Homework Assignments
Paper Review and Mapping Groups
Group Mapping Assignment
1 (Linkage Analysis)
Installing MAPMAKER on a MS Windows computer and completing training
Click here for Mapmaker Assignment
Original Mapmaker Manuscript
MAPMAKER Instructions
Mapping group1 of araba1.raw file
araba.raw - datafile for MAPMAKER instructions
araba.out - output file from
MAPMAKER example
MapDisto Instructions
QTL Mapping Assignment (Individual Analysis)
Assignment
Assignment Datafile
QGene Tutorial
Datafile 1
Datafile 2
Datafile 3
QTL
analysis of flowering time in Arabidopsis thaliana
Study
Questions for: QTL analysis of flowering time...
Comparison
of flowering time genes in Brassica rapa, B. napus and Arabidopsis thaliana
Study
Questions for: Compariosn of flowerng time genes...
Paper To Study for QTL Mapping Assingment
QTL
analysis of flowering time in Arabidopsis thaliana
Study
Questions for "QTL analysis of flowering..."
Comparison
of flowering time genes in Brassica rapa, B. napus and Arabidopsis thaliana
Study
Questions for "Comparison of flowering time genes..."
Exam 1: Electronic Copy (via e-mail) Due: March 10, 2022, 11 AM (10% grade reduction for late submission)
Exam 2: Electronic Copy (via e-mail) Due: May
10, 2022, 11 AM (10% grade reduction for late submission)
What we now know about Mendel
- Mendel's Genes: Toward a Full Molecular Characterization (Required) (January 23) Study questions
- Mendel, 150 Years On (January 23)
- Mendel's Genes
Phylogeny and domestication of crops
- Crop domestication as a long-term selection experiment (Required) (February 4); Study questions
- Evolution of Crop Species: Genetics of Domestication and Diversification (February 4) Study questions
- Patterns and Processes In Crop Domestication: An Historical Review and Quantitative Analysis of 2003 Global Food Crops (Resource paper)
Markers and Marker Development
- Markers and Mapping: We Are All Geneticists Now (February 13) Study questions
- A Molecular Marker-based Linkage Map of Phaseolus vulgaris (February 13) Study questions
- High Density Molecular Linkage Maps of the Tomato and Potato Genomes (February 13) 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)
Molecular Diversity - Markers
- Genetic Diversity of Soybean Cultivars from China, Japan, North America, and North American Ancestral Lines Determined by Amplified Fragment Length Polymorphism (Coming) Study Questions
- Genetic structure and diversity of cultivated soybean (Glycine max (L.) Merr.) landraces in China (Coming) Study questions
- A single domestication for maize shown by multilocus microsatellite genotyping (Coming) Study questions
- A reconsideration of the domestication geography of tetrapolid wheat (Optional) Study questions
Plant Quantitative Genetics
- Mapping and Analysis of Quantitative Trait Loci in Experimental Populations ( ; general background; read after lecture and ask questions during paper review)
- Mapping Quantitative Trati Loci in Plants: Uses and Caveats for Evolutionary Biology( general background; read after lecture and ask questions during paper review)
- 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)
Map-Based Cloning Papers
- fw2.2: A quantitative trait locus key to the evolution of tomato size (Coming)
- Fine mapping of quantitative trait loci Hd-1, Hd-2 and Hd-3,
controlling heading date of rice, as single Mendelian factors - Hd1, a Major Photoperiod Sensitivity Quantitative Trait Locus
in Rice, Is Closely Related to the Arabidopsis Flowering Time
Gene CONSTANS - Control of grain size, shape and quality by OsSPL16 in rice (Coming)
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
Class Discussion Papers
- Candidate Genes and Genetic Architecture of Symbiotic and Agronomic Traits Revealed by Whole-Genome Sequence Based Association Genetics in Medicago truncatula
- Genome-wide Association Study Dissects the Genetic-Architecture of Oil Biosynthesis in Maize
- Genome-wide association mapping of agronomic and morphologic traits in highly structured populations of barley cultivars () Study questions
- Linkage and association mapping of Arabidopsis thaliana flowering time in nature ( no study questions; read on your own)
- Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa ( general class discussion, no study questions) Study questions
Revew Papers
- Status and prospects of association mapping in plants
- Next-generation genetics in plants
- Association mapping for enhancing maize (Zea mays L.) genetic improvement
- Association studies identify natural variation at PHYC linked to flowering time and morphological variation in pearl millet
- Genome-wide association mapping in Arabidopsis identifies previously know flowering time and pathogen resistance genes
- Association mapping of yield and its components in rice cultivars Study Questions
- The genetic architecture of complex traits in teosinte: new evidence from association mapping
- To clone or not to clone plant QTLs: present and future challenges
- Genetic association mapping and genome organizationn of maize
- Association mapping of Stanospora modorum blotch resistance in modern European winter wheat varieties Study questions
- Dwarf8 polymorphisms associate with variation in flowering time
- Association analysis of candidate genes for maysin and chlorogenic acid accumulation in maize silks
- Linkage disequilibrium and association studies in higher plants: present status and future prospects
Transcription Regulation Reviews
- Notes from: The Evolution of Transcriptional Regulation in Eukaryotes
- The Evolution of Transcriptional Regulation in Eukaryotes
- Transcription Regulation and Animal Diversity
- Orchestrated Response- A Symphony of Transcriptional Factors for Gene Control
Plant Small RNAs