A blog for stakeholders in beef cattle and genomics by Jared Decker, He is the MU Extension State Beef Genetics Specialist and uses computational genomics to research cattle genetics. He is passionate about beef cattle genetics and helping beef farmers and ranchers adopt new technologies and best practices.
Viruses typically aren't severe on their own, but they are often the gateway for bacteria infections to start.
Difficulty of BRDC treatment records as phenotypes Disease incidence measured as 0 or 1 Subclinicals/shedders analyzed as healthy
How do we overcome these difficulties? Large sample sizes are needed. USDA MARC is not using a subset of USMARC Germplasm Evaluation Program. MARC is also working to improve the quality of diagnoses/necropsy. They are also looking for indicator traits. They are collecting nasal samples and blood phenotypes. They are also looking at lung lesions scores at slaughter.
USDA-MARC worked with Colorado State University, they collected lung lesion scores from a packing plant in Nebraska.
Tara McDaneld is using metagenomics to look at BRDC. Metagenomics is looking at the genomics of bacterial and viral communities in environmental samples. In metagenomics, you are not looking at a single microbe, but the community of microbes. What distinguishes the microbiomes of sick and healthy cattle?
At sample collection, they collect nasal swabs, blood, fecal swabs, and other tissues. They sampled at prebreeding, preconditioning and weaning. The bacterial profiles change across these 3 time points. Also, there are different profiles of bacteria at different locations at the research center.
In different years there were different bacteria that were present in high numbers.
Smithfield Premium Genetics is the nucleus that provides sows (over 1 million) for Smithfield and the sires of the terminal market pigs. At Smithfield, they mate a Landrace to a Large White to produce the commercial F1 sow. These sows are then breed to a Duroc. The terminal pig then has maximal heterosis (maternal heterosis and direct heterosis). SPG uses single sire semen of Durocs to mate to commerical farms in Missouri and North Carolina. They collect 60,000 carcass data points per year. On the maternal side, it is had to get stayability data because generations are turned over so quickly. They use commercial test herds to collect this data on sows. Howard said that genomic information on purebred animals prior to selection allows them to better predict performance in a commercial setting. This genomic data also allows them to figure out if problematic meat is produced at a company owned farm or an outside source.
Big data is driven by volume and speed at which the data comes in. Their big data is based on pictures, sensors, and sound data, which has minimal human intervention during data collection.
The use of electronic feeder systems use RFID tags to determine which pig is at the feeder, amount of feed consumed, and the body weight of the animal. In a single year there are 2 million animal observations per year in the SPG electronic feeder systems. They use robust regression to identify outlier data points (feeder is empty and has no feed, scale is miscalibrated, etc.). Key piece is for farmers to have a dashboard that alerts them to issues.
They have also collect line speed packing plant data collection.
Research is working on using images and machine learning to classify whether or not the carcass from a pig has had it tail bitten.
Researchers also use a camera to estimate the volume, length, heights and roundness to estimate the body weight of pigs. Right now, these predictions are accurate to within 10 pounds.
Researchers are also working on facial recognition in pigs. If animals have markings on their face, facial recognition is easy. However, for pigs with white faces, facial recognition is much harder. Also, can you track the animal as it ages.
For new technology to be used, researchers have to prove it is useful for genetic prediction and improves the profitability of an operation.
Howard believes big data will make it easier to obtain relevant phenotypes at the commercial level. It's important to not that in swine breeding, all the nucleus animals are genotyped. What is needed is collecting data on their commercial offspring.
His research is outcome, not technology driven. It is not finding shiny new tools and asking how can I use it. Rather, it is looking at problems in the industry and finding solutions, including technology, to help it.
Northern Australia is much more similar to central America that it is to the United States. Southern Australia is similar to the southern US.
There are several tools for stocking rate management, but there is a need to get good tools into these systems. There is now high spatial and temporal satellite data that is now basically available for free. There are emerging radar satellite systems.
There's a lot of hype around "smart tags" and other agtech, but what's the actual need and value? There are three key bits of information producers would love to have from a sensor system:
Producers see lots of applications for smart tags.
Location We went from big backpacks on cattle to neck collars which you had to retrieve the data from the device, to now we receive real-time location information.
Based on where sheep bed for the night and where they graze, they can differentially fertilize a pasture.
They are also looking at activity as a predictor of dark cutters.
Behavior Accelerometers measure changes in gravity forces. Accelerometer data can be used to identify when an animal is standing, walking, running, or laying down. They can also use this data to estimate a fly agitation index. They are working on detecting and quantifying:
calving and dystocia
grazing/ruminating behavior as an indicator of pasture quality
There is also virtual fencing systems. Examples are Agersens, Vence, Nofence, and Halter. Basically the animal wears a collar and receives a small zap to redirect it.
The amount of data is increasing to large levels, lots of data points per animals, rather than small data for paddocks. There is a website called DataMuster (https://www.datamuster.net.au/) which is intended to help cattle producers track and use individual level data.
Trotter also has school education tools to help introduce children to the use of GPS in livestock production (www.gpscows.com).
Why do we use a crossbreeding system? To gain the advantage of heterosis, the cross outperforming the parent average. Retained heterosis is the amount of this advantage that is maintained after multiple generations of mating crossbreed animals (not mating the purebred parents).
Dominance, over dominance, and epistasis likely all contribute to heterosis.
In general, traits with higher heritabilities have lower heterosis and traits with low heritability have higher heterosis.
Why don't commercial producers use crossbreeding? The average herd size is 40 head and 9% of herds have >100 head. It is harder to implement a crossbreeding program in a smaller herd.
Researchers in Canada have developed genomic indicators of retained heterosis. They use the genomic data to infer the breed proportion of the animals. They can then square these breed proportions, add them up, and subtract from zero to estimate the retained heterosis. Another approach is to count the number of heterozygote loci.
The genomic indicator of retained heterosis significantly predicted the heifer pregnancy and stayability of crossed cows in the University of Alberta data. Genho also looked at this in King Ranch and Eldon Farms data, and the genomic measures of heterosis and retained heterosis predicted heifer pregnancy and stayability.
You can't fix heterosis in a herd by selecting for it. Mendelian segregation means that each generation of mating crossbreeds you end up with homozygous loci in the progeny. These homozygous loci result in decreased heterosis.
The GGP-F250 is a very unique assay compared to other SNP panels. All of the other available assays (SNP panels) use common variants. The GGP-F250 has many rare variants, most of which are located in genes or other functional elements.
Why is rare variation important? Most of the variation in mammalian genomes, including the genomes of cattle, contain rare variation. Most of the DNA differences between different individuals are rare variants. We can't tag this rare variation with the common variants included in most SNP panels. To accurately measure genetic differences (and predict EPDs), we have to account for rare variation.
Imputation is the process of: 1. Sorting DNA variants onto each chromosome (phasing) 2. Filling in missing genotypes
We can impute from 50,000 SNPs to 700,000 SNPs to 15 million variants. But, we can't do this accurately for rare variants. However, when we include the GGP-F250 assay into this process, we can now accurately impute rare variants.
Why are imputed rare variants important? Taylor's students just re-analyzed the feed efficiency project samples. The heritability is highest when we include rare variants in the analysis. This is also seen when analyzing Bovine Respiratory Disease as well. When looking at genomic predictions (EPDs) for BRD, the predictions are more accurate when using rare variants.
Taylor then discussed genomic diversity. Genomic diversity is affected 1) by the number of DNA variants and 2) the number of combinations of these DNA variants (haplotypes, strings of variants inherited as a unit). However, we also have to account for the frequency of the different haplotypes. If 90% of the population has one haplotype, then there isn't very much diversity.
When we look at haplotype diversity weighted by frequency, Angus has the fewest number of haplotypes, followed by Brangus, Simmental, Santa Gertrudis, and Beefmaster.
In Brangus, we have selected them to be more like Angus than Brahman. There is more Angus ancestry in Brangus than expected by pedigree. Some examples of this is selection for polled and black.
As Taylor looked at haplotype diversity, he could also look for haplotypes that are never inherited in two copies. These haplotypes carry DNA variants that are embryonic lethals. Taylor repeated this analysis with varrying number of SNPs per haplotype. Taylor finds there are 122 regions in the Angus genome that possibly carry embryonic lethals. Seventy-six (76) of these regions contain genes that are know to be essential for life. These 76 regions are likely responsible for 5% of embryos lost in U.S. registered Angus.
United States beef cattle inventory has decreased since the 1970s. However, over that same time period, we have produced more beef. This means we are more efficiently producing more beef per cow. This is very different compared to other countries such as Brazil and India.
We have seen inflection points in the genetic progress of beef production as various technologies have been adopted? Will gene editing be that next inflection point?
Gene editing technologies are simply scissors that cut DNA. There are various types, such as Zinc Finger Nucleases, TALENS, and CRISPR/Cas9. CRISPR has become very popular recently because it uses a guide RNA to make the cut at a specific location. CRISPR can make site-specific variants (mutations) as the cell repairs the double stranded breaks. CRISPR can also be used to insert new sequence from a different animal, species, or kingdom.
There are 13 papers that describe edits for 12 different traits in cattle.
Gene editing for disease resistance is a win-win for cattle sustainability. We produce animals that have better welfare and need to use fewer antibiotics and treatments.
The Polled allele frequency is 0.0071 in Holstein dairy cattle. If used exclusively, polled sires would increase inbreeding and slow genetic gain.
The public generally supports gene editing for animal welfare issues, such as Polled. However, the public does not realize that there are zero gene edited animals currently in the food chain.
Introducing gene edits into an animal can be complicated and cannot slow down a breeding program. We can do that by editing a cell line and cloning that cell line. Or, you can directly edit an embryo, but this embryo is a mixture of unedited and edited cells. If some of the edited cells are in the germ line, then the animal can pass on the edit to their calves.
Big problem is how gene edits are regulated in plants by the USDA and in animals by the FDA. In plants, if you could have made the change via traditional methods (i.e. cross two lines), then the gene edit is not regulated. The regulations for animals are completely opposite. The FDA is regulating the process of gene editing. Any edit is treated as a new animal drug. Basically, plant breeders can use gene editing and animal breeders can not.
Other countries are taking a much more scientific, risk-based (not processed based) policy. This technology is going to be used in Canada, Argentina, and Brazil. In Australia, the policy doesn't make a lot of sense as non-template edits are not regulated but template-guided edits are regulated. The European Union has said that all mutagenesis processes (if not established before 2001) are regulated. However, if you radiated a plant prior to 2001 and made thousands of mutations, that plant is not regulated.
Mason-Knox Ranch develops heifers to market bred heifers. They like to purchase the heifer calves back from their customers. They also like to breed heifers to producer heifer calves, because we know that heifer calves are lighter compared to bull calves. Mason also sees an opportunity to quick change a cow herd by using sex sorted semen.
Mason said, "Those who know me, know I'm a nervous nelly." The first time they did split time AI, Mason looked at all of the heifers in the hold pen and was nervous. Dave Patterson told him to eat dinner. Mason ate dinner, came back, and still very few heifers in heat. Patterson said, "Just let them be." Next morning, lots of heifers were in heat.
Mason also sees opportunity for sexed-semen in seedstock. Think about breeding that cow who always produces a great bull, to male select semen.
"There is a difference between burlap and satin," Mason quoted a friend. Mason believes in using quality genetics.
Jordan Thomas University of Missouri NAAB Symposium
Why do we care about sex sorted semen? For any on mating, one sex of calf is always more valuable. This is due to genetic potential and your marketing program.
What is the value difference? What is the true cost of using sex sorted semen? Does the value difference justify the cost?
In a perfect world, pregnancy rates would be identical between conventional and sex-sorted semen. But, this is not true. Further, the bull you want to use may not have sex-sorted semen available due to sorting or fertility factors. Sex-sorted semen is also very sensitive to the timing of estrus in a timed synchronization program. Lastly, sex-sorted semen is not free! There are direct costs (cost per straw of semen) and indirect cost (lower pregnancy rates, estrus detection, more complicated protocols).
Unlike the dairy industry, we have a fixed breeding season in the beef industry. If a dairy cow is not breed using sex-sorted semen, we just AI her another time.
Can we optimize male fertility based on how we manage cows in a timed AI program? That is the main research question Thomas is working to answer.
What do we do about cows that don't express estrus at the time of fixed time AI? We can do Split-Time AI, in which we breed cows in groups based on when they express estrus. At 66 hours we bred all of the cows that have expressed estrus. For those cows that have not expressed estrus, we wait 24 hours and breed them.
Ninety percent of heifers express heifers in a split-timed AI protocol. With split-timed AI, Thomas' research observed a 60% pregnancy rate in heifers using conventional semen, and a 52% pregnancy rate when using sexed sorted semen. Non-estrous heifers had a 29% pregnancy rate.
In mature cows, split-timed AI protocols have less consistent results.
George Perry South Dakota State University NAAB Symposium Assume that a cow breeds 30 cows per year for 4 years. Regardless of the year, bull price per calf sired was higher than the cost of semen.
We could have different bulls for different groups of cows. Bulls for heifers, bulls for maternal calves, and bulls for terminal calves. Consider breeding a calving ease bull to mature cows- you are giving up additional growth with that mating.
Sexed semen causes the differences in sexes of the calves that we would expect to see. The number of bulls and heifers in a calf crop can be skewed even if we do one round of artificial insemination followed by natural service.
Perry's groups used 6 herds with 878 cows breed to 5 different bulls. They used conventional semen and sexed semen from each bull. Gender skewed semen had a pregnancy rate of 52.4% and conventional semen had a pregnancy rate of 67%. When cows have displayed estrus (been in heat) at time of AI, pregnancy rate was 69%. Cows that had not been in heat had a pregnancy rate of 49%. If the cow had been in estrus, gender skewed semen had a 65% conception rate compared to 73% for conventional semen. However, for cows that had not been in heat, pregnancy rate for sexed semen was 33% and for conventional semen it was 56%. Gender skewed semen works in the right situation (cows that have displayed estrus).
Sexed semen can allow us to have 2 truck loads of steers to market, rather than 1 and 1/2 truck loads. This has an economic impact. Perry's group is continuing to work on the economic impact of gender skewed semen.
If you are going to use gender skewed semen, you need to know which cows have expressed estrus (been in heat) and which have not.
Written by Jaclyn N. Ketchum, Cliff Lamb, and Michael F. Smith,
Division of Animal Sciences, University of Missouri, and Department of Animal Science, Texas A&M University
Efficiency, sustainability, productivity and profitability – these words are used in conversations around the world including among cattlemen. How do cattlemen assimilate these goals into their herd? One way is by implementing a defined breeding season.
“Heifers that conceive earlier in the breeding season will calve earlier in the calving season and have a longer interval to rebreeding. Calves born earlier in the calving season will also be older and heavier at weaning,” stated Robert Cushman of U.S. Meat Animal Research Center. He added, “Heifers that calved early in the calving season with their first calf had increased longevity and kilograms weaned, compared with heifers that calved later in the calving season.”
Increased longevity and heavier weaning weights are two points that Cushman made. How does one go about increasing the proportion of females that conceive earlier in the breeding season? Perhaps the first place to start is a defined breeding season which translates into a defined calving season. This strategy is attractive not only because of the aforementioned advantages, but also for more uniform group management regarding nutrition and implementation of vaccination protocols.
Once a producer decides to shorten the breeding season, the task may seem daunting. Where do I start? How short a breeding season is practical? What if a large proportion of females come up open the first year? Am I really going to see an increase in profitability? Fortunately, producers can learn from experiences of others who have systematically shortened the breeding season without a decrease in profitability.
The University of Florida-North Florida Research and Education Center Beef Herd provides an excellent example of the benefits of reducing the length of a breeding season. Prior to 2008, bulls were turned in with heifers and cows for a 120-day breeding season. In 2008, Dr. Cliff Lamb, now Department Head at Texas A&M University, and his team implemented multiple reproductive management procedures, including estrous synchronization and fixed-time AI, to increase the proportion of females that conceive early and thereby decrease the length of the breeding season.
Lamb stated, “Prior to 2008 the breeding season was 120 days in length, and we felt that by committing to an estrous synchronization and AI program, we could shorten the breeding season and increase calf value. Committing to a fixed-time AI (FTAI) program required significant work and dedication, especially during the first four years because the length of the breeding season resulted in an extended calving season, such that cows were calving past the initiation of the next breeding season.”
Lamb said that while implementing this strategy required some effort after reducing the breeding season over five years from 120 to 70 days, almost all cows calved prior to initiation of the breeding season and were exposed to a single FTAI at the initiation of the breeding season. The net result was a more compact calving season that increased the value of calves by $169 per calf or an annual increase in calf value for the 300-head operation of $50,700 per year.
Prior to shortening the breeding season, pregnancy rates were 81 to 86 percent. Following implementation of FTAI in 2008, pregnancy rates generally increased from 84 to 92 percent to 94 percent. Also, the average calving date steadily decreased from 79.2 to 38.7 days, indicating that a larger proportion of calves were born earlier in the calving season, which increased calf age and weight at weaning. The first-year that estrous synchronization and AI was implemented, the per calf value increased by $87.
What if this approach is not quite what a producer had in mind or may seem out of reach? Perhaps the producer already has a defined breeding season but wants to shorten it further to obtain additional benefits or maybe the use of estrous synchronization and artificial insemination are not an option for the first few years.
A second example demonstrates how Tellan and Kayla Steffan of Amidon, North Dakota, managed to reduce the breeding season length of their commercial Red Angus herd from 60 to 45 days. Steffan explained why they wanted to reduce the number of days in their breeding season. “The decision to shorten our breeding season to 45 days was based on two factors: 1) we wanted to get away from calving in winter weather; and 2) we wanted a more uniform, consistent calf crop.”
To avoid winter calving, they had to calve later. “We figured that if we could calve later in the year, but have more cows calve in a tighter window of time, the average birth date would not move all that much compared to having a longer breeding season,” said Steffan.
In 2015, a 61-day breeding season was in place. In 2016 the Steffans implemented several changes, including shortening the breeding season to 45 days. “One thing that initially hurt the pocketbook was having about 20 percent of the cows open in the fall after tightening the breeding season,” said Steffan. “However, after looking at the cows in the open pen – mostly hard-doing cows that were less fertile – we saw that there would be beneficial effects long-term. Therefore, we were able to cull some cows that don’t fit our environment.”
In 2017, the Steffans initiated an estrous synchronization protocol and FTAI, however, they left the breeding season length the same as the year before. The 2018 calf crop represented the first set of AI-sired calves. “In 2018, we tightened the breeding season another five days. We artificially inseminated all the cows on one day and left the bulls out for 40 days. Again, the hard-doing cows showed up in the open pen, however, this time there were less of them,” Tellan commented.
“We finally saw a more uniform, consistent calf crop in the fall of 2018. When we started in 2015, we had five different weight groups of steer calves the day we sold. By the fall of 2018, every steer on the place went in the same draft, and that was pretty neat to see,” said Steffan. “The calves were somewhat lighter on shipping day by moving to a later calving date, but with a shorter breeding season they were more uniform. We get paid more per pound, and our inputs of labor, time, fuel and feed have decreased significantly, not to mention our quality of life has improved.”
Since implementing a defined breeding season, Steffan said, “The type of cow that works under our management is starting to become evident. They need to be of moderate frame with the ability to stay in good flesh year-round with minimal supplementation. Red Angus has helped us achieve these goals by being able to meet our needs. We select genetics for a maternal female that will have good feet, a good udder, fleshing ability and longevity. We feel what really sets Red Angus apart is the docility of the cattle. The steer calves from these cows can go into the feedlot and perform with the best in the industry. They really are the complete package.”
Transitioning to a Defined Breeding Season
Producers who have a year-long breeding season but want to implement a defined breeding season should access an article authored by Dr. Les Anderson titled, “Some Ideas on Converting from Year-Round Calving to a Controlled Calving Season.” This article may be accessed at https://u.osu.edu/beef/2016/07/20/some-ideas-on-converting-from-year-round-calving-to-a-controlled-breeding-season/. It outlines eight steps producers should implement to convert from year-round calving to a controlled calving season. Anderson has been collecting data from 75 different farms that have data from pre- and post-implementation of the strategy he proposed. Anderson said, “So far, we have increased pounds weaned per cow exposed 154 pounds on average after the second year.”
Producers who are interested in implementing a defined breeding season but are apprehensive should contact their Extension office or beef specialist for additional ideas better suited for their operation. If you have further questions or wish to see a timeline of how the breeding season was systematically shortened, please contact Jaclyn Ketchum.