely). Crossing-over with recombination is an important additional source of genetic variation. 93 31 ANSC20010 Genetics and Biotech: Section 1 Spring Trimester, 2023-24 Crossing over and recombination takes place in Prophase I of meiosis Note: See Section 3 Urry L. A. et al. (2020) Campbell Biology, 12th edition, Pearson Education, Inc. (page 266). 94 Crossing over and recombination takes place in Prophase I of meiosis Chiasmata (singular chiasma) are the physical points of contact between non-sister chromatids in a tetrad. (NB: sister chromatids in the same homologous chromosome can form chiasmata, but this has no genetic consequences because they are identical.) 95 Random fertilisation generates genetic diversity For humans, independent assortment of chromosomes can produce: ovum [egg] (~8.4 million chromosome combinations) sperm (~8.4 million chromosome combinations) A human zygote generated after fertilisation can have any of ~ 70 trillion (8.4 million × 8.4 million ≈ 7.0 × 1013) diploid combinations (and this ignores crossing-over!) For cattle, there are ~ 1 × 1018 (one quintillion!) possible diploid combinations in a zygote (ignoring recombination). Google sheets demonstration. 96 32 ANSC20010 Genetics and Biotech: Section 1 Spring Trimester, 2023-24 Human females: 300–500 eggs over a reproductive lifespan Human males: more than 500 billion sperm in a lifetime 97 33