SAS Tutorials

These tutorials describe statistical analyses using SAS statistical software.


(Figure 1) Example of SAS code for general linear model procedure and output.  Figure credit: modified from Jennifer Kling

See more on Statistical Inference

 

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How is forward breeding different from backcrossing?

In traditional backcross breeding, a trait, such as disease resistance, from a donor cultivar is introduced into a cultivar of interest, generally high yielding.  Offspring are selected for the introduced trait and crossed back to the high yielding cultivar for multiple generations.  The goal is to develop a cultivar identical to the high yielding cultivar with the exception of the introduced disease resistance trait. Backcross breeding takes several generations and for some species many years.

Forward breeding is a type of backcross breeding. Forward breeding takes advantage of improved cultivars and genetic knowledge that may have been developed during the process of backcross breeding.  In the case of forward breeding the “best” cultivar of interest is used as the recurrent parent, not the original cultivar of interest, allowing for the inclusion of recent breeding advances into the backcross breeding program. Forward breeding is described in United States Patent Application US20090064358, which you may find in on-line databases (http://www.freepatentsonline.com/20090064358.pdf).  Germplasm genotype is often a consideration in forward breeding.  Marker assisted selection is particularly useful when selecting for multiple quantitative traits.

Another modification of backcross breeding involves “background selection” or “donor genome elimination”, where the backcross process is accelerated by coupling phenotypic selection with genomic selection for the genetic background of the recurrent parent.

See more on Breeding and Selection.

Jewels in the Genome

imageJewels in the Genome: Short Reviews of Advancements in Trait Genetics
This series highlights genomic regions that are associated with important plant characteristics. Many of these genomic regions provide the basis for marker assisted breeding efforts.

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Biofortification of Cassava for Africa

Live broadcast from the 2012 Michigan State University Plant Breeding, Genetics and Biotechnology Graduate Programs’s Crop Improvement for Human Nutrition Symposium

Crop Improvement for Human Nutrition Symposium

The main purpose of agricultural production is to efficiently grow food so we can lead healthy, productive and prosperous lives. Historically, plant breeding’s main goal has been increasing yield. However, in the last decades questions have been raised about how much interest should be placed on the importance of food factors associated with human health that are commonly found in deficient levels among populations. In this symposium, we discuss the recent advances of plant breeding for human nutrition and their implications for consumers.

Find all of PBG’s upcoming and archived webinars and broadcasts »

Cassava for Africa: Presented by Richard Sayer

 

Richard Sayre, Los Alamos National Laboratory

Dr. Richard Sayre is the Director of the Biofuels project at the New Mexico Consortium working in conjunction with Los Alamos National Laboratory. Dr. Sayre received his Ph.D. from the University of Iowa and did post-doctoral work at Harvard University. Dr. Sayre is a former member of the Donald Danforth Plant Science Center where he served as the Director of the Enterprise Rent-A-Car Institute for Renewable Fuels. From 2005-2010, he was Director of the BioCassava Plus Program funded by the Bill and Melinda Gates Foundation; and from 2009-2011, was the Director of the Center for Advanced Biofuel Systems a DOE Energy Frontier Research Center. In relation to biofortification, his group currently focuses on increasing bio-available levels of iron in cassava, reducing cyanogen toxicity, increasing root protein content, reducing root post-harvest physiological deterioration, and developing root-specific promoters for transgene expression in cassava. Additional research programs focus on starch metabolism and biofuel production from cassava.

 

 

 

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R Tutorials

These tutorials describe statistical analyses using open source R software.


(Figure 1) Screenshot of the R Project for Statistical Computing Homepage

Download R and Individual R packages
http://www.r-project.org

R is free software for statistical computing and graphics. R runs on a wide variety of platforms; including, UNIX, Windows, and MacOS (See more on Statistical Inference). The following tutorials describe the use of R software in the analysis of breeding experiments.

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Lattice Designs Webinar

This webinar will describe the layout and analysis of lattice field designs.

Part 1

Part 2

Full Recording

Original broadcast: Thursday November 14, 2013 at 12:30 pm Eastern Time (-500 GMT)

About the Presenter

Jennifer Kling image

Dr. Kling is a plant breeder who teaches experimental design to graduate students in Agriculture at Oregon State University. She has considerable experience in the application of recurrent selection methods to improve yield, stress tolerance, and disease and insect resistance in cross-pollinating crops (maize and meadowfoam). She enjoys analyzing data and was the data curator for the Barley Coordinated Agricultural Project (Barley CAP). Dr. Kling received a Bachelors degree in Crop Science from Oregon State University and a Masters in Agronomy from the University of Nebraska-Lincoln. She obtained a Ph.D. in Genetics with a minor in Statistics from North Carolina State University.

Resources from the webinar

Webinar slides (pdf)

5×5 Simple Lattice Example (.xlsx)

Lattice Sample Data (.xlsx)

SAS code (.pdf)

Lattice Design References

  • Cochran, W.G., and G.M. Cox. 1957. Experimental Designs, 2nd ed., Wiley, New York.
  • Hinkelman, K, and O. Kempthorne. 2006. Design and Analysis of Experiments. Volume 2. Wiley, New York.
  • John, J.A., and E.R. Williams. 1995. Cyclic and Computer Generated Designs, 2nd edition. Monographs on Statistics and Probability, No. 38. Chapman and Hall, London, UK.
  • Kuehl, R.O. 2000. Chapt. 10 in Design of Experiments: Statistical Principles of Research Design and Analysis, 2nd edition. Duxbury Press.
  • Patterson, H.D. and E.R. Williams. 1976. A new class of resolvable incomplete block designs. Biometrika 63: 83–92.
  • Piepho, H.P. A. Büchse, and B. Truberg. 2006. On the use of multiple lattice designs and α-designs in plant breeding trials. Plant Breeding 125: 523–528.
  • Yau, S.K. 1997. Efficiency of alpha-lattice designs in international variety yield trials of barley and wheat. Journal of Agricultural Science, Cambridge 128: 5–9.

Find all upcoming and archived webinars »

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Application of Genomics to Strawberry Breeding Webinar

Original broadcast: Thursday, May 1, 2014 at 1:00 pm Eastern Time (-05:00 GMT)

Part 1

Part 2

Part 3

Full Video

Resources

Slides from the presentation (pdf)

About the Presenter

A native of Oak Ridge, North Carolina, Dr. Vance M. Whitaker completed his undergraduate degrees in Horticultural Science and Agricultural Economics at North Carolina State University. He later completed his graduate degrees at the University of Minnesota in Plant Breeding and Molecular Genetics. At Minnesota Dr. Whitaker’s research emphasis was in plant pathology, discovering and developing genetic markers for novel disease resistance genes in landscape roses.

Since 2009 Dr. Whitaker has directed the strawberry breeding program at the University of Florida’s Gulf Coast Research and Education Center, developing cultivars that are widely grown in west-central Florida and around the world. His cultivar development program is enhanced through genetic characterization of traits and through collaborative research with a statewide team of researchers in the areas of genomics, pathology, production and postharvest. In 2012 Dr. Whitaker was named the Outstanding New Researcher for the University of Florida’s Institute of Food and Agricultural Sciences. Dr. Whitaker currently resides in Brandon, FL with his wife Terri and his three children.

Find all upcoming and archived webinars »

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Phenotyping Apple for Project RosBREED

Authors:

Matthew Clark, University of Minnesota; Cari Schmitz, University of Minnesota; Dr. James Luby, University of Minnesota

This page provides a video demonstrating how to phenotype apple. This video was developed to standardize phenotyping of RosBREED’s Crop Reference Sets across the five rosaceous crops: apple, peach, strawberry, sweet cherry, and tart cherry.

You can view the video below or at www.rosbreed.org/resources/fruit-evaluation/phenotyping-videos/apple/

External Links

Luby, J., M. Clark, and C. Schmitz. 2010. Apple—RosBREED [Online]. RosBREED: Enabling Marker-Assisted Breeding in Rosaceae. Available at: http://www.rosbreed.org/resources/fruit-evaluation/phenotyping-videos/ap… (verified 2 Dec 2010).

Funding Statement

Development of this page was supported in part by the USDA’s National Institute of Food and Agriculture (NIFA). Project title: RosBREED: Enabling marker-assisted breeding in Rosaceae is provided by the Specialty Crops Research Initiative Competitive Grant 2009-51181-05808. 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.

 

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Polyploidy

These tutorials provide and introduction to polyploidy and provide examples of analyses using data from polyploid species.

Introduction

Analyses

 

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