Tomato Genetics and Breeding Program       

 HCS 825                          

                                                                    click here for SAS Resources

Introduction

Lecture 1

Lecture 2

Data set for lecture 2 exercise chszero.xls

Lecture 3

Data set for lecture 3 class discussion chsdata2.xls

Data set for lecture 3 exercise 2353master.xls

Lecture 4

Data set for lecture 4 class discussion and exercise lycdat1.xls, 2yrlyc.xls, f2f3lyc.xls

SAS code for Parent-Offspring Regression

Lecture 5

Lecture 6

Power point presentation: introduction to lecture 6

Lecture 7

Genetic Distance Calculations.  The program GDIS.EXE has been compacted. You may download the "zip" file and extract the program using WINZIP.  GDIS1.ZIP

Description of GDIS program GDID1.pdf

Sample Data Set gdid.txt

Sample output gdidout.txt

Soybean Data ssrdt-3.xls

Lecture 8

Lecture 9 (paper discussion)

Lecture 10 (review session)

Midterm

Key to midterm

Minimum Family sizes for Genetic Analysis

Lecture 11

Lecture 12

Linkage analysis and Marker Assisted Selection

Lecture 13

introduction (power point)

Data Set for Exercise

Exercise Key

Lecture 14

Lecture 15

Mapping resources

 Mapmaker from FTP

Example MAPMAKER Run (Holsinger, 2001)

Software documentation

Mapmaker manual

Linkage mapping software at Weizmann Institute

Software at Rockefeller

Genetic Linkage Software at European Bioinformatics Institute

Exercise

Excel data set 2361f2.xls

Text data set 2361f2b.txt

Class Project Example

                In 2000, Marco T. Buenrostro-Nava, a Ph D student in Dr. Finer's lab, chose to learn MAPMAKER for his class project.  I have linked his written report in order to provide an example of the expected format for projects and to provide you more resources for MAPMAKER.  I have also linked the data set that Marco used (RFLPf2.txt) and a second data set RFLPQTL.txt.  The data set used by Marco consisted of 124 f2 progeny from a cross between L. esculentum and L. cheesmanii.  The cross was genotyped with 151 molecular markers. A second data set, RFLPQTL.txt, is an expanded data includes 146 progeny from the same cross and 20 quantitative traits.  

                These data are provided for those of you who want further practice with MAPMAKER or MAPMAKER QTL.

Marco's Presentation

RFLPf2.txt

RFLPQTL.txt

Lecture 16 Power point presentation

Student presentations

Asea

Robin

Rebecca

Edgar

Jianyang

Le-Nguyen

Final Exam

HCS 604.3