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Showing posts from June, 2014

Opportunities and challenges for a new approach to genomic prediction

Dorian Garrick
Henderson originally described breeding values (EPDs) as sums of gene effects. Meuwissen, Hayes, Goddard re-expressed this as sums of effects estimated for genotyped DNA variants.  
In current selection we have two models for genetic prediction, one for genotyped animals and a separate model for animals not genotyped.
You can combine a pedigree based relationship matrix with a genomic based relationship, we call this single-step BLUP or HBLUP (Aguilar et al., 2010).
There is a second approach which Garrick refers to as a hybrid approach. Now breeding values for nongenotyped animals are expressed as the part explained by genotyped relatives and the part not explained by genotyped relatives. This is similar to the animal model where we have the breeding value explained by relatives and the breeding value due to the random shuffle of genes across generations.
This model is in press and should be out later this summer (Fernando, Dekkers and Garrick 2014 GSE).

If everyone is…

Breed Updates on Genomic Prediction

Several of the breed associations gave reports on their progress to implement genomic-enhanced EPDs. When a breed is small it is difficult to obtain genotypes of animals with reliable EPD estimates. More on this later.

The American Gelbvieh Association has implemented and released genomic-enhanced EPDs. See page 30 of the April 2014 Gelbvieh World for more information. Gelbvieh has implemented a solution unique to beef breeds in which a beef producer can either purchase a low density or high density SNP test. The SNPs not genotyped on the low density tests are implemented based on inheritance patterns in the populations. This process is referred to as imputation.

This September, the American Hereford Association will be adding a low-density SNP test that will be marketed at half the cost of the complete SNP test. The SNPs not genotyped on this assay will be imputed from the genotyped DNA variants, the same as the Gelbvieh strategy. When first introduced, AHA genomic predictions had a …

Things that Annoy Thallman About National Cattle Evaluation

Mark Thallman
Mark Thallman recently attended a bull sale with his farther-in-law to help him buy a bull. He was annoyed to find out the embryo transfer calves only had parent average EPDs. This annoyed Thallman because his masters thesis had been focused on calculating EPDs using data from embryo transfer calves.
Thallman also speculates that herds using within herd genetic evaluations are due to frustrations with the genetic evaluations published by breed associations.
Thallman also points out that we need better fertility EPDs. Stayability EPDs were a good first step, but we can do better. He suggests implementing fitting Days to Calving and Pregnant/Open as separate traits. He also envisions fitting each parity as separate pairs of traits in a 6-trait model. Thallman also sees a "build it and the data will come" strategy working best.
We have also failed to implement and use visual scores such as structural soundness, udder soundness, and sheath scores.
Should we score b…

It is possible to genetically change the nutrient profile of beef

Raluca Mateescu
What do consumers want? First taste, second price, and a close third healthfulness. In the last 30 years obesity rates have increased, but beef consumption has decreased. Beef is not causing the rising obesity rates. Previously heart disease has been linked to saturated fat consumption but recent research has questioned this link. On average Americans are overweight and undernourished, in particular their diets are low in iron and B vitamins. Beef can help fix this lack in dietary nutrients!

Iron deficiency is the most common and widespread nutritional disorder, and in aging adults we see an increased risk of sarcopenia (muscle loss likely due to iron and zinc deficiency). We can use genomic predictions to increase the amount of iron in the beef we produce. Increased iron also helps color stability and beef flavor. Genomic prediction of iron content is another example of novel traits that we can tackle with the help of genomic predictions.

Economically Relevant Traits for the 'New Beef Industry'

Bruce Golden
There has been incomplete investment in the strategy of economically relevant traits.

New computational and statistical advancements made genetic prediction possible. From 1975 to 1995 used sire models to predict
By 1989 approximately 20 breed associations were producing genetic estimates.
In 1995 there was whole herd rporting, international cattle evaluation, and online reporting and recording. In 2004 economic selection indexes were implemented.
From 1998 to 2008 breeds moved to in-house or service provider evaluations, rather than using the services of universities.
Golden states that he sees implementation of genomics as an incremental improvement in accuracy of prediction, but not how we "use" the traits.
Shows that genetic predictions have been produced for 75 different traits across many breeds.

There are two categories of traits:
Indicator traits: traits that are genetically correlated with traits that we really want to improveEconomically relevant traits…

Merging genetics and management for improved profitability

Moderator: Tom Field
Panelists: Donnell Brown, Lorna Marshall, and JD Radakovich 
These are some points that stood out to me in panel discussion. It is not organized, but more of a blitz of phrases and talking points.
Commercial producers want to see improved genetic merit for fertility. Commercial producers are also concerned about feet, but what is the science behind feet evaluation?
Radakovich went through a sale catalog and picked out the bulls he wanted based on his ranch's selection criteria. He came home with zero bulls. Lead him to question what bulls did he need rather than the bulls he wanted. If my cow herd is not wrong, how much emphasis should be put on making them a small bit more right.
What is the longivity of the bull's daughters but also what is the longevity of the bull? Does that bull come back in healthy the 3rd and 4th years?
Mark Thallman pointed out that we not only need to cull the bottom end but we also need to apply selection pressure to move our herds…

Economic considerations for profitable cow herds

Clay Mathis
King Ranch Institute for for Ranch Management
Good managers make a multitude of small decisions to keep costs low relative to the cattle they produce and market. But, excellent managers do the same and also find leverage in the production system. These excellent managers make strategic changes that have a systematic impact on their operation. From the SPA data, Mathis shows that the average operation loses money. But, the top quarter of operations make $169 while the bottom quarter of operations lose $308. These bottom quarter have out of control spending and low performance and income. Weaning percentage did not vary dramatically between the top and bottom operations.The top operations are weaning 60 more pounds on average, likely due to older calves from a controlled breeding system and better genetic merit for growth. Increasing weaning weight percentage by 1 percentage unit increases profit by $6 per cow. Labor, depreciation, and feed were the largest expenses in the S…

Heifer intake and feed efficiency as indicators of cow intake and efficiency

Dan Shike
University of Illinois
One of the big questions in feed efficiency has been whether feed efficiency of heifers in the growing stage reflect feed efficiency of cows in the maintenance stage. There is a lot of buzz around efficiency because we are facing a growing world population, increased competition for resources, volatility of feed prices.
Why have we not seen improvement in feed efficiency? One reason is the traditional focus on outputs such as weaning weight, yearling weight and carcass weight. But, feed intake has been difficult to measure in the past.
When we think of feed efficiency in the feedlot, the framework is fairly straightforward, feedlots buy feed and sell beef. But, efficiency in the cow herd is more complicated as there are varying feeding strategies and marketing strategies. We can measure feed efficiency as residual feed intake (eating less than predicted based on body weight and growth is efficient) or as residual gain (gaining more than predicted based…

U.S. Meat Animal Research Center (USMARC) Symposium: 50 Years of Service to the Beef Industry

BIF put together a well respected host of speakers to review the last 50 years of research at the US Meat Animal Research Center.

Larry Cundiff
The Germplasm Evaluation Program was initiated in 1969 after several planning meetings from 1967 to 1969. Because of the quarantine facilities in Canada, the Germplasm Evaluation Program worked very closely with Ag Canada to obtain semen on imported continental bulls. G.E. Dickerson designed the programs to address questions about breed differences and to maintain heterosis among breeds. Over 8 cycles of the program, 37 breeds have been evaluated. In a 7 year period the MARC had amassed a large cow herd as they were trying to evaluate cows from each breed late into their productive years. One of the first lessons was the problems of breeding imported bulls to 2 and 3 year old cows, as calving problems frequently occurred. No one breed was able to excel at all economically important traits in the early years of the Germplasm Evaluation Program. …

LiveAuctions.tv will broadcast 2014 Beef Improvement Federation Annual Meeting and Research Symposium

The 2014 Beef Improvement Federation Annual Meeting and Research Symposium begins this evening and runs through Friday evening, with a post-conference tour on Saturday. LiveAuctions.tv is providing a live video stream of the proceeding. This evening from 6 pm to 9 pm CDT will be a symposium to honor the achievements of the USDA research at the Meat Animal Research Center. A full schedule of presentations can be found here.

American International Charolais Association:
Pathway to Genomic-Enhanced EPDs

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I talked about use of high-throughput DNA sequencing to improve fertility by removing DNA variants from a breed that cause embryonic losses during pregnancy. Here is a link (Managing Broken Genes in the Age of Genomics) to the PowerPoint presentation I gave. I discussed the development of a genomic EPD based on the number of embryonic lethal variants (broken genes) that an animal carries that causes losses of embryos during pregnancy.

 The cost of DNA sequencing has rapidly dropped in the last 15 years. In 2001 it cost about $10,000 to sequence a million base pairs of DNA. In 2014 it costs under 10 cents to sequence a million base pairs. This rapid drop in the price of DNA sequencing has enabled researchers to tackle questions that we previously could not address. With this sequencing data we are identifying loss-of-function variants (broken genes) that lead to pregnacy losses based on the sequences of approximately 200 bulls.

Dorian Garrick discussed the development of genomic-enhanc…

Bovine Respiratory Disease Symposium (BRDS) 2014: New Approaches to Bovine Respiratory Disease Prevention, Management and Diagnosis

The "Bovine Respiratory Disease Symposium (BRDS) 2014: New Approaches to Bovine Respiratory Disease Prevention, Management and Diagnosis" is to be held at the Renaissance Denver Hotel in Denver, Colorado, USA from July 30th to July 31st, 2014.

Registration is open and can be accessed, along with more information, at the Symposium website: http://www.brdsymposium.org

The early registration deadline is June 15, 2014.

The Symposium will include 2 days of presentations and discussions on a variety of topics relevant to BRDS. A research poster session will be held the first night. This meeting is being held in conjunction with the 2014 Summer Academy of Veterinary Consultants (AVC) meeting which will be held July 31st to August 2nd, 2014. We hope to see you there!

As we previously noted, the Bovine Respiratory Disease Complex Coordinated Agricultural Project is using a variety of genetic analyses to better understand BRD and to predict an animal's genetic merit for BRD resist…

Mark Your Calendars For 2014 Field Days
Events are a chance to learn from researchers at your local research center

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Story: Kyle Spradley | spradleyk@missouri.edu
Photos: Kyle Spradley
The main goal of any university is to educate, conduct research and improve the lives of others. Although the University of Missouri is commonly known for instruction at the campus in Columbia, the MU outreach goes beyond the classroom — it stretches to every corner of Missouri. For more than a century MU Extension has provided workshops, assistance programs and connected to the people of the state.  The MU College of Agriculture, Food and Natural Resources’ Agricultural Research Centers also provide an abundance of educational opportunities that many Missourians can find right in their own backyard. “This is a great opportunity to get the latest information from CAFNR researchers and local Extension faculty,” said Marc Linit, associate director of the MU Agricultural Experiment Stations.

The Agricultural Research Centers across the state routinely host Field Days as a chance for the public to learn more about ways to impr…

Dent County Spring Beef Meeting

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Tomorrow evening Dent County Cattlemen’s Association and University of Missouri Extension will sponsor the Dent County Spring Beef Meeting. The meeting will include a presentation by Gregg Barrows about the USDA Drought Assistance Program, which is designed to provide financial assistance to livestock producers who suffered losses during the drought of 2012.

I will be discussing the how using selection indexes and a consistent approach can increase your herd's profits.

The meeting will be held at Bank of Salem Courtesy Room, 100 W. 4th Street, Salem, MO and the program will begin at 7:00 pm.

For more information, please contact Ted Cunningham, MU Extension Livestock Specialist at 573-729-3196 or cunninghamtc@missouri.edu