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ARS Home » Plains Area » Clay Center, Nebraska » U.S. Meat Animal Research Center » Genetics and Animal Breeding » Research » Research Project #433992

Research Project: Developing a Systems Biology Approach to Enhance Efficiency and Sustainability of Beef and Lamb Production

Location: Genetics and Animal Breeding

2019 Annual Report

Objective 1: Improve genomic tools for beef cattle and sheep. Sub-objective 1A: Complete improved reference assemblies for beef cattle and sheep using genome-wide and locus-targeted approaches, in addition to comparative approaches, to improve accuracy and contiguity. Sub-objective 1B: Improve annotation of the reference assemblies by conducting specific assays as outlined in the FAANG consortium guidelines, enhanced with parent-of-origin allele expression pattern data. Sub-objective 1C: Develop comprehensive databases of existing variation with predicted impact of those variations on gene expression and protein sequence. Objective 2: Develop systems to improve performance through combined genetic and genomic approaches. Sub-objective 2A: Improve breeding and management decisions by characterizing current genetic and phenotypic variation within and between predominant beef breeds and crosses. Sub-objective 2B: Identification of genomic variation associated with industry-relevant phenotypes in beef cattle. Sub-objective 2C: Development of low-input production lines of sheep, including genetic and genomic resource development to support characterization of these lines. Objective 3: Identify and characterize microbes, microbial populations, and parasites associated with normal and diseased populations. Sub-objective 3A: Profile microbial populations in the respiratory tract (RT) of cattle throughout the production life-cycle in the context of BRDC. Sub-objective 3B: Characterize genomic variation among sheep parasites, for correlation with anthelmintic resistance and animal genotype. Objective 4: Combine products from Objectives 1, 2, and 3 to synthesize a broader knowledge base. Sub-objective 4A: Synthesize genome annotation from Objective 1 and genetics by selection and assessment of impact of predicted non-functional alleles. Sub-objective 4B: Synthesize parasite and metagenomics from Objective 3 with genetics and genomics from Objective 2. Sub-objective 4C: Synthesize variant genotypes and annotation from Objective 1, animal phenotypes from Objective 2, and microbial profiles from Objective 3, by partitioning microbial variation into host genetic and enviromental influences on phenotypic expression.

Challenges to sustainability of beef and lamb production include aspects of animal health and wellbeing, societal expectations of reduced antibiotic use and/or development of alternatives, and pressure to reduce environmental impact of production. Advances in genomic and related technologies have opened new avenues to better understand the relationships between variants of animal genomes, production traits, and the microbes that are associated with animal production. The technologies support and depend on development of research populations with pertinent phenotypes that broadly sample industry genetics, continuing improvement in annotation of animal genomes, identification and characterization of microbial species relevant to animal production, and continued assessment of the interaction of genome variation and production phenotypes. This project plan will merge previous genetics and genomics projects into a broader systems approach, that will encompass (1) genome annotation and identification of functional variation among genomes, (2) development of phenotyped populations in which the effects of variation can be estimated, (3) characterization of the overall microbial diversity associated with the animals and dependencies of this diversity on animal genome variation, and (4) molecular-level characterization of microbial or parasitic organisms that impact on animal health, productivity, and reproduction. The systems approach will be combined with population management strategies, application of advancements in statistical methodology, and partnering with commercial producers. This combination will enable broader understanding of the components contributing to production efficiency, environmental impact, and animal welfare, while developing specific technologies for release to beef cattle producers and improved strains for the sheep industry.

Progress Report
Important progress was made on the Project Plan this year. For Objective 1, “Improving genomic tools for beef cattle and sheep”, new analysis approaches developed by researchers at Clay Center, Nebraska, and their collaborators, combined with improvements in DNA sequencing technology, have provided a fruitful new direction that was not conceivable at the time the Plan was created. Specifically, the development of a “trio” approach, which uses both sequence data from an individual and its parents (called a trio), supports the creation of two independent genome assemblies representing the chromosomes inherited from each parent (i.e., two genomes for the price of one). In 2019, this trio approach was applied to initiate reference-grade genome assemblies of two sheep breeds (White Dorper and Romanov, using the offspring of a mating of these two breeds), as well as interspecies crosses of Highland breed cattle with yak, Simmental breed cattle with bison, and Piedmontese breed cattle with gaur. Matings for the Pied/gaur cross were made this year, sequencing of a Simmental/bison cross was completed, initial assembly of the White Dorper/Romanov cross, and finished assemblies for the Highland/yak cross were created. The Highland/yak assemblies are now the highest quality genome assemblies of any mammal besides human. In the original Plan Proposal, enhancing the existing Hereford reference genome assembly was the principal goal since resources to create complete new assemblies were not available—the decrease in cost based on advancement in DNA sequencing technology created this new opportunity. The multiple breeds and species assemblies will support enhanced opportunity to use genome comparisons between species to identify functional variation in genes within the cattle and sheep species, as well as contribute to the construction of a “pan-genome”. The pan-genome is a concept that has arisen in the past several years, since formulation of the Project Plan, that posits the existence of variation between individuals of a species that is not confined to small differences in sequence, but instead includes much larger regions of genome that exist only in subset of individuals and can’t be observed using a reference genome assembly from a single individual. Additional progress on Objective 1 included support for the international Functional Annotation of Animal Genomes project, specifically producing data in support of efforts to identify genomic elements that regulate gene expression. This was complemented by efforts to either directly genotype or impute genotypes for over 16,000 markers on 17,880 animals born in the last 18 years in the Germplasm Evaluation (GPE) project. This will be used to support identification of variation directly contributing to phenotype in the other objectives. Progress on Objective 2, “Develop systems to improve performance through combined genetic and genomic approaches”, was equally successful. Matings within the GPE cattle population continued for all 18 sire breeds, and the total number of breeding females was brought to 3,400. The natural service bull group was upgraded to the target 15/16 purebred level, assisting in production of calves available for estimation of breed-specific heterosis. Virtually all calves were measured for important production traits including fertility indicators and lifetime productivity, enhanced by concurrent measure on 475 cows for feed efficiency/feed intake. An additional 800 calves were sampled for response to vaccination for respiratory viruses, among other phenotypes collected across GPE from carcass measurements to rumen microbiome samples. The GPE population and phenotypes supported a release of an update to the across-breed Estimated Progeny Difference (EPD) adjustment factors that are heavily referenced by commercial and seedstock beef cattle producers and breed associations, a major and historically impactful product of this Project Plan and its predecessors. These EPD are being enhanced by addition of new phenotypes such as meat tenderness, mature cow weight, and feed efficiency. The product is being further enhanced by initiating a test of genetics by management/environment interactions in beef cattle by evaluating phenotypes on specific genotypes of animals in El Reno, Oklahoma; Miles City, Montana; Nunn, Colorado; and Woodward, Oklahoma; with each location having different conditions and methods of growing and backgrounding calves before finishing. This across-location activity is supported by a successful Beef Grand Challenge application. In sheep, continued collection of data to evaluate three maternal sheep lines (Easycare composite, Polypay, and Katahdin) was performed. The evaluation of those ewe lines consisted of comparisons of both purebred and terminal mating systems to investigate potential antagonisms between direct sire-breed effects on lamb survival and growth that may occur with prolific ewes in pasture-lambing, low-input production systems. Estimates of ewe productivity have now been collected for all six of the scheduled years with third replicate ewes having produced their fourth parity during 2019 under pasture management. Second replicate ewes that remained and have had opportunities for 4 parities by 2018 and their accumulated performance data was used to identify ewes (n=120) that exhibited differences in lamb survival for subsequent maternal/lamb behavior evaluation for a fifth parity. This data was collected by cameras under barn lambing management in 2019 for the second of three proposed years. Additional data was collected in 2019 on this second replicate of ewes relating to udder morphology traits, and milk was sampled to identify levels of sub-clinical mastitis. Carcass data collection was completed with lambs from the 2017 lambing season. Fecal egg counts have been collected on all lambs at weaning in July from the 2015-2018 lambing seasons allowing estimates of heritability for parasite resistance/tolerance to be generated. Progress on Objective 3, “Identify and characterize microbes, microbial populations, and parasites associated with normal and diseased populations” was also substantial. The Project is on target for generating data on the microbial component, having collected nasal swabs from approximately 5,600 calves at key developmental timepoints like preconditioning (140 days old) and weaning (160 days old), and other timepoints of prebreeding (70 days old) for approximately 2,100 calves. Significantly, 620 calves that exhibited symptoms of respiratory disease were sampled to complement the integration of microbial phenotypes related to feed efficiency and growth, with health-related phenotypes. New techniques for microbial sequencing of animal droppings or rumen contents were developed and more than 100 microbial species previously unknown in the rumen were identified. Novel techniques for examining the immune repertoire of cattle, which is the set of antibody specificities that exist or are elicited by infection in an animal, were developed by researchers in Clay Center, Nebraska in collaboration with university partners. The outputs from Objectives 1-3 are feeding into the “grand synthesis” strategy of Objective 4, “Combine products from Objectives 1, 2, and 3 to synthesize a broader knowledge base”. Breeding based on selection for or against loss-of-function alleles for this Objective are proceeding, and genotyping to evaluate success is on schedule. In summary, the first full year (20 total months) of the new Project have kept us on track to reach the ambitious goals set for the 5-year Project Plan. Significant progress on subordinate project 3040-31000-100-10H, Genomic Analysis of Jersey and Holstein Cattle, was made, including the production of genome assemblies for both breeds. Researchers in Clay Center, Nebraska, used DNA provided by the collaborator to create genome assemblies for both breeds. These assemblies were highly continuous, reference-grade assemblies representing two important dairy breeds of cattle. They are currently undergoing analysis to identify differences from beef breeds of cattle and other attributes.

1. New database for study of bovine respiratory disease. Public release of a comprehensive reference database for conducting microbiome research in the cattle upper respiratory tract (URT). Most microbiome research relies mainly on the characterization of microbial diversity through targeted sequencing of a specific locus, the 16S rRNA gene, that is highly conserved across a wide variety of bacterial species. Generally, this characterization matches short sequences from one or two of the nine highly variable sections of this gene to a database of bacteria, to identify the genus of bacteria present in the DNA extracted from the environment of interest (i.e., the upper respiratory tract in the case of respiratory disease of cattle). Using long-read sequencing technology, ARS researchers in Clay Center, Nebraska, created a specific database of 16S rRNA genes obtained from the URT of over 500 cattle in different environments, including a set with sequence encompassing eight of the nine variable regions. The researchers demonstrated that the use of this database in analysis of bovine URT samples increased the ability to correctly identify microbial components and enhanced the resolution of these components to the species level. Bovine respiratory disease (BRD) is the most important and expensive communicable disease in cattle production, and is the primary disease-related reason for the application of antibiotics to cattle. Many researchers hypothesize that a key to successful strategies for reducing the incidence or severity of disease is understanding the contributions of the URT microbiome to development of disease. Thus, this research provides a new tool to the potential understanding and control of the complex disease of BRD.

2. Cow productivity estimations. ARS scientists at Clay Center, Nebraska, developed genetic evaluations of cow weight and cumulative productivity. Weight and calf production explain a substantial amount of the variation in costs incurred and income generated by individual cows, so breeding values predicted for these traits may be used to select sires for profitability of their daughters. Using random regression techniques, the evaluations incorporate annual measurements of cow weight and calf production, with calf production records reflecting both success and failure to produce a calf following each breeding season. Records start with the first opportunity a heifer has to produce a calf, so predictions are based on records of more females and may be more accurate than waiting for single observations of mature weight and total productivity of aged females. This methodology utilizing all available records from individual cows will improve selection response for beef cattle genetic evaluation programs.

3. Application of interspecies cross to improve efficiency of genome assembly. Created reference-quality assemblies of the Highland breed of cattle and the yak in a single experiment, by using an individual resulting from the mating of a Highland bull and yak cow. Historically, genome assemblies have made use of inbred individuals to minimize the differences between the maternally and paternally derived sets of chromosomes present in each cell, because these differences confused the computer algorithms developed to create assemblies from the short sequence reads generated from the genome. ARS researchers in Clay Center, Nebraska, and Beltsville, Maryland, in collaboration with the National Institutes of Health, University of Nebraska, and University of Kentucky, developed an alternative method that used newer, long-read sequencing technology and highly heterozygous individuals (that is, the maternal and paternal chromosomes are very different) to generate two separate genome assemblies from a single individual, each representing either the maternal or paternal chromosomes. This technique was found to produce the highest quality assemblies, and by applying it to an interspecies hybrid that maximized the contrast between maternal and paternal chromosomes, the researchers created individual genome assemblies for both the yak and cattle, that are of equal or better quality than any existing mammalian assembly including those of humans or biomedical species such as mice or rats.

Review Publications
Freking, B.A., Bennett, G.L. 2019. Rambouillet and Romanov reciprocal breed effects on survival and growth traits of F1 lambs and on reproductive traits of F1 ewes. Journal of Animal Science. 97:578-586.
Bennett, G.L., Tait, R.G., Shackelford, S.D., Wheeler, T.L., King, D.A., Casas, E., Smith, T.P.L. 2019. Enhanced estimates of carcass and meat quality effects for polymorphisms in myostatin and mu-calpain genes. Journal of Animal Science. 97(2):569-577.
Green, B.T., Keele, J.W., Bennett, G.L., Gardner, D.R., Stonecipher, C.A., Cook, D., Pfister, J.A. 2019. Animal and plant factors which affect larkspur toxicosis in cattle: Sex, age, breed, and plant chemotype. Toxicon. 165:31-39.
Snelling, W.M., Kuehn, L.A., Thallman, R.M., Bennett, G.L., Golden, B.L. 2018. Genetic correlations among weight and cumulative productivity of crossbred beef cows. Journal of Animal Science. 97:63-77.
Workman, A.M., Chitko-McKown, C.G., Smith, T.P.L., Bennett, G.L., Kalbfleisch, T.S., Basnayake, V., Heaton, M.P. 2018. A bovine CD18 signal peptide variant with increased binding activity to Mannheimia hemolytica leukotoxin. F1000Research. 7:1985.
Green, B.T., Keele, J.W., Gardner, D.R., Welch, K.D., Bennett, G.L., Cook, D., Pfister, J.A., Davis, T.Z., Stonecipher, C.A., Lee, S.T., Stegelmeier, B.L. 2019. Sex-dependent differences for larkspur (Delphinium barbeyi) toxicosis in yearling Angus cattle. Journal of Animal Science. 97(3):1424-1432.
Green, B.T., Gardner, D.R., Pfister, J.A., Welch, K.D., Bennett, G.L., Cook, D. 2019. The effect of alkaloid composition of larkspur (Delphinium) species on the intoxication of Angus heifers. Journal of Animal Science. 97(3):1415-1423.
Thorson, J.F., Prezotto, L.D., Adams, H., Petersen, S.L., Clapper, J.A., Wright, E.C., Oliver, W.T., Freking, B.A., Foote, A.P., Berry, E.D., Nonneman, D.J., Lents, C.A. 2018. Energy balance affects pulsatile secretion of luteinizing hormone from the adenohypophesis and expression of neurokinin B in the hypothalamus of ovariectomized gilts. Biology of Reproduction. 99(2):433-445.
Green, B.T., Lee, S.T., Keele, J.W., Welch, K.D., Cook, D., Pfister, J.A., Kem, W.R. 2018. Complete inhibition of fetal movement in the day 40 pregnant goat model by the piperidine alkaloid anabasine but not related alkaloids. Toxicon. 144:61-67.
Green, B.T., Gardner, D.R., Cook, D., Pfister, J.A., Welch, K.D., Keele, J.W. 2018. Age-dependent intoxication by larkspur (Delphinium) in Angus steers. Toxicon. 152:57-59.
Lindholm-Perry, A.K., Kuehn, L.A., McDaneld, T.G., Miles, J.R., Workman, A.M., Chitko-McKown, C.G., Keele, J.W. 2018. Complete blood count data and leukocyte expression of cytokine genes and cytokine receptor genes associated with bovine respiratory disease in calves. BMC Research Notes. 11:786.
Workman, A.M., Kuehn, L.A., McDaneld, T.G., Clawson, M.L., Loy, J.D. 2019. Longitudinal study of humoral immunity to bovine coronavirus, virus shedding, and treatment for bovine respiratory disease in pre-weaned beef calves. BioMed Central (BMC) Veterinary Research. 15:161.
Kirkpatrick, B.W., Thallman, R.M., Kuehn, L.A. 2019. Validation of SNP associations with bovine ovulation and twinning rate. Animal Genetics. 50:259-261.
Retallick, K.J., Bormann, J.M., Weaber, R.L., MacNeil, M.D., Bradford, H.L., Freetly, H.C., Hales, K.E., Moser, D.W., Snelling, W.M., Thallman, R.M., Kuehn, L.A. 2017. Genetic variance and covariance and breed differences for feed intake and average daily gain to improve feed efficiency in growing cattle. Journal of Animal Science. 95(4):1444-1450.
Ahlberg, C.M., Allwardt, K., Broocks, A., Bruno, K., McPhillips, L., Taylor, A.A., Krehbiel, C.R., Calvo-Lorenzo, M.S., Richards, C.J., Place, S.E., Desilva, U., Vanoverbeke, D.L., Mateescu, R.G., Kuehn, L.A., Weaber, R.L., Bormann, J.M., Rolf, M.M. 2018. Environmental effects on water intake and water intake prediction in growing beef cattle. Journal of Animal Science. 96:4368-4384.
Murphy Jr, T.W., Stewart, W.C., Notter, D.R., Mousel, M.R., Lewis, G.S., Taylor, J.B. 2019. Evaluation of Rambouillet, Polypay, and Romanov–White Dorper x Rambouillet ewes mated to terminal sires in an extensive rangeland production system: Body weight and wool characteristics. Journal of Animal Science. 97(4):1568-1577.
Liu, H., Smith, T.P., Nonneman, D.J., Dekkers, J.C., Tuggle, C.K. 2017. A high-quality annotated transcriptome of swine peripheral blood. BMC Genomics. 18:479..
Haley, B.J., Smith, T.P., Harhay, G.P., Loneragan, G.H., Webb, H.E., Bugarel, M., Kim, S., Van Kessel, J.S., Harhay, D.M. 2019. Complete genome sequence of a Salmonella enterica subsp. enterica serovar Fresno isolate recovered from beef cattle lymph nodes. Microbiology Resource Announcements. 8(2):e01338-18.
Kalbfleisch, T.S., Murdoch, B.M., Smith, T.P.L., Murdoch, J.D., Heaton, M.P., Mckay, S.D. 2018. A SNP resource for studying North American moose. F1000Research. 7(40):1-17.
Nguyen, S.V., Harhay, G.P., Bono, J.L., Smith, T.P., Harhay, D.M. 2017. Genome sequence of the thermotolerant foodborne pathogen Salmonella enterica serovar Senftenberg ATCC 43845 and phylogenetic analysis of Loci encoding increased protein quality control mechanisms. mSystems. 2:e00190-16.
Harhay, G.P., Harhay, D.M., Bono, J.L., Smith, T.P.L., Capik, S.F., DeDonder, K.D., Apley, M.D., Lubbers, B.V., White, B.J., Larson, R.L. 2017. Closed genome sequences of seven histophilus somni isolates from beef calves with bovine respiratory disease complex. Genome Announcements. 5(40):e01099-17.
Nguyen, S.V., Harhay, D.M., Bono, J.L., Smith, T.P.L., Fields, P.I., Dinsmore, B.A., Santovina, M., Wang, R., Bosilevac, J.M., Harhay, G.P. 2018. Comparative genomics of Salmonella enterica serovar Montevideo reveals lineage-specific gene differences that may influence ecological niche association. Microbial Genomics. 4:1-17.
Parker, C., Cooper, K.K., Huynh, S., Smith, T.P., Bono, J.L., Cooley, M.B. 2018. Genome sequences of eight Shiga toxin-producing Escherichia coli strains isolated from a produce-growing region in California. Genome Announcements. 7(1):1-3.
Harhay, G.P., Harhay, D.M., Bono, J.L., Smith, T.P.L., Capik, S.F., DeDonder, K.D., Apley, M.D., Lubbers, B.V., White, B.J., Larson, R.L. 2018. Closed genome sequences and antibiograms of 16 pasteurella multocida isolates from bovine respiratory disease complex cases and apparently healthy controls. Microbiology Resource Announcements. 7(11):e00976-18.
Workman, A.M., Dickey, A.M., Heaton, M.P., Clawson, M.L., Smith, T.P.L. 2017. Complete genome sequences of two genotype A2 small ruminant lentiviruses isolated from infected U.S. sheep. Genome Announcements. 5(13):e00109-17.
Clemmons, B.A., Reese, S.T., Dantas, F.G., Franco, G.A., Smith, T.P., Adeyosoye, O.I., Pohler, K.G., Myer, P.R. 2017. Vaginal and uterine bacterial communities in postpartum lactating cows. Frontiers in Microbiology. 8:1047.
Beiki, H., Liu, H., Manchanda, N., Nonneman, D.J., Smith, T.P.L., Reecy, J., Tuggle, C. 2019. Improved annotation of the domestic pig genome through integration of Iso-Seq and RNA-seq data. BMC Genomics. 20:344-362.
Johnson, T., Keehan, M., Harland, C., Lopdell, T., Spelman, R.J., Davis, S.R., Rosen, B.D., Smith, T.P., Couldrey, C. 2019. Short communication: Identification of the pseudoautosomal region in the Hereford bovine reference genome assembly ARS-UCD1.2. Journal of Dairy Science. 102(4):3254-3258.
Rexroad III, C.E., Vallet, J.L., Matukumalli, L.K., Ernst, C., Van Tassell, C.P., Cheng, H.H., Reecy, J., Fulton, J., Taylor, J., Lunney, J.K., Liu, J., Cockett, N., Smith, T.P., Van Eenennaam, A., Clutter, A., Telugu, B., Purcell, C., Bickhart, D.M., Blackburn, H.D., Neibergs, H., Wells, K., Boggess, M.V., Sonstegard, T. 2019. Genome to phenome: improving animal health, production, and well-being: a new USDA blueprint for animal genome research 2018–2027. Frontiers in Genetics. 10:327.
Walker, L.R., Engle, T.B., Vu, H., Tosky, E.R., Nonneman, D.J., Smith, T.P.L., Borza, T., Burkey, T.E., Plastow, G.S., Kachman, S.D., Ciobanu, D.C. 2018. Synaptogyrin-2 influences replication of porcine circovirus 2. PLoS Genetics. 14(10):e1007750.