How to Map Thousands of SNPs

Plant Breeding and Genomics October 23, 2012 Print Friendly and PDF

Authors:

Allen Van Deynze, UC Davis; Heather L. Merk, The Ohio State University

During this webinar, Dr. Allen Van Deynze from UC Davis describes an approach to rapidly map tens of thousands of markers. Dr. Van Deynze presents a pipeline to group, order, and determine genetic map distances rapidly using the program Record. He also demonstrates visualization of linkage using heat maps.

Part 1 - Introduction

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Part 2 - MadMapper

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Part 3 - Record

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Part 4 - Check Matrix

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Part 5 - Summary and Discussion

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Full Webinar

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About This Webinar

With the advent of affordable whole genome sequencing and genotyping platforms, tens of thousands of markers can be rapidly developed in any crop, resulting in hundreds of thousands of datapoints even in closely related mapping populations. For example, over 3,000 markers have been mapped using Illumina Infinium chips in both potato and tomato. This has challenged even basic analyses of data, such as the simple generation of genetic maps that geneticists have become accustomed to. Standard softwares are no longer capable of handling these datasets efficiently. We have developed a pipeline to group, order and determine genetic map distances rapidly using the program Record. We then visualize linkage with heat maps using CheckMatrix. This pipeline is presented.

Learning Objectives

At the end of this webinar you should be able to:

  • Describe a pipeline to facilitate genetic mapping with large datasets
  • Use Record to group and order markers and determine genetic map distances
  • Visualize linkage with heat maps

About the Presenter

 

Dr. Allen Van Deynze is a professional researcher at the Seed Biotechnology Center at University of California, Davis. Allen received a BSc. and MSc. degree in plant science from the University of Manitoba, Canada and his Ph. D. in plant breeding from the University of Guelph, Canada.  He did a postdoctorate in molecular genetics at Cornell University in the Dept. of Plant Breeding and Biometry.  Allen worked as a plant breeder for Calgene/Monsanto and Senior Scientist for Celera AgGen where he developed and implemented strategies to incorporate biotechnology into breeding programs. As part of the SBC’s mission to serve as a liaison between public institutions and seed industry, Allen is responsible for developing, coordinating and conducting research and generating and disseminating scientific and informational content for the Seed Biotechnology Center’s educational and outreach programs. His research focuses on developing and integrating genomics into plant breeding of California crops. He has programs on cotton, lettuce, tomato, potato and particularly developing resistance in pepper to root rot and leaf blight. With Dr. Kent Bradford he co-developed and is organizer for the Plant Breeding Academysm and vice chair of the US Plant Breeding Coordinating Committee.

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Funding Statement

Development of this page was supported in part by the National Institute of Food and Agriculture (NIFA) Solanaceae Coordinated Agricultural Project, agreement 2009-85606-05673, administered by Michigan State University. Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the view of the United States Department of Agriculture.

Mention of specific companies is not intended for promotional purposes.

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USDA / NIFA

This work is supported by the USDA National Institute of Food and Agriculture, New Technologies for Ag Extension project.