Dr Ron Lewis
Emeritus Professor, University of Nebraska-Lincoln
Time flies. Over nearly four years I have had the pleasure of working with talented sheep scientists and students, and with nearly forty Katahdin, Polypay, Rambouillet, and Suffolk producers engaged in the National Sheep Improvement Program (NSIP)—our so-called Innovation Flocks—in Sheep GEMS. With this project nearing its finish this December, it seemed timely to share what we have learned so far. In this article, I summarize team members’ insights into the project based on questions that I posed to them.
As a reminder, the “GEMS” in Sheep GEMS stands for Genetics, Environment, Management, and Society. Our aim was to consider how these four key facets of a sheep production system collectively impact robustness and resilience to weather conditions or, more generally, fitness of your flocks. We measured a lot of fitness traits, such as ewe longevity, gastrointestinal parasitism, udder health, and lamb survival, in both Innovation and USDA Agricultural Research Service (ARS) flocks. Such measures help us describe Genetics. The flocks engaged in Sheep GEMS are spread across the U.S., with unique geographies and weather conditions, or Environments. We also conducted a national survey to gather information about on-farm practices, learning about your Management and, to a smaller extent, Society.
Tom Boyer, a third-generation rancher and a Board Member of Sheep Genetics USA, serves as the Chair of our project’s industry advisory board. I asked Tom what aspects of the project stood out as most key to him.
“The broad array of production traits encompassed in the study has been interesting to learn about and see the deep dives that become apparent as we wrap our minds around the power of genetics.”
“Historically, we think of genetics as being the way to identify parentage or carriers of various problems that have plagued the industry. While these have value for our industry, the power comes from identifying individual and flock genetic diversity.”
Tom believes as we become more and more accurate in the prediction of various genetic traits in our breeding programs, we will continue to see greater productivity and profitability through improved breeding and selection decisions every generation.
When asked if he found anything surprising, Tom responded, “It is valuable to stand back and see the changes in crop production, and other livestock species from genetics. The only thing surprising to me is that we have not moved faster to identify and adopt the new technology that will bring the quantum leaps in productivity in the U.S. sheep industry. Some ‘What if’ questions are helpful. What if our entire flock had the productivity of our very best ewe? What if we could wean a 175% lamb crop of 120 or even 130 lb. lambs on grass? What if every ewe had a great udder with ideal teat placement that did not require having jeans with manure-stained knees from kneeling to start lambs nursing? What if every ram could increase loin eye size, improve lamb eating experience, while producing replacement ewes that can raise a set of twins. What if we could ‘stack traits?’ Such questions are all within reach through the power of genetics!”
Dr Luiz Brito is an Associate Professor of Animal Science at Purdue University, specializing in quantitative genetics and genomics. I spoke with Luiz about one of the traits we are considering, ewe longevity.
“Ewe productive longevity basically means how long a ewe stays productive in the flock—most often measured as the number of days between her first and last lambing. Ewes that stay in the flock longer can help improve profitability by lowering the need for replacements, producing more lambs over their lifetime, and often have fewer health or reproduction problems. In our work with Katahdin sheep, we found that about one-third of ewes were removed from the flock before they had a second lamb crop. Even among ewes that lambed at least twice, half had a productive life of less than three years.”
I quizzed Luiz on how we can best incorporate ewe longevity into breeding programs going forward. He replied, “based on records from NSIP producers, Katahdin ewes, on average, had their last lambs at around three years of age, producing about 2.7 litters over their lifetime. But these numbers differed among ewes, which is heritable, meaning we can improve ewe longevity through selection.”
“We recommend that breeders keep track of why and when ewes are culled. This would help improve the way in which we evaluate ewe longevity. We found that the total number of lambs weaned by a ewe over her lifetime was the best measure to use. Selecting for this trait would help increase both ewe productivity and longevity. It also would make the flock more profitable and allow for stronger selection of replacement females.”
The Sheep GEMS team is interested in interconnections among its four facets mentioned above. This leads us to consider a topic known as genotype by environment interaction or GxE. I asked Luiz to explain GxE and how it is evaluated.
“GxE means that the way a sheep performs can depend on both its genetics and the environment it is raised in. In other words, a ram that sires fast-growing, healthy lambs in one type of environment, like a cool, grassy pasture, might not produce offspring that do as well in a hot, dry region with less forage. This concept is especially important in national programs like NSIP, which aim to compare and improve sheep across a wide range of farming and ranching conditions in the U.S. To study GxE, we look at performance and genetic data from sheep raised in different settings to see if certain bloodlines do better in some environments than others. Importantly, we have detected GxE in some key traits around weaning time, namely weight and fecal egg count.”
When asked whether he could speculate on its impact on ranch or farm practices going forward, he responded, “As tools like genomic selection become more common in the sheep industry, understanding GxE will help breeders and producers make better decisions. It could lead to breeding values or selection indexes that are customized to specific weather conditions or production systems. This means farmers and ranchers might eventually choose rams not just based on general performance, but on how well their genetics fit local conditions—whether that is heat, high humidity, arid conditions, or limited feed. In the long run, this approach can lead to more resilient and efficient flocks.”
Dr Brad Freking, a Research Geneticist at U.S. Meat Animal Research Center (USMARC), contributes to Sheep GEMS by evaluating genomic data on the four breeds engaged in the project. At this point, 14,313 Katahdin, 2,414 Polypay, 2,055 Rambouillet, and 1,654 Suffolk genotypes have been accumulated. I asked Brad why collecting genotypes is so important, and why the choice of genotyping tool or platform used in the project, which evaluates 50,000 genetic markers, mattered.
“In Sheep GEMS, the choice of this medium-density genotyping platform was because it currently provides the most cost-effective way to generate the genomic information that achieved three aims: to generate more accurately estimated breeding values from genomic prediction, which we call genomically enhanced EBV; to verify the recorded pedigree information; and to determine some economically important genetic conditions.”
“Genomic prediction uses genetic markers to estimate genetic merit earlier in the life of the animal than just pedigree and phenotypic information alone. For example, two full sibs could be compared at birth and differentiated from each other at birth for carcass merit traits rather than waiting for the traits to be measured later. In addition to genomically enhanced EBV, pedigree errors can be identified and fixed if needed, and genetic status for multiple genetic conditions can be gathered from the same DNA sample.”
Producers participating in Sheep GEMS are provided with information on genetic conditions in their sheep, like ovine progressive pneumonia (OPP) and scrapie susceptibilities. Brad summarized what has been learned this way, “genetic condition status can be useful in selection or culling, and mating, decisions and in marketing programs. For two of the five validated genetic conditions—Booroola fecundity and Callipyge—we find very little or even no occurrence of the causal mutation in our U.S. breeds. Double muscling appears in some breeds to a small extent.”
“The four breeds in Sheep GEMS, however, are at different endpoints in achieving the favored genetic status for low susceptibility to OPP and resistance to scrapie. The Polypay and Rambouillet breeds are already at a high frequency—over 85%—for the favorable forms of genetic markers for low susceptibility to OPP. However, in Katahdin and Suffolk, nearly 60% of the genotyped animals were genetically susceptible to this disease.”
“The U.S. is fast approaching the time where we can be declared scrapie-free as a country. Nearly all Polypay, around 93% of Katahdin and Suffolk, and about 84% of the Rambouillet sheep we genotyped were either resistant or rarely susceptible to scrapie. However, about 16% of Rambouillet were characterized as highly susceptible to scrapie. Selection to increase the amount of scrapie resistant genotypes across breeds and the nation is considered a key part of the National Scrapie Eradication effort in the U.S.”
When asked how this knowledge could be best used, Brad responded, “Breeders can be tempted to test and select only animals with favorable genotypes. However, there is no ‘one size fits all’ approach. In part, it depends on the economic importance of the genetic condition to a sheep enterprise. Culling all animals with less favorable genotypes is seldom the best strategy. From our results, there are clear differences among breeds in OPP and scrapie susceptibilities. That information is useful for designing breeding objectives tailored to the needs and priorities of individual breeds and flocks.”
He added “We encourage breeders to integrate this genetic condition information alongside, rather than instead of, their current breeding objectives. One approach to save genetic diversity in the flock would be to expand and evaluate more sons than needed to obtain a more favorable genetic condition status. A focus on rams and changing the frequencies in the ewe flock over time is a reasonable approach.”
The Sheep GEMS team is also considering parasite resistance, particularly given increasing anthelmintic resistance in our flocks. Dr. Joan Burke is a Research Animal Scientist at the USDA, ARS, Dale Bumpers Small Farms Research Center. Among her contributions to Sheep GEMS is her knowledge of genetic and management tools to control gastrointestinal nematode (GIN) parasites.
When asked what we have learned so far, Joan responded, “I recall over 20 years ago deworming sheep and watching the fecal egg counts, or FEC, skyrocket rather than fall to undetectable levels as expected. It led to examining relative differences in GIN parasite resistance among breed types. We also found variable responses within breeds.”
“Selection for parasite resistance was recognized many years ago in Merino and Romney breeds, and more recently in the Katahdin breed in the U.S. The timing of measuring FEC differs among breed types due to differences in immune response and maturity and should be validated for each breed for optimal selection criteria. Because Katahdins mature more quickly than many wool breeds, FEC can be collected as early as 45 or 60 days of age around weaning, and between 90 and 150 days of age post-weaning. Beyond that, compared with other breeds, FEC often naturally declines, and little variability exists within a contemporary group. In our Booneville, AR, ARS flock, we have heavily selected for parasite resistance. Most lambs never require deworming. In addition, we have simultaneously made progress on all economically important traits included in NSIP.”
Beyond resistance to GIN, there is interest in identifying so-called resilient sheep. I asked Joan “what is the difference between resistance and resilience? In addition to FEC, we are collecting FAMACHA scores in Sheep GEMS. Why so? Is it to help distinguish genetically resilient from resistant sheep?”
“Resistance to GIN parasites in the animal or host is the ability to initiate and maintain an immune response to suppress establishment or eliminate the parasite. That is, the animal resists becoming infected with GIN. The FEC remain low in the presence of GIN on pasture. Resilience, on the other hand, is the ability of the host to remain healthy and productive even when parasitized.”
“Resilient sheep may have high FEC, but do not become anemic or lose body weight or condition like susceptible sheep in the same contemporary group. Resistance is relatively easy to measure by comparing FEC within a group of animals. Resilience can be more difficult to assess. The FAMACHA system examines the color of the lower eye membrane to estimate degree of anemia associated with the barber pole worm, a blood sucking GIN. Farmers can easily use this tool with proper training. GEMS flocks have been recording FAMACHA scores in their lambs. Even with its limited five-point scale, it is a heritable trait. FAMACHA can help us distinguish genetically resilient from susceptible sheep. Both may have high FEC, but the susceptible sheep will become anemic if heavily parasitized. Body weight is also an indicator of resilience and is already recorded routinely in lambs. Resilient lambs continue to grow, but susceptible lambs may grow more slowly.”
Dr Tom Murphy is a Research Geneticist who also is at USMARC. With his interest in udder health, I asked him why udder health is so important.
“In previous sheep industry surveys conducted by the USDA APHIS, he replied, it has been estimated that 14% of the U.S. breeding ewe flock is culled each year and, of these ewes, 15% are culled for udder health issues such as hard bag syndrome and mastitis. While most of us are familiar with clinical mastitis like palpable lumps, abnormal milk, and so on, subclinical mastitis has major economic implications but goes unnoticed in most flocks.”
In follow up, I inquired about what his evaluations of udder health entailed, and what has been learned from them. Tom replied, “To date, we have collected milk samples from over 2,500 ewes of varying ages, breed types, and production systems in our research flocks. These studies have found that approximately 25% of sampled ewes were visually healthy but had milk somatic cell count values indicative of subclinical mastitis. Furthermore, these sub-clinically infected ewes weaned, on average, 13 to 35 lb. less total weight of lamb than healthy ewes, which presents a substantial loss in potential revenue.”
“The problem is that milking ewes to diagnose subclinical mastitis is extremely labor intensive and, while increased ewe milk production generally results in heavier lamb weaning weights, heavy milking ewes are typically more prone to udder health issues. To improve udder health in industry flocks we need to identify traits that are both easier to measure and indicative of udder health while balancing our selection efforts for optimal, rather than maximal, outputs. In many ways, this is easier said than done. However, our preliminary work in Sheep GEMS has found that udder depth and teat placement, both recorded on subjective scales of 1 to 9, are moderately heritable traits (20 to 35%) and most mature ewes have intermediate scores. These early findings are encouraging as we continue to evaluate selection strategies to breed more productive and longer-lived ewes.”
The newest member of the GEMS team is Dr Carrie Wilson, a Research Geneticist at the USDA, ARS, U.S. Sheep Experiment Station (USSES), she is assessing inbreeding in our sheep, a topic of particular interest to her and to sheep producers. I asked Carrie to explain what the team is doing on this topic, and why it is important to evaluate inbreeding levels in our breeds now.
“We have used the full NSIP pedigree to compute inbreeding coefficients for every animal for each breed participating in Sheep GEMS. This allows us to track trends over time and get an understanding of the inbreeding levels and rate of inbreeding for each breed. For animals that have been genotyped, we are able to measure genomic-based inbreeding and get an even better understanding of the realized inbreeding in the breed.”
“It is important to establish a baseline level of genetic diversity prior to the implementation of genomic selection so we can assess the impact, if any, that genomic selection has on the overall genetic diversity of each breed. In the extreme case with dairy cattle, where few elite sires have been heavily used, genomic selection has led to an increased annual rate of inbreeding with negative impacts on fitness traits. While this is unlikely in sheep due to the limited use of A.I., it is still important to monitor and understand the impacts of genomic selection on inbreeding levels over time.”
Evaluating lamb survival is another aspect being studied, and Carrie is taking the lead. when asked, “why do you consider lamb survival as key to improving the robustness of our flocks?”, she replied,
“Any lamb that is born that does not make it to its end goal, whether that is a market lamb or to be retained as a breeder, is affecting profitability. This trait has been reported in the literature for over 75 years, yet we have not been successful as an industry in improving this all-important trait.”
She then described the approaches taken to help better understand ways to improve lamb survival.
“In our flock at the USSES, we evaluated 40 years of lamb survival data and made several conclusions. First, lamb survival is a different trait for a single, twin, or triplet. Second, a lamb’s survival is dependent on the sex composition within its litter, particularly for triplet litters. Third, uniform birth weights within a litter support lamb survival. Lastly, young and old ewes have lower lamb survival and may need closer monitoring to ensure the survival of their lambs. Heritability estimates for lamb survival are extremely low, so I have been evaluating novel models to try to improve genetic selection for this trait. While the initial models still show low heritability for the trait, evaluation of lamb survival for singles, twins, and triplets as separate traits is showing some promise. Once we work through this in our flock, I look forward to seeing what we can do to improve selection for lamb survival across all NSIP flocks.”
Earlier, I mentioned the producer survey conducted to gain insights into producers’ management practices. We are combining what we learned about management practices with weather conditions specific to the location of individual flocks to define their overall production environments. These are called “eco-management clusters”, and we use them as a ‘better’ definition of environment in our investigations of GxE.
The team was also asked about their thoughts on the next steps after Sheep GEMS ends. The consensus was that, with the help of NSIP, genomic selection for traits already evaluated needs to be implemented, along with development of genomically enhanced EBV for novel traits of economic importance to breeders, including lamb survival and ewe longevity. If GxE proves to be important, we need to establish tools for incorporating those interactions into producers’ breeding decisions.
Key to the implementation of Sheep GEMS is for producers to continue – if not expand – their recording of both novel and traditional traits. Without that, many of the advantages of incorporating genomic data into the NSIP genetic evaluation will be lost. There also is a need for tools to assist producers collect and digitize their flocks’ performance data more easily, and for web-based tools to support breeders’ selection and mating decisions. In short, there is a lot left to do.
I would like to finish by returning to Tom Boyer. The value of Sheep GEMS depends on its outcomes being adopted by the U.S. sheep industry. I asked Tom about his thoughts on this.
Boyer replied, “I see many within the industry who will think it is too hard, too expensive, too ‘some other reason’ not to adopt the outcomes of GEMS. Productivity wise, they will stay where they are and have been for decades. There are, however, within the industry a select group of ‘Young Guns’ who are tired of mediocrity, and who have a passion for constant improvement, especially improvement in their profitability. These folks include a powerful set of young educators, extension, and sheep specialists, and early adopter producers who will embrace GEMS and take the industry forward with a quantum leap. I salute this group!”
I would also like to salute and thank everyone participating in Sheep GEMS. Its success is because of you.
Acknowledgements. We thank U.S. sheep associations and breed organizations, NSIP, and sheep producers, for their contributions to this research. This work is supported by the Agriculture and Food Research Initiative Competitive Grant (grant no. 2022-67015-36073/project accession no. 1027785) from the USDA National Institute of Food and Agriculture. The USDA is an equal opportunity provider and employer. 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 USDA.
