Key Terms Gene: The basic unit of heredity, often encoding proteins or non-coding RNAs. Alleles: Variants of a gene at the same locus. Sequence differences, termed polymorphisms, can affect gene function or regulation. Homologs, Orthologs, Paralogs: Homologs: Genes related by common ancestry. Orthologs: Genes in different species from a shared ancestor, maintaining similar functions. Paralogs: Genes within the same organism from duplication, potentially evolving new functions. Reverse Genetics Definition: Hypothesis-driven approach to study gene function by disrupting or silencing specific genes to observe phenotypes. Methods: Mutations: Induce DNA sequence changes. Gene Inactivation (RNAi): Silence gene expression using RNA interference. Protein Depletion: Employ drugs or degradation systems like auxin-induced degradation. Applications: Study gene roles in cellular processes, tissue-specific functions, and gene-environment interactions. Challenges: Functional redundancy can mask phenotypes, requiring temporal and spatial control of gene inactivation. Testing Hypotheses: Correlate gene expression with biological processes using model organisms (e.g., yeast, C. elegans). CRISPR/Cas9 Overview: Genome editing tool for precise DNA modification. Components: Guide RNA (gRNA): Binds target DNA. Cas9 Protein: Cuts DNA at specific sites. Repair Template: Enables precise edits via homology-directed repair (HDR). Mechanism: Recognition: gRNA binds target DNA next to a PAM sequence (e.g., "NGG"). DNA Cutting: Cas9 induces double-strand breaks. Non-Homologous End Joining (NHEJ): Error-prone, causing random mutations. Homology-Directed Repair (HDR): Precise, using a repair template. Applications: Gene knockouts, pathway investigations, disease modeling, and genetically modified organisms. Advantages: High specificity, efficiency, versatility, and multiplexing capabilities. Limitations: Off-target effects, PAM dependence, challenges with essential genes, and ethical concerns. Floral Organ Development ABC Model of Flower Development: A Genes: Sepals (whorl 1) and petals (whorl 2). B Genes: Petals (whorl 2) and stamens (whorl 3). C Genes: Stamens (whorl 3) and carpels (whorl 4). A-C Mutual Inhibition: A and C genes repress each other. Homeotic Mutants: A Mutants: Sepals → Carpels, Petals → Stamens. B Mutants: Petals → Sepals, Stamens → Carpels. C Mutants: Stamens → Petals, Carpels → Sepals. MADS-Box Genes: Encode transcription factors (e.g., AP1, AP3, AG) essential for floral identity. SEPALLATA genes act as cofactors for ABC genes. Testing: Necessity: Gene knockouts reveal required roles. Sufficiency: Misexpression studies show additional factors needed. Genetics of Flowering Time Model Organism: Arabidopsis thaliana (small genome, short lifecycle). Control of Flowering: Regulated by day length, temperature, and circadian rhythms. Long Day Plants (e.g., Arabidopsis): Flower in extended daylight. Short Day Plants (e.g., rice): Flower in shorter daylight. Key Genes: CO (CONSTANS): Light-activated transcription factor. FT (Flowering Locus T): Protein promoting flowering by moving to the shoot apex. FD: Works with FT to activate floral meristem genes like AP1. Photoperiodic Regulation: Long Day: CO stabilizes in light, activating FT. Short Day: CO is degraded, suppressing FT. Grafting Experiments: Confirm FT protein as the mobile "florigen" that induces flowering. Quantitative Traits (Complex Traits) Definition: Traits influenced by multiple genes and environment, showing continuous variation (e.g., height). Types: Threshold Traits: Limited phenotypes (e.g., disease presence). Meristic Traits: Discrete values (e.g., eggs laid). Continuous Traits: Normal distribution (e.g., height). Variance and Heritability: Variance (Vx): Total variation in a trait. Broad-Sense Heritability (H²): Proportion of total variance due to genetics: H 2 = V a + V d V x H 2 = V x ​ V a ​ +V d ​ ​ Narrow-Sense Heritability (h²): Proportion of additive genetic variance: h 2 = V a V x h 2 = V x ​ V a ​ ​ Mapping Traits: QTL Mapping: Identifies genomic regions influencing traits, using genetic markers in controlled populations. GWAS: High-resolution scans of natural populations for associations between traits and genetic variants. Introduction to Epigenetics Epigenome: Chemical modifications influencing gene expression without altering DNA sequence. Mechanisms: DNA Methylation: Silences genes by adding methyl groups (e.g., CpG islands). Histone Modifications: Acetylation, methylation, etc., regulate chromatin states. H3K4me3: Active genes. H3K27me3: Silenced genes. Chromatin Remodeling: Alters large-scale chromatin structure (euchromatin vs. heterochromatin). Epigenetic Landscape: Developmental pathways resemble a ball rolling downhill, where stable cell fates are valleys. Reprogramming fibroblasts into stem cells illustrates forcing the ball uphill. Writers, Erasers, Readers: Writers: Add marks (e.g., methyltransferases). Erasers: Remove marks (e.g., demethylases). Readers: Interpret marks to guide gene expression. Computational Epigenomics Key Tools: ChIP-Seq: Maps histone modifications to study gene regulation. Challenges: Correlation vs. causation: Marks associate with gene expression but may not drive it. Complexity of Post-Translational Modifications (PTMs): Interactions complicate analysis.