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

Homework Assignments Group Assignment 1: Click here for Mapmaker Assignment Original Mapmaker Manuscript MAPMAKER Instructions araba.raw - datafile for MAPMAKER instructions araba.out - output file from MAPMAKER example putty and WinSCP3 instructions Exam 1 Exam 1 2008 Paper 1: Simple sequence repeats reveal uneven distribution of genetic diversity in chloroplast genomes of Brassica oleracea L. and (n=9) wild relatives Paper 2: Domestication patterns in common bean, Phaseolus vulgaris, and the origin of the Mesoamerican and Andean cultivated races Exam 2 Exam 2 2008 Paper 1: Fine Mapping of a Major Quantitative Trait Loci, qSSP7, Controlling the Number of Spikelets Per Panicle as a Single Mendlian Factor in Rice Paper 2: Association Mapping of Partitioning Loci in Barley Paper 3: The Wheat VRN2 Gene Is a Flowering Repressor Down-Regulated by Vernalization Reading Assignments Phylogeny and domestication of crops Crop domestication as a long-term selection experiment (Required) (January 17); Study questions Genetics and geography of wild cereal domestication in the Middle East (Required) (January 17); Study questions Molecular diversity, structure, and domestication of grasses (Required) (January 22); Study questions A reconsideration of the domestication geography of tetrapolid wheat (Required) (January 22); Study questions A single domestication for maize shown by multilocus microsatellite genotyping (Required) (January 22); Study questions The Role of Phylogenetics in Comparative Genetics (Optional) Plant Comparative Genetics After 10 Years (Optional) Beyond The Arabidopsis Genome - Opportunities For Comparative Genomics (Optional) The Site of Einkorn Wheat Domestication Identified by DNA Fingerprinting (Optional) Markers and Marker Development Markers and Mapping: We Are All Geneticists Now (February 7) Study questions A Molecular Marker-based Linkage Map of Phaseolus vulgaris (February 7) Study questions High Density Molecular Linkage Maps of the Tomato and Potato Genomes (February 7) Study questions Gene Mapping With Recombinant Inbreds in Maize (Optional) Identification of Markers Linked to Disease Resistance Genes by Bulked Segregant Analysis: A Rapid Method to Detect Markers in Specific Genomic Regions by Using Segregating Populations (Optional) Target Region Amplification Polymorphism: A Novel Marker Technique for Plant Genotyping (Optional) Sequence-Related Amplified Polymorphism (SRAP), A New Marker System Based On A Simple PCR Reaction: Its Application To Mapping And Gene Tagging In Brassica (Optional) Molecular Diversity - Markers Genetic structure and diversity of cultivated soybean (Glycine max (L.) Merr.) landraces in China (February 9) Study questions Segmental structure of the Brassica napus genome based on comparative analysis with Arabidopsis thaliana (February 11) Study questions Comparative Genome Mapping of Sorghum and Maize (Feb 28) Study Questions Evaluation of soybean RFLP marker diverstiy in adapted germ plasm (Feb 28) Study Questions Similarity coefficeints for molecular markers in studies of genetic relationships between individuals for haploid, diploid, and polyploid species (Optional) Analysis of genetic diversity in crop plants - salient statistical tools and considerations (Optional) Optimization of the Choice of Molecular Markers for Varietal Identification in Vitis vinifera L. (Optional) Genetic Diversity of Soybean Cultivars from China, Japan, North America, and North American Ancestral Lines Determined by Amplified Fragment Length Polymorphism (Optional) AFLP Analysis of the Phenetic Organization and Genetic Diversity of Vigna unguiculata L. Walp. Reveals Extensive Gene Flow Between Wild and Domesticated Types (Optional) Molecular Diversity - Sequence Data Nucleotide sequence variation at two genes of the phenylpropanoid pathway, the FAH1 and F3H genes, in Arabidopsis thaliana (Mar 11) Study Questions Nucleotide sequence diversity at the alcohol dehygrogenase 1 locus in wild barley (Hordeum vulgare ssp. spontaneum): An evaluation of the background selection hypothesis (Mar 11) Study Questions Genetic diversity and selection in the maize starch pathway (Mar 11) Study Questions Plant Quantitative Genetics Mapping and Analysis of Quantitative Trait Loci in Experimental Populations (Apr 2,3; general discussion, bring questions) Mapping Quantitative Trati Loci in Plants: Uses and Caveats for Evolutionary Biology (Apr 2,3; general discussion, bring questions) QTL analysis of flowering time in Arabidopsis thaliana (Apr 3,8) Study Questions Comparison of flowering time genes in Brassica rapa, B. napus and Arabidopsis thaliana (Apr 3,8) Study Questions QTL analysis in plants; where are we now? (Background reading only) Quantitative Traits in Plants: Beyond the QTL (Background reading only) The principles of QTL analysis (a minimal mathematics approach) (Background reading only) Classic Plant Quantitative Genetics Papers The associaiton of size differences with seed-coat pattern and pigmentation in Phaseolus vulagaris Resolution of quantitative traits into Mendelian factors by using a complete map of restriction fragment length polymorphisms The power and deceit of QTL experiments: lessons from comparative QTL studies [in 49th Corn and Sorghum Research Conference (Washington D.C.: American Seed Trade Association) pp 252-268, 1994)] Molecular-marker-facilitated investigations of quantitative trait loci in maize: I. Numbers, genomic distribution, and types of gene action Empirical threshold values for quantitative trait mapping Association Mapping To clone or not to clone plant QTLs: present and future challenges (April 10; introduction) Genetic association mapping and genome organizationn of maize (April 10; introduction) Association mapping of yield and its components in rice cultivars (April 15,16,17) Study Questions Association mapping of Stanospora modorum blotch resistance in modern European winter wheat varieties (April 15,16,17) Study questions Dwarf8 polymorphisms associate with variation in flowering time (April 15,16,17) Association analysis of candidate genes for maysin and chlorogenic acid accumulation in maize silks (April 15,16,17) Linkage disequilibrium and association studies in higher plants: present status and future prospects (Background reading only) Map-based (or Positional) Cloning - Review and Examples Positional cloning in Arabidopsis: Why it feels good to have a genome initiative working for you (Primary review: April 23) Arabidopsis map-based cloning in a post-genomic era (Review: on your own) Map-based cloning of a protein kinase gene conferring disease resistance in tomato (April 24) The barley Mlo gene: A novel control element of plant pathogen resistance (April 24) The Arabidopsis downy mildew resistance gene RPP5 shares similarity to the Toll and Interleukin-1 receptors with N and L6 (April 26) fw2.2: a quantitative trait locus key to the evolution of tomato fruit size (April 26) Cloned Plant QTL A QTL for flowering time in Arabidopsis reveals a novel allele of CRY2 Hd1, a major photoperiod sensitivity quantitative trait locus in rice is closely related to the Arabidopsis flowerint time gene CONSTANS Hd6, a rice quantitative trait locus involved in photoperiod sensitivity, encodes the alpha subunit of protein kinase CK2 Hd3a, a rice ortholog of the Arabidopsis FT gene, promotes transition to flowering downstream of Hd1 under short-day conditions A new class of regulatory genes underlying the cause of pear-shaped tomato fruit Map-based (or Positional) Cloning - Other Papers Phenotypic characterization and molecular mapping of the Arabidopsis thaliana locus RPP5, determining disease resistance to Peronospora parasitica (RPP5 mapping paper) Positional Cloning of the Wheat Vernalization Gene VRN1 The Wheat VRN2 Gene is a Flowering Repressor Down-regulated by Vernalization Plant Disease Resistance - General Plant disease resistance genes - recent insights and potential applications Recognition and response in the plant immune system Transcription Regulation Reviews Notes from: The Evolution of Transcriptional Regulation in Eukaryotes (April 30) The Evolution of Transcriptional Regulation in Eukaryotes Transcription Regulation and Animal Diversity Orchestrated Response- A Symphony of Transcriptional Factors for Gene Control