Location: Livestock Bio-Systems
2022 Annual Report
Objectives
Objective 1: Perform genetic analyses, including genomics and genetic parameters, for a suite of health and performance traits (e.g. mastitis, respiratory disease, milk quality and eating quality).
Objective 2: Evaluate impact of TMEM154 genetic variants on lifetime productivity of sheep.
Approach
The proposed plan will develop comprehensive phenotyped populations in which the effects of genomic variation can be estimated and selection can be performed to improve animal growth and reproductive performance. This approach will generate genomic technologies to increase production efficiency for release to sheep producers.
Progress Report
This is the final report for this project which terminates in September 2022. See the report for the replacement project, 3040-31000-105-000D “Discovery of Novel Traits to Improve Efficiency and Sustainability of Different Sheep Production Systems” for additional information.
In support of Objective 1, research continued on three, multi-year experiments to collect data on economically important health, performance, and behavioral traits which were initiated in fiscal year (FY) 2021 and continued into FY 2022. The first began phenotyping Katahdin lambs for feed intake, growth, health, and carcass traits (approximately 120 lambs per year). This experiment, along with another initiated in FY 2020 which phenotypes Katahdin ewes for health and longevity traits (approximately 300 ewes per year), is part of a multiple ARS location effort to evaluate novel traits for suitability in the National Sheep Improvement Program (NSIP). Currently, the NSIP generates estimated breeding values for traits that can be readily measured on a farm/ranch (e.g., ewe fecundity, lamb weight, etc.). However, many other traits impact sheep enterprise profitability but are too difficult/expensive for producers to measure (e.g., health, longevity, feed efficiency, carcass traits, etc.). A new experiment was initiated in FY 2022 to begin collecting individual feed intake and feed efficiency data in the genetic reference flock lambs, which include Suffolk, Polypay, and Katahdin breeds. By ensuring strong genetic connectedness between ARS and industry purebred sheep flocks, ARS researchers and collaborators can evaluate novel traits for use in the NSIP. Two other experiments were initiated in FY 2021 and continued in FY 2022 in the Composite IV sheep population. Ram breeding capacity (number of ewes mated) is an economically important trait to sheep producers, particularly those that expose ewes to multiple ram mating groups. Past work has estimated large amounts of variation in breeding capacity among fertile rams, which indicates that behaviors toward ewes and other rams have important roles. Composite IV rams were fitted with accelerometers and exposed to small groups of estrus-synchronized ewes for short durations by themselves or with two other rams and behaviors were video recorded. Rams were again fitted with accelerometers and exposed to a larger group of ewes (3 rams: 50 ewes) for a 21-day breeding season. Sire of lambs is determined by genomic testing on progeny DNA using a panel of parentage markers. Two years of ram behavior data have now been collected, with parentage data needed to complete the breeding capacity components. Collected data will enable researchers to identify behavioral characteristics that are indicative of more successful ram mating behavior. The second experiment, utilizing the same Composite IV sheep, seeks to quantify maternal and neonatal behaviors, as well as dam mammary health and conformation traits which contribute to lamb survival in low-input, pasture lambing systems. Low-input production systems are well suited to sheep managed on marginal landscapes but reduce the ability to observe and measure traits that are more easily recorded on sheep managed in varying degrees of confinement. This experiment is a cross-over design which allocates genetically related ewes to be represented within barn or pasture lambing groups each year. A subset of ewes (approximately 120 ewes per year) in the barn lambing group are placed under camera observation to record maternal and lamb behavior for approximately two hours immediately following parturition. Samples are collected on this subset of ewes and lambs to infer colostrum quality and immune transfer to lambs as well as ewe udder health and conformation. Two years of collections for this experiment have been completed. Data from all these experiments will be used to estimate genetic effects/genomic regions contributing to variation in economically important ewe, ram, and lamb traits. Results will be evaluated for their application to the sheep industry in the form of new genetic tools for stakeholder use.
In support of Objective 2, research continued, and final analysis of data was completed for three longitudinal experiments using a natural challenge protocol for exposure to the ovine lentivirus causing ovine progressive pneumonia (OPP). These experiments were designed to evaluate the relative impact of four of the most common genetic variants for a major gene (TMEM154) with host genetic variation for susceptibility to infection in U.S. sheep populations on ewe lifetime productivity. These novel experiments were the first and only example of their kind to evaluate ewes with specific haplotype combinations for TMEM154, yet with a common genetic and management background with repeated performance records and multiple sampling points to recognize when infections were initially established. Prior experiments have always evaluated a snapshot in time for a population. Results from the three overlapping longitudinal studies on an ewe flock over a nine-year period were analyzed and interpreted. The objectives were to estimate additive and dominance effects of four TMEM154 haplotypes on susceptibility to OPP infection and to develop selection guidelines to reduce the prevalence of OPP in industry flocks. TMEM154 diplotype and route of transmission interacted to affect infection status. The susceptible allele haplotypes “2” and “3” are completely dominant to haplotype “1” and the less susceptible alleles “1” and “4” represent equivalent levels of reduced susceptibility and equivalent productivity. Ewes with non-functional TMEM154 (homozygous for haplotype “4”) did not differ for traits evaluated. In addition, a notable outcome was the lack of evidence that there was disease progression in “4,4” positive ewes. Lifetime productivity differences between diplotypes equates to at least $171 in additional lifetime revenue per TMEM154 diplotype “1,1” ewe compared to the susceptible diplotypes. These experiments have allowed us to integrate the knowledge obtained into recommendations for reduction or eradication of OPP in U.S. sheep flocks.
Accomplishments
1. Evaluation of four genetic variants for susceptibility to ovine progressive pneumonia. Ovine progressive pneumonia (OPP) is an incurable disease and results in millions of dollars of annual economic losses to the sheep industry. ARS researchers at Clay Center, Nebraska, analyzed and interpreted data from overlapping longitudinal studies specifically designed to evaluate the effects of each TMEM154 genotype combination, or diplotype, on infection status and ewe lifetime productivity. In a common environment and with similar levels of natural virus exposure, less than 10% the favorable genotype ewes became infected through 5.5 yr. of age whereas > 80% of the unfavorable genotype ewes were infected by 3.3 yr. of age. Over five production years, ewes with the favorable genotype weaned, on average, 2.1 more lambs and 40 kg greater weight of lamb than ewes with the unfavorable genotype. Combined analyses of all three experiments indicated that reduced susceptibility to OPP infection and increased levels of lifetime productivity would be expected from ewes that have two copies of the favorable versions of the TMEM154 gene, and the most susceptible versions cause an equivalent risk of infection with just one copy present. Using average economic conditions during this experiment, these results equate to $171 in additional lifetime revenue for the favorable genotypes. Producers can now select breeding stock that increases the frequency of the favorable genotypes to promotes genetic resilience to OPP.
Review Publications
Page, C.M., Knuth, R.M., Murphy, T.W., Rule, D.C., Bisha, B., Taylor, J.B., Stewart, W.C. 2022. Effects of increasing dietary zinc sulfate fed to gestating ewes: II. Milk somatic cell count, microbial populations, and fatty acid composition. Applied Animal Science. 38(3):285-295. https://doi.org/10.15232/aas.2022-02268.
Murphy, T.W., Chitko-McKown, C.G., Heaton, M.P., Freking, B.A. 2021. Effect of TMEM154 E35K variant (haplotypes 1 and 3) on the incidence of ovine lentivirus infection and ewe productivity during lifetime exposure. Journal of Animal Science. 99(11). Article skab304. https://doi.org/10.1093/jas/skab304.
