NRSP_old8: National Animal Genome Research Program

(National Research Support Project Summary)

Status: Inactive/Terminating

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SAES-422 Reports

Annual/Termination Reports:

[06/10/2019] [03/16/2020] [03/16/2021] [04/22/2022] [03/17/2023]

Date of Annual Report: 06/10/2019

Report Information

Annual Meeting Dates: 01/12/2019 - 01/14/2019
Period the Report Covers: 10/01/2017 - 09/30/2018

Participants

AQUACULTURE
Coordinator: Benjamin J. Reading, North Carolina State University
Co-coordinators: Steven Roberts, Washington State University
Eric Peatman, Auburn University
Species Leaders:
Catfish: Sylvie Quiniou, ARS Stoneville, Mississippi,
John Liu, Syracuse University, New York
Oyster: Dina Proestou, ARS University of Rhode Island, Rhode Island
Salmonids: Yniv Palti, ARS Leetown, West Virginia
Striped Bass: Benjamin Reading, North Carolina State University, North Carolina
Total Attendees
Number: 80
Number of institutes: 43

CATTLE
COOPERATING AGENCY AND PRINCIPAL LEADERS (through 9/30/2018):
University of California, Davis: Juan F. Medrano
University of California, Davis: Alison Van Eenennaam, Co-coordinator
University of Missouri-Columbia: Jerry Taylor, Co-coordinator
COOPERATING AGENCY AND PRINCIPAL LEADERS (starting 10/1/2018):
University of California, Davis: Alison Van Eenennaam, alvaneenennaam@ucdavis.edu
University of Missouri-Columbia: Bob Schnabel, Co-coordinator, schnabelr@missouri.edu
Texas A&M University, Clare Gill, Co-coordinator, clare-gill@tamu.edu
USDA ARS, Beltsville, Ben Rosen, Co-coordinator, Ben.Rosen@ars.usda.gov
Washington State University, Zhihua Jiang, Co-coordinator jiangz@wsu.edu
Table 1. Cattle/Swine Workshop Attendance (count)
Item Before Break After Break Total
Attendees 117 111 194
Countries 21 22 24
U.S. - States 20 24 28
Affiliations 67 77 100
Table 2. Cattle/Sheep/Goats I Attendance (count)
Item Before Break After Break Total
Attendees 63 37 85
Countries 16 7 17
U.S. (States) 20 14 22
Affiliations 63 37 58
Table 3. Cattle/Sheep/Goats II Attendance (count)
Item Before Break After Break Total
Attendees 73 91 138
Countries 15 16 21
U.S. (States) 19 26 28
Affiliations 52 60 80

POULTRY
• Attendance during the 1.5 day workshop averaged n=78 with peak attendance in excess of 115.
• Representatives of 16 agricultural experiment stations attended from across the US including
the membership of NRSP-8 Poultry group: Iowa State, Michigan State, University of Arizona, University of Arkansas, Western University of Health Sciences, Mississippi State University, Univ of Delaware, Univ of Georgia, University of California Davis, University of Minnesota, Beckman Research Institute.
• Attendees also included members of the poultry layer and broiler breeding companies, and scientists from the United Kingdom, Germany, Canada, Sweden, Netherlands, Bangladesh, Australia and China.

EQUINE
Coordinators:
Ernest Bailey, University of Kentucky
Samantha Brooks, University of Florida
Molly McCue, University of Minnesota
NRSP8 Workshop:
Chair: Stephen Coleman, Colorado State University
Co-chair: Annette McCoy, University of Illinois
Attendees:
January 12: 70
January 13: 45
Station Reports were provided by scientists from 20 laboratories including those at Cornell University, University of Florida, Mississippi State University, University of Kentucky, University of Louisville, University of Minnesota, Michigan State University, Illinois State University, University of Nebraska, Texas A&M University, University of California-Davis, Argentina, Uppsala Sweden, Italy, Denmark and France.

SHEEP & GOATS
Cornell University: Heather Huson*
Louisiana State University: James E. Miller*1
North Carolina A & T: Mulumebet (Meli) Worku*1
Oklahoma State University: Udaya DeSilva*
Pennsylvania State University: Wansheng Liu*
Texas A&M University: Clare Gill*1, Penny Riggs*
University of Florida: Raluca Mateescu*
University of Idaho: Brenda Murdoch*1
University of Massachusetts-Amherst: Janice Telfer*, Cynthia Baldwin*
University of Vermont: Stephanie McKay*1
USDA/ARS: Michelle R. Mousel*, Stephen N. White*
USDA ARS: Jennifer Woodward-Greene
Utah State University: Noelle E. Cockett*
Virginia State University: Brian Sayre*, Glenn Harris*
Virginia Tech: Rebecca Cockrum*1
*Voting member.
1In attendance at the 2018 NRSP-8 meeting.

Brief Summary of Minutes

Minutes Attachment:

NRSP 8 Minutes, 1-'19.doc

Accomplishments

SUMMARY OF NRSP-8 ACCOMPLISHMENTS 2018   2018 represented the first year of the new 5-year NRSP-8 funding. The most important accomplishment of the NRSP-8 has been the formation of a large community of scientists working worldwide to advance animal genomics through the sharing of resources, development of open-access multi-species bioinformatic tools, sequencing and assembly of genomes, organization of workshops and conferences, communication of results, support for travel for students and invited speakers, preparation of multi-institutional grant proposals, and formation of large collaborative research groups. The communication and sharing of information among the different species technical committees fostered by NRSP-8 has led to significant achievements under each of the three objectives outlined for 2018-2023 (listed below). Across committees, the experience of one group has often informed and influenced the directions and approaches taken by other groups and this shared knowledge has accelerated tool development and discovery for all supported species. A summary of the major important accomplishments and impacts for each of the technical committees (aquaculture, cattle, horse, poultry, sheep/goat, swine and bioinformatics) are included below.   Objective 1: Advance the quality of reference genomes for all agri-animal species by providing high contiguity assemblies, deep functional annotations of these assemblies, and comparison across species to understand structure and function of animal genomes.   Objective 2: Advance genome-to-phenome prediction by implementing strategies and tools to identify and validate genes and allelic variants predictive of biologically and economically important phenotypes and traits.   Objective 3: Advance analysis, curation, storage, application, and reuse of heterogeneous big data to facilitate genome-to-phenome research in animal species of agricultural interest.     Websites for each coordination group:     Aquaculture : http://www.animalgenome.org/aquaculture/ Bioinformatics : http://www.animalgenome.org/bioinfo/ Cattle : http://www.animalgenome.org/cattle/ Horse: http://www.uky.edu/Ag/Horsemap/ Poultry: http://poultry.mph.msu.edu/ Sheep: http://www.animalgenome.org/sheep/ Swine: http://www.animalgenome.org/pigs/     NRSP-8 Aquaculture 2018 Annual Report   Leadership   Coordinator:                 Benjamin J. Reading, North Carolina State University Co-coordinators:          Steven Roberts, Washington State University Eric Peatman, Auburn University Species Leaders: Catfish:                           Sylvie Quiniou, ARS Stoneville, Mississippi,                                         John Liu, Syracuse University, New York Oyster:                            Dina Proestou, ARS University of Rhode Island, Rhode Island Salmonids:                      Yniv Palti, ARS Leetown, West Virginia Striped Bass:                   Benjamin Reading, North Carolina State University, North Carolina   2019 Aquaculture Workshop Report Workshop Chair 2018-2019: Catherine Purcell (catherine.purcell@noaa.gov) Chair-elect 2019-2020: Louis Plough (lplough@umces.edu) Chair-elect 2020-2021: Moh Salem (Mohamed.Salem@mtsu.edu)   Theme Aquaculture Genomics Workshop 2019   Attendees Number: 80 Number of institutes: 43   Invited Presentations (4 Plenary Speakers)   <ol> <li> FAASG – Functional Annotation of All Salmonid Genomes Ben F. Koop, University of Victoria</li> <li> Editing for Animal Welfare and Environmental Sustainability: Are These Traits Important? Tad S. Sonstegard, Acceligen, Inc.</li> <li> Gene Transcription Data for eQTL Analysis, Variance Component Analysis and Gebv Estimation in Atlantic Salmon Anna K. Sonesson, Nofima AS</li> <li> Use of Atlantic Salmon Gene Editing in Research and Development Anna Troedsson-Wargelius, Institute of Marine Research</li> </ol>   Contributed Presentations (15) Poster Session Participants (20)   Business Meeting Minutes   Time: Saturday January 12, 2019, 5:00-5:46 pm Place: Pacific Salon 3/4, Town and Country Hotel, San Diego, CA Number of Attendees: 9   <ol> <li>Call to order. Catherine Purcell, Ph.D. (2018-19 Workshop Chair, NOAA, California) called the business meeting to order at 5:00 pm, following the Aquaculture Workshop.</li> </ol>   <ol start="2"> <li>Jim Reecy, Ph.D. (2018-19 Bioinformatics Coordinator, Iowa State University) provided a status update of technological resources and plans for data management: the genome database is still under construction; the NAGRP VCF Data Repository (animalgenome.org) will be funded for only five more years and as such, the impetus to store and maintain web resources for genome data is on the species coordinators and associated researchers; a sustainability plan needs to be put into place and is open to suggestions (a current suggestion is to coordinate with librarians at home institutions). Data curation will be led by now-incumbent Co-Coordinators James Koltes, Ph.D. (Present Bioinformatics Co-Coordinator, Iowa State University) and Fiona McCarthy, Ph.D. (Present Bioinformatics Co-Coordinator, University of Arizona).</li> </ol>   <ol start="3"> <li>Benjamin Reading, Ph.D. (Present Aquaculture Coordinator, North Carolina State University) began overview of Species Coordinator reports (not all submitted at the time of meeting due to United States Government shut-down) and status of future meetings and chair positions.</li> </ol>   <ol start="4"> <li>Monies for 2020 meeting will be funded through North Carolina State University and are ear-marked to be available in October of 2019. Eric Peatman, Ph.D. (former Acting NRSP-8 Chair 2018-19 with John Liu 2018-2018; Auburn University) is processing the remainder of the funds from the past funding cycle and deposit for 2020 meeting can be supported through these remaining funds if required prior to Oct. 2019.</li> </ol>   <ol start="5"> <li>Louis Plough, Ph.D. (University of Maryland, Center for Environmental Science) is the Present and Accepted Workshop Chair-Elect for 2019-20. Mohamed Salem, Ph.D. (Middle Tennessee State University) is the Accepted Workshop Chair-Elect for 2020-21.</li> </ol>   <ol start="6"> <li>A note was made for coordinators to mention revenue generated, grants added, and funds leveraged in species updates</li> </ol>   <ol start="7"> <li>NRSP-8 is one of the longest-running NRSPs in the history of their offering. This is attributed to a weakness in terms of progress, but a strength in terms of goals left to achieve. Action plan moving forward is to focus on data curation (see above, bioinformatics) and the development of widely accessible resources and applications.</li> </ol>   <ol start="8"> <li>Industry support is important for each species to obtain a level of impact via industry deliverables, however garnering industry support is important for each species to obtain a certain level of impact, however, this may fragment the solidarity among species-groups by progress made as a function of industry support</li> </ol> . <ol start="9"> <li>For the distribution of monies pending cuts to funding, Bioinformatics is considered the most critical. Mohamed suggested reducing student awards, small funding opportunities, and looking towards large center grants or industry-matching funds. Louis suggested having fewer plannary speakers, although some speakers accepted honorariums.</li> </ol>   <ol start="10"> <li>Meeting was adjourned.</li> </ol>   Objective 1: Advance the status of reference genomes for all species, including basic annotation of worldwide genetic variation, by broad sequencing among different lines and breeds of animals.   Catfish (Quiniou, Liu) Using an innovative approach of a YY channel catfish as the sequencing template and third generation sequencing technologies, we generated, assembled and annotated the YY genome sequence of channel catfish. This represents the very first Y chromosome sequence among teleost fish, and one of the few whole Y chromosome sequences among vertebrate species. The genome sequence assembly had a contig N50 size of 2.7 Mb and a scaffold N50 size of 26.7 Mb.   Oyster (Gómez-Chiarri, Putnam, Guo, Warren, Proestou) Eastern oyster (Crassostrea virginica) genome assembly v. 3.0 was completed; 99% of sequences are assembled into the known number of chromosomes (10). Gene annotation was completed using the automated NCBI pipeline. Computational Analysis of gene Family Evolution (CAFE analysis) was performed to compare expansion of gene families in Eastern oyster with other molluscan genomes. Completed re-sequencing of 92 eastern oyster genomes at 20X coverage. Sequenced specimens derived from 4 geographic regions (Gulf of Mexico, Chesapeake Bay, Delaware Bay, and Maine), 2 salinity regimes within each region (high and low), and wild and selected populations within each region. Sequencing was partially funded through NRSP-8 Aquaculture Program.   Salmonids (Salem, Palti) A chromosome level genome assembly was published for Chinook salmon (Narum et al. 2018) based on the publicly released assembly on NCBI. Atlantic salmon farming in eastern US and Canada is restricted to genetic stocks of North American origin due to ecological and conservation concerns. However, the majority of SNP discovery and SNP chip development efforts in Atlantic salmon have focused on genetic stocks from European origin. High coverage whole genome resequencing within 80 North American Atlantic salmon was conducted to identify 8,395,146 SNPs.   Striped Bass (Fuller, Abernathy, Kovach, Berlinsky, Reading) The striped bass genome assembly v. 2.0 (598 Mb) was completed using a combinatorial approach of Illumina and Pacific Biosciences sequencing and Chicago® and Dovetail™ Hi-C + HiRise™ scaffolding. The number of assembly scaffolds was 629, of which 21 contain most of the genome sequence (L90 = 21 scaffolds), which is consistent with a haploid chromosome number of 24 for striped bass. Ab-initio and evidence-based gene predictions performed using the MAKER Annotation Pipeline identified 27,485 coding genes. Genotyping efforts based on ddRAD-Seq to explore population heterozygosity and genetic variation related to growth performance of domestic striped bass and those of wild-origin derived from 7 geographic locations along the Atlantic Ocean are complete. The white bass genome assembly v. 1.0 (645 Mb) was completed using Illumina sequencing combined with Chicago® and Dovetail™ Hi-C + HiRise™ scaffolding. This approach produced a genome assembly (L90 = 23 scaffolds). Ab-initio gene prediction using produced 28,356 protein-coding genes while evidence-based prediction from alignments of white bass transcriptome sequences produced 24,176 protein-coding genes. Over 2.8 billion paired-end 150 bp reads were generated for white bass using RNA sequencing (transcriptomics studies). These additional sequences will allow for improvement of our white bass transcriptome, provide for a source of gene-associated variation and serve as a guide for annotation of the white bass genome assembly.   Objective 2: Develop strategies to identify and exploit genes and allelic variation that contribute to economically relevant phenotypes and traits, in part through improving functional annotation of the genomes of our species.   Catfish (Quiniou, Liu) Genetic linkage and GWAS analyses placed the sex determination locus of channel catfish within a genetic distance less than 0.5 cM and physical distance of 8.9 Mb. However, comparison of the channel catfish X and Y chromosome sequences showed no sex-specific genes. Comparative RNA-Seq analysis between females and males revealed exclusive sex-specific expression of an isoform of BCAR1 gene in the male during early sex differentiation. Coupling of positional and expression candidates suggest the candidacy of BCAR1 as a sex determination gene, and experimental knockout of BCAR1 gene converted genetic males (XY) to phenotypic females. This indicates that alternative splicing may serve as the molecular mechanism for sex determination in catfish. QTL also were sequenced and mapped for growth performance and disease resistance against enteric septicemia of catfish (ESC).   Oyster (Roberts, Putnam, Lotterhoos, Puritz, Johnson, Eirin-Lopez, Allen, Zhang, Plough, Proestou) Functional annotation is underway by Eastern Oyster Genome Consortium (e.g. Blast2GO, Pfam, DNA methylation patterns). Outlier analysis and environmental association analysis for population genomic analysis of re-sequence data is underway. Over 30,000,000 SNPs were detected from oyster resequence data, thinned and pruned to a working set of 200K for population genomic analysis. Microbiome analysis of naïve and Dermo-infected oysters resistant and susceptible to disease was conducted. RNA-seq analyses are ongoing to understand the genetic and genomic basis for Dermo-resistance in Eastern Oyster breeding populations. Investigation of genetic basis for low-salinity tolerance in eastern oyster continues to quantify heritability for salinity tolerance and identifying QTL underlying tolerant phenotypes.                 Salmonids (Salem, Palti) A total of 10 moderate effect QTL associated with resistance to Infectious hematopoietic necrosis (IHNV; viral disease of salmonids that can result in mass mortality and significant economic losses), which jointly explained up to 42% of the additive genetic variance were detected in genome-wide association analyses of the commercial rainbow trout breeding population of Clear Springs Foods, Inc. using the 57K SNP chip. Two major QTL associated with Bacterial cold water disease (BCWD), a major disease in rainbow trout aquaculture, resistance on chromosomes Omy8 and Omy25 were reported. Whole genome resequencing of 40 fish from resistant and susceptible trout families was conducted to identify new SNPs and to refine the QTL regions. Over 15 million SNPs were identified from resequencing in this population and the two major QTL were narrowed down to regions much smaller than those reported previously. Genomic SNPs associated with thermal adaptation in redband trout were identified. Genotype frequencies for GREB1L were estimated in populations in the Pacific Northwest USA along with individual genotype association for migrating individuals. Genomic SNPs associated with (1) premature/mature arrival to spawning grounds in Chinook salmon and estimated genotype frequencies for the candidate gene greb1L in populations across N. America and (2) age-at-maturity and sex in Chinook salmon also were identified. Genome-wide association study using a 50K transcribed gene SNP-chip identified QTL affecting muscle yield in rainbow trout. A study characterized coding and noncoding genes involved in gonadogenesis-associated muscle atrophy in rainbow trout also was published. Muscle atrophy appears to be mediated by many genes encoding ubiquitin-proteasome system, autophagy related proteases, lysosomal proteases and transcription factors. A study characterized correlation between lncRNA and mRNA expression in rainbow trout families showing variation in body weight, muscle yield, fat content, shear force and whiteness also was published. Three differentially expressed (DE) antisense lncRNAs were co-expressed with sense genes known to impact muscle quality traits. Forty-four differentially expressed lncRNAs had potential sponge functions to miRNAs that affect muscle quality traits.   Striped Bass (Berlinsky, Fuller, Abernathy, Woods, McGinty, Borski, Reading) Expressed quantitative trait loci (eQTL) and small molecule profiling (metabolomics) analyses are ongoing to understand gene pathways related to superior growth traits in sunshine hybrid striped bass (white bass female x striped bass male) and domestic striped bass. Adult, male, domestic striped bass (n=60) were disseminated to major aquaculture producers in the U.S. for hybrid striped bass fry and fingerling production (directly contributing to the $50 million farm gate per year industry). Wild white bass gathered from Arkansas, Texas and Alabama along with available domesticated strains are being used to establish a base breeding population for familywise evaluations of growth and nutrient utilization on alternative, sustainable diets. A genotyping-by-sequencing panel has been developed from white bass populations, where single-nucleotide polymorphisms (SNPs) identified can discriminate domestic stocks from wild-sourced individuals. Additional genetic markers are being developed to rapidly identify gender and parentage.   Objective 3: Facilitate analysis, curation, storage, distribution and application of the enormous datasets now being generated by next-generation sequencing and related "omics" technologies with regard to animal species of agricultural interest.   Oyster (Gómez-Chiarri, Roberts, Proestou) Hands-on comparative genomics workshop was held at the National Shellfisheries Association annual meeting in Seattle, WA, March 18-21, 2018. Eastern Oyster Genome Consortium planning and writing workshop was conducted in Narragansett, RI, October 3-4, 2018.   Salmonids (Salem, Palti) Contributions to the development of FishGen.net database for storage of large-scale genotypes for genetic tagging and monitoring studies were made.   Striped Bass (Reading) JBrowse integrated web portal of the draft striped bass genome resource is hosted online for use as an unrestricted public resource. Progress is being made to produce a similar resource on NCBI. Database URL: <a href="http://appliedecology.cals.ncsu.edu/striped-bass-genome-project/">http://appliedecology.cals.ncsu.edu/striped-bass-genome-project/</a>. Ongoing development of different and novel machine learning-based analytical platforms focused on small molecule (metabolomics) and gene expression (RNA-Seq) profiling to better understand hybrid striped bass growth performance (heterosis effects).   Research support mini-grants (coordinator grants)   Three (3) mini-grants (~$10,000/each) supported projects that fall under all three primary NRSP-8 objectives and include a variety of species. Awards listed:   <ol> <li>Jason Abernathy and Steven J. Micheletti “Mapping sex-linked genes in temperate basses for improved hybrid striped bass culture”, USDA ARS.</li> <li>Hollie Putnam and Steven Roberts “Functional Re-annotation of Oyster Genomes with Epigenetic Resources (FROGER)”, University of Rhode Island.</li> <li>Moh Salem “The landscape of histone modifications in the rainbow trout genome: preliminary data for FAASG”, Middle Tennessee State.</li> </ol>   Travel Support & Opportunities for Trainings   The travel of seven students/postdocs was funded to attend the Aquaculture Workshop at PAG 2019. The purpose of the travel award program is to help graduate students and postdoctoral fellows to travel to the annual PAG meetings and present their research. The awardees of PAG 2019 are as follows:   <ol> <li>Pratima Chapagain, Middle Tennessee State University (TN, USA), “Gut Microbiome Analysis of Fast- and Slow-growing Rainbow Trout (Oncorhynchus mykiss)”.</li> <li>Valentina Cordova, University of Chile (Chile), “Development of a SNP baseline for genetic stock identification in a commercially important species of the South-east Pacific (Genypterus chilensis)”.</li> <li>Konstantin Divilov, Oregon State University (OR, USA), “Genetics of Pacific Oyster Uniformity in Different Environments”.</li> <li>Garrett McKinney, NOAA National Marine Fisheries Service, Northwest Fisheries Science Center (WA, USA), “Development of a universal sex assay and identification of y-chromosome haplotypes in Chinook salmon”.</li> <li>Ivan Pocrnic, University of Georgia (GA, USA), “Exploiting the dimensionality of genomic information in channel catfish”.</li> <li>Noemie Valenza-Troubat, The New Zealand Institute for Plant & Food Research Limited (New Zealand), “Genomics of New Zealand trevally: exploring the interactions genetic basis of quantitative traits to inform a newly developed breeding programme”.</li> <li>Wenwen Wang (Auburn University (LA, USA), “Identification of QTL associated with Aeromonas disease resistance in catfish throughout a genome-wide association study”.</li> </ol>   Leveraged funds and stakeholders’ use of project outputs Leveraged funds from diverse projects totaling more than one million dollars from federal sources. Selected grants are highlighted below: Egg Yolk, Egg Buoyancy and Striped Bass Recruitment: A Common Link? (PI Reading) $205,495. North Carolina Coastal Recreational Fishing License Program (CRFL), Division of Marine Fisheries. The Hybrid Striped Bass: Understanding Heterosis to Improve Food-Animal Agriculture. (PI Reading) $300,000 (+$300,000 industry matching funds). Foundation for Food and Agriculture Research (FFAR), New Innovator in Food and Agriculture Research Award.   Major impact products (could be potential impact) The new genome references should help to identity genes that control economically important aquaculture production traits. Draft genomes were assembled for striped bass v. 2.0, white bass v 1.0, eastern oyster (Crassostrea virginica) v. 3.0, and an additional re-sequencing of 92 eastern oyster genomes at 20X coverage also was completed. A chromosome level genome assembly was published for Chinook salmon (Narum et al., 2018) based on the publicly released assembly on NCBI. The shrimp genome sequence also was published in Nature Communications (Zhang et al., 2019). An improved reference genome also was reported for YY channel catfish (Bao et al., 2019).                               ANNUAL REPORT OF COOPERATIVE REGIONAL PROJECTS Supported by Allotments of the Regional Research Funds, Hatch Act January 1 to December 31, 2018   PROJECT:  NRSP-8 Cattle Genome Coordinators   COOPERATING AGENCY AND PRINCIPAL LEADERS (through 9/30/2018): University of California, Davis: Juan F. Medrano University of California, Davis: Alison Van Eenennaam, Co-coordinator University of Missouri-Columbia: Jerry Taylor, Co-coordinator   COOPERATING AGENCY AND PRINCIPAL LEADERS (starting 10/1/2018): University of California, Davis: Alison Van Eenennaam, <a href="mailto:alvaneenennaam@ucdavis.edu">alvaneenennaam@ucdavis.edu</a> University of Missouri-Columbia: Bob Schnabel, Co-coordinator, <a href="mailto:schnabelr@missouri.edu">schnabelr@missouri.edu</a> Texas A&M University, Clare Gill, Co-coordinator, <a href="mailto:clare-gill@tamu.edu">clare-gill@tamu.edu</a> USDA ARS, Beltsville, Ben Rosen, Co-coordinator, <a href="mailto:Ben.Rosen@ars.usda.gov">Ben.Rosen@ars.usda.gov</a> Washington State University, Zhihua Jiang, Co-coordinator <a href="mailto:jiangz@wsu.edu">jiangz@wsu.edu</a>   2019 Cattle Workshop Report   Workshop Chair 2018-2019:      Rebecca Cockrum (<a href="mailto:rcockrum@vt.edu">rcockrum@vt.edu</a>) Chair-elect 2019-2020: Ben Rosen (<a href="mailto:Ben.Rosen@ARS.USDA.GOV">Ben.Rosen@ARS.USDA.GOV</a>) Co-Chair-elect 2020-2021:         Darren Hagen  (<a href="mailto:darren.hagen@okstate.edu">darren.hagen@okstate.edu</a>) Erdogan Memeli (<a href="mailto:em149@msstate.edu">em149@msstate.edu</a>)   International Plant and Animal Genome XXVII Workshop Attendance     <table> <tbody> <tr> <td colspan="4" width="617"> Table 1. Cattle/Swine Workshop Attendance (count) </td> </tr> <tr> <td width="174"> Item </td> <td width="164"> Before Break </td> <td width="140"> After Break </td> <td width="139"> Total </td> </tr> <tr> <td width="174"> Attendees </td> <td width="164"> 117 </td> <td width="140"> 111 </td> <td width="139"> 194 </td> </tr> <tr> <td width="174"> Countries </td> <td width="164"> 21 </td> <td width="140"> 22 </td> <td width="139"> 24 </td> </tr> <tr> <td width="174"> U.S. - States </td> <td width="164"> 20 </td> <td width="140"> 24 </td> <td width="139"> 28 </td> </tr> <tr> <td width="174"> Affiliations </td> <td width="164"> 67 </td> <td width="140"> 77 </td> <td width="139"> 100 </td> </tr> </tbody> </table>     <table> <tbody> <tr> <td colspan="4" width="617"> Table 2. Cattle/Sheep/Goats I Attendance (count) </td> </tr> <tr> <td width="174"> Item </td> <td width="164"> Before Break </td> <td width="140"> After Break </td> <td width="139"> Total </td> </tr> <tr> <td width="174"> Attendees </td> <td width="164"> 63 </td> <td width="140"> 37 </td> <td width="139"> 85 </td> </tr> <tr> <td width="174"> Countries </td> <td width="164"> 16 </td> <td width="140"> 7 </td> <td width="139"> 17 </td> </tr> <tr> <td width="174"> U.S. (States) </td> <td width="164"> 20 </td> <td width="140"> 14 </td> <td width="139"> 22 </td> </tr> <tr> <td width="174"> Affiliations </td> <td width="164"> 63 </td> <td width="140"> 37 </td> <td width="139"> 58 </td> </tr> </tbody> </table>     <table> <tbody> <tr> <td colspan="4" width="617"> Table 3. Cattle/Sheep/Goats II Attendance (count) </td> </tr> <tr> <td width="174"> Item </td> <td width="164"> Before Break </td> <td width="140"> After Break </td> <td width="139"> Total </td> </tr> <tr> <td width="174"> Attendees </td> <td width="164"> 73 </td> <td width="140"> 91 </td> <td width="139"> 138 </td> </tr> <tr> <td width="174"> Countries </td> <td width="164"> 15 </td> <td width="140"> 16 </td> <td width="139"> 21 </td> </tr> <tr> <td width="174"> U.S. (States) </td> <td width="164"> 19 </td> <td width="140"> 26 </td> <td width="139"> 28 </td> </tr> <tr> <td width="174"> Affiliations </td> <td width="164"> 52 </td> <td width="140"> 60 </td> <td width="139"> 80 </td> </tr> </tbody> </table>     Old NRSP8 Objectives: Objective 1: Create shared genomic tools, reagents and sequence information to enhance the understanding and discovery of genetic mechanisms affecting traits of interest. Objective 2: Facilitate the development and sharing of animal populations and the collection and analysis of new, unique and interesting phenotypes. Objective 3: Develop, integrate and implement bioinformatics resources to support the discovery of genetic mechanisms that underlie traits of interest.   Progress toward Objective 1.  Shared genomic tools and reagents and sequence information. An important focus of the community has been towards improving the bovine genome assembly.   Publication of the new ARS-UCD 1.2  Dominette bovine genome reference assembly A group of collaborating scientists (Tim Smith, Juan Medrano, Ben Rosen, Sergey Koren, Robert Schnabel, Derek M. Bickhart, Aleksey Zimin, and Chris Elsik) worked toward developing an improved bovine reference genome assembly and its annotation. The ARS-UCD 1.2 Bovine Assembly was released April 2018 – and details are below. <ul> <li>The ARS-UCD assembly represents a vast improvement in the continuity of the bovine genome. The quality of the assembly including the 100-fold improvement in the number of gaps compared to the Btau_5.0.1 assembly and almost 200-fold improvement over UMD3.1.</li> <li>See Table 1 (Rosen, Bickhart et al. 2018). Funding for this project came from Cattle Genome Coordinator Funds, USDA/MARC, UC Davis, Neogen/Geneseek and Zoetis.</li> </ul> Table 1. Bos taurus Reference Genome Comparisons. Rosen, Bickhart et al., (2018)   ARS-UCD1.2 <a href="https://www.ncbi.nlm.nih.gov/assembly/GCF_002263795.1">https://www.ncbi.nlm.nih.gov/assembly/GCF_002263795.1</a> Isolate: L1 Dominette 01449 registration number 42190680 Sex: female BioSample:  <a href="https://www.ncbi.nlm.nih.gov/biosample/SAMN03145444/">SAMN03145444</a> BioProject: <a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA391427/">PRJNA391427</a> Coordinator funds were also used to perform long read sequence on the F1 male (Angus sire x Brahman dam F1 hybrid) in collaboration with John Williams at University of Adelaide and Tim Smith at MARC. This hybrid enabled the development of a Brahman and Angus assembly that are available <a href="https://www.ncbi.nlm.nih.gov/assembly/GCF_003369695.1">UOA_Brahman_1</a> <a href="https://www.ncbi.nlm.nih.gov/assembly/GCF_003369695.1">https://www.ncbi.nlm.nih.gov/assembly/GCF_003369695.1</a> <a href="https://www.ncbi.nlm.nih.gov/assembly/GCA_003369685.2">UOA_Angus_1</a> <a href="https://www.ncbi.nlm.nih.gov/assembly/GCA_003369685.2">https://www.ncbi.nlm.nih.gov/assembly/GCA_003369685.2</a>   An assembly of a Holstein bull, and both a Jersey and Holstein bull from New Zealand are in development.   USDA Cattle FAANG project (USDA-NIFA-AFRI 2018-67015-27500)   An AFRI-NIFA grant was awarded to a consortium of multiple US institutions to generate and analyze cattle FAANG data. The objectives of the project are to generate detailed transcriptome and chromatin state information from a comprehensive set of cattle tissues and to integrate transcriptome and chromatin state data sets into readily accessible maps of functional elements in the bovine genome. For this, 60 different cattle tissues, in two biological replicates, including tissues from adult and fetal L1 Hereford animals, primary cell lines, and Holstein mammary gland tissues are being subjected to analysis using 4 assays aimed at identifying transcribed regions (RNA-seq, smRNA-seq, RAMPAGE, WTTS-seq) and 9 assays aimed at characterizing chromatin state (WGBS, ATAC-seq, ChIP-seq for 6 histone marks and CTCF). Integration of transcriptomic and epigenomic data will assist in the annotation of the functional regions in the bovine genome.   USDA Cattle FAANG project participants include: University of California Davis, University of Vermont, Texas A&M University, University of Idaho, USDA-ARS, Washington State University, Iowa State University, Virginia Tech, Pennsylvania State University, The University of Arizona, University of Wisconsin, University of Pennsylvania, Colorado State University, University of Guelph and Zoetis.   Progress towards Objective 3: Bioinformatics and database resources Cattle GRIN Genomics Database The front and back ends for the Animal-GRIN genomic component will be completed before March 2019. Therefore this component of Animal-GRIN will be available for scientists receiving USDA funding to archive their genomic data as part of completing their project. Any questions can be directed to Harvey Blackburn (Harvey.blackburn@ars.usda.gov). The Animal-GRIN system can be found at: <a href="https://nrrc.ars.usda.gov/A-GRIN/database_collaboration_page_dev">https://nrrc.ars.usda.gov/A-GRIN/database_collaboration_page_dev</a>   Database and bioinformatics activities are also coordinated by Jim Reecy (NRSP8 Bioinformatics Coordinator) at the NAGRP site (<a href="http://www.genome.iastate.edu/cattle/">http://www.genome.iastate.edu/cattle/</a>).   Zhiliang Hu at Iowa state collated data from the sequence read archive – there are 4,885 cattle samples available there  <a href="https://www.animalgenome.org/other/pubSeqSum">https://www.animalgenome.org/other/pubSeqSum</a>   Meetings: Coordinator funds supported student travel awards for PAG-XXVI in January 2019, and will do the same for more students for PAG XXVII in January 2020. Plans for the future: The new NRSP8 (10/1/2018 to 9/30/2023) has updated priorities.   New NRSP8 Objectives:   Objective 1: “Advance the status of reference genomes for all species, including basic annotation of worldwide genetic variation, by broad sequencing among different lines and breeds of animals.” Objective 2: “Develop strategies to identify and exploit genes and allelic variation that contribute to economically relevant phenotypes and traits, in part through improving functional annotation of the genomes of our species.” Objective 3: “Facilitate analysis, curation, storage, distribution and application of the enormous datasets now being generated by next-generation sequencing and related "omics" technologies with regard to animal species of agricultural interest.”   Sequencing cattle Y chromosome (Objective 1) <ul> <li>Discussion of doing finished Y chromosome for bovine</li> <li>larger project that would benefit everyone in the community</li> <li>work with Brenda Murdoch to fund FACS sorting of sex chromosomes at Stanford to develop enriched library followed by long read sequencing</li> </ul>   Iso-Seq on Dominette tissues (Objective 1) <ul> <li>Do Iso-Seq on 15 fetal tissues from late gestation calf collected by C-section of L1 Dominette to enable genome annotation</li> <li>Tim Smith at MARC will perform PAC-Bio long read sequencing on fetal tissues</li> </ul>   Perform long read sequencing on F1 hybrid (Objective 1) <ul> <li>Tim Smith will run long reads using Oxford Nanopore PromethION on the F1 male (Angus sire x Brahman dam F1 hybrid)</li> </ul>   NRSP-8 Poultry Annual Report October 1, 2017 – September 30, 2018   Poultry Genome Coordinators: Huaijun Zhou (UC Davis); Hans Cheng (USDA-ARS) Chair: Kent Reed (University of Minnesota) The NRSP-8 Poultry Workshop held January 12-13, 2019 in conjunction with NC1170 Poultry Workshop at the Plant & Animal Genome Conference, San Diego CA, attendance overview: <ul> <li>Attendance during the 1.5 day workshop averaged n=78 with peak attendance in excess of 115.</li> <li>Representatives of 16 agricultural experiment stations attended from across the US including</li> </ul> the membership of NRSP-8 Poultry group: Iowa State, Michigan State, University of Arizona, University of Arkansas, Western University of Health Sciences, Mississippi State University, Univ of Delaware, Univ of Georgia, University of California Davis, University of Minnesota, Beckman Research Institute. <ul> <li>Attendees also included members of the poultry layer and broiler breeding companies, and scientists from the United Kingdom, Germany, Canada, Sweden, Netherlands, Bangladesh, Australia and China.</li> </ul> Poultry Coordination funds partially supported a total 12 scientists attending the workshop.  In pariticar, partially supported three speakers specially focusing on microbiome work in livestock: David Mills from UC Davis described lessons learned from a naturally evolved system to enrich a functional microbiome: The wonders of mammalian milk; Glenn Zhang from Oklahoma State University talked about important role of gut microbiota on adiposity in pigs. Third speaker was not able to make it due to flight delay. We have a total of 20 station reports with research areas of heat stress, disease, gut physiology, bioinformatics analysis, epigenomic analysis etc. The 2018 poultry Jorgensen Travel award winners Kelly Chanthavixay (UCD) and Lei Liu (UM) were then introduced and each gave a lightning talk on their area of research. Finally, we had 8 junior scientists given 2 minutes lightning talks about their research. Grants <ul> <li>Kent Reed, Univ of Minnesota:</li> </ul> o Effect of AFB1 on immune tissues of turkeys from diverse genetic backgrounds. USDAUMN Multi-State Project, 2016-2018, $94,221; o USDA National needs fellowship for enhancing animal production: Addressing national need in poultry production. USDA-NIFA-NNF. 2016-2021, $241,000; o Antibiotic-free alternatives to improve health and performance in commercial turkeys. USDA-NIFA-AFRI. 2016-2018, $464,000; o Influence of thermal challenge on turkey muscle development and meat quality. USDANIFA-AFRI. 2014-2018, $975,000. <ul> <li>Susan Lamont: Iowa State University. US-UK Collaborative Research: Host Resistance to Avian Pathogenic E. coli. USDA-NIFA-AFRI/BBSRC; $499,999</li> <li>Marcia Miller: Beckman Research Institute, City of Hope Medical Center, CA: USDA NIFA</li> </ul> Foundational Program Understanding Antimicrobial Resistance. Award: $387,518.00. Period of Performance: 06/01/2017-05/31/2020. MHC-Y-Directed Immune Responses during colonization of Chickens by Campylobacter. <ul> <li>Doug Rhoads: University of Arkansas. Validation of a SNP panel for breeding against ascites in broilers. NIFA-AFRI; 3/2018-2/2021; $500,000;</li> <li>Yvonne Dreshsler, Western University of Health Sciences: Genome-wide annotation of cis-regulatory elements in the chicken genome. NIFA AFRI; $1,000,000;</li> <li>Hans Cheng, USDA-ARS: Genome biology of Marek’s disease: Viral integration and genome alterations in genetically resistant and susceptible stocks. NIFA AFRI; $499,997; Genomic screens to identify regulatory elements with causative polymorphisms accounting for Marek’s disease genetic resistance in chicken, NIFA; $498,116.</li> <li>H. Zhou, UC Davis: $11,212,800 from USAID, USDA.including newly funded $10,000,000 during that period as PI, co-PIs.</li> </ul> Impacts Our members are highly focused on fundamental, translational and applied research to benefit U.S. Agriculture and through genomics improve poultry health and contribute to the productivity of the relevant industries. Below are listed some of the highlights from 2017-18 research. Many of the efforts are focused on projects that directly impact poultry health and production. Principal impact is providing evidence that the MHC-Y region contributes to immune responses.  The work has provided a) determination of the sequence for MHC-Y haplotype in the RJF, b) evidence for rapid changes in MHC-Y gene expression during early immune responses and c) data revealing a correlation between MHC-Y genotype and immune response phenotype. Establishment of various omic assays to identify and characterize epigenetic elements in the chicken to aid poultry research. Identification of genes that are associated with resistance to heat stress and Newcastle disease virus and can be used to genetic enhancement of disease resistance of chicken in adaption to hot climate. Knowledge of genes associated with enhanced immune response may inform further information on vaccine efficacy in poultry production. ChIP-seq and ATAC-seq assays developed and other omic data generated for regulatory elements annotation will be important for animal genome community. A new brain structure involved in regulating the stress response in broilers has been identified.  It is called the nucleus of the hippocampal commissure (NHpC) and may function as part of the classical hypothalamo-pituitary-adrenal (HPA) axis in avian species. Providing new molecules and additional key mechanisms into the cellular pathways for muscle growth and muscle mass development in breast muscle of broilers will improve production efficiency and hopefully prevent metabolic myopathy such as ‘woody breast’. Identification of the genetics of ascites will allow breeders to select against ascites and reduce production losses Genes, pathways and genomic regions associated with important biological traits such as heart development, and response to heat stress and pathogen infection, in chickens were identified. Genetic variation was characterized in commercial lines, research lines and indigenous lines of chickens.  Important factors for optimal use of genetic evaluation models were identified. The feasibility of applying molecular genetics and genomics to analysis of variation in structure, function and gene expression within the chicken genome was demonstrated. Development of management strategies to reduce lameness caused by BCO is critical for reducing a significant animal welfare issue in broilers.Our efforts at the University of Minnesota are focused on projects that directly impact poultry health and production. Extreme temperature variations threaten the quality of poultry muscle as a healthy, high quality food product. Our collaborative project with Michigan State University and Ohio State University seeks to quantify climate change impacts on poultry breast muscle growth and development, morphological structure, intramuscular fat deposition, and protein functionality to develop appropriate strategies to mitigate the undesirable changes in meat quality. Identification of molecular mechanisms associated with altered muscle development will result in development of mitigation strategies based on improved genetic selection, nutritional intervention, and other strategies to improve poultry muscle food quality and quantity. Our collaborative project with Utah State University is investigating the genetic response to of turkeys to aflatoxin exposure.  Aflatoxin B1 (AFB1) causes annual industry losses estimated in excess of $500 M. Increasing innate resistance to AFB1 could result in numerous health benefits. Transformational improvements in AFB1 resistance require a multidisciplinary approach to identify protective alleles with potential to reduce disease. Genetic markers to improve AFB1-resistance have a potentially high commercial value and positive economic impact to industry, owing to improvements in health and well-being, productivity, and a safer product for consumers.  The gastrointestinal health of an animal is key to its successful growth and development.  Our collaborative project at UMN seeks to advance our understanding of the interactions between the turkey gastrointestinal microbiome and host during maturation and microbiome modulation. Elimination of sub-therapeutic antibiotics for growth promotion and health in poultry will leave a critical void. This project will improve our mechanistic understanding of host-microbiome interactions in the avian host, and identify feasible approaches towards modulating the turkey intestinal microbiome resulting in enhanced health and performance.   NRSP-8 Equine 2018 Annual Report   Leadership: <h4>Coordinators:</h4> Ernest Bailey, University of Kentucky Samantha Brooks, University of Florida Molly McCue, University of Minnesota   NRSP8 Workshop: Chair: Stephen Coleman, Colorado State University Co-chair: Annette McCoy, University of Illinois   2018 Equine Workshop Report The workshop met Saturday afternoon (Jan 12) and Sunday morning (Jan 13) at the Plant and Animal Genome Conference in San Diego, CA.   Attendees: January 12: 70 January 13: 45   Station Reports were provided by scientists from 20 laboratories including those at Cornell University, University of Florida, Mississippi State University, University of Kentucky, University of Louisville, University of Minnesota, Michigan State University, Illinois State University, University of Nebraska, Texas A&M University, University of California-Davis, Argentina, Uppsala Sweden, Italy, Denmark and France.   PAG 2019 Workshop Presentations Invited Speaker: Gene W. Yeo, University of California, San Diego: “RNA binding proteins as engineers of human health”.   In addition, there were presentations on the new Y chromosome assembly, population structure studies using genomic tools, investigations of gene expression in different health and physiological states, and investigations and discoveries for specific genes in horses.   Travel support: The Jorgenson Travel Award was won by Anna Dahlgren of the University of California, Davis for the presentation entitled, “Functional Investigation of Putative Variant for Atypical Equine Thrombasthenia in Thoroughbreds”.   Additional Travel Awards were also made to 21 other students using the NRSP8 Coordinator Funds.    Progress on the Workshop Objectives:   1: Advance the status of reference genomes for all species, including basic annotation of worldwide genetic variation, by broad sequencing among different lines and breeds of animals.   The new assembly of the horse genome, Ecab 3.0, was published and made available on NCBI and ENSEMBL genome browsers.  The new assembly is based on the existing Sanger sequence data along with Illumina HiSeq short reads, CHiCago and Hi-C long-insert libraries, Gap-filling with PacBio and a 10x Chromium library to identify and phase variants. The final assembly has 4.5Mb contig N50, 85Mb scaffold N50, and 70Mb more sequence assigned to chromosomes.   An assembly of the Y chromosome was published and reported based on sequencing 94 BACs from a 192 mapped BAC tile array, plus 265 STs and FISH mapping.  An assembly of 9,497,449 was descirbed, although the true size is likely to exceed 12 Megabases if gaps were accounted for.  The work led to discovery of 52 genes and a transcript that has high homology to DNA sequences in a horse parasite, Parascaris, suggesting evidence of horizontal transfer of DNA between these species.   2: Develop strategies to identify and exploit genes and allelic variation that contribute to economically relevant phenotypes and traits, in part through improving functional annotation of the genomes of our species. For the Functional Annotation of Animal Genomes (FAANG) initiative, sampling and preservation of 86 tissues, 2 cell lines, and 5 fluids from two Thoroughbred mares was completed in 2016 (Burns, et. al 2018). This biobank has been instrumental in the development of epigenetic assays and data collection for the horse, including RNA-seq, ChIP-seq, and CTCF-binding assays. While the initial study prioritized eight tissues for sampling (liver, lung, ovary, adipose, heart, lamina, parietal cortex and longissimus dorsi muscle), notably, over $61,000 contributed by individual members of the research community allowed for collection of RNA-seq data from 46 tissues, rather than only the 8 initially funded. This sequencing was completed in 2018 and uploaded to EMBL-ENA (https://www.ebi.ac.uk/ena/data/view/PRJEB26698). ChIP-Seq on four prioritized histone marks (H3K27me3, H3K4me3, H3K27ac, and H3K4me1) from eight prioritized tissues were recently completed.  Three additional tissues (spleen, metacarpus III and sesamoid bone) have subsequently been supported for ChIP-seq assays and are currently underway. In 2018, the profiling of CTCF, the major eukaryotic insulator, was initiated. Like histone marks, CTCF assays required optimization across tissues. To date, successful CTCF antibody selection and immunoprecipitation has been performed in equine ovary. CTCF-ChIP-seq of the additional seven prioritized tissues is underway. ATAC-seq has been completed in equine liver, with lamina samples currently undergoing immunoprecipitation. To augment the efforts for equine functional annotation, seven laboratories also voluntarily conducted additional assays, including karyotype analyses, centromere mapping of fibroblast cells, reduced representation bisulfite sequencing (RRBS), fibroblast functional assays, and further phenotyping through sequencing of microbiome samples. The biobank was additionally leveraged to generate external funding of $40,000 for functional assays on the suspensory apparatus (PIs: Dr. Hamilton (University of Sydney) and Dr. Finno [co-PD] and Dr. Bellone [co-investigator]). Because of the “adopt-a-tissue” effort, we have also identified a set of tissues for which functional annotation will have the greatest impact on immediate research endeavors being conducted by members of the community. Additionally, USDA Species Coordinator Funds were appropriated for ChIP-seq analysis of equine spleen. Lastly, numerous breed associations have provided letters of support for this project. 3: Facilitate analysis, curation, storage, distribution and application of the enormous datasets now being generated by next-generation sequencing and related "omics" technologies with regard to animal species of agricultural interest. Datasets from whole-genome sequencing of the two mares (https://www.ebi.ac.uk/ena/data/view/PRJEB26698), mRNA-seq  (<a href="https://www.ebi.ac.uk/ena/data/view/ERA1487553">https://www.ebi.ac.uk/ena/data/view/ERA1487553</a>) and smRNA-seq (in submission) across 47 tissues from the two mares and reduced read bisulfate sequencing (RRBS) across 8 tissues (in submission) on the two mares is publicly available at EMBL-ENA. ChIP-seq data on the 8 prioritized tissues will be submitted by August 2019.   Communication:  The coordinators maintain an email list and use it to broadcast information for USDA-NRSP8, the USDA, the Havemeyer Foundation and other information relevant to the workshop.  In addition to the PAG conference, workshops are held once every two years at a Dorothy Russell Havemeyer Workshop and at a conference of the International Society for Animal Genetics.  Many of the NRSP8 members also participant in the biennial Equine Science Society Conferences.   Website:  A new website for the International Horse Genome program was set up including reports from the different meetings, identification of participants and tools.  The website can be found at:  <a href="https://horsegenomeworkshop.com/">https://horsegenomeworkshop.com/</a>   September 2019 Havemeyer International Equine Genome Workshop A workshop meeting was held in connection with this program. Details can be found at the following website:  <a href="https://havpav.com/">https://havpav.com/</a>   Summary of Additional Funding Reported in support of Equine Genomics to NRSP8 Stations and Affiliates: Based on 19 Stations reporting: 6 international and 13 US   Institution          Internal                          Industry                         Federal US                        $471134                          $1009327                        $978786 Internat'l $109304                          $695320                          $597004 Total                    $580518                          $1704647                        $1575790     ANNUAL REPORT OF MULTI-STATE RESEARCH ACTIVITY   PROJECT:  NRSP-8 PROJECT TITLE: NRSP-8 Sheep/Goats Species Committee PERIOD COVERED: January 1 to December 31, 2018 DATE OF THIS REPORT:  March 4, 2019 ANNUAL MEETING DATES: January 12-13, 2019   PARTICIPANTS:        Cornell University: Heather Huson* Louisiana State University:  James E. Miller*1 North Carolina A & T: Mulumebet (Meli) Worku*1 Oklahoma State University:  Udaya DeSilva* Pennsylvania State University:  Wansheng Liu* Texas A&M University: Clare Gill*1, Penny Riggs* University of Florida:  Raluca Mateescu* University of Idaho: Brenda Murdoch*1 University of Massachusetts-Amherst:  Janice Telfer*, Cynthia Baldwin* University of Vermont: Stephanie McKay*1 USDA/ARS: Michelle R. Mousel*, Stephen N. White* USDA ARS: Jennifer Woodward-Greene Utah State University:  Noelle E. Cockett* Virginia State University:  Brian Sayre*, Glenn Harris* Virginia Tech:  Rebecca Cockrum*1   *Voting member. 1In attendance at the 2018 NRSP-8 meeting.   BRIEF SUMMARY OF MINUTES OF ANNUAL MEETING:   The 2019 annual meeting of the NRSP-8 Cattle, Sheep, and Goat committee was held on Jan 12-13 in conjunction with the Plant and Animal Genome XXVII meeting.  The morning session of the scientific meeting on Jan 12th was held as a joint session in with the Swine Committee with a total of 8 presentations. These presentations included an overview of genome assembly tools and improvements, adaptability to high altitude, feature selection for genomic prediction, DNA methylation, breed of origin effects, and haplotypes affecting reproduction. The Saturday afternoon and Sunday morning sessions of the combined Cattle/Sheep/Goat workshops included 22 presentations covering a wide variety of topics, from the goat ADAPTmap, international bovine genomics consortia, Angus genomic selection, long noncoding RNAs linked to parasite immune responses of sheep, RNA editing, and microbiomics.  Attendance at the sessions was good with delegates from Academia, Industry and Governments representing more than 20 countries.  Additionally, there were 51 cattle and 20 sheep and goat posters presented.  Rebecca Cockrum was thanked for serving as President of the NRSP-8 Cattle, Sheep and Goat Committee in 2018-19.  Ben Rosen will serve as President in 2019-20. Erdogan Memili was elected as the 2019-2020 Secretary, and he will serve as President in 2020-2021.   ACCOMPLISHMENTS AND IMPACTS:   Objective 1: Advance the quality of reference genomes for all agri-animal species through providing high contiguity assemblies, deep functional annotations of these assemblies, and comparison across species to understand structure and function of animal genomes.   The Ovine FAANG Project represents state-of-the-art integrated functional annotation with genome assembly from the same individual. This project was based on collaborative work organized by many NRSP8 Sheep and Goat genomics members. This project includes performance of FAANG assays on tissues from the reference genome Rambouillet sheep. In so doing, this work will contribute to the core FAANG activities by provision of transcriptome data, detailed gene annotation, and multiple regulatory elements in the sheep genome.    Objective 2: Advance genome-to-phenome prediction by implementing strategies and tools to identify and validate genes and allelic variants predictive of biologically and economically important phenotypes and traits.   The genetics of goat scrapie resistance took a step forward when commercial genotyping services for the S146 and K222 mutations were released. An experimental challenge demonstrated that animals singly heterozygous for either PRNP S146 or K222 did not develop scrapie for times that now extend beyond the commercial lifetimes of many goats. The experiment is ongoing with a few very old animals to see how long

Publications

Impact Statements

Date of Annual Report: 03/16/2020

Report Information

Annual Meeting Dates: 01/11/2020 - 01/13/2020
Period the Report Covers: 10/01/2018 - 09/30/2019

Participants

Aquaculture NRSP-8 Report 2019
Coordinator: Benjamin J. Reading, North Carolina State University
Co-coordinators: Steven Roberts, Washington State University
Moh Salem, University of Maryland
Eric Peatman, Auburn University
Species Leaders:
Catfish: Sylvie Quiniou, ARS Stoneville, Mississippi,
Oyster/shellfish: Dina Proestou, ARS University of Rhode Island, Rhode Island
Salmonids: Yniv Palti, ARS Leetown, West Virginia
Striped Bass: Benjamin Reading, North Carolina State University, North Carolina
Workshop Chair 2019-2020: Louis Plough (lplough@umces.edu)
Workshop Chair-elect 2020-2021: Moh Salem (Mohamed.Salem@mtsu.edu)
Workshop Chair-elect 2021-2022: Rafet Al-Tobasei (Rafet.Al-tobasei@mtsu.edu)
Aquaculture Workshop
There were 17 oral presentations including presentations by 6 graduate students and postdocs who were presented with travel awards ($1000 each) and 3 invited plenary speakers.
Attendees
The number of attendees: 100 (80, 2019)
The number of institutes/organizations: 49 (43, 2019)
The number of countries: 13
Aquaculture dinner reception and poster session were sponsored in part by Illumina, National Breeding Program for the Hybrid Striped Bass Industry, and NC State University.
Participants: 80
Posters: 15 (20, 2019)

Bovine NRSP-8 Report 2019
COOPERATING AGENCY AND PRINCIPAL LEADERS
University of California, Davis: Alison Van Eenennaam, alvaneenennaam@ucdavis.edu
University of Missouri-Columbia: Bob Schnabel, Co-coordinator, schnabelr@missouri.edu
Texas A&M University, Clare Gill, Co-coordinator, clare-gill@tamu.edu
USDA ARS, Beltsville, Ben Rosen, Co-coordinator, Ben.Rosen@ars.usda.gov
Washington State University, Zhihua Jiang, Co-coordinator jiangz@wsu.edu
2020 Cattle Workshop Report
Workshop Chair 2019-2020: Ben Rosen (Ben.Rosen@ARS.USDA.GOV)
Co-Chair-elect 2020-2021: Darren Hagen (darren.hagen@okstate.edu)
Erdogan Memeli (em149@msstate.edu)
Co-Chair-elect 2021-2022 Cedric Gondro (gondroce@msu.edu).
International Plant and Animal Genome XXVIII Workshop Attendance:
Cattle/swine
Item Total
Attendees 170
Countries 18
U.S. - States 25
Affiliations 89
Cattle/sheep/goat 1
Item Total
Attendees 113
Countries 12
U.S. (States) 22
Affiliations 60
Cattle/sheep/goat 2
Item Total
Attendees 95
Countries 16
U.S. (States) 16
Affiliations 59

Poultry NRSP-8 Report 2019
NRSP-8 Poultry Annual Report October 1, 2018 – September 30, 2019
Poultry Genome Coordinators: Huaijun Zhou (UC Davis); Hans Cheng (USDA-ARS)
Chair: Kent Reed (University of Minnesota)
Secretary: Bindu Nanduri (Mississippi State University)
The NRSP-8 Poultry Workshop held January 11-12, 2020 in conjunction with NC1170 Poultry Workshop at the Plant & Animal Genome Conference, San Diego CA, and attendance overview:
• Attendance during the 1.5 day workshop averaged n=45 with peak attendance in excess of 90.
• Representatives of 16 agricultural experiment stations attended from across the US including the membership of NRSP-8 Poultry group: Iowa State, Michigan State, University of Arizona, University of Arkansas, Western University of Health Sciences, Mississippi State University, Univ of Delaware, Univ of Georgia, University of California Davis, University of Minnesota, Beckman Research Institute.
• Attendees also included members of the poultry layer and broiler breeding companies, and scientists from the United Kingdom, Germany, Canada, Sweden, Netherlands, Bangladesh, Australia and China.

NRSP-8 Equine 2019 Annual Report (Coordinator and Workshop)
Leadership:
Coordinators:
Ernest Bailey, University of Kentucky
Samantha Brooks, University of Florida
Molly McCue, University of Minnesota
NRSP8 Workshop:
Chair: Annette McCoy, University of Illinois
Co-chair: Mike Mienaltowski, University of California, Davis
2019 Equine Workshop Report
The workshop met Saturday afternoon (Jan 11, 2020) and Sunday morning (Jan 12, 2020) at the Plant and Animal Genome Conference in San Diego, CA.
Attendees:
January 12: 80
January 13: 55
Station Reports were provided by scientists from 20 laboratories including those at Cornell University, University of Florida, University of Kentucky, University of Louisville, University of Minnesota, Michigan State University, Illinois State University, University of Nebraska, Texas A&M University, University of California-Davis, Argentina, Brazil, Sweden, Denmark, South Korea and China.

NRSP-8 Sheep/Goats Species Committee Report
PARTICIPANTS:
Cornell University: Heather Huson*
Louisiana State University: James E. Miller*
North Carolina A & T: Mulumebet (Meli) Worku*1
Oklahoma State University: Udaya DeSilva*
Pennsylvania State University: Wansheng Liu*
Texas A&M University: Clare Gill*1, Penny Riggs*
University of Florida: Raluca Mateescu*
University of Idaho: Brenda Murdoch*1
University of Massachusetts-Amherst: Janice Telfer*, Cynthia Baldwin*
University of Vermont: Stephanie McKay*1
USDA/ARS: Michelle R. Mousel*1, Stephen N. White*1
USDA ARS: Jennifer Woodward-Greene
Utah State University: Noelle E. Cockett*1
Virginia State University: Brian Sayre*, Glenn Harris*
Virginia Tech: Rebecca Cockrum*1
*Voting member.
1In attendance at the 2019 NRSP-8 meeting.

Brief Summary of Minutes

Minutes Attachment:

NRSP-8 Business Meeting Minutes1.12.20.docx

Accomplishments

NRSP-8 2019 Annual Multispecies Report Summarizing the 2019 accomplishments of National Animal Genome Research Program (NRSP-8) is a tall order, given the productivity and prolificacy of this group of researchers from land-grant universities and research institutions throughout the nation. The importance of animal agriculture to the U.S. agricultural economy should be kept in perspective. In 2017, U.S. cash receipts were almost evenly divided between plant (52%) and animal agriculture (48%). <table width="100%"> <tbody> <tr> <td> </td> </tr> </tbody> </table> The value of agricultural production in the United States rose over most of the past decade due to increases in production as well as higher prices. In 2017, the cattle industry had the highest value of livestock production at roughly $50.2 billion.  The poultry industries were the next largest commodity with production valued at around $42.7 billion, followed by hogs and pigs at $19.2 billion. The value of milk production was about $38.1 billion. Cumulatively, the 2017 value of U.S. animal agriculture was > $151 billion. A major contributing factor to productivity increases (Figure 1) is the genetic improvement of animals through research. As outlined the newly published “Genome to phenome: improving animal health, production, and well-being–a new USDA blueprint for animal genome research 2018–2027<a href="#_ftn1" name="_ftnref1">[1]</a>”, NRSP-8 scientists across the country were instrumental in creating many of the genomic tools and resources that enabled genetic improvements such as: <ul> <li>The lifetime net merit (NM$) index, a gauge of dairy animal profitability, doubled over the past 10 years resulting in over $4 billion return (and counting) on a $100 million investment</li> <li>Poultry and swine and poultry breeding companies actively use genome information to accelerate genetic improvement by about 30%, resulting in considerable exports (Figure 2).</li> </ul> NRSP-8 is an umbrella organization of animal scientists who use genomics to provide solutions for the animal agriculture community. The membership of the NRSP-8 come from experiment stations throughout the nation AL, AR, AZ, CA, CO, DE, FL, IA, ID, IL, KY, MA, MD, MI, MN, MO, MS, NC, NE, NY, OK, PA, TX, UT, VA, VT, WA, WI, WY), non-land grant institutions (California State University, Fresno, City of Hope Beckman Research Institute, Middle Tennessee State University, National Research Institute of Animal Production, National University of La Plata, Norwegian University of Life Sciences, Racing Australia Equine Genetics Research Centre, Swedish University of Agricultural Sciences, The Laboratory of Racing Chemistry, Tufts University School of Veterinary Medicine, North Grafton, MA, University of Louisville, University of Sydney, USDA-ARS Beltsville Agricultural Research Center, USDA-ARS-Avian Disease & Oncology Laboratory, Western University of Health Sciences) and encompasses scientists from the dairy and beef cattle, poultry, equine, sheep, goat, swine, and aquaculture sectors. The impact of NRSP-8 on agriculture reaches every state and region of the U.S. The use of genomics to improve the genetics of US animal-based commodities has been adopted by nearly all the food and fiber animal-breeding industries for which tools have been developed.   The annual coordinator funds allocated to each NRSP-8 species group (including bioinformatics), help to provide critical infrastructure and tools for agri-animal genomic discoveries including; genomics and bioinformatics tools and databases, genetic resource populations with economically-important phenotypes, education and training of students, scientists, and outreach to the public.   Highlights and impacts summarized in this report for 2019 include: <ul> <li>Leveraging of $65,000 coordinator funds to attract new grants e.g. the aquaculture group attracted $7,532,332 in new funding. This equates to over a 1:115 return on investment for the coordinator funds. Other species groups report leveraging seed funding to secure millions of dollars in matching industry, state and federal funds.</li> <li>The improved poultry genome assemblies have allowed for the identification of genes associated with heat stress, aflatoxin, and disease resistance in poultry. Validation of these regions for commercial breeding stocks will allow significant improvements in resistance to diseases will help with selection of animals that can tolerate extreme environmental fluctuations, and avoid diseases that cost the poultry industry >$100 million annually in the absence of antimicrobial therapies.</li> <li>The new horse genome assembly has been used in a multitude of research projects, ranging from identification of genetic defects to the origins of the modern horse, with the equine species group publishing an impressive 88 papers in 2019.</li> <li>Collectively the NRSP-8 group of researchers are prolific with over 200 basic and applied peer-review papers published in 2019, in addition to multiple industry collaborations, and outreach.</li> <li>Graduate students and postdocs are being trained in genomics and bioinformatics by all species groups, and coordinator funds are being used to bring students to conferences and training events, including a bioinformatics training in advance of the NRSP-8 Annual Meeting at PAG, these students/postdocs will be the future leaders in agriculture-oriented computational science.</li> <li>Over 4,685 users worldwide subscribe and are informed by the AnGenMap email list serve (<a href="https://www.animalgenome.org/community/angenmap/">https://www.animalgenome.org/community/angenmap/</a>); and information about NRSP-8 is made publicly available through the <a href="https://www.animalgenome.org/">https://www.animalgenome.org/</a> website maintained at Iowa State University.</li> </ul> Aquaculture NRSP-8 Report 2019 Coordinator:             Benjamin J. Reading, North Carolina State University Co-coordinators:       Steven Roberts, Washington State University Moh Salem, University of Maryland Eric Peatman, Auburn University Species Leaders: Catfish:                       Sylvie Quiniou, ARS Stoneville, Mississippi, Oyster/shellfish:          Dina Proestou, ARS University of Rhode Island, Rhode Island Salmonids:                  Yniv Palti, ARS Leetown, West Virginia Striped Bass:               Benjamin Reading, North Carolina State University, North Carolina   Workshop Chair 2019-2020: Louis Plough (lplough@umces.edu) Workshop Chair-elect 2020-2021: Moh Salem (Mohamed.Salem@mtsu.edu) Workshop Chair-elect 2021-2022: Rafet Al-Tobasei (Rafet.Al-tobasei@mtsu.edu)   Aquaculture Workshop There were 17 oral presentations including presentations by 6 graduate students and postdocs who were presented with travel awards ($1000 each) and 3 invited plenary speakers. Attendees The number of attendees: 100 (80, 2019) The number of institutes/organizations: 49 (43, 2019) The number of countries: 13   Aquaculture dinner reception and poster session were sponsored in part by Illumina, National Breeding Program for the Hybrid Striped Bass Industry, and NC State University. Participants: 80 Posters: 15 (20, 2019)   Leveraged funds 4 small research projects were funded at $10,000 each for 2020 to provide preliminary data for grants: $40,000 (2019-2020); $30,000 (2018-2019).   Leveraged funds from diverse projects based on previously funded small research projects totaled more than seven million and a half dollars from federal sources in 2019.   Total Leveraged Funding in 2019: $7,532,332 This is over 1:100 return on investment for the aquaculture coordinator funds. Extramural funding agencies include NOAA, USDA NIFA, USDA AFRI, USDA Southern Regional Aquaculture Center and the Ratcliffe Foundation (non-profit). In particular the marine finfish and shellfish aquaculture initiatives of USDA and NOAA are to be thanked. There were 29 publications in 2019 including one in the journal Nature. Specific major activities include:   Catfish Channel catfish genome assembly refined with optical mapping; blue catfish genome assembly released. DNA methylation profiles revealed differential methylation patterns between the two genders that underlie sex determination.   Shellfish and Crustaceans Pacific white shrimp genome published; sequencing of whiteleg shrimp genome was initiated. Re-sequencing of wild and selected eastern oyster populations derived from multiple geographic regions along the US east Coast and Gulf of Mexico also were initiated. 600K and 50K SNP chips developed for eastern oyster were applied to different populations and RNA-seq analyses are ongoing to understand genomic basis for Dermo-resistance in Eastern Oyster. Three Eastern Oyster workshops were held: Epigenetics Workshop, Genome Workshop, Breeding Consortium Round Table.   Trout and Salmon Genome assembly of doubled-haploid rainbow trout based on PacBio long read sequencing and scaffolding with Bionnano optical map and Hi-C contact map; genome assembly for Atlantic salmon is in progress using the tri-binning approach; Genome resequencing is underway in Chinook salmon and steelhead for broad representation of genomic variation across populations for each species. Genome-wide association studies identified genomic loci that affect fillet firmness, protein content, egg quality, fecundity, and egg size in rainbow trout. Allelic variation for candidate genes associated with migration timing/age at maturity was validated with markers in over 50,000 Chinook salmon and 20,000 steelhead. Contributions were made to development of FishGen.net database for storage of large-scale genotypes for genetic tagging and monitoring studies   Striped Bass The second striped bass genome draft was uploaded to GenBank; transcriptome data is currently being processed by NCBI for annotation. A machine learning pipeline developed to analyze single nucleotide (SNP) markers (expressed quantitative trait loci, eQTL) related to growth in different strains of hybrid striped bass. Different and novel machine learning-based analytical platforms are focused on small molecule (metabolomics), gene expression (RNA-Seq), and protein (proteomics) profiling to better understand hybrid striped bass growth performance (heterosis effects) and reproductive success in several different wild stocks of striped bass in watersheds of the mid-Atlantic region. Different strains of white bass from the midwest were assembled to establish a base breeding population for familywise evaluations of growth and nutrient utilization on alternative, sustainable diets; genotyping-by-sequencing panel was developed from these white bass populations. Genetically improved striped bass and white bass transferred to industry from National Breeding Program for the Hybrid Striped Bass Industry.   Bovine NRSP-8 Report 2019   COOPERATING AGENCY AND PRINCIPAL LEADERS University of California, Davis: Alison Van Eenennaam, <a href="mailto:alvaneenennaam@ucdavis.edu">alvaneenennaam@ucdavis.edu</a> University of Missouri-Columbia: Bob Schnabel, Co-coordinator, <a href="mailto:schnabelr@missouri.edu">schnabelr@missouri.edu</a> Texas A&M University, Clare Gill, Co-coordinator, <a href="mailto:clare-gill@tamu.edu">clare-gill@tamu.edu</a>  USDA ARS, Beltsville, Ben Rosen, Co-coordinator, <a href="mailto:Ben.Rosen@ars.usda.gov">Ben.Rosen@ars.usda.gov</a> Washington State University, Zhihua Jiang, Co-coordinator <a href="mailto:jiangz@wsu.edu">jiangz@wsu.edu</a>   2020 Cattle Workshop Report Workshop Chair 2019-2020: Ben Rosen (<a href="mailto:Ben.Rosen@ARS.USDA.GOV">Ben.Rosen@ARS.USDA.GOV</a>) Co-Chair-elect 2020-2021:     Darren Hagen  (<a href="mailto:darren.hagen@okstate.edu">darren.hagen@okstate.edu</a>) Erdogan Memeli (<a href="mailto:em149@msstate.edu">em149@msstate.edu</a>) Co-Chair-elect 2021-2022      Cedric Gondro (<a href="mailto:gondroce@msu.edu">gondroce@msu.edu</a>).   International Plant and Animal Genome XXVIII Workshop Attendance:   Cattle/swine <table> <tbody> <tr> <td width="175"> Item </td> <td width="141"> Total </td> </tr> <tr> <td width="175"> Attendees </td> <td width="141"> 170 </td> </tr> <tr> <td width="175"> Countries </td> <td width="141"> 18 </td> </tr> <tr> <td width="175"> U.S. - States </td> <td width="141"> 25 </td> </tr> <tr> <td width="175"> Affiliations </td> <td width="141"> 89 </td> </tr> </tbody> </table>   Cattle/sheep/goat 1 <table> <tbody> <tr> <td width="175"> Item </td> <td width="141"> Total </td> </tr> <tr> <td width="175"> Attendees </td> <td width="141"> 113 </td> </tr> <tr> <td width="175"> Countries </td> <td width="141"> 12 </td> </tr> <tr> <td width="175"> U.S. (States) </td> <td width="141"> 22 </td> </tr> <tr> <td width="175"> Affiliations </td> <td width="141"> 60 </td> </tr> </tbody> </table>   Cattle/sheep/goat 2 <table> <tbody> <tr> <td width="175"> Item </td> <td width="141"> Total </td> </tr> <tr> <td width="175"> Attendees </td> <td width="141"> 95 </td> </tr> <tr> <td width="175"> Countries </td> <td width="141"> 16 </td> </tr> <tr> <td width="175"> U.S. (States) </td> <td width="141"> 16 </td> </tr> <tr> <td width="175"> Affiliations </td> <td width="141"> 59 </td> </tr> </tbody> </table>       Objective 1: “Advance the status of reference genomes for all species, including basic annotation of worldwide genetic variation, by broad sequencing among different lines and breeds of animals.”   We generated >1M pass filter CCS reads for 12 tissues (total CCS reads 14.6M), which produced an average of 50k polished high-quality isoforms per tissue using IsoSeq3 analysis protocol.  Tissues were from the 180d gestation Dominette fetus and included Abomasum, Adipose (SubQ), Adrenal Cortex, Cerebellum, Frontal Cortex, Kidney, Liver, Lung, Lymph Node, Skeletal Muscle, Thyroid, Tongue. We plan to do an analysis including all data to find total number of unique isoforms across all tissues, but it is computationally intensive so we have been waiting for the server to have a relatively idle period.  The data are being shared with Jim Reecy to perform analysis/comparison with adult tissues and across species (Tim Smith, US MARC).   We also generated 15 PromethION flow cells of data for the Angus_x_Brahman fetus, producing 301 Gb of data including the one flow cell run at UC Davis.  Ben Rosen has run an assembly of just the nanopore data to see how it would compare to the PacBio assembly. Initial contig (highly confident, uninterrupted sequence assembly) N50 for Angus and Brahman PacBio assemblies were 29.4 Mb and 23.4 Mb respectively. Preliminary results of the nanopore only assembly are encouraging, with these lengths more than doubling to 69.8 Mb and 71.8 Mb respectively..  Total data is >450x coverage, so we are hopeful that the assembly of sex chromosomes will be greatly improved.  We only got about 5x coverage of reads >100 kb, was hoping for more but DNA quality was a bit limiting due to age of the sample and shipping from Australia (Tim Smith, US MARC).   We also generated >60M reads (FAANG standard) RNAseq for each of the fetal tissues that had IsoSeq, for quantitation purposes (Tim Smith, US MARC).   Bovine Y-Chromosome Since January of 2019 Brenda Murdoch from the University of Idaho ran 25 cycles of cells for chromosome isolation and fluorescence-activated cell sorting (FACS) preparation. Thirteen of these trails have been done with cultured white blood cells isolated from whole blood, and twelve have been done with a fibroblast cell line. Chromosome samples were initially sent for fluorescence-activated cell sorting (FACS) at Stanford’s FACS facility; however, several FACS trials did not return an adequately isolated sample, and the project has begun implementation of a magnetic streptavidin-bead capture method as an alternative to FACS. DNA has been extracted from isolated chromosomes and sent to Tim Smith for validation of enrichment.  This project is ongoing (Brenda Murdoch, University of Idaho).    Wansheng Liu at Penn State reported in previous years that two of the lost Holstein Y lineages, namely ZIMMERMAN ALSTAR PILOT (born in 1954) and ROSAFE CALIBAN (born in 1953), were recovered and produced 3 and 5 male offspring, respectively. We have completed the evaluation of these young bulls and submitted a manuscript to J. Dairy Sci. Here is the abstract of this paper: More than 99 percent of all known Holstein artificial insemination bulls in the United States can be traced through their male lineage to just two bulls born in the 1950s and all Holstein bulls can be traced back to two bulls born in the late 1800s. As the Y-chromosome is passed exclusively from sire to son, this suggests there is limited variation for much of the Y-chromosome and that there has been significant loss of genetic diversity in the artificial insemination era. Two additional male lineages that are separate from modern lineages prior to 1890 were present at the start of the artificial insemination era and had semen available from the USDA–National Animal Germplasm Program; semen from representatives of those lineages were used for in vitro  embryo production by mating to elite modern genetic females, resulting in the birth of seven bulls and eight heifers. Genomic evaluation of the bulls suggested that lineages from the beginning of the AI era could be reconstituted to breed average for total economic merit in one generation when mated to elite females due to high genetic merit for fertility, near average genetic merit for fat and protein yield, and below average genetic merit for udder and physical conformation. Semen from the bulls is commercially available to facilitate Y-chromosome research and efforts to restore lost genetic diversity. Sequence and Assembly of the Holstein Y Chromosome. The objective of this study was to sequence and assemble the Holstein Y by using multiple types of whole genome sequencing data from a single bull. The sequence data sets include the illumina paired-end (PE), illuminia mate pair (MP), PacBio long reads (PB), and Dovetail Chicago reads (Hi-C). The initial contigs was assembled from the PE reads. The total length of the contigs was 17.3M. Then the contigs were scaffolded with MP reads, and the total length was 19.2 M with the largest contig increased from 36K to 123K. The gaps of the scaffolds were filled with PB reads, and the total scaffold length was improved into 24.2M. At last the scaffolds were improved by Hi-C reads, and the final assembly was 24.3Mb with 7208 contigs, and the N50 is 7618 bp. Gene annotation indicated that all 12 known X-degenerate (Xd) and 5 known Y-ampliconic (Ya) genes are present in the draft Holstein Y assembly, and the copy number of these Y-linked genes were estimated. Differing from the Hereford Y, we found that RBMY and UBE1Y genes are multicopy in the Holstein Xd region.   Functional Annotation of Animal Genomes (FAANG) initiative Brenda Murdoch from the University of Idaho completed the collection of fetal cattle tissues from four (3 males and 1 females) 14 month old Line 1 Hereford animals. The samples from eight tissues (skeletal muscle, liver, adipose, spleen, hypothalamus, brain cortex/whole, cerebellum, and lung) from the animals have been collected for RNA-Seq, DNase-Seq, ATAC-Seq, ChIP-Seq, DNA-methylation, Hi-C and other assays. Data are being integrated to functionally annotate regulatory elements within the bovine genome. We expect that the FAANG cattle initiative will be significantly expanded with added collaborations and assays supported by the recent FAANG Program Area NIFA funding (Brenda Murdoch, University of Idaho).   Wansheng Liu at Penn State oversees the bovine tissue RNA extraction and RNA-seq and small RNA-seq library construction and sequencing (at Zoetis). The accomplishments for the cattle FAANG project in 2019 are summarized below. This project seeks to generate high quality transcript and chromatin status datasets from a comprehensive set of assays in tissues collected from animals closely related to Dominette L1, the individual from which the reference genome was sequenced. Moreover, multiple developmental stages, mammary gland tissue from Holstein cows, and cultured cells are being evaluated for a wide-ranging list of agriculturally important tissues/cell types. So far, transcriptomic data, including RNA-seq, small RNA-seq, and ATTS-seq has been collected from two biological replicates of 28 adult tissues and 10 fetal tissues. Current datasets include 65 ATTS libraries with a total of 388M sequenced reads, 123 RNA-seq libraries, and 123 small RNA-seq libraries. Analysis of these data will provide a comprehensive characterization of the expressed regions of the genome as well as accurate comparisons of differential gene expression across multiple tissues that will be harnessed for the identification of regulatory elements active in the bovine genome (Wansheng Liu, Pennsylvania State University). .   Identify relationships between sensor data and feed intake in Holstein dairy cattle.  Associations were identified between adjusted daily dry mater intake (i.e. feed intake) and health events with rumen bolus pH, temperature and activity and ear tag temperature, activity and rumination measurements from two ear tag technologies (P < 0.05).  Daily changes in feed intake were estimated in response to animal health events to determine the daily impact on feed intake.  The impact of ambient temperature on feed intake and health events was also evaluated.  Results indicate automated sensor traits act as indicators of feed intake. Health events appear to have long lasting influence on sensor trait and feed intake phenotypes.  Objective 1b: Participation in national effort to develop a feed efficiency genetic evaluation in US dairy cattle.  Feed intake was collected on 48 lactating cows in 2019 towards the goals and objectives of the FFAR/ CDCB funded project:  Improving dairy feed efficiency, sustainability and profitability by impacting farmers’ breeding and culling decisions, headed by lead PI Dr. Mike Vandehaar at Michigan State University.  This research program links the use of molecular and quantitative genetics data as well as new high-throughput phenotyping technologies for use in applied animal breeding by AI companies and breeders (James Koltes, Iowa State University).   Characterization of the bovine PRAMEY protein in testis, epididymis and spermatozoa. We reported last year the characterization of PRAMEY protein dynamic in spermatozoa, fluid and tissues from testis and caput and cauda segments of the epididymis by western blot with a PRAMEY-specific antibody. We continued to work on this project in 2019 to further study the potential role of PRAMEY during sperm capacitation and acrosome reaction, and we hope to complete this work in 2020 (Wansheng Liu, Pennsylvania State University). Determine the functional role of PRAME in spermiogenesis using a Prame-knockout (KO) mouse model. We continued to work on the KO mouse models to study the functional role of PRAME during spermiogenesis. We have finished the characterization of the Prame cKO mice and found that the cKO mice are fertile with a distinctively reproductive phenotype,  i.e. the testis size (P<0.01) and sperm count (P<0.05) are significantly reduced by 12% at 4 months of age when compared to the Prame floxed mice. Histological, immunofluorescence with germ cell-specific markers and TUNEL analyses of testis cross-sections at postnatal day 7 (P7), P14, P21, P35, P120, and P365 indicated a significant increase in apoptotic germ cells at P7 and P14, and an increase in abnormal seminiferous tubules at P21 and P35. Germ cells were gradually lost resulting in two different phenotypes in the Prame cKO testes: Sertoli-cell-only (SCO) for some of the affected tubules in young mice (at P35) and germ cell arrest at spermatogonia stage for other affected tubules in mature mice. Both phenotypes were a consequence of disruption in RAR signal pathway by the depletion of Prame at a different time point during the first and subsequent rounds of spermatogenesis. The results suggest that Prame plays a minor, but important role in spermatogenesis and different paralogs in the Prame gene family may be functionally and partially redundant (Wansheng Liu, Pennsylvania State University). Generated high –throughput RNA sequence of microRNAs from 74 longissimus lumborum biopsies from F3 Bos indicus x Bos taurus steers.  These sequence data are coupled with extensive meat and carcass phenotypes (Penny Riggs, Texas A&M).   Objective 2: “Develop strategies to identify and exploit genes and allelic variation that contribute to economically relevant phenotypes and traits, in part through improving functional annotation of the genomes of our species.” Genetic associations with antral follicle count in beef cattle Antral follicle number was counted on 216 heifers from the University of Idaho’s Nancy M. Cummings Research, Education and Extension Center. The heifers used were between 10 and 14 months at the time of sampling and samples were taken during two different years, 70 from year one and 146 from year two. The herd is a crossbred herd with sires from Angus, Hereford, Simmental, and SimAngus breeds. Antral Follicle Count (AFC) was determined using an ultrasound probe with follicles greater than 3mm in diameter being recorded. The Bovine 50K GGP Single Nucleotide Polymorphism (SNP) marker chip and then was imputed up to 850K SNP markers (with Bob Schnabel). The most significant SNPs are located on chromosome 23 and 2 and are located in regions with genes of biological significance to AFC as they affect transcription, anti-apoptosis, intracellular calcium levels, angiogenesis, energy production/metabolism, and cell proliferation (Brenda Murdoch, University of Idaho).   Single cell RNA-sequencing Single cell RNA-sequencing was performed in fetal gonads at 35 and 49 days of gestation.  Gonads were collected from fetuses recovered from timed-pregnant heifers, two male fetuses were used for day 35 collection and one male fetus for day 49. The genital ridge/gonad was dissected and dissociated to achieve a single cell suspension, which was then cryopreserved until single-cell library preparation. On September 10th, 4,000 and 12,000 cells corresponding to day 35 and 49 samples, respectively, were submitted to the UC Davis Genome Center for 10X Genomics Chromium single Cell RNA-seq preparation. The libraries were sequenced in a single HiSeq4000 lane. Sequencing data is being processed to assess library quality. Another sequencing lane is expected to be necessary to achieve sufficient read coverage. (Pablo Ross, UC Davis).   Ovaries were harvested immediately after slaughter of heifers at days 35 and 49 of gestation and transported to the laboratory.  Small fragments of ovarian cortex from the first heifer (slaughtered on 8/14/19) were cryopreserved at -80 °C in medium composed of 90% fetal bovine serum and 10% DMSO immediately after slaughter, and the cell isolation procedure was performed in thawed tissue. For the second heifer (slaughtered on 8/27/19), fresh ovarian tissue was processed into a single cell suspension, and the cells were then cryopreserved in the same freezing medium and temperature until sequencing. Preparations of cell suspension: ovarian cortex was cut into fragments of approximately 5 mm and processed into a single cell suspension. The cell suspension was then filtered through a 100 mm and 40 mm cell strainers, centrifuged at 300g for 5 minutes and resuspended in 1mL of HBSS with 0.04% (v/v) BSA. Trypan blue cell viability test was used to ensure at least 80% cell viability before and after thawing. Cell suspensions were transported in ice to the Genome Center for 10X Genomics Chromium single Cell RNA-seq preparation on 9/6/2019 and 9/10/2019. Libraries were sequenced in a single HiSeq4000 lane. (Anna Denicol, UC Davis)   Single-cell transcriptome analysis of germ cells at postnatal day 7 from Prame cKO and floxed mice. Cells from the entire testis of 3 Prame cKO and 1 WT mice at P7 were subjected to single-cell RNA-seq using 10X Genomics. Approximately 4000 cells from each sample and 130K reads (pair-end, 100 bp per read) per cell were obtained and analyzed. All cells in the P7 testis were clustered into 5 clusters based upon the transcriptome profile. Cell type in each cluster was identified by germ cell-specific markers, such as Nanos3 and c-Kit. Sertoli and other non-germ cells were clustered in groups II and V. All germ cells were clustered in three groups: undifferentiated (III) and differentiated spermatogonia (I) and an undefined cluster of germ cells (IV). Interestingly, Cluster IV shows substantial difference between the cKO and WT mice. The proportion of Cluster IV cells was 5% in the WT testis, while 8.3% in average (6-10%) in cKOs. (Wansheng Liu, Pennsylvania State University).   Work towards this objective involves studies characterizing a major gene for bovine ovulation rate in cattle.  Current work involves creating a de novo sequence assembly of a homozygote for the allele which will be used to identify the probably variant.  The variant will be validated by creating a cell line containing the putative causative polymorphism using gene editing and verifying the mutations effect on gene expression (Brian Kirkpatrick, University of Wisconsin)   Objective 3: “Facilitate analysis, curation, storage, distribution and application of the enormous datasets now being generated by next-generation sequencing and related "omics" technologies with regard to animal species of agricultural interest.”   NRSP8 Bioinformatics Training Workshop @PAG supported by Bovine Coordinator Funds Provided $3,000 support to the Workshop as well as covered registration for 6 students, and travel costs for 5 graduate students to attend PAG.   A pilot study was done to better understand what aspects of the maternal environment influence the developing rumen microbiome in calves. Currently, samples from this study have been collected and 16S amplicon sequencing of the microbial DNA is complete. Bioinformatic analysis is currently ongoing where I am training 2 M.S. students and 1 Ph.D. to utilize these tools of metagenomic sequencing to characterize the microbiome. (Hannah C. Cunningham-Hollinger, University of Wyoming)   The effect of the rumen microbiome and the effects on feed efficiency is a major theme in our lab. Utilizing Next Generation Sequencing of the rumen microbiome, we are able to characterize not only what microbes are present but also their functional role. Recent studies investigating the maternal factors that impact early colonization of the rumen microbiome have been underway.  The long-term potential impact is discovering management, feeding, or other intervention strategies that may allow for programming of the microbiome to improve efficiency in offspring later in life.  This project was funded by the Wyoming INBRE ($10,000) (Hannah C. Cunningham-Hollinger, University of Wyoming)   While the DNA samples we collect are not necessarily from the host but rather used to identify microbial communities at various locations (rumen, vagina, placenta, etc.) these samples are coupled with phenotypic information and will be used to develop selection tools based on the microbiome to select for improved efficiency. Host genetics plays a critical, however, the rumen microbiome has a strong connection to feed efficiency and as such should also be considered when making selection decisions (Hannah C. Cunningham-Hollinger, University of Wyoming)   Recent work has been published utilizing key microbial taxa to predict feed efficiency in sheep. There is an effort in our lab to utilize various data sets that have GrowSafe feed intake data and rumen microbiome data, to evaluate the use of this strategy in beef cattle. This has the potential to predict efficiency based on the rumen microbiome and/or to understand which microbes are most critical in animals with desirable feed efficiency. There are various new sequencing techniques that make the possibility of chute-side testing a reality (MinION, iSeq, etc.). It is imperative that a host of candidate microbial populations be well established so this chute-side testing can be effective and beneficial (Hannah C. Cunningham-Hollinger, University of Wyoming)   Impacts <ul> <li>There are now several high quality “reference” genomes for major cattle breeds, which has open up the possibility of developing a pangenome. Several groups have recently used this data to develop successful grants to develop tools to develop a bovine pangenome. This will be a more generally useful resource for industry as compared to a single reference genome.</li> <li>This has also revealed New insights into mammalian sex chromosome structure and evolution using high-quality sequences from bovine X and Y chromosomes</li> <li>Genomic data is being used widely in both the beef and dairy industry for genomic prediction</li> </ul>   Funding Secured: <ul> <li>2019-2020 University of Wyoming Agricultural Experiment Station Competitive Grant Program. Late gestation maternal nutrition influence on the developing rumen microbiome in cattle. Funded. $9,866.64. (Hannah C. Cunningham-Hollinger, University of Wyoming)</li> <li>2019-2020 Private industry funding. Investigations of RumaCell on post-weaned calf performance, efficiency, rumen microbiome, and coccidia prevalence. Funded by Pacer Technology. ($20,000) (Hannah C. Cunningham-Hollinger, University of Wyoming)</li> <li>2018-2019 Wyoming INBRE Sequencing and Bioinformatic Analysis Program. Survey of the maternal/reproductive microbiomes influence on the neonatal rumen microbiome in cattle. Funded. $8,594.72 (Hannah C. Cunningham-Hollinger, University of Wyoming)</li> <li>Prenatal Stress Modulation of the Hypothalamic-Pituitary- Adrenal Axis and Telomere Length, Funded by USDA NIFA (May 1, 2019 - April 30, 2021), awarded May 1, 2019 (Funded - In Progress, Spring 2019, PI Thomas Welsh with CoPI Charles Long, CoPI David Riley, CoPI Penny Riggs, CoPI Rodolfo De Carvalho Cardoso, CoPI Ronald Randel</li> <li>IPA at the US Department of the Interior (October 1, 2018 - August 31, 2019), awarded October 2, 2018 ($191,030.00), Completed, Summer 2019, PI Penny Riggs</li> <li>Pilot Project to Develop Feasibility Data for Bovine Germline Complementation. Rustici Rangeland and Cattle Research Endowment Grant. $50,000 A.L. Van Eenennaam (PD) 1/1/2019 – 12/31/2019</li> <li>Functional Annotation of the Bovine Genome; 2018-67015-27500; P. Ross (PI), H. Zhou, J. Medrano et al; 1/15/2018-1/14/2022;. $2,500,000.</li> </ul>     Poultry NRSP-8 Report 2019   NRSP-8 Poultry Annual Report October 1, 2018 – September 30, 2019 Poultry Genome Coordinators: Huaijun Zhou (UC Davis); Hans Cheng (USDA-ARS) Chair: Kent Reed (University of Minnesota) Secretary: Bindu Nanduri (Mississippi State University) The NRSP-8 Poultry Workshop held January 11-12, 2020 in conjunction with NC1170 Poultry Workshop at the Plant & Animal Genome Conference, San Diego CA, and attendance overview: <ul> <li>Attendance during the 1.5 day workshop averaged n=45 with peak attendance in excess of 90.</li> <li>Representatives of 16 agricultural experiment stations attended from across the US including the membership of NRSP-8 Poultry group: Iowa State, Michigan State, University of Arizona, University of Arkansas, Western University of Health Sciences, Mississippi State University, Univ of Delaware, Univ of Georgia, University of California Davis, University of Minnesota, Beckman Research Institute.</li> <li>Attendees also included members of the poultry layer and broiler breeding companies, and scientists from the United Kingdom, Germany, Canada, Sweden, Netherlands, Bangladesh, Australia and China.</li> </ul> Poultry Coordination funds partially supported a total 11 scientists attending the workshop. The 2020 poultry Jorgensen Travel award winner Nnamdi Ekesi was then introduced and each gave a lightning talk on their area of research. Finally, we had 4 junior scientists given 2 minutes lightning talks about their research. Grants University of Arkansas: <ul> <li>Empowering US broiler production for transformation and sustainability; USDA-NIFA Sustainable Agriculture Systems; 9/2019 - 8/2024; $9,919,300; PD Bottje CoPIs Dridi, Rochell, Hargis, Erf, Kong, Kidd, Kuenzel, Owens, Kwon, Sun, Rhoads, Alrubaye, Tabler (MS), and others.</li> <li>Global expression pathway analysis training: target obesity. Chancellor’s Discovery, Creativity, Innovation, and Collaboration Fund. 9/2017-7/2019; $76,500; PI: W. Bottje CoPI: D. Rhoads, B. Kong.</li> </ul> Douglas Rhoads, Univ of Arkansas: <ul> <li>Validation of a SNP panel for breeding against ascites in broilers. NIFA-AFRI; 3/2018-2/2021; $500,000; PI: Rhoads</li> <li>Evaluation of Zinpro micronutrients for protection against BCO lameness and improving bone health for broilers raised on litter flooring with bacterial challenge. Zinpro; 2/2018-12/2018; $47,797; PI: Rhoads</li> <li>Whole Genome Resequencing to Identify Genetic Determinants of Resistance to Bacterial Chondronecrosis with Osteomyelitis Leading to Lameness. Cobb-Vantress, Inc; 9/2018-8/2019; $55,846; PI: Rhoads</li> </ul> Wayne Kuenzel, Univ of Arkansas: <ul> <li>Antistress compounds as effective tools for addressing chronic stress. Arkansas Biosciences Institute. 7/2018 to 6/2019; $50,000; PI: W. Kuenzel, Co-PIs: S. Krishnaswamy, S.W. Kang.</li> </ul> Byung-Whi Kong, Univ of Arkansas: <ul> <li>Gene editing and transgenic poultry production. Chancellor’s Discovery, Creativity, Innovation, and Collaboration Fund. 7/01/2019-6/30/2021; $115,665; PI: B. Kong CoPI: W. Kuenzel.</li> <li>Determination of roles of mitochondrial small RNAs in metabolic disease phenotypes using isocitrate dehydrogenase 2 (IDH2) knock out mouse and genetically selected chicken models. Arkansas Bioscience Institute. 7/2017-6/2020; $148,500; PI: B. Kong.</li> </ul> Huaijun Zhou, University of California, Davis: <ul> <li>Genomics for improving animal production; USDA NIFA National Need Training Grant 2014-38420-21796; H. Zhou, J. Murray, P. Ross;$238,000.</li> <li>Genomic Editing for Enhanced Animal Production; USDA NIFA National Need Training Grant; P. Ross, H. Zhou., J. Murray; $238,000.</li> <li>Improving food security in Africa by enhancing resistance to disease and heat in chickens; Feed the future innovation lab for genomics to improve poultry; USAID AID-OAA-A-13-00080; H. Zhou, S. J. Lamont, J. Dekkers etc; $5,000,000.</li> <li>Functional Annotation of the Swine Genome;2018-67015-27501;C. Tuggle (PI), H. Zhou, et al; 1/15/2018-1/14/2022; $2,500,000.</li> <li>High throughput characterization of gene transcript variants by full-length single-molecule sequencing to improve farm animal genome annotation; P. Ross(PI), H. Zhou, J. Mendaro; 1/1/2017-12/31/2019; $460,000.</li> <li>Genome wide identification and annotation of functional regulatory regions in livestock species; 2015-67015-22940;H. Zhou (PI), P. Ross, I. Korf; 1/1/2015 – 12/31/2019; $500,000.</li> </ul> Susan Lamont, Iowa State University: <ul> <li>US-UK Collaborative Research: Host Resistance to Avian Pathogenic E. coli. USDA-NIFA-AFRI/BBSRC; $499,999.</li> <li>Industry funding: Aviagen Limited, EW Group, Hy-Line, International.</li> </ul> Jack Dekkers, Iowa State University: <ul> <li>Industry Funding: Iowa Egg Industry Center</li> </ul> Marcia Miller; Beckman Research Institute, CA: <ul> <li>MHC-Y-Directed Immune Responses during colonization of Chickens by Campylobacter; USDA NIFA; Grant No. 2016-10247; 06/01/2017-05/31/2020; $387,518.00.</li> </ul> Kent Reed, Univ of Minnesota: <ul> <li>USDA National needs fellowship for enhancing animal production: Addressing national need in poultry production; USDA-NIFA-NNF; 2016-2021; $241,000; PI: Reed.</li> </ul> Hans. H. Cheng, USDA-ARS: <ul> <li>ARS CRIS Project, Employing Genomics, Epigenetics, and Immunogenetics to Control Diseases Induced by Avian Tumor Viruses.</li> <li>ARS CRIS Project, Genetic and Biological Determinants of Avian Herpesviruses Pathogenicity, Transmission, and Evolution to Inform the Development of Effective Control Strategies.</li> <li>USDA, AFRI, award no. 2017-05741, Genomic screens to identify regulatory elements with causative polymorphisms accounting for Marek’s disease genetic resistance in chicken. PI, Cheng; co-PIs, Erez Lieberman Aiden (Baylor) and Bill Muir (Geneysis Bioinformatic Services). $498,116.</li> </ul>     Impacts <ul> <li>Our members are highly focused on fundamental, translational and applied research to benefit U.S. Agriculture and through genomics improve poultry health and contribute to the productivity of the relevant industries. Below are listed some of the highlights from 2018-19 research. Many of the efforts are focused on projects that directly impact poultry health and production.</li> <li>We have been using the existing assemblies for high resolution (10 kb regions) QTL mapping through whole genome resequencing. We have mapped 42 regions for ascites and 11 regions for bacterial resistance.  We are working with primary breeding companies to validate these regions and to expand the analysis to commercial products.  Validation of these regions for commercial breeding stocks will allow significant improvements in resistance to two diseases that cost the industry >$100 million annually.</li> <li>Additional data have been published to support our proposed suggestion that the nucleus of the hippocampal commissure (NHpC) be added to the classical hypothalamo-pituitary-adrenal (HPA) axis in avian species due to its early activation of corticotropin releasing hormone gene expression within that structure following an imposed stressor.</li> <li>Providing new molecules and additional key mechanisms into the cellular pathways for muscle growth and muscle mass development in breast muscle of broilers will improve production efficiency and hopefully prevent metabolic myopathy such as ‘woody breast’.</li> <li>Identification of genes that are associated with resistance to heat stress and Newcastle disease virus and can be used to genetic enhancement of disease resistance of chicken in adaption to hot climate.</li> <li>Knowledge of genes associated with enhanced immune response may inform further information on vaccine efficacy in poultry production.</li> <li>ChIP-seq and ATAC-seq assays developed and other omic data generated for regulatory elements annotation will be important for animal genome community.</li> <li>Genetic variation was characterized in commercial, research and indigenous lines of chickens.</li> <li>Genes, pathways and genomic regions associated with important biological traits in chickens were identified.</li> <li>The feasibility of applying molecular genetics and genomics to analysis of variation in structure, function and gene expression within the chicken genome was demonstrated.</li> <li>The improved typing method makes it feasible to expand efforts to understand the impact of MHC-Y genetic variability on immunity and disease resistance in chickens.</li> <li>Evidence continues to accumulate supporting the likelihood that MHC-Y contributes to the genetics of immune responses in chickens.</li> <li>Identification of molecular mechanisms associated with altered muscle development will result in development of mitigation strategies based on improved genetic selection, nutritional intervention, and other strategies to improve poultry muscle food quality and quantity.</li> <li>AFB1 causes annual industry losses estimated in excess of $500 M. Increasing innate resistance to AFB1 could result in numerous health benefits. Transformational improvements in AFB1 resistance require a multidisciplinary approach to identify protective alleles with potential to reduce disease.</li> <li>Genetic markers to improve AFB1-resistance have a potentially high commercial value and positive economic impact to industry, owing to improvements in health and well-being, productivity, and a safer product for consumers.</li> <li>The gastrointestinal health of an animal is key to its successful growth and development. Elimination of sub therapeutic antibiotics for growth promotion and health in poultry will leave a critical void. This project will improve our mechanistic understanding of host-microbiome interactions in the avian host, and identify feasible approaches towards modulating the turkey intestinal microbiome resulting in enhanced health and performance.</li> <li>Determining the purity of tumor samples has aided our efforts to identify Ikaros and other candidates as the first driver genes for MD. This supports our hypothesis that somatic mutations are required in addition to MDV infection to get tumors in susceptible birds.</li> <li>The TCR genes and usage play a role in response to MDV infection. As the TCR interactions with the MHC, this makes sense as the MHC has a major influence on MD genetic resistance.</li> <li>Advancement in understanding the underlying genetic and epigenetic factors that modulate vaccine efficacy would greatly improve the development of strategy in design of new vaccines, and therefore better control of the disease. The findings that MD vaccines-induced differentially expressed microRNAs in primary lymphoid organ, bursae, suggest the epigenetic factors are highly likely involved in modulating vaccine protective efficacy in chicken.</li> <li>Functionally annotating the chicken genome will benefit research in agricultural animals. Epigenetic modifications such as histone tail modifications and DNA methylation are not only key to the regulation of unique transcriptome patterns, these modifications are indispensable as genome annotators to uncover cell- and tissue-specific regulatory elements. Uncovering the location of regulatory elements and determining their interactions will provide the necessary framework to understand how regulatory networks govern gene expression and how genetic and environmental influences alter these networks to impact animal growth, health and disease susceptibility or resistance.</li> <li>HPIDB (https://hpidb.igbb.msstate.edu/) allows agricultural researchers to predict host-pathogen protein-protein interaction (HPI) data for proteins of their interest, where none exist in the literature. This in turn allows researchers to interrogate high through put datasets (RNA-Seq and proteomics) in the context of HPI to better understand infectious diseases of relevance to US agriculture.</li> <li>We provided information about poultry gene functions (via the AgBase database) and developed and deployed analysis tools on CyVerse. This includes the development of iMicrobe (http://openwetware.org/wiki/Imicrobe), a resource that makes large scale microbial data accessible and queryable for all researchers, and Chickspress, a chicken gene expression resource (http://geneatlas.arl.arizona.edu). Another resource is VERVE Net (http://vervenet.us), a virus ecology research and virtual exchange network.</li> <li>We improved standardized naming across chicken genes, enabling researchers to consistently and unambiguously report their scientific findings. These efforts enable researchers to have equal access to tools that help them analyze their genomics data sets, and data to support these anlayses. Analyzing and understanding genomics data sets in turn ensures that poultry researchers can translate their finding into gains for the industry.</li> </ul>     NRSP-8 Equine 2019 Annual Report (Coordinator and Workshop) Leadership: Coordinators: Ernest Bailey, University of Kentucky Samantha Brooks, University of Florida Molly McCue, University of Minnesota   NRSP8 Workshop: Chair:   Annette McCoy, University of Illinois Co-chair: Mike Mienaltowski, University of California, Davis   2019 Equine Workshop Report The workshop met Saturday afternoon (Jan 11, 2020) and Sunday morning (Jan 12, 2020) at the Plant and Animal Genome Conference in San Diego, CA.   Attendees: January 12: 80 January 13: 55   Station Reports were provided by scientists from 20 laboratories including those at Cornell University, University of Florida, University of Kentucky, University of Louisville, University of Minnesota, Michigan State University, Illinois State University, University of Nebraska, Texas A&M University, University of California-Davis, Argentina, Brazil, Sweden, Denmark, South Korea and China.   PAG 2019 Workshop Presentations Invited Speaker: Dr. Marcio Costa, from the University of Montreal, who presented his perspective on what is known about the equine intestinal microbiota.   There were eleven abstract presentations, including two sharing results from the Equine FAANG initiative. Brief station reports were provided by 15 lab groups in the U.S. and three international lab groups during which they shared their ongoing research efforts and made requests for future collaborations and students/post-docs. There was also an update for the upcoming Havemeyer equine genetics/genomics workshop to be hosted by Cornell University July 26-29, 2020. A portion of the Saturday workshop was dedicated to a community discussion, as part of the larger animal genomics community discussion regarding the future of NRSP8. There were four questions posed for discussion: <ol> <li>What are the next steps we are taking as a community in terms of discovery science? What will we be investigating over the next 5-10 years? What tools do we need to build?</li> <li>What would help us the most? Where do investments need to be made that will do the most good in driving discovery forward?</li> <li>How will we get our results out to the industry? Who are the stakeholders that we need to engage as our champions?</li> <li>What are our options for community funding moving forward once NRSP8 ends?</li> </ol> A white paper will be generated summarizing the results of this discussion. Briefly, the following key points were brought forth: <ul> <li>We are poised to make the jump from genome to phenotype, and from there to clinical management including the development of informative biomarkers. Phenotype can be defined at many levels (cell, tissue, organism, herd). This work will allow us to work towards the goal of personalized medicine for horses, which is something that owners and breeders are looking for.</li> <li>We need to consider moving away from a single reference genome. Can we move to data-driven rather than reference driven discovery? This involves taking the machinery for making genomes and turning it to annotating genomes.</li> <li>Tools that need to be developed include shareable repositories for data of all types (SNP, long-read data, functional annotation etc.) and a shared biobank.</li> <li>We need to invest in translating our discoveries to our stakeholders (veterinarians and owners/breeders) so that they will provide support for infrastructure development/maintenance and further discovery research. We should leverage existing extension frameworks through the agricultural experiment station directors to accomplish this, as well as use industry media contacts. We need to effectively communicate what tools are available, how to use them, and what the underlying science means. This communication will also allow us to get feedback about what is important to our stakeholders.</li> <li>The horse is well-poised to be used as a model for sports medicine/performance-related traits and diseases. We can propose a comparative biology/genomics angle to funding agencies (e.g. NIH). There is also a new NSF call with a specific line for investigation of complex traits, and IOS is focusing on “reunifying biology” with an interest in cross-disciplinary collaboration.</li> <li>The best bet for the horse to be a part of a new multispecies NRSP would be if it was focused on phenotype prediction (and development of bioinformatics tools to facilitate this).</li> <li>There may be an opportunity to tap industry for money (pharma, feed/supplement companies, breed organizations), but we need to include them in our meetings so we know where their interests lie.</li> </ul> At the conclusion of the workshop, Felipe Avila of the University of California, Davis was elected co-chair for the 2020 workshop (meeting at PAG in January 2021).  Mike Mienaltowski will assume major responsibilities as chair of the workshop meeting.   Travel support: The Jorgenson Travel Award was won by Sian Durward-Akhurset of the University of Minnesota for the presentation entitled, “The frequency of loss of function alleles in the equine population”.   Additional Travel Awards were also made to 24 other students using the NRSP8 Coordinator Funds.        Progress on the Workshop Objectives:   1: Advance the status of reference genomes for all species, including basic annotation of worldwide genetic variation, by broad sequencing among different lines and breeds of animals.   The new assembly of the horse genome, Ecab 3.0, was published in 2018 and made available on NCBI and ENSEMBL genome browsers.  The assembly has been used extensively in research during the current year with exceptions and problems being reported to the team that organized the new assembly. The assembly was based on the existing Sanger sequence data along with Illumina HiSeq short reads, CHiCago and Hi-C long-insert libraries, Gap-filling with PacBio and a 10x Chromium library to identify and phase variants. The final assembly has 4.5Mb contig N50, 85Mb scaffold N50, and 70Mb more sequence assigned to chromosomes.   2: Develop strategies to identify and exploit genes and allelic variation that contribute to economically relevant phenotypes and traits, in part through improving functional annotation of the genomes of our species. For the Functional Annotation of Animal Genomes (FAANG) initiative, sampling and preservation of 86 tissues, 2 cell lines, and 5 fluids from two Thoroughbred mares was completed in 2016 (Burns, et. al 2018) and data continues to be added to the community databases.  During 2019, work began to add two stallions to this project and tissues will be available for testing during 2020.   This biobank has been instrumental in the development of epigenetic assays and data collection for the horse, including RNA-seq, ChIP-seq, and CTCF-binding assays. This sequencing was completed in 2018 and uploaded to EMBL-ENA (https://www.ebi.ac.uk/ena/data/view/PRJEB26698). Because of the “adopt-a-tissue” effort, we have also identified a set of tissues for which functional annotation will have the greatest impact on immediate research endeavors being conducted by members of the community. Additionally, USDA Species Coordinator Funds were appropriated for ChIP-seq analysis of additional tissues.   3: Facilitate analysis, curation, storage, distribution and application of the enormous datasets now being generated by next-generation sequencing and related "omics" technologies with regard to animal species of agricultural interest.   Datasets from whole-genome sequencing of the two mares (https://www.ebi.ac.uk/ena/data/view/PRJEB26698), mRNA-seq (<a href="https://www.ebi.ac.uk/ena/data/view/ERA1487553">https://www.ebi.ac.uk/ena/data/view/ERA1487553</a>) and smRNA-seq (in submission) across 47 tissues from the two mares and reduced read bisulfate sequencing (RRBS) across 8 tissues (in submission) on the two mares continue to be publicly available at EMBL-ENA.   Communication:  The coordinators maintain an email list and use it to broadcast information for USDA-NRSP8, the USDA, the Havemeyer Foundation and other information relevant to the workshop.  In addition to the PAG conference, workshops are held once every two years at a Dorothy Russell Havemeyer Workshop and at a conference of the International Society for Animal Genetics.  Many of the NRSP8 members also participant in the biennial Equine Science Society Conferences.   International Society for Animal Genetics (ISAG) Conference 2019: A workshop meeting for the horse genome project was held at the ISAG meeting in Lleida, Spain, July 7-12, 2019.  More information about that meeting can be found at the conference website: <a href="https://www.isag.us/2019/">https://www.isag.us/2019/</a>   Website:  A new website for the International Horse Genome program was set up including reports from the different meetings, identification of participants and tools.  The website can be found at:  <a href="https://horsegenomeworkshop.com/">https://horsegenomeworkshop.com/</a>   September 2020 Havemeyer International Equine Genome Workshop A workshop meeting will be held in connection with this program. Details can be found at the following website:   <a href="https://havemeyergenome2020.com/">https://havemeyergenome2020.com/</a>     Funding in 2019 Reported by 9 US Stations and 7 International Stations   Internal                      Industry                     Federal $311,400

Publications

<ol start="29"> <li> <ol> <li>Liu R, Low WY, Tearle R, Koren S, Ghurye J, Rhie A, Phillippy AM, Rosen BD, Bickhart DM, Smith TPL, Hiendleder S, Williams JL. New insights into mammalian sex chromosome structure and evolution using high-quality sequences from bovine X</li> </ol> and Y chromosomes. BMC Genomics. 2019 Dec 19;20(1):1000 <ol start="2"> <li>Fang L, Zhou Y, Liu S, Jiang J, Bickhart DM, Null DJ, Li B, Schroeder SG, </li> </ol> Rosen BD, Cole JB, Van Tassell CP, Ma L, Liu GE. Comparative analyses of sperm DNA methylomes among human, mouse and cattle provide insights into epigenomic evolution and complex traits. Epigenetics. 2019 Mar;14(3):260-276. <ol start="3"> <li>Liu S, Kang X, Catacchio CR, Liu M, Fang L, Schroeder SG, Li W, Rosen BD,</li> </ol> Iamartino D, Iannuzzi L, Sonstegard TS, Van Tassell CP, Ventura M, Low WY, Williams JL, Bickhart DM, Liu GE. Computational detection and experimental validation of segmental duplications and associated copy number variations in water buffalo ( Bubalus bubalis ). Funct Integr Genomics. 2019 May;19(3):409-419. <ol start="4"> <li>Johnson T, Keehan M, Harland C, Lopdell T, Spelman RJ, Davis SR, Rosen BD,</li> </ol> Smith TPL, Couldrey C. Short communication: Identification of the pseudoautosomal region in the Hereford bovine reference genome assembly ARS-UCD1.2. J Dairy Sci. <ul> <li>;102(4):3254-3258.</li> </ul> <ol start="5"> <li>Rowan TN, Hoff JL, Crum TE, Taylor JF, Schnabel RD, Decker JE. A multi-breed reference panel and additional rare variants maximize imputation accuracy in cattle. Genet Sel Evol. 2019 Dec 26;51(1):77.</li> <li>Smith JL, Wilson ML, Nilson SM, Rowan TN, Oldeschulte DL, Schnabel RD, Decker JE, Seabury CM. Genome-wide association and genotype by environment interactions for growth traits in U.S. Gelbvieh cattle. BMC Genomics. 2019 Dec 4;20(1):926.</li> <li>Zwane AA, Schnabel RD, Hoff J, Choudhury A, Makgahlela ML, Maiwashe A, Van Marle-Koster E, Taylor JF. Genome-Wide SNP Discovery in Indigenous Cattle Breeds of South Africa. Front Genet. 2019 Mar 29;10:273.</li> <li>Hoff JL, Decker JE, Schnabel RD, Seabury CM, Neibergs HL, Taylor JF. QTL-mapping and genomic prediction for bovine respiratory disease in U.S. Holsteins using sequence imputation and feature selection. BMC Genomics. 2019 Jul 5;20(1):555.</li> <li>Crum TE, Schnabel RD, Decker JE, Regitano LCA, Taylor JF. CRUMBLER: A tool for the prediction of ancestry in cattle. PLoS One. 2019 Aug 26;14(8):e0221471. =</li> <li>Maldonado MBC, de Rezende Neto NB, Nagamatsu ST, Carazzolle MF, Hoff JL, Whitacre LK, Schnabel RD, Behura SK, McKay SD, Taylor JF, Lopes FL. Identification of bovine CpG SNPs as potential targets for epigenetic regulation via DNA methylation. PLoS One. 2019 Sep 12;14(9):e0222329.</li> <li>Koltes JE, Cole JB, Serao N, McCue M, Woodward J, Zhang H, McKay S, Lunney J, Kramer L, Schroeder M, Clemmens R, Murdoch B, Rexroad C, Rosa G, Mateescu R, White S, Worku M, Reecy J. A vision for development and utilization of high-throughput phenotyping and big data analytics in livestock. Frontiers in Genetics (2019) Dec 17</li> <li>Cantrell B, Lachance H, Murdoch B, Sjoquist J, Funston R, Weaber R, McKay S. Global DNA methylation in the limbic system of cattle. Epigenomes – feature cover (2019) 3(2).</li> <li>Kern C, Wang Y, Chitwood J, Korf I, Delany M, Cheng H, Medrano JF, Van Eenennaam AL, Ernst C, Ross P, Zhou H. Genome-wide identification of tissue-specific long non-coding RNA in three farm animal species. BMC Genomics. 2018 19(1):684.</li> <li>Mueller, M.L., Cole, J.B., Sonstegard, T.S., Van Eenennaam, A.L. 2019. Comparison of gene editing vs. conventional breeding to introgress the POLLED allele into the U.S. dairy cattle population. Journal of Dairy Science. 102(5): 1-12.</li> <li>Mueller, M.L., Cole, J.B., Sonstegard, T.S., Van Eenennaam, A.L. Simulation of introgression of the POLLED allele into the Jersey breed via conventional breeding vs. gene editing, Translational Animal Science, Volume 2, Issue suppl_1, September 2018, Pages S57–S60</li> <li>Van Eenennaam, A.L., Wells, K.D. and Murray, J.D. Proposed U.S. regulation of gene-edited food animals is not fit for purpose. npj Science of Food, 3(3).</li> <li>Rexroad, C.,Vallet, J., Kumar, L., Reecy, J., Bickhart, D., Blackburn, H., Boggess, M., Cheng, H., Clutter, A., Cockett, N., Ernst, C., Fulton, J., Liu, J., Lunney, J., Neibergs, H., Purcell, C., Smith, T., Sonstegard, T., Taylor, J., Telugu, B., Van Eenennaam, A., Van Tassell, C., and Wells, K. 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.</li> <li>Dubrovsky, S., Van Eenennaam, A. L., Karle, B. M., Rossitto, P., Lehenbauer, T. and Aly, S. 2019. Epidemiology of Bovine Respiratory Disease (BRD) in preweaned calves on California dairies: The BRD 10K study. Journal of Dairy Science. 102:7306-7319.</li> <li>Dubrovsky, S., Van Eenennaam, A. L., Karle, B. M., Rossitto, P., Lehenbauer, T. and Aly, S. 2019. Bovine Respiratory Disease (BRD) cause-specific and overall Mortality in preweaned calves on California dairies: The BRD 10K study. Journal of Dairy Science. 102:7320-7328.</li> <li>Maier GU, Love WJ, Karle BM, Dubrovsky SA, Williams DR, Champagne JD, Anderson, RJ, Rowe JD, Lehenbauer TW, Van Eenennaam AL, Aly SS. 2019. Management factors associated with bovine respiratory disease in preweaned calves on California dairies: The BRD 100 study. Journal of Dairy Science. 102: 7288-7305</li> <li>Upperman, L.R., Kinghorn, B.P., MacNeil, M.D., Van Eenennaam, A.L. 2019. Management of lethal recessive alleles in beef cattle through the use of mate allocation software. Genetics, Selection, Evolution. 6;51(1):36.</li> <li>Van Eenennaam, A.L. 2019. Application of genome editing in farm animals: cattle. Transgenic Research. 28(Suppl 2):93-100.</li> <li>Young, A.E., T.A. Mansour, B.R. McNabb, J.R. Owen, J.F.Trott, C.T. Brown, and A.L. Van Eenennaam, 2020. Comparative evaluation of the phenotype and genome from offspring of a genome edited, hornless bull and controls. Nature Biotechology. 38:225–232.</li> <li>Kirkpatrick, B.W., R.M. Thallman and L.A. Kuehn. Validation of SNP associations with bovine ovulation and twinning rate.  Animal Genetics 50(3):259-261. doi: 10.1111/age.12793. Epub 2019 Apr 12.</li> <li>Lam, P.T., S.L. Padula, T.V. Hoang, J.E. Poth, L. Lin, C. Liang, A.S. LeFever, L.M. Wallace, R. Ashery-Padan, P.K. Riggs, J.E. 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Riggs. 2018. “The Outbreak That Changed Meat and Poultry Inspection Systems Worldwide.” ANIMAL FRONTIERS 8 (4): 4–8.</li> <li>Littlejohn, Brittni P., Deborah M. Price, Don A. Neuendorff, Jeffery A. Carroll, Rhonda C. Vann, Penny K. Riggs, David G. Riley, Charles R. Long, Thomas H. Welsh Jr., and Ronald D. Randel. 2018. “Prenatal Transportation Stress Alters Genome-Wide DNA Methylation in Suckling Brahman Bull Calves.”J. Anim. Sci. 96 (12): 5075–99.</li> </ol> </li> <li>Phillips, C.A., Reading, B.J., Livingston, M., Livingston, K. and Ashwell, C.M. Accepted. Evaluation via Supervised Machine Learning of the Broiler Pectoralis Major and Liver Transcriptome in Association with the Muscle Myopathy Wooden Breast. Frontiers in Physiology, in press.</li> <li>Hornick, K.M. and Plough, L.V., 2019. Tracking genetic diversity in a large-scale oyster restoration program: effects of hatchery propagation and initial characterization of diversity on restored vs. wild reefs. 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Genes (Basel), 10 (8) 2019.</li> <li>Loux SC, Dini P, El-Sheikh Ali H, Kalbfleisch T, Ball BA. Characterization of the placental transcriptome through mid-late gestation in the mare. PLOS ONE 14(11): e0224497, </li> <li>Loux SC, Fernandes CB, Dini P, Wang K, Wu X, Baxter D, Troedsson MH, Squires EL, Ball BA. Small RNA expression in the chorioallantois, endometrium and serum of mares following experimental induction of placentitis.  Rep Fertil Devel 31:1144-1156, 2019.</li> <li><a href="https://pubmed.ncbi.nlm.nih.gov/?sort=date&term=Sol%C3%A9+M&cauthor_id=31640551">Marina Solé</a>, <a href="https://pubmed.ncbi.nlm.nih.gov/?sort=date&term=Ablondi+M&cauthor_id=31640551">Michela Ablondi</a>, <a href="https://pubmed.ncbi.nlm.nih.gov/?sort=date&term=Binzer-Panchal+A&cauthor_id=31640551">Amrei Binzer-Panchal</a>, <a href="https://pubmed.ncbi.nlm.nih.gov/?sort=date&term=Velie+BD&cauthor_id=31640551">Brandon D Velie</a>, <a href="https://pubmed.ncbi.nlm.nih.gov/?sort=date&term=Hollfelder+N&cauthor_id=31640551">Nina Hollfelder</a>, <a href="https://pubmed.ncbi.nlm.nih.gov/?sort=date&term=Buys+N&cauthor_id=31640551">Nadine Buys</a>, <a href="https://pubmed.ncbi.nlm.nih.gov/?sort=date&term=Ducro+BJ&cauthor_id=31640551">Bart J Ducro</a>, <a href="https://pubmed.ncbi.nlm.nih.gov/?sort=date&term=Fran%C3%A7ois+L&cauthor_id=31640551">Liesbeth François</a>, <a href="https://pubmed.ncbi.nlm.nih.gov/?sort=date&term=Janssens+S&cauthor_id=31640551">Steven Janssens</a>, <a href="https://pubmed.ncbi.nlm.nih.gov/?sort=date&term=Schurink+A&cauthor_id=31640551">Anouk Schurink</a>, <a href="https://pubmed.ncbi.nlm.nih.gov/?sort=date&term=Viklund+%C3%85&cauthor_id=31640551">Åsa Viklund</a>, <a href="https://pubmed.ncbi.nlm.nih.gov/?sort=date&term=Eriksson+S&cauthor_id=31640551">Susanne Eriksson</a>, <a href="https://pubmed.ncbi.nlm.nih.gov/?sort=date&term=Isaksson+A&cauthor_id=31640551">Anders Isaksson</a>, <a href="https://pubmed.ncbi.nlm.nih.gov/?sort=date&term=Kultima+H&cauthor_id=31640551">Hanna Kultima</a>, <a href="https://pubmed.ncbi.nlm.nih.gov/?sort=date&term=Mikko+S&cauthor_id=31640551">Sofia Mikko</a>, <a href="https://pubmed.ncbi.nlm.nih.gov/?sort=date&term=Lindgren+G&cauthor_id=31640551">Gabriella Lindgren</a>. Inter- And Intra-Breed Genome-Wide Copy Number Diversity in a Large Cohort of European Equine Breeds. BMC Genomics, 20 (1), 759, 2019 (Oct 22).</li> <li>Marquardt SA, Wilcox CV, Burns EN, Peterson JA, Finno CJ*. Previously identified genetic variants in ADGRL3 are not associated with risk for equine degenerative myeloencephalopathy across breeds. Genes (Basel) 2019;10(9):</li> <li>McClellan, A., Paterson, Y. Z., Paillot, R. & Guest, D. Equine fetal, adult and embryonic stem cell derived tenocytes are all immune privileged but exhibit different immune suppressive properties in vitro. Stem Cells Dev, doi:10.1089/scd.2019.0120 (2019).</li> <li>McCoy, A.M., Beeson, S.K., Rubin, C.-J., Andersson, L., Caputo, P., Lykkjen, S., Moore, A., Piercy, R.J., Mickelson, J.R., McCue, M.E. Identification and validation of genetic variants predictive of gait in Standardbred horses. 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The expression profile of genes involved in osteoclastogenesis detected in whole blood of Arabian horses during 3 years of competing at race track, Research in Veterinary Science, 123, 59-64.</li> <li>Stefaniuk-Szmukier M., Szmatoła T., Łątka J., Długosz B., Ropka-Molik K., 2019, The blood and muscle expression pattern of equine TCAP gene during the race track training of Arabian horses, Animals, 9, 574.</li> <li>Stejskalova K, Cvanova M, Oppelt J, Janova E, Horecky C, Horecka E, Knoll A, Leblond A, Horin P.Genetic susceptibility to West Nile virus infection in Camargue horses. Res Vet Sci. 2019 Jun;124:284-292. doi: 10.1016/j.rvsc.2019.04.004. Epub 2019 Apr 10.</li> <li>Stejskalova K, Janova E, Horecky C, Horecka E, Vaclavek P, Hubalek Z, Relling K, Cvanova M, D'Amico G, Mihalca AD, Modry D, Knoll A, Horin P. Associations between the presence of specific antibodies to the West Nile Virus infection and candidate genes in Romanian horses from the Danube delta. Mol Biol Rep. 2019 Aug;46(4):4453-4461. doi:</li> <li>Tezuka A, Takasu M, Tozaki T, Nagano AJ. 2019. Genetic analysis of Taishu horses on and off Tsushima Island: Implications for conservation. J Equine Sci. 30:33-40.</li> <li>Todd, K. Jadervkist Fegraeus, P.C. Thomson, C.F. Ihler, E. Strand, G. Lindgren and B.D. Velie. Premie race participation is associated with increased career longevity and prize money earnings in Norwegian-Swedish Coldblooded Trotters. Acta Agri Scand, Section A: Animal Sci, Volume 68 (2), 2019, pages 112-116. doi: 10.1080/09064702.2018.1563211.</li> <li>Tozaki T, Kikuchi M, Kakoi H, Hirota K, Nagata S, Yamashita D, Ohnuma T, Takasu M, Kobayashi I, Hobo S, Manglai D, Petersen JL. 2019. Genetic diversity and relationships among native Japanese horse breeds, the Japanese Thoroughbred and horses outside of Japan using genome-wide SNP data. Anim Genet. 2019. 50:449-459.</li> <li>Tozaki T, Miyake T, Kikuchi M, Kakoi H, Hirota KI, Kusano K, Ishikawa Y, Nomura M, Kushiro A, Nagata SI. 2019. Heritability estimates of fractures in Japanese Thoroughbred racehorses using a non-linear model. J Anim Breed Genet. 136:199-204.</li> <li>Tozaki T, Ohnuma A, Takasu M, Kikuchi M, Kakoi H, Hirota KI, Kusano K, Nagata SI. 2019. Droplet digital PCR detection of the erythropoietin transgene from horse plasma and urine for gene-doping control. Genes (Basel). 10: E243.</li> <li>Twenter H, Klohonatz K, Davis K, Bass L, Coleman SJ, Bouma GJ, Bruemmer JE.  (2019) Transfer of microRNAs from epididymal epithelium to equine spermatozoa. J, Equine Vet. Sci. <a href="https://doi.org/10.1016./j.jevs.2019.102841">https://doi.org/10.1016./j.jevs.2019.102841</a>.  </li> <li>Ueda T, Tozaki T, Nozawa S, Kinoshita K, Gawahara H. 2019. Identification of metabolomic changes in horse plasma after racing by liquid chromatography-high resolution mass spectrometry as a strategy for doping testing. J Equine Sci. 30:55-61.</li> <li>Valberg SJ, Soave K, Williams ZJ, Perumbakkam S, Schott M, Finno CJ, Gardner KL, Petersen JL, Fenger F, Autry JM, Thomas DD. Coding sequences of sarcoplasmic reticulum calcium ATPase regulatory peptides and expression of calcium regulatory genes in recurrent exertional rhabdomyolysis. J Vet Intern Med. 2019;33(2): 933-941 doi: 10.1111/jvim.15425.</li> <li>Velie BD, Jäderkvist Fegraeus K, Ihler CF, Lindgren G, Strand E. <a href="https://www.ncbi.nlm.nih.gov/pubmed/29969157">Competition lifespan survival analysis in the Norwegian-Swedish Coldblooded Trotter racehorse.</a> Equine Vet J. 2019: 51 (2), 206-211. doi: 10.1111/evj.12989.</li> <li><a href="https://pubmed.ncbi.nlm.nih.gov/?sort=date&term=Velie+BD&cauthor_id=31461557">Velie</a>, <a href="https://pubmed.ncbi.nlm.nih.gov/?sort=date&term=Smith+PM&cauthor_id=31461557">P M Smith</a>, <a href="https://pubmed.ncbi.nlm.nih.gov/?sort=date&term=Fjordbakk+CT&cauthor_id=31461557">C T Fjordbakk</a>, <a href="https://pubmed.ncbi.nlm.nih.gov/?sort=date&term=Sol%C3%A9+M&cauthor_id=31461557">M Solé</a>, <a href="https://pubmed.ncbi.nlm.nih.gov/?sort=date&term=J%C3%A4derkvist+Fegraeus+K&cauthor_id=31461557">K Jäderkvist Fegraeus</a>, <a href="https://pubmed.ncbi.nlm.nih.gov/?sort=date&term=Rosengren+MK&cauthor_id=31461557">M K Rosengren</a>, <a href="https://pubmed.ncbi.nlm.nih.gov/?sort=date&term=R%C3%B8ed+KH&cauthor_id=31461557">K H Røed</a>, <a href="https://pubmed.ncbi.nlm.nih.gov/?sort=date&term=Ihler+CF&cauthor_id=31461557">C F Ihler</a>, <a href="https://pubmed.ncbi.nlm.nih.gov/?sort=date&term=Lindgren+G&cauthor_id=31461557">G Lindgren</a>, <a href="https://pubmed.ncbi.nlm.nih.gov/?sort=date&term=Strand+E&cauthor_id=31461557">E Strand</a>. Exploring the Genetics Underpinning Dynamic Laryngeal Collapse Associated With Poll Flexion in Norwegian-Swedish Coldblooded Trotter Racehorses. Equine Vet J. 2019 Aug 28 [Online ahead of print].</li> <li>Yokomori T, Tozaki T, Mita H, Miyake T, Kakoi H, Kobayashi Y, Kusano K, Itou T. 2019. Heritability estimates of the position and number of facial hair whorls in Thoroughbred horses. BMC Res Notes. 12:346.</li> <li> <ol> <li>Rexroad C, Vallet J, Matukumalli LK, Reecy J, Bickhart D, Blackburn H, Boggess M, Cheng H, Clutter A, Cockett N, Ernst C, Fulton JE, Liu J, Lunney J, Neibergs H, Purcell C, Smith TPL, Sonstegard T, Taylor J, Telugu B, Eenennaam AV, Tassell CPV, Wells K. Genome to Phenome: Improving Animal Health, Production, and Well-Being - A New USDA Blueprint for Animal Genome Research 2018-2027. Front Genet. 10:327. 2019. doi: 10.3389/fgene.2019.00327.</li> <li>Murphy, T. W., Stewart, W. C., Notter, D. R., Mousel, M. R., Lewis, G. S., and Taylor, J. B. 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(2019) Molecular profiling demonstrates modulation of immune cell function and matrix remodeling during luteal rescue. Biology of Reproduction 100(6), 1581–1596.</li> <li> Beiki H, Liu H, Huang J, Manchanda N, Nonneman D, Smith TPL, Reecy JM, Tuggle CK. Improved annotation of the domestic pig genome through integration of Iso-Seq and RNA-seq data. BMC Genomics. 2019 May 7;20(1):344. doi: 10.1186/s12864-019-5709-y. </li> </ol> </li> </ol> </li> </ol> </li> </ol>

Impact Statements

• Over 4,685 users worldwide subscribe and are informed by the AnGenMap email list serve (https://www.animalgenome.org/community/angenmap/); and information about NRSP-8 is made publicly available through the https://www.animalgenome.org/ website maintained at Iowa State University.

Date of Annual Report: 03/16/2021

Report Information

Annual Meeting Dates: 09/30/2020 - 09/30/2020
Period the Report Covers: 01/01/2020 - 09/01/2020

Participants

Brief Summary of Minutes

Please see attached file below for NRSP8's 2020 annual report.

Minutes Attachment:

NRSP8 ANNUAL REPORT OF COOPERATIVE REGIONAL PROJECTS_2020[6].pdf

Accomplishments

Publications

Impact Statements

Date of Annual Report: 04/22/2022

Report Information

Annual Meeting Dates: 04/03/2022 - 04/03/2022
Period the Report Covers: 04/30/0202 - 04/01/2022

Participants

Brief Summary of Minutes

Please see attached file below for NRSP8's annual report.

Minutes Attachment:

NRSP8 ANNUAL REPORT OF COOPERATIVE REGIONAL PROJECTS_2021_final.pdf

Accomplishments

Publications

Impact Statements

Date of Annual Report: 03/17/2023

Report Information

Annual Meeting Dates: 01/15/2023 - 01/15/2023
Period the Report Covers: 01/01/2022 - 12/31/2022