A Steak in Genomics™

The Thompson Research Field Day will be Thursday, September 21, 2017. This year we will be having an evening program, hopefully to better accommodate more people's schedules. See the flyer below for program details. Dinner will be provided.

PALMYRA, Mo. – The fourth and final spring Show-Me-Select heifer sale topped the average price of all at $1,928. “Buyers were light, but bidders came to buy heifers,” said Daniel Mallory, University of Missouri Extension livestock specialist, New London. He noted that many new buyers came from northern Missouri and Iowa. Consignors were mostly longtime members of the MU Show-Me-Select Replacement Heifer Program. “That shows the quality of the program,” Mallory said. “Farmers see the added value built for the past 21 years.” The Palmyra sale sold 120 heifers from 12 consignors. They went to 16 buyers. The top price was $2,550 at F&T Livestock Market, June 3. That was for a single black-baldy heifer from Richards Farm, Keytesville. She was a Tier Two, AI-bred. Price averages for the other sales: Farmington, $1,813; Fruitland, $1,764; Joplin, $1,714. Tops at the first two sales were $2,500 per head. The top at Joplin was $3,200. Those were for a new class of SMS heifers called S...

Guest post by Tamar Crum , University of Missouri Scott Speidel Colorado State University The concept of stayability was developed ~23 years ago. Stayability is simply, generally, the survivability to a certain age given the opportunity to reach that age. Multi-breed stayability analyses are difficult because of different definitions of stayability. Is the female present in the herd at 6 years old? (basic/generic definition) Did she wean a calf at 6 years old? Did she wean a calf at 6 years old while also calving at 2 years of age? Did she calve 5 consecutive times within the same calving season? Successful females for stayability varies depending on which of the definitions of stayability the breed association has adopted. It is shown that stayability to 6 years of age is a heritable trait. Stayability is a HUGE driver of herd profitability and accounts for 53-77% of the value of of the maternal indices. Currently, stayability is recorded as a binary trait. ...

Guest post by Tamar Crum, University of Missouri Tom Brink Red Angus Association of America Fitting that the Georgia peach is in the logo for this year’s BIF, as we have learned throughout the conference that the industry has been provided with many types of “fruit” to choose form when it comes to our technology and genetic tools. Do EPDs work?  Are you a skeptic? If so, you are not alone! Believe it or not there are still skeptics out there. Numerous studies have been completed on carcass traits, milk, and weaning weight EPDs in the late 1990s and 2000s.  After that period, the research coming out proving EPDs worth got a little sparse.  Why? We convinced ourselves and our scientists that EPDs work, but skeptics remained in the industry.  They wanted to belief in EPDs but still need to see more. This study was in conducted in conjunction with Gardiner Angus Ranch, Zoetis, and Top Dollar Angus. The field test wanted to make comparisons between high...

John Genho Livestock Genetic Services In challenging environments, we need to use heterosis. We need cross-bred cows in these challenging environments. Deseret Ranches Deseret Ranches uses three different herds. They have a Simbrah sired cowherd, Brangus sired cowherd, and a Deseret Red sired cowherd. A Deseret Red is 3/8th Red Poll, 3/8th South Devon, and 1/4 Brahman. The Simbrah sired cows are breed by Brangus bulls, the Brangus sired cows are mated to Deseret Red bulls, and Deseret Red sired cows are mated to Simbrah bulls. King Ranch The Santa Gertrudis breed was developed at King Ranch 90 years ago. They have a seedstock Santa Gertrudis herd where they perform selection with an internal EPD system. They then have a multiplier herd where they make Red Angus x Santa Gertrudis F1 bulls. These bulls are then used in the commercial herd. Replacement females are developed from the commercial herd. They have Heifer Pregnancy EPD and Breed Back EPD from their internal EPD evaluat...

Gary Fike Tri County Steer Carcass Futurity Cooperative The Tri County Steer Carcass Futurity Cooperative first helps producers collect growth and carcass data. They help them benchmark their cattle related to the industry. It is hoped that this information will be used to make genetic improvement. The cooperative also works to help encourage and educate about retained ownership in the beef industry. It all comes down to profit. From an analysis of 25 states, the most profitable group make $216 per head, the least profitable group lost $120 per head. Out of 6 groups, the 4th and 5th groups basically broke even. What are the big things that drive whether or not a consignment of cattle was profitable? The least profitable group came in as the heaviest group. The most profitable cattle cost the least as feeders (bought cheap and sold high). The most profitable group had the fastest growth rates and were heaviest at slaughter. The most profitable cattle gained well during the war...

Justin Rhinehart University of Tennessee A step-by-step guide for heifer development: Breed early in the first breeding season Minimize calving difficulties Wean acceptable calves Breed early in the second breeding season Optimize profit Improve genetics In our nutritional development, we can have steady growth, fast early growth then plateau, slow early growth and fast late growth. We can develop heifers to a lower target weight and still get good pregnancy weights. If we have range development vs feedlot development of heifers, we see higher pregnancy rates in the range developed heifers. The range developed heifers also stay in the herd longer. One month before breeding season, reproductive tract scores heifers and cull heifers that have not reached sexual maturity. Estrus synchronization is also a great tool for jump starting heifers using the progesterone in a CIDR. With a limited approach to heifer development, using estrus synchronization is very important...

Donnell Brown R. A. Brown Ranch Darrh Bullock University of Kentucky Larry Keenan Red Angus In the history of selection, we used used visual appearance and local adaptation to create some breed creation. We then moved to actual performance. We started weighing and measuring cattle. Then scientist used statistics to analyze this data and produce sire summaries and EPDs. We have now added genomics to this process. Prior to the release of Milk EPD there was no change in milking ability in Angus cattle. We started with visual appraisal. We then did visual + actual weights, visual + adjusted weights, visual + EPDs, visual + EPDs for economically relevant traits, and visual + GE-EPDs. Now, we need to move to visual + economic selection indexes. Don't overload producers with too much information! We don't need to be double reporting data. Genomics goes into GE-EPDs; no need to publish genomic percentiles. Indexes simplify the information we presen...

Alison Van Eenennaam UC-Davis The grant dubbed the "heifer fertility project" is really looking for embryonic lethal variants. These are DNA variants that if an embryo inherits two copies of the variant, that embryo is aborted. The DNA variant breaks a gene. If an animal inherits two copies, it can't live. The project sequenced the entire genome of hundreds of cattle. This is not genotyping thousands of DNA variants, it is looking at all 2.6 billion base pairs of the genome. From sequencing these bulls, the team identified millions of DNA variants. They selected 200,000 of these DNA variants that are predicted to affect proteins encoded by genes to build a new SNP chip. This chip is called the GGP-F250. They then genotyped 17,000 cattle with the GGP-F250 chip. Taylor then looked for DNA variants for which there are not observed in two copies. If a DNA variant is at high frequency, but is never seen as two copies, then we have evidence that this is a lethal DNA vari...

Bruce Golden Theta Solutions IGS Analysis: 12 breed associations 12 million pedigree records 10 million observation records 15 different EPDs The IGS primary goals are: Improve accuracy EPDs that can be compared between breeds Weekly run Advanced methods In order for the data to be comparable across breeds, there has to be connectedness between pedigrees. There have to be sires that are in Simmental pedigrees that are also in Red Angus and Gelbvieh pedigrees. With all of these breeds using Angus sires to produce hybrids, there is a good possibility that there will be good linkages between breeds. Models seem to be robust to methods used or not used to adjust for heterosis. Have to adjust for heterosis effects, as they are not additive, to effectively predict EPDs (additive effects). Larry Kuehen USDA-MARC The center uses 2,200 AI matings each year that result in about 1,000 AI-sired pregnancies.  Adjustment factors will be coming in July of ...

Matt Spangler University of Nebraska-Lincoln Alison Van Eenennaam University of California-Davis   Early DNA tests with 1 or 2 markers had little predictive ability. As tests improved, more markers were added. Eventually there was a switch to genomic predictions.  Unfortunately, early on, these DNA test results were published along side adjusted phenotypes, ratios, and EPDs.  Quantitative genetic methods solved this problem by combining the molecular breeding value (MBV) with the EPD. Two approaches were used to combine MBVs with EPDs. One approach is to fit the MBV as an indicator or correlated trait. This is similar to combining carcass records with ultrasound records. The other approach is to blend the two predicts, MBVs and EPDs, as an index.  There are two fundamental camps for implementing single-step. UGA- ssGBLUP Misztal Theta Solutions/ISU - BOLT Garrick, Golden, Fernando Before, we were trying to fit genomic prediction into ...

Tom Lawlor Holstein Association USA Lawlor cited Jerry Taylor's article saying that Holsteins are the genomic prediction poster cows . Genotyping has increased and genetic improvement has increased in the dairy industry. But, not everyone is happy. From The Bullvine website: "How Genomics is killing the dairy breeding industry" "What the Experts Won't Tell You About The Future of the A.I. Industry" The dairy industry has had to change their data structures and analysis methods. Everyone in the dairy industry is winning, but some breeders are winning more than others. The Holstein breed is rapidly turning over their population and seeing more profitable animals. Genomics also allows them to look at genetic merit, inbreeding, undesirable genetic defects, and breed composition. One in five animals are expected to be a carrier of a genetic defect causing early embryonic loss. We have to abandon our old beliefs about not using animals with gene...

Daniela Lourenco The University of Georgia Before genomics, we were fairly happy with genetic prediction. Traditional evaluation combined pedigree, individual performance and progeny information. This was equal to summing all of an animal's genetics effects and dividing by 2. SNPs are used as markers for genes, or regions of the genome that impact production. The color of a banana peel (green vs. yellow) is a marker for banana ripeness. SNP markers are used in the same way. Marker assisted selection did not work. Why? Most traits are polygenic, meaning they are controlled by hundreds or thousands of genes. Trying to predict quantitative traits with a small number of DNA markers doesn't work well. What is 100,000 times cheaper now than in 2001? Airline flights are 2 times cheaper. Computers are 5 times cheaper. DNA sequencing is 100,000 times cheaper now than in 2001. A Holstein bull named Freddy was the best bull according to genomic predictions in 2009. In 2012, ...