Brief Summary of Minutes of Annual Meeting

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)

1. FAASG – Functional Annotation of All Salmonid Genomes Ben F. Koop, University of Victoria
2. Editing for Animal Welfare and Environmental Sustainability: Are These Traits Important? Tad S. Sonstegard, Acceligen, Inc.
3. Gene Transcription Data for eQTL Analysis, Variance Component Analysis and Gebv Estimation in Atlantic Salmon Anna K. Sonesson, Nofima AS
4. Use of Atlantic Salmon Gene Editing in Research and Development Anna Troedsson-Wargelius, Institute of Marine Research

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

1. 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.

2. 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).

3. 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.

4. 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.

5. 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.

6. A note was made for coordinators to mention revenue generated, grants added, and funds leveraged in species updates

7. 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.

8. 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

.

9. 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.

10. Meeting was adjourned.

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: http://appliedecology.cals.ncsu.edu/striped-bass-genome-project/. 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:

1. Jason Abernathy and Steven J. Micheletti “Mapping sex-linked genes in temperate basses for improved hybrid striped bass culture”, USDA ARS.
2. Hollie Putnam and Steven Roberts “Functional Re-annotation of Oyster Genomes with Epigenetic Resources (FROGER)”, University of Rhode Island.
3. Moh Salem “The landscape of histone modifications in the rainbow trout genome: preliminary data for FAASG”, Middle Tennessee State.

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:

1. Pratima Chapagain, Middle Tennessee State University (TN, USA), “Gut Microbiome Analysis of Fast- and Slow-growing Rainbow Trout (Oncorhynchus mykiss)”.
2. 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)”.
3. Konstantin Divilov, Oregon State University (OR, USA), “Genetics of Pacific Oyster Uniformity in Different Environments”.
4. 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”.
5. Ivan Pocrnic, University of Georgia (GA, USA), “Exploiting the dimensionality of genomic information in channel catfish”.
6. 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”.
7. Wenwen Wang (Auburn University (LA, USA), “Identification of QTL associated with Aeromonas disease resistance in catfish throughout a genome-wide association study”.

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, 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

2019 Cattle Workshop Report

Workshop Chair 2018-2019:      Rebecca Cockrum (rcockrum@vt.edu)

Chair-elect 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)

International Plant and Animal Genome XXVII Workshop Attendance

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.

• 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.
• 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.

Table 1. Bos taurus Reference Genome Comparisons. Rosen, Bickhart et al., (2018)

ARS-UCD1.2 https://www.ncbi.nlm.nih.gov/assembly/GCF_002263795.1

Isolate: L1 Dominette 01449 registration number 42190680

Sex: female

BioSample:  SAMN03145444

BioProject: PRJNA391427

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

UOA_Brahman_1 https://www.ncbi.nlm.nih.gov/assembly/GCF_003369695.1

UOA_Angus_1 https://www.ncbi.nlm.nih.gov/assembly/GCA_003369685.2

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:

https://nrrc.ars.usda.gov/A-GRIN/database_collaboration_page_dev

Database and bioinformatics activities are also coordinated by Jim Reecy (NRSP8 Bioinformatics Coordinator) at the NAGRP site (http://www.genome.iastate.edu/cattle/).

Zhiliang Hu at Iowa state collated data from the sequence read archive – there are 4,885 cattle samples available there  https://www.animalgenome.org/other/pubSeqSum

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)

• Discussion of doing finished Y chromosome for bovine
• larger project that would benefit everyone in the community
• work with Brenda Murdoch to fund FACS sorting of sex chromosomes at Stanford to develop enriched library followed by long read sequencing

Iso-Seq on Dominette tissues (Objective 1)

• Do Iso-Seq on 15 fetal tissues from late gestation calf collected by C-section of L1 Dominette to enable genome annotation
• Tim Smith at MARC will perform PAC-Bio long read sequencing on fetal tissues

Perform long read sequencing on F1 hybrid (Objective 1)

• Tim Smith will run long reads using Oxford Nanopore PromethION on the F1 male (Angus sire x Brahman dam F1 hybrid)

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:

• 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.

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

• Kent Reed, Univ of Minnesota:

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.

• Susan Lamont: Iowa State University. US-UK Collaborative Research: Host Resistance to Avian Pathogenic E. coli. USDA-NIFA-AFRI/BBSRC; $499,999
• Marcia Miller: Beckman Research Institute, City of Hope Medical Center, CA: USDA NIFA

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.

• Doug Rhoads: University of Arkansas. Validation of a SNP panel for breeding against ascites in broilers. NIFA-AFRI; 3/2018-2/2021; $500,000;
• Yvonne Dreshsler, Western University of Health Sciences: Genome-wide annotation of cis-regulatory elements in the chicken genome. NIFA AFRI; $1,000,000;
• 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.
• H. Zhou, UC Davis: $11,212,800 from USAID, USDA.including newly funded $10,000,000 during that period as PI, co-PIs.

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:

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

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  (https://www.ebi.ac.uk/ena/data/view/ERA1487553) 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:  https://horsegenomeworkshop.com/

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:  https://havpav.com/

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 12^th 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