Progress 01/01/16 to 12/31/16

Outputs
Target Audience:Application of new genetic and genomic technologies to enhance fertility in beef cattle offers the potential to improve reproductive efficiency. The objective of this project is to improve reproductive rates in cattle by identifying genes which cause embryonic or early developmental mortality. The long-term goal of this project is to improve reproductive rates of US beef cattle based on improvements in selection to improve overall profitability to the herd enterprise. Audiences targeted from outcomes stemming from this project include various segments of the beef cattle industry, including: breed associations; seedstock and commercial beef producers; the AI industry; the academic community; and extension livestock specialists. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Regional extension livestock specialists, beef producers and allied industry representatives have been provided with updates from the project through continuing education events, news releases, field days, and regional extension meetings. However, more extensive training and development opportunities are scheduled in subsequent years of the project. How have the results been disseminated to communities of interest?Regional extension livestock specialists, beef producers and allied industry representatives have been provided with updates from the project through continuing education events, news releases, field days, and regional extension meetings. However, more extensive training and development opportunities are scheduled in subsequent years of the project. What do you plan to do during the next reporting period to accomplish the goals?1. Identify, validate and characterize the impact of recessive developmentally lethal alleles associated with reproductive failure in Angus cattle. Goals for 2017. Sequencing of the 150 bulls in addition to the analysis of all of the collected sequences for the discovery of putative loss of function alleles will have been completed. This includes identification of animals predicted to be homozygous for such alleles to enable the prioritization of functional candidates which have the potential to be early embryonic or developmental lethals. We have identifiedthe most cost-effective and highest content custom genotyping assay available from Illumina and Affymetrix and use the generated sequences to design the content for the functional genotyping assay. The assay is designed and delivered to the project. 2. Develop a male fertility expected progeny difference (EPD) and enhanced heifer pregnancy rate EPD based upon LOFgenotype information. Goals for 2017. After completion of DNA and phenotypicsampling of the 11,506heifers inMissouri and cooperating herds in other states, an assay of functional variantsidentified in the sequencing project will be completed to identify those that are never seen in homozygous form, implying them to be lethals.Based upon allele frequencies estimated from the sample we will generate molecular EPDs for fertility based upon genotypesgenerated in Angus. 3A. Development of selection indexes that support multi-trait selection, inclusive of fertility traits. Goals for 2017.Continue refining the fertility index ($F) in collaboration with Mike MacNeil and in discussion with cooperators to determine if the index appears to be appropriately weighting reproduction against the other traits of economic importance. 3B. Develop sector-level economic effects of increasing reproductive rates in Angus cattle. Goals for 2017. Sector-level economic effects of increasing reproductive rates determined from the research and extension portions of the grant will be determined. 4. Develop decision support software to optimize breeding schemes via the implementation of selection indexes and mate selection based upon sire and dam recessive lethal genotypes. Goals for 2017.We are meeting with Brian Kinghorn in November 2016 to customize mate selection software for US Angus parameters and develop working example using the University of Missouri Thompson ranch phenotypes and genotypes. We are also meeting with American Angus Association to determine how to best utilize the recessive lethal information into their genetic improvement program. 5A. Develop a web-based comprehensive educational training program for extension livestock specialists, allied industries, producers, veterinarians, and students. Goals for 2017. Content for the remaining modules to be completed inyear 4 and 5 will be in cooperation with ITLE. 5B. Develop a simulation exercise that demonstrates the effect of DGV for heifer and sire fertility on reproductive performance and profitability. Goals for 2017. The primary goal for 2017is to complete the development of specific learning objectives and develop an overall plan for the simulation exercise. Upon completion, individual components of the simulation plan will begin being constructed. 5C. Develop innovative educational and outreach materials and enhancement of the Beef Cattle Community of Practice. Goals for 2017. Van Eenennaam, Rolf, and Decker have worked with collaborators to re-launch the beef cattle communityof practice (CoP) on eXtension and addedto site traffic through the development of a site called eBEEF. The newCoP re-launch includes a revitalized content database focused towards genomics information and will be curated andupdated by a team of beef genetics/genomics extension personnel. As additional resources are developed within thisproposal and other genomics proposals, they will be added to the new CoP and disseminated on the site. We will also havethe ability to archive and retain this content well past the life of this proposal which will ensure the broadest disseminationpossible.

Impacts
What was accomplished under these goals? 1. Identify, validate and characterize the impact of recessive developmentally lethal alleles associated with reproductive failure in Angus cattle. Accomplishments. Genomes of 99 Angus bulls were sequenced and analyzed to identify putative loss of function alleles which are being tested for the absence of homozygosity in 11,506 genotyped heifers to implicate those that are embryonic or early developmental lethals. Eighteen US beef breed associations which annually register at least 10,000 animals are participatingin this project and contributed financially to the sequencing of 5-15 bulls from each breed. We secured ~$250K in additional support from the American, Argentine, Australian and New Zealand Angus Associations; inaddition to the US Hereford, Beefmaster, Gelbvieh, Charolais, Simmental, and Maine-Anjou Associations. Genome sequencedata was contributed from Genome Canada, USDA/BARC and breed associations. We have shared sequence on Angus animals for sequence on Red Angusanimals with the Genome Canada sequencing project, andprovided sequence data on 17 Angus bulls to the 1000 bullgenome project to allow us access to that database of over 35 million variants in 1147 animals. The majority of the bullssequenced in these projects were shallow skim sequenced (~8X coverage) however, by increasing thenumber of animals represented in our data we increased the number of identified loss of function variants and decreased thenumber of candidate lethals via the identification of animals homozygous for certain alleles. Preliminary results indicate thatour approach is correctly identifying loci that directly affect fertility in beef cattle. 2. Develop a male fertility expected progeny difference (EPD) and enhanced heifer pregnancy rate EPD based upon LOFgenotype information. Accomplishments. We proposed to genotype a sample of 10,000 Angus females to identify lethals withhigh-confidence and their allele frequencies. DNA and phenotypic sampling was completed on 11,506 heifersfrom 52 herds. We characterized 86 of the sequenced Angus bulls (those with Heifer Pregnancy EPDs) for the numberof LOF alleles that they carry in genes that are predicted to be essential for life and likely to directly impact the fertilityof these bulls. We have identified the number of alleles carried per bull and the sum of the frequencies of these alleles in eachbull (inversely proportional to the molecular breeding value for fertility of each bull based on these loci). The mean number ofLOF alleles in essential genes carried by each bull ranged from 5 to 23 with an average of 12.04. Our data indicate that it isnot only the number of lethals that are carried by each bull but the frequency at which these alleles occur in the Angus breedthat impacts the predicted fertility of each bull. 3A. Development of selection indexes that support multi-trait selection, inclusive of fertility traits. Accomplishments.Mike MacNeil developed a model that simulates a herd of 10,000 breeding age females with age specific rates of fertility and survival. MacNeil is working this into a fertility index ($F) that uses the economic values derived in the model to develop an Angus straight bred whole industry index that includes fertility as one of the criteria - weighted by its relative economic merit. The recessive loci identified in this project will be treated as a genetic load rather than an EPD as the impact of the alleles on fertility will be dependent upon the genotype of their mate. We are awaiting an estimate of the approximate number of recessive lethal loci. 3B. Develop sector-level economic effects of increasing reproductive rates in Angus cattle. Accomplishments. Activity related to this specific aim will not begin until year 5 of the project. 4. Develop decision support software to optimize breeding schemes via the implementation of selection indexes and mate selection based upon sire and dam recessive lethal genotypes. Accomplishments.Currently, Lindsay Upperman, UC Davis graduate student,is working on running two simulations in MateSel. The first simulation is with 100 loci at rare frequencies in the population, while the second is with 10 loci at intermediate frequencies. Also, she is running these simulations with different genotyping percentages within the population, thus to show which percentage would be best for producers. Furthermore, she will be working with Dr. Brian Kinghorn from November 6th, 2016 to November 20th, 2016 in Armidale to further explore and understand using the program, MateSel. 5A. Develop a web-based comprehensive educational training program for extension livestock specialists, allied industries,producers, veterinarians, and students. Accomplishments. The Institute for Teaching and Learning Excellence (ITLE) atOklahoma State University is the service provider working with Rolf to develop the web interface and educational content fordevelopment of the teaching modules.In the past year, Dr. Rolf worked with ITLE to develop a website for the project, which is intended to host the educational video modules produced in this project as well as direct interested website visitors to additional educational materials.The project's educational website, hosted http://beefreproduction.org/, was launched this year and currently includes space for both videos and links to fact sheets and other educational materials. The first module on genetic correlations and antagonisms was launched and is currently available. Several others are in development with ITLE and three more, "What is the Genome?", "What is an EPD?", and "History of Selection and Genetic Change in Beef Cattle", are nearing release. Additional topics that will be covered in subsequent modules include:Introduction to the Central Dogma of Biology;Mendelian Inheritance;Risk Management of Genetic Defects;LOF Mutations;Parentage testing;Selection Indexes;Recombination;Genome sequencing, annotation, and assembly;Use of DGVs and Genomic-Enhanced EPDs;EPD Accuracy;Formulating breeding objectives;Optimizing vs maximizing for trait selection;Heterosis and Mating systems;Fitting to the Environment; and Use of MateSel in multi-trait selection.Approximately half of the content for the modules in this list has been delivered to ITLE and is awaiting module development. The remainder of the content for the modules will be delivered in subsequent years and we will continue to work with ITLE to develop and release these modules on the website. 5B. Develop a simulation exercise that demonstrates the effect of DGV for heifer and sire fertility on reproductive performanceand profitability. Accomplishments. The overall goal of the simulation exercise will be to educate extension livestock specialists, allied industries, producers, veterinarians, and undergraduate students on how to incorporate principles of selection and genomic information into breeding management decisions.During the past year, the original "Cowgames" was converted from disk format to a web application currently hosted on a local server. Players breed their bulls to a predetermined number of females, andEPDs are provided for each animal's birth weight, weaning weight, and yearling weight. Additionally, each animal has a genotype representing the locus of an unidentified lethal recessive. Players must determine how to best manage this lethal in their particular herd. 5C. Develop innovative educational and outreach materials and enhancement of the Beef Cattle Community of Practice. Accomplishments. Accomplishments are summarized under Specific Aim 5A because of the overlap betweenSpecific Aims 5A and 5C.

Publications

• Type: Other Status: Other Year Published: 2015 Citation: Current grants with an eye to future research directions (June 2015)UC Davis Animal Science Annual Retreat, Davis, CA, 6/5/15
• Type: Other Status: Other Year Published: 2015 Citation: "Needs and Challenges in Agricultural Production: The Livestock Perspective" APEC Manila, Philippines 6/8/15
• Type: Other Status: Other Year Published: 2015 Citation: Utilizing Molecular Information in Beef Cattle Selection, Angus Genomics Forum, Modesto Jr College, Modesto, CA 8/4/15
• Type: Other Status: Other Year Published: 2015 Citation: Targeting multiple end uses in beef cattle breeding programs Applied Reproductive Strategies in Beef Cattle, Davis, CA 8/18/15
• Type: Other Status: Other Year Published: 2015 Citation: Food for Thought: Innovations and Opportunities for Animal Breeding, Explorit Science Center lecture series, Davis, CA 9/1/15
• Type: Other Status: Other Year Published: 2016 Citation: Rolf, MM. 2016. What is the Genome? Educational module hosted @ http://beefreproduction.org/
• Type: Other Status: Other Year Published: 2015 Citation: Producer Uptake: How might genomic information to translated to industry outcomes BRD Symposium, American Association of Bovine Practitioners conference (AABP) conference, New Orleans, LA 9/18/15
• Type: Other Status: Other Year Published: 2016 Citation: Utilizing DNA Information in Cattle Selection Programs Western Canadian Association of Bovine Practitioners (WCABP), Calgary, AB, Canada 1/15/16
• Type: Other Status: Other Year Published: 2016 Citation: Genome selection: Basics and experience in animal systems, UC Davis Seed Biotechnology Center Breeding with Genomics Class, Davis, CA 2/17/16
• Type: Other Status: Other Year Published: 2016 Citation: Genomics and Bull Selection, UCCE meeting, Alturas, CA 2/18/16
• Type: Other Status: Other Year Published: 2016 Citation: Genomics and Bull Selection, Siskiyou Cattlemens Association Pie Night, Montague, CA 2/18/16
• Type: Other Status: Other Year Published: 2016 Citation: Genomics and Bull Selection, Willows, Tehama UCCE meeting, Willows, CA 2/19/16
• Type: Other Status: Other Year Published: 2016 Citation: Genomics and Bull Selection, Redding, Shasta UCCE meeting, Cottonwood, CA 2/19/16
• Type: Other Status: Other Year Published: 2016 Citation: Genomics and Bull Selection, Southern San Joaquin UCCE Livestock Symposium, Bakersfield, CA 2/27/16
• Type: Other Status: Other Year Published: 2016 Citation: Genomics and Bull Selection, Southern San Joaquin UCCE Livestock Symposium, Exeter, CA 2/27/16
• Type: Other Status: Other Year Published: 2016 Citation: New developments in selection for replacement heifers, disease resistance and other economically relevant traits, 2016 Texas A&M Beef Cattle Short Course, College Station, TX 8/2/2016
• Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Taylor JF, RD Schnabel, B Simpson, JE Decker, MF Smith and DJ Patterson. 2016. Detection and selection against early embryonic lethals in US beef breeds. Abstract 15118. Translational Genomics for Improved Fertility of Animals Workshop. Joint Animal Meetings. Salt Lake City, UT. July 21.
• Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Taylor JF. 2016. Adventures in next-generation sequencing. Teagasc Grange Research Center, Meath Ireland. September 21.
• Type: Other Status: Other Year Published: 2015 Citation: Commercial Replacement Heifer Selection 12/2015 http://articles.extension.org/pages/73404/commercial-replacement-heifer-selection
• Type: Other Status: Other Year Published: 2016 Citation: Recent Developments in Genetic Evaluations and Genomic Testing 1/2016 http://articles.extension.org/pages/73461/recent-developments-in-genetic-evaluations-and-genomic-testing
• Type: Other Status: Other Year Published: 2016 Citation: How To Get Started With DNA Testing 4/2016 http://articles.extension.org/pages/73798/how-to-get-started-with-dna-testing
• Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Rolf, MM and A. Van Eenennaam. 2016. Turning Loss into Gain: Managing Genetic Risk to Improve Fertility.
• Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Taylor JF. 2016. Identification and Management of Alleles Impairing Heifer Fertility while optimizing genetic gain in Angus cattle. USDA AFRI Animal Breeding, Genetics and Genomics annual program director meeting. San Diego, CA January 8. Invited presentation.
• Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Taylor JF, EB Simpson, DM Larkin, JL Hoff, JE Decker and RD Schnabel. 2016. Design and Application of the Cattle GGP-F250 Array. Plant and Animal Genome Conference XXIV. San Diego, CA. Jan 9-13. Presentation 22333.
• Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Taylor JF and Schnabel RD. 2016. Identifying Important New Traits In Cattle  An Update On The GGP F-250 Array. GeneSeek Innovation Seminar. Beef Improvement Federation, Manhattan KS, June 14.
• Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Taylor JF. 2016. Adventures in next-generation sequencing. Irish Cattle Breeding Federation. Bandon Ireland. September 19.
• Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Taylor JF, RD Schnabel, B Simpson, JE Decker, MM Rolf, BW Kinghorn, AL Van Eenennaam, MD MacNeil, S Brown, M Smith and D Patterson. 2016. Detection and selection against early embryonic lethals in US beef breeds. National Beef Cattle Evaluation Consortium Brown Bagger Seminar Series. Via Internet. October 5.
• Type: Journal Articles Status: Published Year Published: 2016 Citation: Decker JE, JF Taylor, J Kantanen, A Millbrooke, RD Schnabel, LA Alexander and MD MacNeil. 2016. Origins of cattle on Chirikof Island, Alaska, elucidated from genome-wide SNP genotypes. Heredity 116:502-505.
• Type: Journal Articles Status: Published Year Published: 2016 Citation: Bickhart DM, L Xu, JL Hutchison, JB Cole, DJ Null, SG Schroeder, J Song, JF Garcia, TS Sonstegard, CP Van Tassell, RD Schnabel, JF Taylor, HA Lewin, and GE Liu. 2016. Diversity and population-genetic properties of copy number variations and multicopy genes in cattle. DNA Res 23:253-262.
• Type: Journal Articles Status: Published Year Published: 2016 Citation: Taylor JF, LK Whitacre, JL Hoff, PC Tizioto, JW Kim, JE Decker and RD Schnabel. 2016. Lessons for livestock genomics from genome and transcriptome sequencing in cattle and other mammals. Genet Sel Evol 48:59.
• Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Taylor, JF, RD Schnabel, EB Simpson, JE Decker, MM Rolf, BP Kinghorn, AL Van Eenennaam, MD Macneil, DS Brown, MF Smith, and DJ Patterson. 2016. Detection and selection against embryonic lethals in US beef breeds. J. Anim. Sci. 94, E-Suppl.5: pp 324.
• Type: Other Status: Other Year Published: 2016 Citation: Rolf, MM. 2016. History of Selection and Genetic Change in Beef Cattle. Educational module hosted @ http://beefreproduction.org/
• Type: Conference Papers and Presentations Status: Published Year Published: 2016 Citation: Van Eenennaam, AL. 2016 Use of genetic marker information in beef cattle selection. In: Proceedings, Applied Reproductive Strategies in Beef Cattle. September 7-8. Des Moines, IA. pp. 234-241.
• Type: Websites Status: Other Year Published: 2016 Citation: Rolf, MM. 2016. http://beefreproduction.org/
• Type: Other Status: Other Year Published: 2016 Citation: Rolf, MM. 2016. What is an EPD? Educational module hosted @ http://beefreproduction.org/
• Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Kinghorn, B.P., Van Eenennaam, A.L., MacNeil, M.D. 2015. Targeting Multiple End-Uses in Beef Cattle Breeding Programs. Proceedings of the 2015 Applied Reproductive Strategies in Beef Cattle conference, August 17-18, 2015, Davis, CA. http://appliedreprostrategies.com/2015/documents/proceedings/17Kinghorn-VanEeen-pg250-257.pdf
• Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Van Eenennaam, A.L. 2015. Producer uptake: how might genomic information get translated into industry outcomes? Proceedings of the American Association of Bovine Practitioners (AABP), September 17-19, 2015, New Orleans, LA. The AABP Proceedings 48: 164-168.
• Type: Other Status: Published Year Published: 2016 Citation: Van Eenennaam, A.L. 2016. How might genomic information get translated into industry outcomes? ASAS/ADSA Joint Annual Meeting, July 19-23, 2016, Salt Lake City, UT, J. Animal Sci. 94(E-suppl. 5)/J. Dairy Sci. 99(E-suppl. 1): 134.

Progress 01/01/15 to 12/31/15

Outputs
Target Audience:Application of new genetic and genomic technologies to enhance fertility in beef cattle offers the potential to improve reproductive efficiency. The objective of this project is to improve reproductive rates in cattle by identifying genes which cause embryonic or early developmental mortality. The long-term goal of this project is to improve reproductive rates of US beef cattle based on improvements in selection to improve overall profitability to the herd enterprise. Audiences targeted from outcomes stemming from this project include various segments of the beef cattle industry, including: breed associations; seedstock and commercial beef producers; the AI industry; the academic community; and extension livestock specialists. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Regional extension livestock specialists, beef producers and allied industry representatives have been provided with updates from the project through continuing education events, news releases, field days, and regional extension meetings. However, more extensive training and development opportunities are scheduled in subsequent years of the project. How have the results been disseminated to communities of interest?Regional extension livestock specialists, beef producers and allied industry representatives have been provided with updates from the project through continuing education events, news releases, field days, and regional extension meetings. However, more extensive training and development opportunities are scheduled in subsequent years of the project. What do you plan to do during the next reporting period to accomplish the goals?1. Identify, validate and characterize the impact of recessive developmentally lethal alleles associated with reproductive failure in Angus cattle. Goals for 2016. In 2016,sequencing of the 150 bulls in addition to the analysis of all of the collected sequences for the discovery of putative loss of function alleles will have been completed. This will include the identification of animals predicted to be homozygous for such alleles to enable the prioritization of functional candidates which have the potential to be early embryonic or developmental lethals. We shall also identify the most cost-effective and highest content custom genotyping assay available from Illumina and Affymetrix and use the generated sequences to design the content for the functional genotyping assay. The assay will be fully designed and delivered to the project. 2. Develop a male fertility expected progeny difference (EPD) and enhanced heifer pregnancy rate EPD based upon LOF genotype information. Goals for 2016. DNA and phenotype sampling will have been completed on 10,000 + heifersin Missouri andcooperating herds in other states. These animals willthen begenotyped with an assay of functional variants identified in the sequencing project to identify those that are never seen in homozygous form, implying them to be lethals. Based upon allele frequencies estimated from the sample we will generate molecular EPDs for fertility based upon genotypes generated in Angus. 3A. Development of selection indexes that support multi-trait selection, inclusive of fertility traits. Goals for 2016. Continue refining the fertility index ($F) in collaboration with Mike MacNeil and in discussion with cooperators to determine if the index appears to be appropriately weighting reproduction against the other traits of economic importance. 3B. Develop sector-level economic effects of increasing reproductive rates in Angus cattle. Goals for 2016. Activity related to this specific aim will not begin until year 5 of the project. 4. Develop decision support software to optimize breeding schemes via the implementation of selection indexes and mate selection based upon sire and dam recessive lethal genotypes. Goals for 2016. Continue working with Brian Kinghorn to customize mate selection software for US Angus parameters and develop examples for demonstration of operation to cattle producers. Work with select breeders to demonstrate program and obtain feedback as to perceived usefulness of the program, and suggestions for improvement. 5A. Develop a web-based comprehensive educational training program for extension livestock specialists, allied industries, producers, veterinarians, and students. Goals for 2016.Content for the first module, a review of genetic correlations and their use in decision making with multiple-trait selection, will be completed. Content for the remaining modules to be completed in year 4 and 5 will be outlined and a plan will be developed for completion of those modules in upcoming years. 5B. Develop a simulation exercise that demonstrates the effect of DGV for heifer and sire fertility on reproductive performance and profitability. Goals for 2016. The primary goal for 2016 is to complete the development of specific learning objectives and develop an overall plan for the simulation exercise. Upon completion,individual components of the simulation plan will begin being constructed. 5C. Develop innovative educational and outreach materials and enhancement of the Beef Cattle Community of Practice. Goals for 2016. Van Eenennaam, Rolf, and Decker will work with collaborators towards re-launching the beef cattle community of practice (CoP) on eXtension and adding to site traffic through the development of a site called eBEEF. The new CoP re-launch will include a revitalized content database focused towards genomics information and will be curated and updated by a team of beef genetics/genomics extension personnel. As additional resources are developed within this proposal and other genomics proposals, they will be added to the new CoP and disseminated on the site. We will also have the ability to archive and retain this content well past the life of this proposal which will ensure the broadest dissemination possible.

Impacts
What was accomplished under these goals? 1.Identify, validate and characterize the impact of recessive developmentally lethal alleles associated with reproductive failure in Angus cattle. Accomplishments. Genomes of 99 Angus bulls were sequenced and analyzed to identify putative loss of function alleles which we shall later test for the absence of homozygosity in 10,000 genotyped heifers to implicate those that are embryonic or early developmental lethals. We invited 18 US beef breed associations which annually register at least 10,000 animals to participate in this project and to contribute financially to the sequencing of 5-15 bulls from each breed. We have secured ~$250K in additional support from the American, Argentine, Australian and New Zealand Angus Associations; in addition to the US Hereford, Beefmaster, Gelbvieh, Charolais, Simmental, and Maine-Anjou Associations. Genome sequence data was contributed from collaborators at Genome Canada, USDA/BARC and breed associations. These funds werethe industry utility of the project. We secured ~$750K in university fundingfor purchase of a second Illumina HiSeq instrument and another $100K to build an additional 5 multi-core servers each with 500 Gb of memory and a total of 60 TB of external storage to facilitate this project. Weleveraged opportunities for data sharing to increase the extent of the number of animals that can be included in our variant calling analyses. We have shared sequence on Angus animals for sequence on Red Angus animals with the Genome Canada sequencing project. We have provided sequence data on 17 Angus bulls to the 1000 bull genome project to allow us access to that database of over 35 million variants in 1147 animals. The majority of the bulls sequenced in these projects are being shallow skim sequenced (~8X coverage) however, we anticipate that increasing the number of animals represented in our data will increase the number of identified loss of function variants and decrease the number of candidate lethals via the identification of animals homozygous for certain alleles. Preliminary results indicate that our approach is correctly identifying loci that directly affect fertility in beef cattle. 2. Develop a male fertility expected progeny difference (EPD) and enhanced heifer pregnancy rate EPD based upon LOF genotype information. Accomplishments. We proposed to genotype a sample of 10,000 Angus females to identify lethals with high-confidence and their allele frequencies. To date, DNA and phenotypic sampling has been completed on 10,252 heifers from 52 herds. We have characterized 86 of the sequenced Angus bulls (those with Heifer Pregnancy EPDs) for the number of LOF alleles that they carry in genes that are predicted to be essential for life and are thus likely to directly impact the fertility of these bulls. We have identified the number of alleles carried per bull and the sum of the frequencies of these alleles in each bull (inversely proportional to the molecular breeding value for fertility of each bull based on these loci). The mean number of LOF alleles in essential genes carried by each bull ranged from 5 to 23 with an average of 12.04. Our data indicate that it is not only the number of lethals that are carried by each bull but the frequency at which these alleles occur in the Angus breed that impacts the predicted fertility of each bull. 3A. Development of selection indexes that support multi-trait selection, inclusive of fertility traits. Accomplishments. Mike MacNeil developed a model that simulates a herd of 10,000 breeding age females with age specific rates of fertility and survival. These females are characterized according to a Brody-type growth curve, level of milk production, and annual intake of metabolizable energy. Direct and maternal effects on dystocia and on weaning weight are jointly considered. The weaned progeny are characterized by growth and feed intake during a two-stage post-weaning period and by carcass weight, quality grade and yield grade at harvest. Income is derived from the sale of cull females and harvested progeny. Expenses are incurred for feed consumed by the cow herd and associated offspring, with non-feed costs prorated on a per head basis and calving difficulty assessed a charge per event. Economic values for various phenotypes are predicted based on changes in profit resulting from perturbation of a simulated phenotype by one unit compared to a baseline simulation in which the phenotype is unperturbed. MacNeil is working this into a fertility index ($F) that uses the economic values derived in the model to develop an Angus straight bred whole industry index that includes fertility as one of the criteria - weighted by its relative economic merit. 3B. Develop sector-level economic effects of increasing reproductive rates in Angus cattle. Accomplishments. Activity related to this specific aim will not begin until year 5 of the project. 4. Develop decision support software to optimize breeding schemes via the implementation of selection indexes and mate selection based upon sire and dam recessive lethal genotypes. Accomplishments. Collaborators on the project met following the NBCEC meeting in March 2013. Brian Kinghorn suggested that a simulation could be developed for LOF genotypes in an existing pedigree with EPDs. Mike Kasten's herd (Millersville, MO) was used as a prototype dataset to demonstrate how mate allocation would occur given loss of function mutations. During the meeting, it was recommended that we, as a group, now refer to these loss of function mutations, as FERTILITY REDUCING MARKERS (FRMS). The $Fertility EPDs are being derived for all of the Angus animals in Mike Kasten's herd and this, in addition to his herd pedigree file, are being used as input files to enable Brian Kinghorn to customize his mate selection software to work with US Angus EPDs and herd pedigree files. 5A. Develop a web-based comprehensive educational training program for extension livestock specialists, allied industries, producers, veterinarians, and students. Accomplishments.The Institute for Teaching and Learning Excellence (ITLE) at Oklahoma State University is the service provider working with Rolf to develop the web interface and educational content for development of the teaching modules. The first set of contentis scheduled tobe delivered on the web interface in December 2015 by ITLE. 5B. Develop a simulation exercise that demonstrates the effect of DGV for heifer and sire fertility on reproductive performance and profitability. Accomplishments. Acomputer-based genetic selection tool is being revised(Cowgame) to teach principles of sire selection. Genomic data and lethal alleles will be includedin the program to teach students and producers how to manage the frequency of lethal alleles in a group of animals without completely sacrificing genetic gain. 5C. Develop innovative educational and outreach materials and enhancement of the Beef Cattle Community of Practice. Accomplishments. Rolf and Van Eenennaam met with a number of the various breed associations to gauge interest and determine the feasibility of developing an app for EPD lookup across multiple breeds; however, a variety of concerns from individual associations have slowed progress in this goal. The second stage of the app development project for year 2 outlined in this proposal was completed by the American Angus Association. Their app, launched in 2013, allows EPD and information lookup synced with the association information on their server. It also has the ability to look up inbreeding coefficient details for individual animals and herds within the application.

Publications

• Type: Journal Articles Status: Published Year Published: 2014 Citation: Rolf MM, JE Decker, SD McKay, PC Tizioto, K Branham, L Whitacre, JL Hoff, LCA Regitano, and JF Taylor. 2014. Genomics in the United States Beef Industry. Livest. Sci. 66:84-93.
• Type: Journal Articles Status: Published Year Published: 2014 Citation: Tizioto PC, LL Coutinho, JE Decker, RD Schnabel, KO Rosa, PSN Oliveira, MM Souza, GB Mour�o, RR Tullio, AS Chaves, DPD Lanna, A Zerlotini Neto, MA Mudadu, JF Taylor and LCA Regitano. 2015. Global liver gene expression differences in Nelore steers with divergent residual feed intake phenotypes. BMC Genomics 16:242
• Type: Conference Papers and Presentations Status: Other Year Published: 2014 Citation: Van Eenennaam, A, Implications of Improper Management of Known Genetic Abnormalities, Applied Reproductive Strategies in Beef Cattle, Oklahoma City, OK 10/9/2014
• Type: Conference Papers and Presentations Status: Other Year Published: 2014 Citation: Van Eenennaam, A. MateSel: A Software Mating Tool to Aid in Selection for Improved Fertility  NBCEC Brownbagger, Internet presentation 10/22/2014.
• Type: Conference Papers and Presentations Status: Other Year Published: 2014 Citation: Van Eenennaam, A. Beef Heifer Replacement: Considerations Related to Breed and Biological Type, Oregon Cattlemens Association Annual Convention, Redmond, OR 12/4/2014.
• Type: Conference Papers and Presentations Status: Other Year Published: 2015 Citation: Van Eenennaam, A. Can early embryonic losses that reduce reproduction efficiency be managed through genetics? Kentucky Beef Efficiency Conference, Owensboro Convention Center, KY 1/16/2015
• Type: Other Status: Other Year Published: 2015 Citation: Van Eenennaam, A. http://www.cattlenetwork.com/advice-tips/cow-calf/tale-missing-homozygotes. 2015.
• Type: Other Status: Other Year Published: 2015 Citation: Van Eenennaam, A. Genetic Defects. 2015. http://www.extension.org/pages/72661/genetic-defects#
• Type: Other Status: Other Year Published: 2015 Citation: Van Eenennaam, A. Managing Genetic Defects. 2015. http://www.extension.org/pages/72662/managing-genetic-defects#
• Type: Other Status: Other Year Published: 2014 Citation: Taylor JF. 2014. Confessions of a genome sequencing addict. Saturday Morning Science series. University of Missouri, Columbia MO. October 18.
• Type: Conference Papers and Presentations Status: Other Year Published: 2014 Citation: Taylor JF. 2014. Sequencing the genomes of 250 bulls. World Brangus Congress. Merida, Mexico. November 11.
• Type: Conference Papers and Presentations Status: Other Year Published: 2015 Citation: Taylor JF, S Albarella, RD Schnabel, GS Johnson, F Strozzi, C Ferrandi and J Williams. 2015. Using Sequence Data to Localize Developmental Mutations. Buffalo genome workshop, Plant and Animal Genome XXIII, January 10. Presentation W111.
• Type: Conference Papers and Presentations Status: Other Year Published: 2015 Citation: Taylor JF, JE Decker, L Whitacre, J Hoff, D Patterson and RD Schnabel. 2015. Identification of Causal Variants using Next-Generation Sequencing Data. Cattle and Swine Workshop. Plant and Animal Genome XXIII, January 10. Presentation W154.
• Type: Conference Papers and Presentations Status: Other Year Published: 2015 Citation: Taylor JF. 2015. Identification and management of alleles impairing heifer fertility while optimizing genetic gain in Angus cattle. USDA PD Meeting. San Diego, CA. January 9.
• Type: Conference Papers and Presentations Status: Other Year Published: 2015 Citation: Taylor JF. 2015. From sequence to loss of function  getting to the underlying causation. GeneSeek Science Advisory Council. Lincoln NE. May 12.
• Type: Conference Papers and Presentations Status: Other Year Published: 2015 Citation: Hoff JL, JE Decker, RD Schnabel and JF Taylor. 2015. Lethal haplotype detection and characterization in Angus population. Plant & Animal Genome XXIII. January 10-14, San Diego, CA. Poster P0275.
• Type: Conference Papers and Presentations Status: Other Year Published: 2015 Citation: Whitacre LK, PC Tizioto, JW Kim, TS Sonstegard, LJ Alexander, JF Medrano, RD Schnabel, JF Taylor and JE Decker. 2015. Whats in your next-generation sequencing data? An exploration of unmapped reads from DNA and RNA sequencing. Life Sciences Week. University of Missouri. Poster presentation. April 15.
• Type: Conference Papers and Presentations Status: Other Year Published: 2015 Citation: Whitacre LK, PC Tizioto, JW Kim, TS Sonstegard, LJ Alexander, JF Medrano, RD Schnabel, JF Taylor and JE Decker. 2015. Whats in your next-generation sequencing data? An exploration of unmapped reads from DNA and RNA sequencing. Missouri Informatics Symposium. University of Missouri. April 27.
• Type: Conference Papers and Presentations Status: Other Year Published: 2015 Citation: Worley KC, AC English, X Qin, SC Murali, DST Hughes, Y Han, V Vee, T Smith, JE Decker, B Dalrymple, J Kijas, NE Cockett, JF Taylor, J Medrano, DC Schwartz, S Zhou, DM Muzny and RA Gibbs. 2015. Improving the Reference through Long Read Technology - Better Genomes for the Sheep and the Cow. Biology of Genomes. Cold Spring Harbor NY. May 5-9.
• Type: Conference Papers and Presentations Status: Published Year Published: 2015 Citation: Kinghorn, BP, AL Van Eenennaam, and MD MacNeil. Targeting multiple-end uses in beef cattle breeding programs. In: Proceedings, Applied Reproductive Strategies in Beef Cattle. August 17-18, Davis, CA. pp. 250-257.
• Type: Conference Papers and Presentations Status: Other Year Published: 2015 Citation: Taylor JF, PC Tizioto, NV Grupioni, JW Kim, JE Decker and RD Schnabel. 2015. Adventures in next generation sequencing of transcriptomes and genomes. Functional Genomics Symposium. Midwest Animal Science Conference. Des Moines, IA. March 17.
• Type: Conference Papers and Presentations Status: Other Year Published: 2015 Citation: Taylor J.F. 2015. Whats In Your Next-Gen Sequence Data? Department of Animal Science, Iowa State University. April 17.
• Type: Conference Papers and Presentations Status: Other Year Published: 2015 Citation: Taylor JF. 2015. Latest Happenings in Genetics. Plenary presentation. National Pedigreed Livestock Council Annual Meeting. Lafayette, IN. May 5.
• Type: Conference Papers and Presentations Status: Other Year Published: 2015 Citation: Taylor JF. 2015. Adventures in Next-Generation Sequencing. Niemeyer Lecture. College of Veterinary Medicine, University of Missouri. Columbia, MO. May 8.

Progress 01/01/14 to 12/31/14

Outputs
Target Audience: Application of new genetic and genomic technologies to enhance fertility in beef cattle offers the potential to improve reproductive efficiency. The objective of this project is to improve reproductive rates in cattle by identifying genes which cause embryonic or early developmental mortality. The long-term goal of this project is to improve reproductive rates of US beef cattle based on improvements in selection to improve overall profitability to the herd enterprise. Audiences targeted from outcomes stemming from this project include various segments of the beef cattle industry, including: breed associations; seedstock and commercial beef producers; the AI industry; the academic community; and extension livestock specialists. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? Regional extension livestock specialists, beef producers and allied industry representatives have been provided withupdates from the project through continuing education events, news releases, field days, and regional extension meetings. However, more extensive training and development opportunities are scheduled in subsequent yearsof the project. How have the results been disseminated to communities of interest? Regional extension livestock specialists, beef producers and allied industry representatives have been provided withupdates from the project through continuing education events, news releases, field days, and regional extension meetings. However, more extensive training and development opportunities are scheduled in subsequent yearsof the project. What do you plan to do during the next reporting period to accomplish the goals? 1. Identify, validate and characterize the impact of recessive developmentally lethal alleles associated with reproductive failure in Angus cattle. Goals for 2015. In 2015, the sequencing of the 150 bulls will be complete in addition to the analysis of all of the collected sequencesfor the discovery of putative loss of function alleles. This will include the identification of animals predicted to be homozygous for such alleles to enable the prioritization of functional candidates which have the potential to be early embryonic or developmental lethals. We shall also identify the most cost-effective and highest content custom genotyping assay available from Illumina and Affymetrix and use the generated sequences to design the content for the functional genotyping assay. The assay will be fully designed and delivered to the project in 2015. 2. Develop a male fertility expected progeny difference (EPD) and enhanced heifer pregnancy rate EPD based upon LOF genotype information.Goals for 2015. DNA and phenotype sampling will continue on heifers enrolled in the Missouri Show-Me-Select Replacement Heifer Program along with cooperating herds in Missouri and other states. Sample collection on the 10,000 heifers will be completed by the spring of 2015. These animals will be genotyped with an assay of functional variants identified in the sequencing project to identify those that are never seen in homozygous form, implying them to be lethals. Based upon allele frequencies estimated from the sample we shall be able to generate molecular EPDs for fertility based upon genotypes generated in Angus. 3A. Development of selection indexes that support multi-trait selection, inclusive of fertility traits. Goals for 2015. Continue refining the fertility index ($F) in collaboration with Mike MacNeil and in discussion with cooperators to determine if the index appears to be appropriately weighting reproduction against the other traits of economic importance. 3B. Develop sector-level economic effects of increasing reproductive rates in Angus cattle. Goals for 2015. Activity related to this specific aim will not begin until year 5 of the project. 4. Develop decision support software to optimize breeding schemes via the implementation of selection indexes and mate selection based upon sire and dam recessive lethal genotypes. Goals for 2015. Continue working with Brian Kinghorn to customize mate selection software for US Angus parameters and develop examples for demonstration of operation to cattle producers. Work with select breeders to demonstrate program and obtain feedback as to perceived usefulness of the program, and suggestions for improvement. 5A. Develop a web-based comprehensive educational training program for extension livestock specialists, allied industries, producers, veterinarians, and students.Goals for 2015. Proposal content will be outlined for activities starting in year 3. Content for the first module, a review of genetic correlations and their use in decision making with multiple-trait selection, will be developed and delivered to the collaborating company in 2015. Content for the remaining modules to be completed in year 4 and 5 will be outlined and a plan will be developed for completion of those modules in upcoming years. 5B. Develop a simulation exercise that demonstrates the effect of DGV for heifer and sire fertility on reproductive performance and profitability. Goals for 2015. The primary goal for 2015 is to develop the specific learning objectives and an overall plan for the simulation exercise. Once this is accomplished we will be able to begin constructing the individual components of the simulation plan. 5C. Develop innovative educational and outreach materials and enhancement of the Beef Cattle Community of Practice. Goals for 2015. Van Eenennaam, Rolf, and Decker have been working with collaborators towards re-launching the beef cattle community of practice (CoP) on eXtension and adding to site traffic through the development of a site called eBEEF. The new CoP will re-launch late 2014 or early 2015 with a revitalized content database that is focused towards genomics information and will be curated and updated by a team of beef genetics/genomics extension personnel. As additional resources are developed within this proposal and other genomics proposals, they will be added to the new CoP and disseminated on the site. We will also have the ability to archive and retain this content well past the life of this proposal, which will ensure the broadest dissemination possible.

Impacts
What was accomplished under these goals? 1. Identify, validate and characterize the impact of recessive developmentally lethal alleles associated with reproductive failure in Angus cattle. Accomplishments. Genomes of 99 Angus bulls have each been sequencedand are currently being analyzed to identify putative loss of function alleles which we shall later test for the absence of homozygosity in 10,000 genotyped heifers to implicate those that are embryonic or early developmental lethals. We invited 18 US beef breed associations which annually register at least 10,000 animals to participate in this project and to contribute financially to the sequencing of 5-15 bulls from each breed. We have secured ~$250K in additional support from the American, Argentine, Australian and New Zealand Angus Associations; in addition to the US Hereford, Beefmaster, Gelbvieh, Charolais, Simmental, and Maine-Anjou Associations. Genome sequence data has also been contributed from collaborators at Genome Canada, USDA/BARC and breed associations. These funds are being used in conjunction with USDA NIFA funds to sequence a total of ~150 bulls from 9 breeds (including Shorthorn and Limousin) to increase the industry utility of the project. We secured ~$750K in university funding to allow the purchase of a second Illumina HiSeq instrument and another $100K to build an additional 5 multi-core servers each with 500 Gb of memory and a total of 60 TB of external storage to facilitate this project. We have discussed opportunities for data sharing so as to increase the extent of the number of animals that can be included in our variant calling analyses. We have verbal agreements with the USMARC and the Genome Canada sequencing project to share data and have already exchanged data with the Genome Canada Project. We have also provided sequence data on 17 Angus bulls to the 1000 bull genome project to allow us access to that database. The majority of the bulls sequenced in these projects are being shallow skim sequenced (~8X coverage) however, we anticipate that increasing the number of animals represented in our data will increase the number of identified loss of function variants and decrease the number of candidate lethals via the identification of animals homozygous for certain alleles. Preliminary results indicate that our approach is correctly identifying loci that directly affect fertility in beef cattle. 2. Develop a male fertility expected progeny difference (EPD) and enhanced heifer pregnancy rate EPD based upon LOF genotype information. Accomplishments. We proposed to genotype a sample of 10,000 Angus females to identify lethals with high-confidence and their allele frequencies. To date DNA and phenotypic sampling has been completed on 6,050 heifers from 52 herds. We have characterized 86 of the sequenced Angus bulls (those with Heifer Pregnancy EPDs) for the number of LOF alleles that they carry in genes that are predicted to be essential for life and are thus likely to directly impact the fertility of these bulls. We have identified the number of alleles carried per bull and the sum of the frequencies of these alleles in each bull (inversely proportional to the molecular breeding value for fertility of each bull based on these loci). The mean number of LOF alleles in essential genes carried by each bull ranged from 5 to 23 with an average of 12.04. Our data indicate that it is not only the number of lethals that are carried by each bull but the frequency at which these alleles occur in the Angus breed that impacts the predicted fertility of each bull. 3A. Development of selection indexes that support multi-trait selection, inclusive of fertility traits. Accomplishments. Mike MacNeil developed a model that simulates a herd of 10,000 breeding age females with age specific rates of fertility and survival. These females are characterized according to a Brody-type growth curve, level of milk production, and annual intake of metabolizable energy. Direct and maternal effects on dystocia and on weaning weight are jointly considered. The weaned progeny are characterized by growth and feed intake during a two-stage post-weaning period and by carcass weight, quality grade and yield grade at harvest. Income is derived from the sale of cull females and harvested progeny. Expenses are incurred for feed consumed by the cow herd and associated offspring, with non-feed costs prorated on a per head basis and calving difficulty assessed a charge per event. Economic values for various phenotypes are predicted based on changes in profit resulting from perturbation of a simulated phenotype by one unit compared to a baseline simulation in which the phenotype is unperturbed. MacNeil is working this into a fertility index ($F) that uses the economic values derived in the model to develop an Angus straight bred whole industryindex that includes fertility as one of the criteria – weighted by its relative economic merit. 3B. Develop sector-level economic effects of increasing reproductive rates in Angus cattle.Accomplishments. Activity related to this specific aim will not begin until year 5 of the project. 4. Develop decision support software to optimize breeding schemes via the implementation of selection indexes and mate selection based upon sire and dam recessive lethal genotypes. Accomplishments. Collaborators on the project met following the NBCEC meeting in March 2013. Brian Kinghorn suggested that a simulation could be developed for LOF genotypes in an existing pedigree with EPDs. Mike Kasten’s herd (Millersville, MO) was used as a prototype dataset to demonstrate how mate allocation would occur given loss of function mutations. During the meeting, it was recommended that we, as a group, now refer to these loss of function mutations, as FERTILITY REDUCING MARKERS (FRMS). The $Fertility EPDs are being derived for all of the Angus animals in Mike Kasten’s herd and this, in addition to his herd pedigree file, are being used as input files to enable Brian Kinghorn to customize his mate selection software to work with US Angus EPDs and herd pedigree files. 5A. Develop a web-based comprehensive educational training program for extension livestock specialists, allied industries, producers, veterinarians, and students. Accomplishments. Work on this aspect of the proposal is funded starting in year 3. 5B. Develop a simulation exercise that demonstrates the effect of DGV for heifer and sire fertility on reproductive performance and profitability. Accomplishments. Progress on this objective is not scheduled to begin until 2014. 5C. Develop innovative educational and outreach materials and enhancement of the Beef Cattle Community of Practice. Accomplishments. Megan Rolf and Alison Van Eenennaam met with a number of the various breed associations to gauge interest and determine the feasibility of developing an app for EPD lookup across multiple breeds; however, a variety of concerns from individual associations have slowed progress in this goal. The second stage of the app development project for year 2 outlined in this proposal was completed by the American Angus Association. Their app, launched in 2013, allows EPD and information lookup synced with the association information on their server. It also has the ability to look up inbreeding coefficient details for individual animals and herds within the application. Taylor, Van Eenennaam, and Patterson reviewed the overall goals and objectives for the project with regional extension livestock specialists during their annual in-service training in February 2013, and the project was reviewed again in 2014 with the same audience. At this time, specialists were asked to continue participating in sample collection from heifers to be used in the project.

Publications

• Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Hayes B, H Daetwyler, H Pausch, I Macleod, C VanDerJagt, P Stothard, X Liao, B Guldbrandtsen, C Schrooten, A Chamberlain, P Bowman, R Fries, M Lund, D Boichard, R Veerkamp , M Goddard C Van Tassell , T Druet, B Gredler, J Vilkki, Mullaart , A Bagnato, D Berry, DJ deKoning, E Santus, J Reecy, J Taylor, F Schenkel, C Droegemueller. 2014. Genomic Prediction from Whole Genome Sequence in Livestock: The 1000 Bull Genomes Project. 10th World Congress on Genetics Applied to Livestock Production. Vancouver, CA. August 17-22.
• Type: Journal Articles Status: Published Year Published: 2014 Citation: Saatchi M, RD Schnabel, JF Taylor and DJ Garrick. 2014. Large-effect pleiotropic or closely linked QTL segregate within and across ten US cattle breeds. BMC Genomics 15:442.
• Type: Journal Articles Status: Published Year Published: 2014 Citation: Rolf MM, JE Decker, SD McKay, PC Tizioto, K Branham, L Whitacre, JL Hoff, LCA Regitano, and JF Taylor. 2013. Genomics in the United States Beef Industry. Livest. Sci. 166:84-93.
• Type: Journal Articles Status: Submitted Year Published: 2014 Citation: Noyes HA, D Daly, IB Goodhead, SM Kaye, SJ Kemp, JG Kenny, I Saccheri, RD Schnabel, JF Taylor, and N Hall. 2014. A simple procedure for directly obtaining haplotype sequences of diploid genomes. Genome Biol.
• Type: Journal Articles Status: Submitted Year Published: 2014 Citation: Bickhart DM, JL Hutchison, L Xu, RD Schnabel, JF Taylor, J Reecy, S Schroeder, CP Van Tassell, TS Sonstegard, and GE Liu. 2014. RPSR: a hybrid algorithm for the detection of structural variants. Bioinformatics.
• Type: Other Status: Other Year Published: 2014 Citation: Rolf MM, JF Taylor, DS Brown, MF Smith, RD Schnabel, SE Poock, JE Decker, FD Dailey, DJ Patterson, AL Van Eenennaam, BP Kinghorn, and MD MacNeil. 2014. Identification and management of alleles impairing heifer fertility while optimizing genetic gain in cattle. National Beef Cattle Evaluation Consortium Brown Bagger Webinar Series. October 22.
• Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Decker JE, RD Schnabel and JF Taylor. 2014. Applications of high-throughput sequencing for fertility, demography, and genome improvement. Midwest American Society of Animal Science. Des Moines, IA March 17-19.
• Type: Conference Papers and Presentations Status: Published Year Published: 2104 Citation: Schnabel RD, JF Taylor, AL Van Eenennaam, S. Brown, MF Smith, MM Rolf, MD MacNeil, BP Kinghorn, S Pook and DJ Patterson. 2014. Reducing the incidence of early embryonic mortality in beef cattle. Proceedings of the10th World Congress on Genetics Applied to Livestock Production. Vancouver, CA. August 17-22.
• Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Van Eenennaam, AL, and BP Kinghorn. 2014. Use of Mate Selection software to manage lethal recessive conditions in livestock populations. Proceedings, 10th World Congress of Genetics Applied to Livestock Production. August, 2014. Vancouver, BC, Canada.
• Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Taylor, JF. Identification and management of loss of function alleles impacting fertility. Proceedings, Applied Reproductive Strategies in Beef Cattle. October, 2014. Stillwater, OK.
• Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Van Eenennaam, AL.Implications of improper management of known genetic abnormalities. Proceedings, Applied Reproductive Strategies in Beef Cattle. October, 2014. Stillwater, OK.
• Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Taylor JF. 2013. Whole genome resequencing identifies functional variation within the bovine genome. 5th International Symposium on Animal Functional Genomics - ISAFG Guaruja, S�o Paulo, Brazil. September 8-11.
• Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Taylor JF. 2013. Identification of loss-of function alleles underlying embryonic loss in cattle. Presidents Symposium, Society for the Study of Reproduction 46th Annual Meeting, Montr�al, Qu�bec, Canada. July 2226.
• Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Taylor JF. 2013. Molecular genetic approaches to the improvement of beef cattle. Workshop on Genomic Applications in Livestock. S�o Paulo State University, Jaboticabal, Brazil. August 12-14.
• Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Taylor JF. 2013. Current status of genomic evaluation of Angus cattle. PGG Wrightson World Angus Forum. Rotorua, New Zealand. Keynote Presentation. October 13-17.
• Type: Conference Papers and Presentations Status: Published Year Published: 2013 Citation: Taylor JF. 2013. Updates on USDA Bovine Respiratory Disease, feed efficiency, and heifer fertility projects. Beef Improvement Federation Annual Meeting, Oklahoma City, OK. June 14.
• Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Taylor JF. 2014. Genome resequencing to identify loss of function variants underlying disease, fertility, inbreeding depression and heterosis. ASGSA distinguished lecturer, University of Florida, Gainesville, FL. March 20.
• Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Taylor JF. 2014. Genome resequencing to identify loss of function variants underlying disease, fertility, inbreeding depression and heterosis. AB Chapman Lecture, University of Wisconsin, Madison, WI. April 29.
• Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Taylor JF, JE Decker and RD Schnabel. 2014. Genome resequencing identifies loss of function variants underlying fertility, inbreeding depression and heterosis. Plenary presentation. 21st International Colloquium on Animal Cytogenetics and Gene Mapping. Ischia, Italy. June 7.
• Type: Conference Papers and Presentations Status: Awaiting Publication Year Published: 2014 Citation: Taylor JF, JE Decker and RD Schnabel. 2014. Animal Breeding in the Next-Generation Sequencing Era. Plenary presentation. Abstract #10659 - 10th World Congress on Genetics Applied to Livestock Production. Vancouver, CA. August 17-22.
• Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Hoff JL, JE Decker, RD Schnabel and JF Taylor. 2014. Lethal haplotype detection and characterization in a beef cattle population. Biology of Genomes. Cold Spring Harbor NY. May 6-10.
• Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Hoff JL, JE Decker, RD Schnabel and JF Taylor. 2014. Lethal haplotype detection and characterization in a beef cattle population. Graduate Forum. Division of Animal Science, University of Missouri. May 29.
• Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Taylor JF. 2014. The future of genomic selection. ARC Irene, South Africa. March 4.
• Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Taylor JF. 2014. Applications of next-generation sequencing. ARC Pretoria, South Africa. March 7.
• Type: Other Status: Other Year Published: 2014 Citation: Taylor JF. 2014. The future of genomic selection. AB Chapman Lecture, University of Wisconsin, Madison, WI. April 30.
• Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Bickhart DM, L Xu, JL Hutchison, TS Sonstegard, CP Van Tassell, SG Schroeder, JF Garcia, JF Taylor, RD Schnabel, HA Lewin and GE Liu. 2014. Population sequencing reveals breed and sub-species specific CNVs in cattle. International Plant & Animal Genome XXII. January 11-15, San Diego, CA. Poster P078.
• Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Bickhart DM, L Xu, JL Hutchison, TS Sonstegard, CP Van Tassell, SG Schroeder, JF Garcia, JF Taylor, RD Schnabel, HA Lewin and GE Liu. 2014. Population sequencing reveals breed and sub-species specific CNVs in cattle. Advances in Genome Biology and Technology. February 12-15, Marco Island, FL.
• Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Bickhart DM, L Xu, JL Hutchison, TS Sonstegard, CP Van Tassell, SG Schroeder, JF Garcia, JF Taylor, RD Schnabel, HA Lewin and GE Liu. 2014. Population sequencing reveals breed and sub-species specific CNVs in cattle. Biology of Genomes. Cold Spring Harbor NY. May 6-10.
• Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Whitacre LK, JE Decker, JW Kim, RD Schnabel, JF Taylor and the US Consortium for the Genetic Improvement of Feed Efficiency in Beef Cattle. 2014. Candidates for the Hereford Spotted locus. Biology of Genomes. Cold Spring Harbor NY. May 6-10.
• Type: Conference Papers and Presentations Status: Published Year Published: 2014 Citation: Whitacre LK, JE Decker, JW Kim, JF Medrano, RD Schnabel, DC Schwartz, S Zhou, the US Consortium for Genetic Improvement of Feed Efficiency in Beef Cattle and JF Taylor. 2014. Structural variation at the KIT locus is responsible for spotted coat color phenotypes in Hereford and Simmental cattle. Graduate Forum. Division of Animal Science, University of Missouri. May 29.

Progress 01/01/13 to 12/31/13

Outputs
Target Audience: Application of new genetic and genomic technologies to enhance fertility in beef cattle offers the potential to improve reproductive efficiency. The objective of this project is to improve reproductive rates in cattle by identifying genes which cause embryonic or early developmental mortality. The long-term goal of this project is to improve reproductive rates of US beef cattle based on improvements in selection to improve overall profitability to the herd enterprise. Audiences targeted from outcomes stemming from this project include various segments of the beef cattle industry, including: breed associations; seedstock and commercial beef producers; the AI industry; the academic community; and extension livestock specialists. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? Nothing Reported How have the results been disseminated to communities of interest? Nothing Reported What do you plan to do during the next reporting period to accomplish the goals? Identify, validate and characterize the impact of recessive developmentally lethal alleles associated with reproductive failure in Angus cattle. Goals for 2014. In 2014 we shall complete the sequencing of the 150 bulls and also complete the analysis of the sequences for the discovery of putative loss of function alleles. This will include the identification of animals predicted to be homozygous for such alleles to enable the prioritization of functional candidates which have the potential to be early embryonic or developmental lethals. We shall also identify the most cost-effective and highest content custom genotyping assay available from Illumina and Affymetrix and use the generated sequences to design a the content for the functional genotyping assay. The assay will be designed and delivered to the project in 2014. Develop a male fertility expected progeny difference (EPD) and enhanced heifer pregnancy rate EPD based upon LOF genotype information. Goals for 2014. DNA and phenotype sampling will continue on heifers enrolled in the Missouri Show-Me-Select Replacement Heifer Program along with cooperating herds in Missouri and other states. The goal by the end of calendar year 2014 is to have sampled over 10,000 heifers in support of this Specific Aim. These animals will be genotyped with an assay of functional variants identified in the sequencing project to identify those that are never seen in homozygous form implying them to be lethals. Based upon allele frequencies estimated from the sample we shall be able to generate molecular EPDs for fertility based upon genotypes generated in Angus. 3A. Development of selection indexes that support multi-trait selection, inclusive of fertilitytraits. Goals for 2014. Continue refining the fertility index ($F) in collaboration with Mike MacNeil and in discussion with cooperators to determine if the index appears to be appropriately weighting reproduction against the other traits of economic importance. 3B. Develop sector-level economic effects of increasing reproductive rates in Angus cattle. Goals for 2014. Activity related to this specific aim will not begin until year 5 of the project. 4. Develop decision support software to optimize breeding schemes via the implementation ofselection indexes and mate selection based upon sire and dam recessive lethal genotypes. Goals for 2014. Continue working with Brian Kinghorn to customize mate selection software for US Angus parameters and develop examples for demonstration of operation to cattle producers. Work with select breeders to demonstrate program and obtain feedback as to perceived usefulness of the program, and suggestions for improvement. In discussion with Kinghorn it was decided we would put together a paper on use of MateSel; and also GeneProb in the management of deleterious recessive lethal alleles as a part of this project. It was suggested it might be a good idea to submit a portion of this to WCGALP – with abstracts due in February. Two main topics of the paper would be: 1. Consequences of different management approaches to lethal recessives – 1. Ignore them and just focus on making maximum rate of genetic gain (ΔG) 2. focus on nothing else and do not allow the use heterozygous carriers 3. use matesel to do sire allocation after selecting them for Maximum ΔG What is the measure of impact? - % decrease in ΔG in 2 and 3 as compared to 1, as compared to the number of live calves (1-number of dead calves) expected as a result of the matings proposed. If give up on $index what is that worth in terms of increased number of first conception calves? What is the value of a first conception calf? Depending upon gene frequency will impact decisions differently – with draconian actions on low gene frequency allele having disproportionately expensive costs in terms of decreased ΔG. What is the optimal balance for culling? Comparison of using GeneProb versus not for different proportions (0-100%) of the population genotyped. At 0 GeneProb=HW; at 100% GeneProb = true knowledge – at all levels in between it is likely that GeneProb will do a better job of avoiding carrier matings in potential carriers than based on H-W equilibrium, and both will compared to situation of true knowledge of actual phenotypes (i.e. 100% genotyped). Compare knowledge on hand versus reality based on known genotypes. Ultimately result in graph with proportion of animals genotypes on X axis and number of live first service calves conceived on Y axis (= fertility). Aim to get this paper done by end of Q1 2014. Van Eenennaam will take lead on writing paper. 5A. Develop a web-based comprehensive educational training program for extension livestockspecialists, allied industries, producers, veterinarians, and students. Goals for 2014. Proposal content will be outlined for activities starting in year 3. 5B. Develop a simulation exercise that demonstrates the effect of DGV for heifer and sirefertility on reproductive performance and profitability. Goals for 2014. The primary goal for 2014 is to develop the specific learning objectives and an overall plan for the simulation exercise. Once this is accomplished we will be able to begin constructing the individual components of the simulation plan. However, specific learning objectives for the simulation exercise are being established in 2013 in preparation for developing the exercise in 2014. 5C. Develop innovative educational and outreach materials and enhancement of the BeefCattle Community of Practice. Goals for 2014. Work towards establishing a beef cattle genomics eXtension community of practice.

Impacts
What was accomplished under these goals? Specific Aim 1; Accomplishments. We proposed to resequence the genomes of 89 Angus bulls each to a depth of coverage of 30X to bring the total number of sequenced Angus bulls to 100. These sequences were proposed to be used to identify putative loss of function alleles which we shall later test for the absence of homozygosity in 10,000 genotyped heifers to implicate those that are embryonic or early developmental lethals. We invited 13 US breed associations which annually register at least 10,000 animals to participate in this project and to contribute financially to the sequencing of 5-15 bulls for each breed. We have secured ~$250K in additional support from the American, Argentine, Australian and New Zealand Angus Associations; in addition to Hereford, Beefmaster, Gelbvieh, Charolais, Simmental, and Maine-Anjou Associations. These funds will be used in conjunction with USDA NIFA funds to sequence a total of ~150 bulls from 9 breeds (including Shorthorn and Limousin) to increase the industry utility of the project. We secured ~$750K in university funding to allow the purchase of a second Illumina HiSeq instrument and another $100K to build an additional 5 multi-core servers each with 500 Gb of memory and a total of 60 TB of external storage to facilitate this project. We have completed the sequencing of 70 animals to a depth of ~30X coverage andhave libraries constructed for an additional 45 animals scheduled to be run on the sequencer by January 2014. We anticipate that we will complete all sequence generation andvariant calling by Spring, 2014. Table 1. Summary of sequence data generated to date. Breed N Total unique reads Total bases Angus 52 39,317,317,188 3,886,996,281,747 Hereford11 8,122,866,724 808,242,798,713 Beefmaster 9 6,988,253,172695,246,722,677 We have discussed opportunities for data sharing so as to the extent of the number of animals that can be included in our variant calling analyses. We have verbal agreements with the USMARC and the Genome Canada sequencing project to share data and have agreed to provide 30X of sequence data on 10 Angus bulls to the 1000 bull genome project to allow us access to that database. The majority of the bulls sequenced in these projects are being shallow skim sequenced (~8X coverage) however, we anticipate that increasing the number of animals represented in our data will increase the number of identified loss of function variants and decrease the number of candidate lethals via the identification of animals homozygous for certain alleles. Specific Aim 2; Accomplishments. We proposed to genotype a sample of 10,000 Angus females to identify lethals with high-confidence and their allele frequencies. Hair samples have been collected from 1697 heifers on 24 farms and ranches in MO and SD. Complete phenotypic data accompanies each of these samples. Additionally, samples are being obtained this fall from another 3400 heifers in MO and CA. By the end of calendar year 2013, samples will have been collected on roughly 5100 heifers in support of this project. Specific Aim 3A; Accomplishments. Mike MacNeil developed a model that simulates a herd of 10,000 breeding age females with age specific rates of fertility and survival. These females are characterized according to a Brody-type growth curve, level of milk production, and annual intake of metabolizable energy. Direct and maternal effects on dystocia andweaning weight are jointly considered. The weaned progeny are characterized by growth and feed intake during a two-stage postweaning period and by carcass weight, quality grade and yield grade at harvest. Income is derived from the sale of cull females and harvested progeny. Expenses are incurred for feed consumed by the cow herd and associated offspring, with non-feed costs prorated on a per head basis and calving difficulty assessed a charge per event. Economic values for various phenotypes are predicted based on changes in profit resulting from perturbation of a simulated phenotype by one unit compared to a baseline simulation in which the phenotype is unperturbed. MacNeil is working this into an fertility index ($F) that uses the economic values derived in the model to develop an Angus straight bred whole industry good index that includes fertility as one of the criteria – weighted by its relative economic merit. Specific Aim 3B; Accomplishments. Activity related to this specific aim will not begin until year 5 of the project. Specific Aim 4; Accomplishments. Collaborators on the project met in St. Joseph, MO in March 2013. Brian Kinghorn indicated that mate allocation will be required for the program to work properly, so it was suggested that a simulation could be developed for LOF genotypes in an existing pedigree with EPD. Mike Kasten’s herd (Millersville, MO) is being used as a prototype dataset to demonstrate how mate allocation would occur given loss of function mutations. During the meeting, it was recommended that we, as a group, now refer to the loss of function mutations, as FERTILITY REDUCING MARKERS (FRMS). This $Fertility value will be derived for all of the Angus animals in Mike Kasten’s EPD file and this, in addition to his herd pedigree file, will be used as input files to enable Kinghorn to customize his mate selection software to work with US Angus EPDs and herd pedigree files. Van Eenennaam worked with Kinghorn October 28-31, 2013 in Armidale, NSW, Australia to learn how to use the mate selection software using the Kasten herd files. Developed files using Kasten’s pedigree file and simulated genotypes to run on Matesel using assumptions of 6 SNPs – a couple with fairly high frequencies, and then 100 lethal recessives all at fairly low frequencies – both of these run in MateSel and can be used for demonstration purposes. This required development of simulated genotypes using GenePop and modification of the code to kill any progeny that inherited the “aa” (i.e. lethal recessives). Also included a couple of new “traits” in the MateSel file including number of alleles carried by a given bull, and also number of Aa versus aA (later would be important in case of imprinted alleles – else equivalent). Index used in this simulation was $Beef (American Angus Association), and all modeled with linked markers on 1 Morgan genome. A demonstration of this work will be reported to the research team at an in-person team meeting scheduled for December 12th, 2013 in Kansas City, MO. Specific Aim 5A; Accomplishments. Work on this aspect of the proposal is funded starting in year 3. Specific Aim 5B;Accomplishments. Progress on this objective is not scheduled to begin until 2014. Specific Aim 5C; Accomplishments. Rolf and Van Eenennaam met with a various breed associations to gauge interest and determine the feasibility of developing an app for EPD lookup. The first stage of the app development project for year 1 outlined in this proposal was completed by the American Angus Association. Their app allows EPD and information lookup synced with the association information on their server. Rolf and Van Eenennaam are currently working with several major US beef breed associations to explore the generation of a collaborative EPD lookup app that will work across several different breeds. This work is currently ongoing. Taylor, Van Eenennaam, and Patterson reviewed the overall goals and objectives for the project with regional extension livestock specialists during their annual in-service training in February 2013. At this time, specialists were asked to participate in sample collection from heifers to be used in the project. Van Eenennaam has planned a meeting of beef cattle genomics specialists 13th December, 2013 in conjunction with the BIF Genetic Prediction Workshop that is being held in Kansas City, MO.

Publications

• Type: Book Chapters Status: Published Year Published: 2013 Citation: Van Eenennaam, A.L. 2013. Considerations related to breed and biological type. Chapter 3 in Management considerations in beef heifer development and puberty. D. J. Patterson and M. F. Smith Eds. Veterinary Clinics of North America: Food Animal Practice. 29(3): 493-516