Introduction to Genetic Analysis

The Genetics Revolution in the Life Sciences The nature of biological information How information becomes biological form Genetics and evolution Genetics has provided a powerful new approach to biological research Model organisms have been crucial in the genetics revolution Genetics changes society Genetics and the future PART I: TRANSMISSION GENETICS Single-Gene Inheritance Single-gene inheritance patterns The chromosomal basis of single-gene inheritance patterns The molecular basis of Mendelian inheritance patterns Some genes discovered by observing segregation ratios Sex-linked single-gene inheritance patterns Human pedigree analysis Independent Assortment of Genes Mendel's law of independent assortment Working with independent assortment The chromosomal basis of independent assortment Polygenic inheritance Organelle genes: inheritance independent of the nucleus Mapping Eukaryote Chromosomes by Recombination Diagnostics of linkage Mapping by recombinant frequency Mapping with molecular markers Centromere mapping with linear tetrads Using the chi-square test for testing linkage analysis Accounting for unseen multiple crossovers Using recombination-based maps in conjunction with physical maps The molecular mechanism of crossing over The Genetics of Bacteria and Their Viruses Working with microorganisms Bacterial conjugation Bacterial transformation Bacteriophage genetics Transduction Physical maps and linkage maps compared Gene Interaction Interactions between the alleles of a single gene: variations on dominance Interaction of genes in pathways Inferring gene interactions Penetrance and expressivity PART II: FROM DNA TO PHENOTYPE DNA: Structure and Replication DNA: the genetic material The DNA structure Semiconservative replication Overview of DNA replication The replisome: a remarkable replication machine Replication in eukaryotic organisms Telomeres and telomerase: replication termination RNA: Transcription and Processing RNA Transcription Transcription in eukaryotes Intron removal and exon splicing Small functional RNAs that regulate and protect the eukaryotic genome Proteins and Their Synthesis Protein structure The genetic code tRNA: the adapter Ribosomes The proteome Gene Isolation and Manipulation Overview: isolating and amplifying specific gene fragments Generating recombinant DNA molecules Finding a specific clone of interest Determining the base sequence of a DNA segment Aligning genetic and physical maps to isolate specific genes Genetic engineering Regulation of Gene Expression in Bacteria and Their Viruses Gene regulation Discovery of the lac system: negative control Catabolite repression of the lac operon: positive control Dual positive and negative control: the arabinose operon Metabolic pathways and additional levels of regulation: attenuation Bacteriophage life cycles: more regulators, complex operons Alternative sigma factors regulate large sets of genes Regulation of Gene Expression in Eukaryotes Transcriptional regulation in eukaryotes: an overview Lessons from yeast: the GAL system Dynamic chromatin Short-term activation of genes in a chromatin environment Long-term inactivation of genes in a chromatin environment Gender-specific silencing of genes and whole chromosomes Post-transcriptional gene repression by miRNAs The Genetic Control of Development The genetic approach to development The genetic toolkit for Drosophila development Defining the entire toolkit Spatial regulation of gene expression in development Posttranscriptional regulation of gene expression in development From flies to fingers, feathers, and floor plates: the many roles of individual toolkit genes Development and disease Genomes and Genomics The genomics revolution Obtaining the sequence of a genome Bioinformatics: meaning from genomic sequence The structure of the human genome Comparative genomics Functional genomics and reverse genetics PART III: MUTATION, VARIATION, AND EVOLUTION The Dynamic Genome: Transposable Elements Discovery of transposable elements in maize Transposable elements in prokaryotes Transposable elements in eukaryotes The dynamic genome: more transposable elements than ever imagined Epigenetic regulation of transposable elements by the host Mutation, Repair, and Recombination The phenotypic consequences of DNA mutations The molecular basis of spontaneous mutations The molecular basis of induced mutations Biological repair mechanisms Cancer: an important phenotypic consequence of mutation Large-Scale Chromosomal Changes Changes in chromosome number Changes in chromosome structure Overall incidence of human chromosome mutations Population Genetics Detecting genetic variation The gene pool concept and the Hardy--Weinberg law Mating systems Genetic variation and its measurement The modulation of genetic variation Biological and social applications The Inheritance of Complex Traits Measuring quantitative variation A simple genetic model for quantitative variation Broad sense heritability: nature versus nurture Narrow sense heritability: predicting phenotypes Mapping QTL in populations with known pedigrees Evolution of Genes and Traits Evolution by natural selection Molecular evolution: the neutral theory Natural selection in action: an exemplary case Cumulative selection and the paths to functional change Morphological evolution The origin of new genes and protein functions A Brief Guide to Model Organisms Appendix A: Genetic Nomenclature Appendix B: Bioinformatics Resources for Genetics and Genomics

'The author does an excellent job of showing how genetics is used today (one of the major strengths of the text).' - Kurt Dubear Kroening, University of Wisconsin, USA 'Its major strength is reflected in its title: that it introduces students to genetics as a mode of analysis. Not all students will become practicing geneticists, but what they can take away from learning through this text is how to construct knowledge by analyzing data and solving problems.' - Lynn A. Petrullo, College of New Rochelle, USA

ANTHONY GRIFFITHS Professor of Botany, Emeritus, at the University of British Columbia, Canada. His research focuses on the developmental genetics of fungi, using the model fungus Neurospora crassa. He has served as President of the Genetics Society of Canada and Secretary-General of the International Genetics Federation.

SUSAN R. WESSLER Distinguished Professor of Genetics in the Department of Botany and Plant Sciences at the University of California, USA. Her research focuses on plant transposable elements and their contribution to gene and genome evolution. Wessler was elected to the National Academy of Sciences in 1998. As a Howard Hughes Medical Institute Professor, she developed and teaches a series of Dynamic Genome Courses where undergraduates can experience the excitement of scientific discovery.

SEAN B. CAROLL Investigator at the Howard Hughes Medical Institute and Professor of Molecular Biology and Genetics at the University of Wisconsin, USA. Carroll is a leader in the field of evolutionary developmental biology and was elected to the National Academy of Sciences in 2007. He is also the author of Endless Forms Most Beautiful, The Making of the Fittest, and Remarkable Creatures (a finalist for the National Book Award, non-fiction, 2009).

JOHN DOEBLEY Professor of Genetics at the University of Wisconsin-Madison, USA. He studies the genetics of crop domestication, using the methods of population and quantitative genetics. He was elected to the National Academy of Sciences in 2003 and served as the President of the American Genetic Association in 2005.