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What do Google, Amazon, Facebook, and IGS All Have in Common?

January 07, 2020 Industry News ASA
Data is their lifeblood! By Jackie Atkins, Ph.D. International Genetic Solutions (IGS) partner organizations, representing 18.9 million beef cattle, gathered in Bozeman on October 22-24, 2019, for a meeting of the minds. Thirty guests including executive vice…

2019 Recipients of the Walton-Berry Graduate Student Support Grant Announced

December 26, 2019 Industry News ASA
By Emme Troendle, Editor | Since 2013, the Walton-Berry Graduate Student Support Grant has aided graduate education with an emphasis on genetic improvement of livestock. Six years later, the grant continues to support the progress of livestock research. The…

Check Out What We Have Done So Far

By Lauren Hyde, Ph.D.            |         

Nearly a year and a half ago, on Saturday, May 5, 2018, the American Simmental Association released the first full suite of multi-breed EPDs powered by the state-of-the-art BOLT software. I have to admit that the ASA staff, with the exception of very few (maybe only Steve McGuire), was very scared as to what we would find in our email, voicemail, Facebook Messenger, and so on come Monday morning. However, it wound up being so quiet, we all heard that mythical pin drop.   I’m not saying that we were perfect in our execution, but as you members started to evaluate the new EPDs, you had some well-deserved comments and questions that we were expecting.   We knew that the software wasn’t “done”. It never will be. In fact, I was still revising the 30-year-old Cornell software as recently as two short years ago. As with the old Cornell software, we will continue to update, revise, and improve the EPDs produced by the new BOLT software. 

 

 

Check out what we have done so far:

June 2018

• Developed evaluation audit reports on incoming record counts for ASA staff and IGS partners

• Developed quality control (QC) reports for incoming genomic data

• Started clearing up erroneous and missing genotypes among all associations

• American Shorthorn Association released IGS EPDs

July 2018

• Started parallel (aka beta) testing for IGS partners yet to release IGS EPDs

• Started delivering weekly QC reports to each association through the genomic pipeline, which routes genomic data from all genomic labs to the IGS partners and then the IGS database

August 2018

• American Gelbvieh Association, North American Limousin Foundation, and Canadian Simmental Association released IGS EPDs

• Added embryo transfer data to the evaluation

• Discovered and corrected duplicate animal IDs

• Began collecting feed intake and heifer pregnancy data from IGS partners

September 2018

• Canadian Shorthorn Association released IGS EPDs

• Initiated monthly IGS partner conference calls to discuss issues and updates with the evaluation

October 2018

• Red Angus Association of America released IGS EPDs

• Developed a web-based interface for bull lookups and QC error checking for ASA staff and IGS partners

• Established a “white list” to keep animals with insignificant genomic discrepancies in the evaluation 

• Adjusted the evaluation system to add genomic data on animals without carcass or ultrasound phenotypes 

November 2018

• Implemented a Java script to compute breed composition of all animals in the IGS database at a much faster rate

• Began a research project with CSU to develop a days-to-finish EPD

• Initiated a project known as Work Order 1 (WO1) in order to:   

– Remove erroneous birth weights from the evaluation   

– Separate birth contemporary groups between calves out of two-year-old dams from calves out of older ones   

– Include heterogeneous variances for weaning weight based on sex of calf   

– Remove the moderately negative genetic correlation between weaning weight direct and maternal and set it to zero   

– Implement an updated marker subset of genomic data 

December 2018

• Added trio (sire + dam + calf) mating checks to the QC error reports

January 2019

• Began investigating multi-breed imputation

• Started evaluating the latest version of the FImpute software package

February 2019

• Began refining the Zoetis arm of the genomic pipeline

• Received preliminary results on the days- to-finish EPD research project

• Combined the heifer pregnancy (HPG) data from the IGS partners and began refining it

March 2019

• Started to investigate potential improvements to the carcass weight-ribeye area (CW-REA) evaluation

• Fixed minor bugs in the online bull lookup tool

• Added birth dates and other supplemental data to the HPG dataset

• Received the first set of health data courtesy of Darr Feedlot

• Upgraded the Postgres evaluation database

April 2019

• Started exploring modifications to the utilization of external EPDs

• Tested several scenarios in the investigation to potentially improve the CW-REA evaluation

• Updated carcass breed differences with new data from USMARC

• Fixed a small bug in the docility evaluation scripts

May 2019

• Canadian Angus released IGS EPDs

• North American South Devon Association submitted external EPDs

• Began planning for the IGS partner meeting to be held October 23-24 in Bozeman

• Started building and developing server #5

June 2019

• Developed a standard format for sharing pedigree extracts among IGS partner associations in order to catch dual-registered animals more quickly

• Released data to Colorado State University (the leaders in PAP EPD development) for development of a PAP EPD

July 2019

• Implemented multi-breed imputation software

• Installed and configured FImpute

• Implemented updates to the CW-REA evaluation

August 2019

• Added Australian Shorthorn Association data

• Added updated American Angus Association externals

• Re-calculated progeny equivalents for each trait computed by IGS


I am writing this article on September 18. In just a few days, I will be traveling from Denver to the Rhine River in Germany to find out where my maternal grandparents lived before they immigrated to Chicago and met in English school. After my excursion, I will be finishing up all of my outstanding projects so that I can retire on December 31 to pursue my dream of coaching and teaching swimming.

I am fortunate to have worked with the best team in the beef cattle industry. The ASA staff is knowledgeable, hard-working, creative, and fun. This fantastic group of individuals has shown time and time again that it is more than capable of developing and implementing innovative science-based products to help you produce cattle that make a significant genetic contribution to the beef industry. I truly wish all of you — ASA members and staff alike — much success in your efforts to keep moving the breed forward and ensuring that SimGenetics continue to have a major influence in the global market.

 

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