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Plant Breeding for Drought Tolerance: Short Course June 2-13, 2014

Colorado State University will offer a three-credit, graduate-level, field-oriented course in Plant Breeding for Drought Tolerance, June 2-13, 2014. The course will be held in and around Fort Collins, Colorado, USA and is targeted to graduate students in the plant sciences, as well as to professionals in the public and private sectors interested in increasing their knowledge in this area.

Additional information on the course content, format, cost, and registration is available at For questions, pleasecontact the Program Assistant, Kierra Jewell ( Applications will be accepted through March 15, 2014 or until the class is full (20 students).

Breeding with Genomics Course at UC Davis February 11, 2014

The Seed Biotechnology Center at UC Davis is having their Breeding with Genomics Course on February 11 - 13, 2014.

PBG's own David Francis and our former content coordinator Shawn Yarnes are part of this event. 

Below is some information provided by the Seed Biotechnology Center. Visit their webpage to learn more and to register! The early bird registration ends this Sunday, December 15. 

The course covers the basics of DNA markers, quantitative trait loci and the transition from maker assisted selection with a highlight on breeding for disease resistance.

New for 2014!
Extended modules on genomic selection, the latest integration of genomics to breeding, and a hands-on workshop on software support to marker application in breeding including the Integrated Breeding Platform and BLUPS.

Who should attend?
The course is aimed at professionals who are directly or indirectly involved in plant breeding and germplasm improvement.  It is an opportunity for breeders who are already using these tools to expand their knowledge of new strategies and technologies and for laboratory personnel to appreciate how the marker data that they generate are applied in breeding programs.

The course is taught by experts from both industry and academia.  This is a great chance to interact with experts and technology specialists in plant breeding. They include:

Allen Van Deynze, UC Davis
Hamid Ashrafi, UC Davis
Kent Bradford, UC Davis
Jorge Dubcovsky, UC Davis
David Francis, The Ohio State University
Shawn Yarnes, The Integrated Breeding Platform Initiative
Graham McLaren, The Integrated Breeding Platform Initiative
Alison Van Eenennaam, UC Davis

December 2013

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Join the symposium live from Michigan State University by registering at the link below.

Title: Genetics of Seed Quality, Germination and Evolution
Date: Friday, December 13, 2013
Time: 9:00 am - 4:00 pm Eastern Time


9:10 - 10:00 Dr. Hiro Nonogaki, Oregon State University
“Transcriptional and Post-transcriptional Regulation of Gene Expression Associated with Hormone Signaling in Seeds.”

10:40 - 11:30 Dr. Kristin Mercer, Ohio State University
“Evolutionary Ecology Of Seeds In Crop-Wild Hybrid Zones.”

1:35 - 2:25 pm Dr. Chris Richards, US National Center for Genetic Preservation
"Genetic Dynamics in Conservation Collections"

3:05 - 3:55 pm Dr. Oswald Crasta, Leader, Genomics Assisted Breeding, Dow AgroSciences
"Next-generation breeding"

Publications of Interest

Plant breeding can be broadly defined as alterations caused in plants as a result of their use by humans, ranging from unintentional changes resulting from the advent of agriculture to the application of molecular tools for precision breeding. The vast diversity of breeding methods can be simplified into three categories: (i) plant breeding based on observed variation by selection of plants based on natural variants appearing in nature or within traditional varieties; (ii) plant breeding based on controlled mating by selection of plants presenting recombination of desirable genes from different parents; and (iii) plant breeding based on monitored recombination by selection of specific genes or marker profiles, using molecular tools for tracking within-genome variation. The continuous application of traditional breeding methods in a given species could lead to the narrowing of the gene pool from which cultivars are drawn, rendering crops vulnerable to biotic and abiotic stresses and hampering future progress. Several methods have been devised for introducing exotic variation into elite germplasm without undesirable effects. Cases in rice are given to illustrate the potential and limitations of different breeding approaches.
Neglected and underutilized species (NUS) are those to which little attention is paid or which are entirely ignored by agricultural researchers, plant breeders and policymakers1. Typically, NUS are not traded as commodities. They are wild or semi-domesticated varieties and non-timber forest species adapted to particular, often quite local, environments. Many of these varieties and species, along with a wealth of traditional knowledge about their cultivation and use, are being lost at an alarming rate. Yet NUS present tremendous opportunities for fighting poverty, hunger and malnutrition. And they can help make agricultural production systems more resilient to climate change. Not least, acknowledgment of the value of NUS in traditional foods and cultures can empower indigenous communities (women in particular) and reaffirm their identity. The time for action on NUS is now. There is a growing realization that agriculture must diversify. NUS have an important role to play in advancing agricultural development beyond the Green Revolution model of improving and raising the yields of staple crops.
Most methods for next-generation sequencing (NGS) data analyses incorporate information regarding allele frequencies using the assumption of Hardy–Weinberg equilibrium (HWE) as a prior. However, many organisms including those that are domesticated, partially selfing, or with asexual life cycles show strong deviations from HWE. For such species, and specially for low-coverage data, it is necessary to obtain estimates of inbreeding coefficients (F) for each individual before calling genotypes. Here, we present two methods for estimating inbreeding coefficients from NGS data based on an expectation-maximization (EM) algorithm. We assess the impact of taking inbreeding into account when calling genotypes or estimating the site frequency spectrum (SFS), and demonstrate a marked increase in accuracy on low-coverage highly inbred samples. We demonstrate the applicability and efficacy of these methods in both simulated and real data sets.


Reminder: Lattice Designs Webinar This Week

Join PBG for our webinar this week:

Title: Lattice Designs

When: Thursday, November 14 at 12:30 pm ET (New Time!)

Presenter: Dr. Jennifer Kling, Oregon State University

Registration Link:

Hope to see you there!

Find us on eXtensionGoogle+, Facebook, Twitter, or YouTube



November 2013

Plant Breeding and Genomics News

News from Plant Breeding and Genomics on


Shawn Yarnes, the PBG Content Coordinator, to Join the Generation Challenge Program's Integrated Breeding Platform

My time with the Plant Breeding and Genomics Community of Practice on has been a fantastic opportunity to see plant breeding from a multi-crop and multi-trait perspective. It has been a privilege to be involved in plant breeding extension through the development of open-source tutorials ( and Plant Breeding and Genomics News ( I look forward to applying this experience in my new position as Genotyping Support Scientist with the Generation Challenge Program. Thank you to everyone who contributes to the Plant Breeding Community of Practice.

Shawn Yarnes

Other Events






Recent Publications



Plant Breeding and Genomics News, 25 September 2013

Plant Breeding and Genomics News

Upcoming Events from eXtension

This webinar is the second in a two part series on high throughput field phenotyping. This presentation describes how to handle data generated by a field-based sensor array.

Publications from the Past Month



Plant Breeding and Genomics News: Special Edition Sustainable Intensification of Agriculture , 22 August 2013

Plant Breeding and Genomics News

Upcoming Events from eXtension









Animal Health Science. Plant Breeding and Genetics. Crop production and Management. 

These fields of study don’t receive the glitz and glamour of other programs in many schools, but training experts in these areas is crucial for the future of agriculture. That’s why, USDA Chief Scientist and Under Secretary for Research, Education, and Economics Dr. Catherine Woteki will answer questions in a Twitter chat this Friday at 2pm. EST to discuss how we all can keep the pipeline filled with promising students.

Please join us on Twitter tomorrow and use the hashtag #StudyAgScience to keep up with conversation. Please use the #StudyAgScience hashtag in all of your tweets. You can tweet questions, comments or just follow along. We will answer as many as we can in one hour from the @ScienceAtUSDA Twitter account. We hope to see you tomorrow at 2pm EDT.


Other Event Announcements


Publications from the Past Month














Sustainable Agriculture Research 
Intersection of Plant Breeding, Climate Change, and Food Security

Research Publications from Last 6 Months


Sustainable Agriculture Intensification Policy Recommendations

Policy Publications from Last 6 Months













Plant Breeding and Genomics News

Our Upcoming Events

Webinar Broadcast August 12-14: International Quinoa Research Symposium - eXtension

August 21 Noon EDT Webinar: Selective Sequencing Through Combinatorial Pooling


Our Recent Tutorial Publication

Genomic Relationships and GBLUP

This tutorial describes calculations of realized genomic relationships from DNA markers and the application of GBLUP for genomic estimated breeding values in animal and plant breeding. Two demos are provided using R and ASReml software. The tutorial was recorded as a live webinar on August 1, 2013.


Upcoming Thursday Webinar Rescheduled

NEW DATE: Wednesday 21 August 2013 at Noon EDT

Selective Sequencing Through Combinatorial Pooling

Register Now (If you previously registered to participate this Thursday, you remain registered for the new date.)

Presented By Stefano Lonardi and Timothy Close

Related Publication
Stefano Lonardi, Denisa Duma, Matthew Alpert, Francesca Cordero, Marco Beccuti, Prasanna R. Bhat, Yonghui Wu, Gianfranco Ciardo, Burair Alsaihati, Yaqin Ma, Steve Wanamaker, Josh Resnik, Serdar Bozdag, Ming-Cheng Luo, Timothy J. Close (2013). Combinatorial Pooling Enables Selective Sequencing of the Barley Gene Space. PLOS Computational Biology, 9(4), e1003010.

Funding Statement
Development of this resource was supported in part by the National Institute of Food and Agriculture (NIFA) Solanaceae Coordinated Agricultural Project, Dry Bean Root Health East Africa, and the Triticeae Coordinated Agriculture Project.  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.

Plant Breeding and Genomics Newsletter, June 28, 2013

PBG Webinar Series

Selective Sequencing Through Combinatorial Pooling
July 11 at noon EDT – Register Now
Presented by Stefano Lonardi and Timothy Close

View upcoming webinars and archive here.

Feed the Future Partnering for Innovation  

Private manufacturers, research and development institutes, universities, scientists, and other entrepreneurs are invited to submit concept papers that highlight an outstanding problem and either a new technology or adoption of an existing one to solve it. Those that are simple, cost-effective, and show he most potential for smallholder adoption and replication, particularly by women, will be shortlisted in a competitive selection process. The program is seeking technologies that are labor saving, boost productivity, and show promise for sustainability under the Feed the Future initiative.  For more information visit

Examples include

Seed varieties
Biological controls
Animal genetics and vaccines
Drip irrigation and water harvesting systems
Postharvest and value-added technologies
Farm tools

First International Conference on Rapid Cycle Crop-Breeding

January 7-10, 2014
Landsdowne, Virginia   
Registration Due November 1st, 2013

This conference seeks to gather experts in the fields of plant breeding, genetics, molecular biology, horticulture, forestry, plant physiology and related fields to discuss approaches and present the latest findings related to the shortening of breeding cycles in long-generation cycle crops in order to more efficiently and effectively face the challenges of improving the world’s production of food and fiber (see attached document for more information).

Connect to Plant Breeding and Genomics News



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