Sheep GEMS was born in January as a collaboration between the American sheep industry, two land-grant universities and three U.S. Department of Agriculture Agricultural Research Service locations. GEMS’ aim is two-fold. First, to incorporate innovations in molecular technologies into routine genetic evaluation of American sheep. Second, to broaden the scope of those evaluations to improve the robustness and climatic resilience of our flocks. With funding from the USDA National Institute of Food and Agriculture and the American sheep industry, both aims are in reach.
This article summarizes excerpts from interviews with members of the Sheep GEMS team. Through their words, it tells the full story about the ambitions and relevance of this project.
Dr. Ron Lewis is a geneticist at the University of Nebraska-Lincoln, and Technical Advisor for the National Sheep Improvement Program. He is also the Project Director for Sheep GEMS.
“Why the name Sheep GEMS?” He explained. “The acronym GEMS stands for Genetics, Environment, Management and Society, all of which are captured in the project. As a further play on words, we are very hopeful the outcomes will be gems to our industry.”
Apparently, a key element of Sheep GEMS is to work in partnership with sheep producers, particularly those engaged in NSIP. Why is that important?
“For this project to truly matter, our discoveries must be seen as important enough to be adopted by the industry,” Lewis said. “By seeking the input and involvement of producers from the start, we believe we can foster the commitment and enthusiasm to achieve just that. As the bottom line, Sheep GEMS is about joining together records collected on-farm and on-ranch – some new and some traditional, with information at the DNA level – to do a better job of evaluating our sheep. It is through the structure of NSIP, that combination is possible.”
Sheep GEMS has a project advisory board made up of key industry groups. Tom Boyer, a third-generation rancher and the chair of Sheep Genetics USA, is also the chair of the Sheep GEMS Board.
“I see a variety of roles for this board, including encouraging eligible flock producers to participate in the project,” Boyer said. “In the world of data – particularly production-related data – the more we have, the better. We need Rambouillet, Suffolk and Polypay producers to become passionately engaged in GEMS. The fourth breed, Katahdin, has set the participation standard as they are already anxiously engaged in the project.
“Our role also involves keeping a focus on the scope of work, mileposts and achievements gained along the way, and disseminating results. Receiving input from and keeping each industry group up to date on project status will maximize outcomes and project success.”
How do you think the planned outcomes will best serve and benefit the industry?
“This project has the potential to create a paradigm shift in the U.S. sheep industry. This is the first time for a project of this size and scope to focus on the foundational genetic building blocks. Viewing resilience, adaptability and key productivity traits through a combined genetic and environmental [climatic] lens will provide exciting new insights into advances that will provide quantum leaps in selective breeding and management.”
Dr. Luiz Brito is at Purdue University specializing in quantitative genetics and genomics. He also is the co-director of Sheep GEMS. Brito was asked about the aims of improving robustness and climatic resilience. What do those terms mean?
“Robustness is an animal’s ability to remain healthy and productive within a defined environment or set of management conditions. In the same line, climatic resilience is the animal’s ability to either be minimally affected by or recover from changes in climatic conditions, such as extremes in temperature or humidity.”
Why do they matter?
“Most U.S. sheep are raised in pasture-based systems or in facilities with limited environmental control,” Brito explained. “Therefore, animals need to be able to cope with various environmental challenges, including thermal stress, gastrointestinal parasites, low-quality pastures and greater prevalence of infectious diseases. These stressors negatively influence animal survival, productivity and well-being, and consequently, the profitability of sheep farms.
“As climate change becomes more evident, extreme climatic events will affect lamb survival, ewe longevity and reproduction, and overall productivity. Breeding more robust and climatic resilient animals will ensure the long-term sustainability of sheep farming in the U.S.”
A proposed outcome of Sheep GEMS is to provide sheep producers with genomic enhanced estimated breeding values, or GEBV, for a suite of traits. What are GEBV?
“Accurately identifying the best individuals to become the parents of the next generation is not a trivial task. Fortunately, the integration of performance records, pedigree and genomic data is a powerful tool to help sheep producers with this undertaking. By combining this information, geneticists can calculate GEBV, which predict the genetic potential of an animal for each trait evaluated based on thousands of genomic markers.”
What do they offer beyond what is already available to sheep producers?
“GEBV tend to be more accurate for young animals than traditional EBV, especially for traits that are difficult or expensive to measure, such as robustness and climatic resilience. GEBV also allow us to evaluate and differentiate lambs from the same litter even before they themselves have been measured. This allows us to make selection decisions earlier and make more progress.”
Why is the project using Katahdin, Polypay, Rambouillet and Suffolk breeds?
“They were selected because they are among the largest – in terms of total number of records – of NSIP breeds and they are each reared at one or more USDA/ARS locations,” said Dr. Tom Murphy, a research geneticist at the U.S. Meat Animal Research Center in Clay Center, Neb. “The Katahdin is reared at all three locations, Polypay and Suffolk at USMARC and the U.S. Sheep Experiment Station, and Rambouillet at the USSES. We have been exchanging rams and ewes of common breeds to strengthen genetic connectedness across USDA/ARS sites.”
Murphy is leading efforts to establish reference populations in each of the breeds involved in Sheep GEMS by connecting genetically flocks at USDA/ARS centers with those in industry. But why is this necessary?
“The basic concept of the USDA/ARS Genetic Reference Flocks is to bring in genetically representative rams from industry NSIP flocks and collect standard and novel traits on their progeny,” Murphy said. “Firstly, this will help us ‘work the kinks out’ of potential new NSIP traits before we ask industry breeders to begin recording them. Secondly, although current traits evaluated in NSIP are economically important, they are limited in scope to what can be collected on farm or ranch, or by a qualified technician.
“While performance in many other health, longevity and efficiency traits impacts flock productivity, specialized equipment or increased labor may be required to accurately collect them. The resources needed to do so are available at USDA/ARS locations.
“We are collecting the same information on our ewes in our reference flocks as the Sheep GEMS participants are in their flocks, along with many other novel traits. This will allow NSIP breeders to select for these novel traits without having to record them all in their own operations.”
What are examples of novel traits?
“Udder health is one of them,” Murphy replied. “Recent surveys have estimated that about half of ewes are culled in the U.S. before they reach the end of a ‘normal’ productive life, say at 6 or 7 years of age. Udder health also affects ewe longevity as approximately 15 percent of ewes are culled for mastitis or hard bag. Subclinical mastitis – the form of the disease we cannot diagnose without testing ewe milk – is also common and negatively impacts ewe productivity.”
At USMARC, we are evaluating 10 traits associated with udder health and conformation on ewes at lambing and at weaning. We are also collecting milk samples to quantify subclinical mastitis. Since these measures are labor intensive, we have selected only a subset of these traits – udder depth and teat placement – for other Sheep GEMS flocks to collect.”
An important element of Sheep GEMS is genomics, with more than 10,000 sheep to be genotyped. Dr. Brad Freking – also a research geneticist at USMARC – is contributing his expertise in molecular genetics to the team. Among the information participating flock owners will receive back are genotypes for conditions such as Scrapie and Ovine Progressive Pneumonia susceptibility. Still, there is some uncertainty in the industry as to exactly what is meant by a genetic condition and how they are best used.
“A genetic condition,” Freking explained, “can be described as variation that has a known genetic basis. An animal’s status for a known condition can be determined directly from a DNA sample. For each genetic condition, prior knowledge of the specific type of gene action and which alleles are either favorable or unfavorable is needed. For example, the favorable allele from the TMEM154 gene associated with susceptibility to OPP is required to be present as two copies in an animal to confer the desired lower risk category.”
As an important stipulation, he added, “each genetic condition requires understanding these associations and what your goals are for the animals tested. Selection to move a population toward the most favorable versions for these conditions is an accurate and effective tool but requires long-term planning for the breeding objective.”
Another novel trait being considered in Sheep GEMS is lamb survival. Is there work already underway to better understand lamb survival? If so, how does it dovetail with the aims of Sheep GEMS?
“We have an experiment at USMARC that we hope has relevance to lamb survival and the overall aims of Sheep GEMS. It is being conducted within a maternal composite breed we refer to as our Composite IV flock – which is half Romanov, one-quarter White Dorper and one-quarter Katahdin. We are measuring several indicator traits of maternal fitness under intensive conditions of barn lambing. Our objective, though, is predicting how well individuals will perform under more extensive pasture lambing conditions.
“Genetically, matched halves of the flock will alternate annually between lambing in the barn and on pasture. When on pasture, we will only be able to measure lamb weaning survival on ewes. However, when in the barn, we will measure uniformity of lamb birth weight, ewe colostrum quality, transfer of immune function to the lambs, reproductive hormone status, udder morphology, subclinical mastitis status, and maternal behavior traits at parturition. These are all indicator traits of weaning survival.”
In circling back to Sheep GEMS, he continued, “By better understanding the genetic relationships between these more intensive measures and lamb survival in ewes at pasture, we can provide better advice on what to measure in producers’ flocks to make gains.”
Parasite resistance is another trait being considered in Sheep GEMS. Dr. Joan Burke is a research animal scientist at the USDA/ARS Dale Bumpers Small Farms Research Center in Arkansas. Among her contributions to Sheep GEMS is her knowledge of genetic and management tools to control gastrointestinal parasites.
Anthelmintic resistance is a growing concern in our sheep industry.
How should the sheep industry best strategize to deal with GIN?
“The best strategy is a holistic approach that includes tools best suited to individual farms. For sheep living in warmer, more humid climates, tools include genetic resistance, good nutrition, optimum body condition – 3.5 out of 5 is best – rotational grazing and dewormers that work to selectively treat animals in need,” Burke said. “Dewormer resistance by GIN can be catastrophic for those relying only on anthelmintics. Use of copper oxide wire particles alone or in combination with a dewormer can be effective for acute barber pole or mixed worm infections.”
In Sheep GEMS, fecal egg counts and FAMACHA scores are both being collected. How are those measurements best combined to improve genetic control of GIN?
“Fecal egg counts determined on a group of animals can indicate which animals are resistant to GIN infection and which ones are more susceptible that might be culled,” Burke said. “Fecal egg count data are submitted to NSIP to give an EBV on parasite resistance. The more negative the value, the more resistant the animal.
“FAMACHA scores – on the other hand – are an indication of how resilient the animals are to infection. A high FAMACHA score – a score of 3 or greater – indicates that an animal is anemic and likely in need of deworming. Lower scores mean that the animal would not need to be dewormed, even if it had a high fecal egg count. Both indicator traits are heritable and can be used to improve genetic resistance and resilience to GIN infection.”
FAMACHA is scored from 1 to 5 based on inspecting the inner membrane of the eye, with lower scores indicating less anemia. Is formal training needed to reliably collect FAMACHA scores? If so, how can someone receive such training?
“Yes, formal training is necessary to use the FAMACHA system to understand the biology and dynamics of the worms and the animal. It involves watching a video or slides on integrated parasite management and proper FAMACHA technique. Training may be available through your extension agent or veterinarian, or through the University of Rhode Island or Virginia State University (Wormx.info/online-famacha-certification).”
Dr. Bret Taylor is a research animal scientist and the research leader at the USDA/ARS U.S. Sheep Experiment Station. The pioneering program he oversees focuses on sheep managed under extensive Western grazing conditions.
Ewe longevity is another of the traits being considered in Sheep GEMS. Is it of particular importance in your environment?
“Because of harsher environments – resulting from extreme climates, sparse forage and rugged terrain – ewe longevity in U.S. Western range flocks is generally shorter than what may be observed in pasture-based systems. Nevertheless, ewe longevity nationwide has suffered in the last 20 years, with a 20 percent increase in ewe replacement rate and in mature sheep a 6 percent death rate. This is problematic given that enterprise profitability is directly linked to how long a ewe remains reproductively successfully in a flock.
“Older ewes are generally the best mothers, drop the most lambs, and wean the most pounds,” Taylor continued. “Annual ewe costs are greatest for young ewes, and unfortunately, they return the least marketable products. As the average age of the flock increases, annual ewe costs decrease and pounds of marketable products – both lamb and wool – increase. Considering the ever-decreasing national ewe inventory and limited supply of affordable replacement ewes, increasing the average age of a ewe flock is critical for sustaining and hopefully growing the U.S. sheep industry.”
The U.S. Sheep Experiment Station is the one USDA/ARS location collaborating in this project that has flocks in each of the four breeds involved. Why is that important to the project?
“The station is the birthplace of the Polypay – in around 1980 – and the source of much of the modern-day Rambouillet genetics found in the U.S. West reaching way back to 1917. Suffolks were imported to the USSES in 1979 and immediately selected for range hardiness. Overall, maternal genetics from the USSES are present in some proportion at most sheep farms and ranches across the U.S. Furthermore, since 2014, the USSES has made significant efforts in linking its genetics to the nation’s sheep flocks. Well over 140 sires – most from NSIP flocks – from various breeds have been imported to the USSES and incorporated into the purebred flock breeding programs. This in addition to migrating much of the USSES genetics database over to NSIP. Having genotype data for thousands of these sheep has provided an incredible resource foundation for the project.”
Describing the recent addition of a Katahdin flock to USSES, Taylor explained, “As the growing popularity of this breed has crept West, many producers have asked, ‘Is the Katahdin breed a viable alternative to wool-type sheep in the open range, herder-managed systems of the U.S. West?’ As the ‘foster origin’ for the Katahdin Hair Sheep International Association – not the breed, just the association – it made perfect sense to finally house a study group of Katahdin sheep at the USSES. Beginning in 2016, the USSES set in place a plan to acquire several productive NSIP Katahdin ewes from USMARC. These ewes have arrived and are now being compared to Rambouillet and Polypay breeds in an open-range, herder-managed production system. Again, this current project provides a vastly expanded foundation for the project and its ultimate success.”
Although this set of interviews provided great background to Sheep GEMS, a question remained unanswered. How do flock owners join in the project?
“By contacting me at firstname.lastname@example.org,” said Lewis. “We already have had a lot of engagement by Katahdin breeders, but we are looking to recruit more Polypay, Rambouillet and Suffolk flocks. They do need to be part of NSIP. So that we can accumulate enough years of data, it would certainly help if those flocks were on board by this year’s breeding season. If you are interested, please send me an email.”
How does a flock owner benefit from joining in?
“Perhaps foremost is knowing that they have contributed to a project designed to benefit the entire sheep industry. By improving the sustainability of our flocks, making them more robust and resilient, we ensure the economic vitality of sheep enterprises.
“However, more specifically, participating flocks – Innovation Flocks – will benefit from substantial support of their genotyping costs. As that genotyping is done – which has already begun in the project – they will receive DNA-based pedigree verification and genetic conditions on some key disease susceptibility and muscling traits. Given enough buy-in among producers, at the end of the project, GEBV will be introduced in the Polypay, Rambouillet and Suffolk breeds, and bolstered in Katahdin. These GEBV will be available for current NSIP traits and, in due-course, important new ones.
“We are asking Innovation Flock owners to collect several new measures, which we certainly understand places more demands on their already busy schedules. We very much appreciate that extra effort. Yet for us – and I truly mean us collectively – to take full advantage of what Sheep GEMS can offer, we need you to join in heart and soul. Together, we can accomplish a lot.”
Boyer perhaps said it best.
“This project has the potential to create a paradigm shift in the US sheep industry … Viewing resilience, adaptability and key productivity traits through a combined genetic and environmental [climatic] lens will provide exciting new insights into advances that will provide quantum leaps in selective breeding and management.”
Acknowledgement: Sheep GEMS is supported by the Agriculture and Food Research Initiative Grant number 2022-67015-36073 from the USDA National Institute of Food and Agriculture, Animal Breeding and Functional Annotation of Genomes program, A1201. USDA is an equal opportunity provider and employer. The mention of trade names of commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the USDA.