Tariq Ahmad Bhat · Aijaz Ahmad Wani Editors Chromosome Structure and Aberrations Chromosome Structure and Aberrations [email protected] Tariq Ahmad Bhat • Aijaz Ahmad Wani Editors Chromosome Structure and Aberrations [email protected] Editors Tariq Ahmad Bhat Aijaz Ahmad Wani Department of Education Department of Botany Government of Jammu and Kashmir University of Kashmir Srinagar, India Srinagar, Jammu and Kashmir, India ISBN 978-81-322-3671-9 ISBN 978-81-322-3673-3 (eBook) DOI 10.1007/978-81-322-3673-3 Library of Congress Control Number: 2017930685 © Springer India 2017 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. The publisher, the authors and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, express or implied, with respect to the material contained herein or for any errors or omissions that may have been made. Printed on acid-free paper This Springer imprint is published by Springer Nature The registered company is Springer (India) Pvt. Ltd. The registered company address is: 7th Floor, Vijaya Building, 17 Barakhamba Road, New Delhi 110 001, India [email protected] [email protected] Foreword Chromosomes have always fascinated me as remarkably condensed DNA thread- like structures regulating all the phenotypic features and physiological processes of an organism. Equally fascinating is the history of its discovery. Starting right from 1869, when the genetic material was first reported as “nuclein” in pus cells by Friedrich Miescher, followed by unequivocal experimental evidence provided by Oswald Avery, Colin MacLeod and Maclyn McCarty in 1944 for DNA as the genetic material in the cell and then the revolutionary DNA double helical structure of James Watson and Francis Crick in 1953 based upon X-ray diffraction analysis done by Rosalind Franklin and Maurice Wilkins – all have proven to be turning points in our understanding of life processes. The knowledge gained as a result of global interest in the DNA molecule led us into the era of recombinant DNA tech- nology, transgenesis, animal cloning and ultimately embarking on Human Genome Project. The DNA molecule with its fundamental nucleotide base composition has been the driving force behind all the biological phenomena. The simple organisms had few base pairs (bp), which continued to grow in number depending upon the complexity of the organisms along the evolutionary scale. The smallest number of base pairs (bp) has been reported from a virus – porcine circovirus type with 1.8 × 103 bp. The number of bp continued to increase with the increase in complex- ity during the course of evolution spanning billions to millions of years. The bacte- rium Escherichia coli has 4.6 × 106 bp (4288 genes), Caenorhabditis elegans 10 × 107 bp (19,000 genes), Arabidopsis thaliana 15.7 × 107 bp (25,498 genes), Drosophila melanogaster17.6 × 107 bp (13,600 genes), Mus musculus 6.4 × 109 bp (20,000 genes) and Homo sapiens 6.9 × 109 bp (30,000 genes). In prokaryotes, the organisms could manage to accommodate this DNA (chromosome) in their proto- plasms, but with the evolution of eukaryotes, the increasing size of DNA/chromo- some ultimately delimited itself from the cytoplasm by nuclear envelope. In order to accommodate large size of DNA within a limited space, the DNA molecule under- went process of packaging, for which histone protein and variety of looping, coiling and coiled coiling helped in condensation of chromosomes. During the course of evolution, the long DNA broke into smaller pieces, which later became the charac- teristic karyotype of the organisms. These chromosomes are in their relaxed state during interphase when the cell is not dividing but are condensed into specific num- ber and shape of typical metaphase structure during dividing phase. This cycle of condensation and decondensation is such an organized and orchestrated sequence of vii [email protected] viii Foreword events that organisms remain healthy and normal, both phenotypically and geno- typically. Any mishap during interphase and more so during mitotic or meiotic dividing phases results in genetic abnormalities. There are a variety of genetic syn- dromes which are the result of accidental changes in the number of chromosomes or loss or rearrangement of segments of chromosomes particularly during mitotic metaphase and anaphase and meiotic prophase, which are passed on to the next generation and become the basis of mild to severe abnormalities and in several cases become fatal. These biological phenomena prompted the preparation of this book. The history of development of concept of chromosomal basis of inheritance and the molecular structure of chromosomes is given in Chap. 3. Chapter 12 encom- passes the phenomena of number of chromosomes, which is normally fixed for a particular species, and the consequences of accidental increase or decrease in the chromosomal number. Chapter 13 describes the abnormalities arising due to struc- tural rearrangements of chromosomes or chromosomal segments such as inversions, deletions, translocations, etc., which have far-reaching genetic implications with physical, physiological and mental debilities. Chapter 6 deals with two more cate- gories of chromosomal abnormalities, i.e. asynapsis and desynapsis. Conjugation of the chromosomes during the first meiotic prophase is referred to as synapsis, and the lack of this pairing is referred to as asynapsis. Desynapsis is the condition when chromosomes initially pair at pachytene but fail to remain paired at subsequent meiotic stages. Such conditions usually result in chromosomal imbalance. Usually, eukaryotic cells are diploid, but there are some eukaryotes that contain more than two sets of chromosomes. Such cells are called as polyploid and are common in plants. Rice, for example, are diploid plants, banana is triploid, cotton is tetraploid, wheat is hexaploid, and sugarcane is octaploid. On the basis of number of chromo- somes, polyploidy can be divided into euploidy and aneuploidy. Chapter 10 deals with polyploidy and its role in crop improvement. In addition to normal karyotype, wild populations of animals, plants and fungi contain B chromosomes, also known as supernumerary or accessory chromosomes. These chromosomes are not essential for life. Most of them are entirely or mainly heterochromatic, though some contain euchromatic segments. These chromosomes have been dealt with in Chap. 2. Chromosomes can be studied under the light microscope using different types of chromogenic dyes. Chapter 14 gives a broad outline of all the cytogenetic tech- niques prevalent for understanding structure of chromosome. Over the past few decades, versatile methods based on fluorescence in situ hybridization (FISH) have transformed cytogenetics into a molecular science and provided cytogeneticists with powerful new tools. FISH procedures are now routinely employed in clinical cytogenetics. Although chromosomes may appear to be static structures when viewed under a microscope, cytogeneticists know that chromosomes are actually dynamic assemblies made up of a DNA-protein complex called chromatin. This chapter takes stock of all the prevalent techniques, highlighting the principals involved in each method. Karyotyping, genetic mapping, fluorescence in situ hybridization (FISH), multiplex FISH, spectral karyotyping, flow cytometry and microarray have been described. New trends in cytogenetics to understand the molecular mechanism have been discussed under new generation sequencing. [email protected] Foreword ix Chapter 16 describes the FISH techniques and its applications, while Chap. 4 pro- vides guidelines to cytological techniques written specifically for the plant chromo- somes. Chapter 8 describes banding techniques to study different parts of the chromosomes. The chapter describes G, Q, R banding which requires heating in a saline buffer prior to staining with Giemsa or quinacrine and is often called T band- ing, since it also highlights telomeres. C stains heterochromatin in the centromeres, and NOR silver nitrate stains selectively the satellite stalk of the acrocentric chro- mosome. Flow cytometry is another cytogenetic technique, which measures optical and fluorescence characteristics of single chromosome preparation. The informa- tion obtained is both qualitative and quantitative. The principle involved and its applications have been discussed in Chap. 5. The 2000s witnessed an explosion of genome sequencing and mapping in evolutionarily diverse species. While full genome sequencing of mammals is rapidly progressing, the alignment of whole chromosomal regions from more than a few species is not possible. Building of comparative maps for domestic, laboratory and agricultural animals has tradition-