Preface The book is basically intended to accompany course in cytogenetics for students of Genetics and Plant Breeding in Agricultural universities. Present book with the help of diagrams and explanations it has been attempted that even a beginner could grasp the core elements of the subject. The book has been strictly organized on the basis of course curriculum of post graduate and PhD programs especially for courses “Principles of Cytogenetics1” (GP502) and “Molecular and Chromosomal Manipulation for Crop Breeding” (GP604) being taught inAgricultural Universities. This book also covers majority of the course outlines of course of Genetics for B Sc and BSc(Ag.) students. All the topics covered in the book have been ordered in a crisp and comprehensible manner avoiding complexities of a traditional textbook since it is a simply a guide book to supplement but not supplant the main texts. Moreover, this book is also open one for genuine suggestions, comments and corrections from any source/s which would be duly acknowledged and incorporated in the present text. The main objective of the book is just to help the students to prepare themselves for examination and competition in a quick way in short period. I would like to thank the many people without whose help or influence this book would not have been possible. Thanks to Prof. P.K.Gupta, my teacher and mentor who taught me the alphabet of this subject which helped me throughout my service period from assistant professor to Faculty Dean of RVSKVV, Gwalior(MP).Thanks to Prof. A.K Singh, Director Instruction, RVSKVV, Gwalior, Prof.A.K Sharma Deptt. of Plant Breeding and Genetics and Prof.(Smt) Reeti Singh who suggested me to put up my scrawled lecture notes in order and be published. I also extend my thanks to Mr. Sarman Karosiya and Rajesh Pal (computer operator) who helped immensely to prepare the manuscript on computer. Finally thanks to my wife Usha Malik and childern Ajeeta Singh, Ira Malik andAbhijeet Singh who always motivated me tofocus on academic persuits. Last but not least I would extend my thanks to publisher, New India Publishing Agency, New Delhi for expressing his keen interest to publish this book.

Most of the DNA of an living organism is packaged and organized in a chromosome as well as in mitochondria and cell organelles (Feulgen and Rossenbeck 1924). DNA is not found on its own but rather is structured in long strands wrapped around protein complex called nucleosome consisted of a protein called histone. During most of the duration of cell cycle a chromosome consists of long double helix DNA molecule (with associated proteins)During S phase the chromosome gets replicated resulting in X –shaped structure (chromatids) and still attached to a single centromere. The basic role of the chromosome is to provide a frame work which allows each linear segment of the genome to replicate and segregate efficiently. Failure in either of processes cause chromosome imbalance in daughter cells. Three specific cis-acting sites are required for stable chromosome maintenance, i.e., an origin of replication, a centromere and telomeres. Classical studies of the morphologyof individual chromosomesof the plant species begun by S. Nawaschin 1910-16 and continued by Taylor (1925), Sharp (1929) and Mc Clintock (1929-30). And eventually it was possible to set up working models which account for the internal structure and chemistry of the chromosome and the genetic material as well as genetical facts. The use of aceto-carmine with iron (Belling, 1921) and application of heat greatly improved the staining differentiation of chromosomes. Smears have practically replaced the paraffin techniques of studying chromosome. The gross morphology of chromosomes is generally worked out either at prophase stages of meiosis or metaphase in somatic tissues. The chromosomes may differ in thickness, total length, position of centromere or spindle fiber attachment region, chromomere pattern and number and position of secondary constriction. The total length of chromosomes at metaphase also differs in different tissues of a species and also in certain tissues chromosome present may be very different in appearance. Figure 1 shows various morphological features of a eukaryotic chromosome

The relationship between gene and chromosome was suspected at the time of rediscovery of Mendelian, Laws. During that period Montgomery (1901) and Walter Sutton (1902) working on grasshoppers showed that chromosomes occur in distinct pairs, often of recognizable shape and size, and that synapsis involves the union of maternal and paternal chromosomes, while Winiwarter (1901) concluded from his studies in rabbit ovaries that bivalents in the first meiotic division resulted from the chromosome pairing side by side and not end to end as believed by some other workers of that time . Theodor Bovery (1902) showed from his work on polyspermy in the fertilization of sea urchin eggs that the chromosomes of an individual were not equivalent (genetic information) to one another and hence a full chromosomal complement is essential for normal development of cell. Correns (1902) and Cannon (1902) pointed out close parallelism between Mendelian segregation and chromosome reduction during meiosis and concluded that genes are located on chromosomes but they, like de Vries, supposed that maternal and paternal chromosomes move to opposite poles during meiosis. In the same year Guyer established an understanding that random assortment between different pairs of chromosomes would give the independent assortment of genes required by Mendel. Ultimately Sutton (1903) brought together the ideas from cytology and genetics to clearly show the role of chromosomes in heredity and hence to establish the field of cytogenetics. Boveri also through his work, advanced many of the same ideas and thus the hypothesis correlating genes and chromosome transmission was established, which is known as the “Sutton-Boveri Hypothesis or chromosome theory of inheritance”.

The chromosomes provide physical basis by which genetical stability and continuity of individuals and populations are maintained in each generation. Chromosomes also play an important role to generate variation which is an essential component of evolutionary process. Although crossing over during meiosis is responsible for generation of variability, but structural changes in chromosome too are important for causing variation and evolution, since genetic and cytological analysis of individuals of related species or isolated populations within the species have shown that they may differ by various kinds of changes in their chromosomal structure. The structural changes usually may result from spontaneous chromosome breakage. But under normal condition/s such breakage is an rare event and its frequency is dependent upon environmental conditions, i.e., temperature, various high energy radiations (e.g. X, λ and β-rays) and some chemicals. Chromosome breakage is reported to be higher in some hybrids and in presence of particular genes. Certain chromosomes and chromosomal segments (centromeric and other heterochromatic regions) are more likely to undergo breakage. But stability and continuity of structural changes in the chromosomes depend on the behavior of the broken ends. There is no change if broken end rejoins at the same chromosome but a change may occur if it rejoins with the end of other chromosome or if remains unattached. In case of a pair of homologous chromosomes if one chromosome has any structural change and other one is normal we customarily call it a structural hybrid.

The intervarietal chromosome substitution lines of wheat (T. aestivum) are utilized to study the effects of individual whole chromosome/s on agronomic characters of interest to improve crop plants to be selected for preferred traits (Law and Worland 1973). The common method to develop subsitutiion lines involves development of monosomics lines first of that variety which are used later as recipient variety or recurrent parent for substitution. Presently monosomic lines of several wheat varieties are available. However, the development of substitution lines for a specific chromosome by using monosomics sometimes may be erroroneus due replacement of specific monosome by another one of the 21 chromosome set from the donor to the recipient and consequently monosomic becomes monosomic for another chromosome or a recombined chromosome (univalent shift.). Therefore, to maintainand confirmthe identityof a chromosome involved in monosomy are tagged with either genetic marker/s or confirmed cytologically or with the help of molecular markers.

The newly synthesized autopolyploids, having few or more undesirable features, e. g; meiotic instability, low seed setting and late maturity etc, are usually not suitable for immediate commercial use, are known as raw polyploids. This is specifically more applicable for those sexually propogated polyploids which are developedfor seed. In early generations due to polyploid chromosome constitution and polysomic inheritance they predominanantly do not breed true. Further more, due to meiotic instability chromosome number in their progeny is not always constant or equal to as in synthesized autotetraploid which may vary from few more to few less than the standard autotetraploid. The raw polyploids usually reverts back to diploid parental constitution due chromosome elimination (Randolph and Fischer, 1939). The mechanism responsible for reverting back to diploid status is similar to that of which give rise haploids from diploids. Presently cases are known where either spontaneously or due to specific treatments the chromosome number was reduced to half in somatic tissues. The phenomenon causing such chromosomal reduction is termed as somatic reduction or reduced mitosis Earlier reports suggested it probably to be caused due to spindle organizer abnormalities or some other unknown mechanism/s. The treatment of seed or seedling by colchicine, chloramphenicol and paraflurophenylalanine are reported to have induced chromosome reduction and production of haploids.

Wide hybridization (interspecific/intergeneric) is basically attemped to introduce new genetic variability from wild or distantly related species into cultivated ones or to synthesize new plant type/s like Triticale and Raphanobrassica. Majority of the commercial crop plants are usually deficient for one or the other desirable traits which are usually available in their wild relatives. However, crossability between commercial varieties and their wild relatives is very limited which is naturally imposed by certain genetically controlled reproductive barriers. These reproductive barrier/s usually operate either at pre or post fertilization stage/s in plant species (Stebbins1958). Since a species is constituted of individuals who share a common gene pool, reproduce among themselves only / exchange genes and share a common habitat. Hence at natural level gene flow remains strictly confined only among members of a particular species otherwise among the members of unrelated species a genetic barrier exists to create reproductive isolation. Therefore, wide crossing basically requires the overcoming of such barriers whch are imposed by temporal and spatial isolation of parents. The reproductive isolation consists of premating and post mating isolation mechanisms like habitat isolation or geographical isolation, sexual isolation and mechanical barrier depending upon incompatibility or mismatching of ganitalia (animals). Sexual isolation in animal kingdom is usually enforced by type of sexual displays and mating calls which are attractivce only to particular members of a species , however other potential intermating species also do exist in the same habitat or locality at that particular period of time.

Index A Aberrant segregatin 35, 40, 131 Achiasmate meiosis 33 Acrocentric, 2, 44, 68, 69, 122 Aegilops umbellulata 78, 167, 174 Alien addition 145, 146, 148, 167 Alien gene introgression 160, 164 Alien substitution 145, 146 Allo-hexaploids 104 Allopolyploidization 93, 94, 164 Allopolyploidy 81, 94, 95, 97, 160 Alternate disjunction 70, 73, 75