Instructor Textbook Course Description Grading Honor System Course Topics Homework Mini-reviews

COURSE TOPICS Molecular Markers: Tools of Molecular Genetics Molecular Markers Study Guide Classes of Molecular Markers Lecture Notes Classes of Molecular Markers Lecture Notes Annotated Molecular Marker Detection Systems Molecular Marker Detection Systems-Annotated Mapping Populations Required Paper: Jones et al. Markers and Mapping: We Are All Geneticists Now Jones et al. Study questions Required Paper: Vallejos et al. A Molecular Marker-based Linkage Map of Phaseolus vulgaris Vallejos et al. Study questions Required Paper:Tanksley et al. High Density Molecular Linkage Maps of the Tomato and Potato Genomes Tanksley et al. Study questions Mendel's Discoveries and Molecular Genetics Mendel Genes Study Guide Required Paper: Reid and Ross. Mendel's Genes: Toward a Full Molecular Characterization (Required reading) Study questions for Reid and Ross paper Resource Paper: Mendel, 150 Years On (This will help your understanding of the cloning of the genes.) Mendel's Genes Plant Domestication Plant Domestication Study Guide Plant Domestication Lecture Notes Plant Domestication Lecture Notes Annotated Required Paper: Meyer and Purugganan. Evolution of Crop Species: Genetics of Domestication and Diversification Study questions for Meyer and Purugganan paper Resource Paper: Gepts. Crop domestication as a long-term selection experiment Study questions for Gepts paper Resource Paper:Meyer et al. Patterns and Processes In Crop Domestication: An Historical Review and Quantitative Analysis of 2003 Global Food Crops Resource Paper: Lenser and Theissen. Molecular mechanisms involved in convergent crop domestication Molecular Phylogenetics and Population Structure and Differentiation Molecular Population Genetics Analysis Study Guide Molecular Population Genetics Analysis Lecture Notes Molecular Population Genetics Analysis Lecture Notes - Annotated Wright - Analysis of Local Variability of Flower Color in Linanthus parryae (Paper of Histotric Importance) Epling and Dobzhansky - Genetics of Natural Populations. VI. Microgeographic Races in Linanthus parryae (Paper of Histotric Importance) Mapping Quantitative Trait Loci Mapping Quantitative Trait Loci Study Guide Fornara et al. (2010) SnapShot: Control of Flowering in Arabidopsis Mapping Quantitative Trait Loci Lecture Notes Mapping Quantitative Trait Loci Lecture Annotated Notes Clarke et al – QTL analysis of flowering time in Arabidopsis thaliana (Required Paper) Study questions for Clarke et al QTL paper Osborn et al - Comparison of flowering time genes in Brassica rapa B napus and Arabidopsis thaliana (Required Paper) Study questions for Osborn et al Flowering Time paper Sax - The association of size differences iwht seed-coat pattern and pigmentation in Phaseolus vulgaris (Paper of Histotric Importance) Linkage Disequilibrium and Association Mapping Linkage Disequilibrium and Association Mapping Study Guide Linkage Disequilibrium and Association Mapping Lecture Notes Linkage Disequilibrium and Association Mapping Lecture Notes-annotated Map-Based Cloning of Plant Genes: On-line Resources Study Guide Study Guide: Comments on Learning Objectives Added Map-Based Cloning of Plant Genes: Highlighted pdf notes Map-Based Cloning of Plant Genes: Graphic notes Cloning Qualitative and Quantitative Genes: On-line Lecture Pto Cloning Paper: Martin et al. 1993 Pto Cloning Paper: Martin et al. 1993-Study Questions fw2.2 Cloning Paper #1: Alpert and Tanksley 1996 fw2.2 Cloning Paper #2: Frary et al. 2000 fw2.2 Cloning Paper #2: Frary et al. 2000-Study Questions Hd1 Cloning Paper #1: Yamamoto et al. 1998 Hd1 Cloning Paper #2: Yano et al. 2000 Hd1 Cloning Paper #2: Yano et al. 2000-Study Questions DNA Sequencing Technologies DNA Sequencing Notes Genome Sequencing: On-line Resources Study Guide Genome Sequencing: Highlighted pdf notes Genome Sequencing: On-line Lecture Illumina Sequencing Technology Video PacBio Sequencing Video Pea Genome Paper - Kreplak et al. 2019 Maize Mo17 Genome Paper: Sun et al. 2019 Plant Genome Evolution: On-line Resources Study Guide Plant Genome Evolution: Highlighted pdf notes Plant Genome Evolution: On-line Lecture 1000 Plant Transcriptome/Phylogenetics Paper- OPTPI 2019 Bean Photoperiod Gene Paper: Weller et al. 2019 Sequencing and Evolution of Plant Genomes Sequencing and Evolution of Plant Genomes Overheads Evolution of Plant Genomes Narrative BLAST for Geneticists Plant Transposable Elements: On-line Resources Study Guide Plant Transposable Elements: Highlighted pdf notes Plant Transposable Eements: On-line Lecture TEs Effect on Phenotypic Variation: Wei and Cao 2017 TE Control of Blood Orange Expression: Butelli et al. 2012 Plant Transcription, Transcription Factors, and Chromatic Remodeling: On-Line Resources Study Guide Plant Transcription, etc: Highlighted pdf notes Plant Transcription, etc: On-line Lecture Cloning Rice QTL GLW7: Si et al. 2016 Transcription Animations Transcription mRNA Splicing mRNA Processing Regulated Transcription Plant Non-Coding RNAs: On-Line Resources Study Guide Plant Non-coding RNA: Highlighted pdf notes Plant Non-Coding RNA: On-line Lecture Micro RNA control of grape fruit color: Tirumalai et al. 2019 General lecture of non-coding RNAs miRNA Video (Arty and General) miRNAVideo (Detailed) Yu et al. - Plant Non-coding RNAs - Hidden Players in Development and Stress Responses (Background information) Rai et al. - Classification and Experimental Identification of Plant Long Non-coding RNAs (Background information) Higher Order Concepts: Second Half of Semester Second-Half Summary: Higher Order Concepts to Learn Control of Plant Gene Expression by Cis-Acting Elements and Trans-Acting Factors Genes Controlling Flower Development in Plants: Mendelian Genetics to Molecular Sequence Transposon Tagging of Plant Gene Analyzing Plant Gene Expression with Transgenic Plants