Brief Summary of Minutes of Annual Meeting

SUMMARY OF NRSP-8 ACCOMPLISHMENTS (2013-2017)

Overview of accomplishments for all NRSP-8 technical committees

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 2013-2017. 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 important accomplishments and impacts for each of the technical committees (aquaculture, cattle, horse, poultry, sheep/goat, swine and bioinformatics) are included below. Here we highlight a few of the accomplishments shared across multiple species for each of the three 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. Between 2013 and 2017, reference genomes were assembled for the pig, turkey, sheep, goat, catfish pacific oyster, rainbow trout and striped bass. In addition, genome reference assemblies were improved for the chicken, cow, horse, pig and rainbow trout with researchers capitalizing on short-read sequencing technologies, optical mapping, Pacific Biosciences sequencing and other technologies. Across all species, these improved assembles reached high-quality chromosome levels, eliminated most of the regions with ambiguous sequences, and in some cases provided sequence for previously unsequenced autosomes. Genome annotation and gene predictions were enhanced in several species using a variety of methods including RNA sequencing (RNA-Seq) of protein coding RNA, micro RNA (miRNA), and long non-coding RNA (lncRNA), full-length transcript sequencing using Iso-seq, and coordinated efforts to manually annotate genes.

Efforts were initiated in the cow, pig, chicken, horse, sheep, rainbow trout and pacific oyster to annotate additional functional elements of the genome as part of a new initiative, the Functional Annotation of ANimal Genomes (FAANG) consortium. The FAANG consortium was formed in 2014 with the goal of accelerating genome-to-phenome discovery in NRSP-8 species. In the first phases of this effort, a number of investigations have been proposed or initiated across 80-105 tissues, depending on the species. These include whole genome sequencing; whole genome bisulfite sequencing; RNA sequencing (mRNA, miRNA, ncRNA) and transcriptome assembly; ATAC-seq; ChIP-seq with DNAse I, histone modification marks, insulator-binding protein CCCTC-binding factor, and important transcription factors; and the study of the genome-wide chromatin interactome using Hi-C. Is it worth noting that this is the first time some of these technologies have been applied to some of these species.  Work is ongoing among members of the FAANG project to standardize collection techniques, experimental protocols, and data analysis pipelines to maximize the utility of the data produced by this effort.

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.  From 2013 to 2017, single nucleotide polymorphism (SNP) high-throughput genotyping arrays were developed for several species including Equine (54K, 65K, 670K and 2M arrays), chicken (670K), cattle (250K functional allele array), sheep (600K), goat (52K), swine (670K) and rainbow trout (57K, 50K functional allele arrays). For all species, the impacts of these SNP genotyping arrays include: permitting genome-wide analyses such as genome-wide association studies (GWAS) and genomic signatures of selection for identification of genomic regions harboring alleles for traits of interest; allowing for, and improving the accuracy of predicted breeding values; enabling genomic selection; and permitting estimation of genetic diversity in breeds and populations of interest. Across species tools developed under this objective have allowed for identification of alleles responsible for important economic and disease traits, including alleles important in infectious diseases such as GBP5 associated with resistance/susceptibility to primary PRRS virus infection in pigs. In addition, the dairy industry has used SNP-chips to genotype nearly over one million dairy cattle allowing application of genomic selection which has reduced animal selection generation interval (from 5 years to less than one year) and has increased genetic merit prediction accuracy by more than 30 percent with an estimated annual benefits of $100 million per year.

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. Successful efforts have been made to develop platforms to facilitate collaborative research for collection and analysis of new, unique, and interesting phenotypes, and to develop, integrate, and implement bioinformatic resources to support the discovery of genetic mechanisms underlying agriculturally important traits. For example, the Animal Quantitative Trait Loci database (Animal QTLdb) was updated with 104,272 new quantitative trait loci (QTL). To date, the database contains 95,332 cattle, 6,633 chicken, 1,245 horse, 16,516 pig, 1,412 sheep and 127 rainbow trout loci that have been associated with many traits of interest. Further, the data repository for the aquaculture, cattle, chicken, horse, pig, and sheep communities to share their genome analysis data has proven to be very useful for the community with 1,140 data files, totaling 140 GBGb, shared through this platform. Finally, a collaborative VCF information-mining platform was developed to allow for sharing discovered genetic variants between researchers.

In addition to direct contributions to each of the three objectives, NRSP-8 participants have leveraged the NRSP-8 investment in tools and infrastructure into at least $94.5 million dollars in funding to study diverse animal models to investigate fundamental mechanisms of genome biology and physiology and pathophysiology affecting production efficiency, product quality, animal health, disease resistance and food safety and to develop additional bioinformatics resources (see Table 1). Finally, the annual NRSP-8 workshops have become an essential component for the development of collaborations, training and dissemination of new information to government, academic, and industry stakeholders in animal agriculture. NRSP-8 species coordinators’ funds have been used to support travel for 146 postdoctoral and graduate students to the NRSP-8 meetings that are held in conjunction with the annual Plant and Animal Genome (PAG) meeting. 

AQUACULTURE

http://www.animalgenome.org/aquaculture/

Direct contributions to Objective 1:

• Reference genome for catfish (2016). Impact(s): The genome reference will allow understanding the genes controlling performance traits. Technologies can be developed based on this information allowing superior catfish breeds that will help farmers increase profits.
• Rainbow trout high-density 57K SNP chip was developed and characterized (2013). Approximately 50K of the SNPs were validated in a panel of 18 rainbow trout populations at the standard 97% call rate of the Affymetrix SNP polisher software. Impact(s): The SNP chip allowed improved accuracy of predicting breeding values for bacterial cold water disease resistance compared to a traditional pedigree-based model in rainbow trout aquaculture.
• Reference genome for the Pacific oyster (2012). Impact(s): This genome provides a basis for numerous phenotype studies and provides insight into performance under changing environmental conditions.
• Striped Bass Genetic Map (2012). The first genetic map of the genome of the striped bass was developed and published. Impact(s): This medium-density linkage map was based on 298 microsatellite markers and is enabling detection of QTL affecting production traits.
• Rainbow Trout Reference Genome sequence (2012): A pooling and tagging scheme was used for sequencing of ~15,000 clones from the BAC fingerprinted physical map minimal tiling path (MTP). Impact(s): The map helped in assembling the trout genome.
• Improved Rainbow Trout Reference Genome sequence (2017): The longest available read length of the Illumina technology was used to improve the genome sequence producing longer and better anchored scaffolds to chromosomes. Impact(s): The genome assembly led to SNP genotyping tools that are being used to accelerate genetic improvement.
• Striped bass genome sequence assembly containing ~35 K scaffolds was produced (2015). Impact(s): The assembly should accelerate analysis of the striped bass genome, to identify and characterize genes affecting important production traits.

Direct contributions to Objective 2:

• A 675K SNPs array was developed for catfish (2017). Impact(s): This array allowed for genetic mapping and validation of the reference genome sequence assembly as well as for identification of a genetic markers associated with aquaculture production traits in catfish.
• A 57K SNPs array was developed for rainbow trout (2014). Impact(s): This array allowed for genetic mapping and improving assembly of the reference genome and evaluation genomic selection in rainbow trout.
• A 50K cSNPs array was developed for rainbow trout (2016). Impact(s): This array allowed for allelic-imbalance analysis of genes that are associated with muscle yield and fillet quality traits and also with bacterial cold-water disease survivability.
• Bulked segregant RNA-seq (BSR-Seq) was used to analyze differentially expressed genes and associated SNPs with disease resistance against enteric septicemia of catfish (ESC) (2013). A total of 1,255 differentially expressed genes were found between resistant and susceptible fish. Impact(s): These genes are candidates for further functional genomics work to validate their role in providing catfish with susceptibility to ESC.
• QTL mapping families for stress response and bacterial cold-water resistance (BCWD) in rainbow trout (2013). Impact(s): The families are being used to study genes responsible for stress response and BCWD.
• Illumina GoldenGate genotyping arrays were designed for Crassostrea gigas and Ostrea edulis (2014). Impact(s): These assays were used to genotype 1,000 individuals from wild and selected populations as well as families bred for commercially important traits.
• Large intergenic noncoding RNAs (lncRNAs) were identified by RNA-Seq analysis of rainbow trout transcriptome (2016). Impact(s): Many of the lncRNAs are tissue-specific and functionally associated with important biological processes including resistance to the rainbow trout BCWD and muscle growth.
• RNA-Seq analysis of miRNAs associated with different production quality traits in trout (2015 and 2017). Impact(s): Several miRNAs with epigenetic role associated with egg quality and muscle quality traits were identified.

Direct contributions to Objective 3:

• Rainbow trout QTL database (2012) available through the Animal Genome website of the NRSP-8 bioinformatics group (http://www.animalgenome.org/cgi-bin/QTLdb/index) and is being continually updated. Impact(s): QTLs are available for industry to improve aquaculture production traits in rainbow trout.
• Bioinformatics pipeline was developed for genotyping SNPs from raw sequence data for the GT-seq method (2014). Impact(s): The pipeline provides significant cost reduction for genotyping.
• gigas transcriptome information derived from 2.2 billion sequences from 114 RNA-seq datasets has been organized and deposited into a publicly available database: GigaTON (2015). Impact(s): The user interface provides powerful and user-friendly tools to search and retrieve annotation, expression, and polymorphism information of important genes related to aquaculture traits.

Communication:

• A strategic planning workshop for aquaculture genomics, genetics and breeding was held at Auburn University (2016). Impact(s): The workshop led to a white paper published in BMC Genomics that placed goals and priorities for future research in the aquaculture genomics, genetics and breeding in the US.
• NRSP-8 Aquaculture leaders participated in establishing the FAASG (Functional Annotation of All Salmonid Genomes) consortium. Impact(s): The consortium will allow coordinating data sharing and establish an infrastructure for providing high quality functional annotation of salmonid genomes.

Research support mini-grants (coordinator grants):

• Approximately 25 mini-grants (~$10,000/each) supported projects that fall under all three primary objectives and include a variety of species.

Travel support and opportunities for trainings:

• Travel of 25 students/postdocs was funded to attend the Aquaculture workshop at PAG meetings (2012-2016). The purpose of the travel award program is to help graduate students and postdocs to travel to the annual PAG meeting to present their research.

Leveraged funds and stakeholders’ use of project outputs

Leveraged funds from diverse projects totaling more than $5,553,103 from federal sources. Selected grants are highlighted below.

• Whole genome mapping of disease resistance/susceptibility-associated SNPs in catfish. USDA National Institute of Food and Agriculture Competitive Grant no. 2015-67015-22975. $500,000. John Liu (PD).

This project is designed to address the following two objectives: 1). Genome wide scan of QTLs conferring resistance to ESC and columnaris using F2 and F4 fish using the 250K catfish SNP array; and 2). Fine QTL analysis by genotyping a large number of F2 and F4 individuals using evenly-spaced markers from mapped QTL regions. Impact(s): The impact of this grant will be to determine genes that will be used to select for fish resistant catfish

• Closing the tilapia genome assembly. USDA National Institute of Food and Agriculture Competitive Grant no. 67015-23088. $270,000. Tom Kocher (PD).

       This project aims to improve the platform for genetic improvement of tilapia by developing a definitive sequence of the tilapia genome. Impact(s): The ultimate goal of the project is to improve the health and production of tilapia and related aquaculture species.

• Sequencing the Genome of the Eastern Oyster. USDA National Institute of Food and Agriculture Competitive Grant no. 2015-67016-22942. $242,051 Marta Gonez-Chiarri (PD).

       This project propose to develop these key resources and tools by performing the sequencing, assembly, and annotation of a reference genome and transcriptome for the Eastern oyster C. virginica. Genome researchers and bioinformatics experts, in collaboration with the Eastern Oyster Genome Consortium, will use state-of-the-art sequencing and assembly strategies to achieve these aims. Impact(s): The reference genome and transcriptomes for the Eastern oysters will aid the research community in the discovery of candidate genes and markers associated with traits of commercial, biological, and ecological importance in oysters.

• Development of 675K SNP arrays for whole genome mapping and genetic studies in catfish. USDA National Institute of Food and Agriculture Competitive Grant no. 2015-67015-22907. $485,000 John Liu (PD).

       This project addresses major limitations to adopting genome technologies in aquaculture that currently are the lack of a high- throughput technology for the analysis of genomic variations in relation to phenotypic variations. We need a high-density SNP array technology that allows high- efficiency, cost-effective, whole-genome coverage, analysis of genetics of important performance traits such as disease resistance. This project is poised to resolve these challenges, with three specific objectives: 1) Developing the catfish 675K SNP arrays; 2). Genetic mapping of whole genomic sequence scaffolds; 3). Enhancing and validating the catfish whole genome assembly. Impact(s): This project will address the most significant problem currently existing in catfish genomics. This project will develop a technology for the most efficient analysis of performance traits, and will literally transform the isolated whole genome sequence tags into a well-assembled reference genome assembly, thereby enabling its application in breeding and selection programs.

• Homozygous clonal rainbow trout lines as genomic resources. USDA National Institute of Food and Agriculture Competitive Grant no. 2016-67015-24472. $485,000. Gary Thorgaard (PD).

       Doubled haploid lines have unique value as genomic tools because they have minimal heterozygosity and allow full chromosomal haplotypes to be identified. These lines have been used for the rainbow trout genome sequencing project and for QTL studies. The experimental objectives will include: (1) Establish at least 12 lines within the USDA. (2) Transfer cryopreserved semen from each line as an ongoing repository. (3) Generate a repository of frozen tissues and genomic DNA. (4) Conduct baseline karyotype analysis and SNP typing by re-sequencing of two of the lines. (5) Attempt to induce sex reversal to females in the YY lines and test their fertility. Impact(s): The project will assure continued availability of the lines to the trout research community, develop sperm, tissue and DNA repositories and improve propagation methods.

• SNP markers for muscle, growth and fillet quality traits in rainbow trout. USDA National Institute of Food and Agriculture Competitive Grant no. 2014-67015-21602. $500,000. Mohamed Salem (PD).

       The project aims to find genes and to develop genetic markers that would be used in USDA marker-assisted selection programs to develop food fish strains with superior muscle growth and fillet quality in rainbow trout. This project is expected to produce a large number of true genetic markers that provide a valuable resource for determination of genetic merit of growth and carcass traits in rainbow trout. Project outcomes including, knowledge, expertise, methods, tools, and technologies, will be disseminated to the US aquaculture industry/stakeholders including the US largest producers of rainbow trout food fish and eggs. Impact(s): These genetic markers may be quickly adapted to other species and give the US aquaculture industry a competitive advantage.

Major impact products (could be potential impact):  

Recently, the first genome-wide SNP arrays have been developed and applications of the SNP-chip technology in genomic selection have just begun to be adapted by commercial breeders of some aquaculture species including catfish (600K), salmon (286K), rainbow trout (57K) and oyster (190K).

CATTLE

http://www.animalgenome.org/cattle/

Direct contributions to Objective 1:

• An improved bovine genome reference sequence assembly of Dominette (the reference animal) based on multiple data types developed by the bovine community (optical map, Illumina paired-end, PacBio sequence, and improved gene predictions based on RNA-Seq and Iso-Seq data) will be released in Fall of 2017. Impact(s): This improved assembly will help with the identification of genetic markers associated with economically important traits in cattle.

Direct contributions to Objective 2:

• A 250K functional variant assay was made available to cattle researchers. The assay was designed using various sources of sequence data derived from AFRI-funding and is focused on the detection of genic variants likely to be functional in taurine cattle. Impact(s): This tool will assist researchers to identify genetic identifying causative SNPs that are associated with economically important traits and which are likely to be useful in marker-assisted selection across multiple breeds.

Direct contributions to Objective 3:

• A database (Animal-GRIN) has been developed to serve as a permanent archive for DNA data, germplasm/tissue samples, and phenotypic and production system data from large animal genomics projects. Impact(s): This database will allow for future data mining and value capture from the data and samples collected by publicly funded research.

Communication: 

• A bovine genome newsletter was prepared by the bovine coordinators and distributed to the AnGenMap listserve. Impact(s): This helped inform the bovine research community of ongoing developments with the bovine genome.
• Two industry conferences were held, the “2015 Applied Reproductive Strategies in Beef Cattle (ARSBC) Conference Grant”, and “New Approaches to Bovine Respiratory Disease Prevention, Management, and Diagnosis” with support from USDA, National Institute of Food and Agriculture Conference Grants (2014-67015-21562; 2015-67015-23693). Proceedings were produced from both conferences, and the latter was published in Animal Health Reviews.

Research support mini-grants (coordinator grants):

• Livestock FAANG project (lead by H. Zhou, P. Ross and I Korf) Coordinator funds ($30,000)]. [The project allowed for sample collection from 4 individuals (2 males and 2 females). These funds were used as leverage that resulted in ~$500,000 grant from the USDA NIFA and another ~$100,000 from National Pork Board, Aviagen etc. for FAANG data collection on these samples.

Leveraged funds and stakeholders’ use of project outputs:

From 2013-2017, the investigators and stakeholders leveraged the tools and resources generated through NRSP-8 to obtain at least $27,904,461 additional funding from federal sources, in funding from private foundations and industry sources. Selected grants are highlighted below.

• Integrated program for reducing bovine respiratory disease complex in beef and dairy cattle. USDA National Institute of Food and Agriculture Competitive Grant no. 2011-68004-30367. $9,750,000. Jim Womack (PD). The objective of this Coordinated Agricultural Project was to use genomic tools to identify genetic markers associated decreased susceptibility to bovine respiratory disease. This is the most important disease in both the beef and dairy cattle industry with estimated losses of more than one billion dollars annually. This project used genome sequences to fine map genetic variants associated with respiratory disease, with the aim of delivering a tool that the industry can use to select for cattle that are less susceptible to respiratory disease. Impact(s): The impact of this grant will be decreased morbidity and antibiotic use in cattle production, and improved animal health and welfare.
• 2015-2017: USDA NIFA 2015-67015-23183. “Application of a functional variant assay and sequence imputation to identify large-effect QTL underlying feed efficiency and component traits in beef cattle.” Taylor JF, RD Schnabel, JE Decker, CS Seabury and HL Neibergs. 4/1/15-03/31/17. $500,000. This grant supported the development of the GGP-F250 functional assay. The accomplishment is that we successfully designed an assay for which 173,609 variants can be assayed with a marker call rate of at least 90%. These variants are highly enriched for rare functional variation within the bovine genome and include 82,979 variants that alter amino acids within gene products, 665 Indels that either alter frame or add/delete amino acids, 2017 splice site variants and 44,358 variants within untranslated regions. The assay is currently publicly available through GeneSeek. Impact(s): Impacts of this grant include 23,541 variants within QTL regions detected in the BRD and Feed Efficiency grant that were identified and included on the assay and 1978 BRD case-control and 4609 Feed Efficiency project animals have been genotyped with the assay to fine-map QTL. The assay also contains 2,224 variants for which no homozygotes were detected. These are currently being mapped to genes known to be essential for life to identify candidates for lethal alleles segregating in cattle. Finally, the assay is expected to aid in the process of imputing genotypes to whole genome sequence, because, contrary to the currently used assays which are strongly enriched for common variants, the GGP-F250 is enriched for rare variants and the linkage disequilibrium that exists among rare variants will aid in the imputation of genotypes for this class of variant.
• 2013-2017: USDA-NIFA-AFRI. 2013-68004-20364. “Identification and management of alleles impairing heifer fertility while optimizing genetic gain in Angus cattle.” Patterson DJ, JF Taylor, A Van Eenennaam, S Brown and M Smith. $2,997,040. This grant supported the whole genome sequencing of the 100 registered Angus bulls that have had the greatest impact on the breed as determined by the number of registered descendants. These animals, along with sequences obtained on 162 additional animals from 12 other taurine breeds, were used to identify variants genome wide. With support from the three other USDA grants (Bovine Respiratory Disease, Feed Efficiency and Functional Variant), we designed the GGP-F250 assay for which 173,609 variants can be assayed with a marker call rate of at least 90%. These variants are highly enriched for rare functional variation within the bovine genome and include 82,979 variants that alter amino acids within gene products, 665 Indels that either alter frame or add/delete amino acids, 2017 splice site variants and 44,358 variants within untranslated regions. Impact(s): The assay is currently publicly available through GeneSeek allowing genetic gain assessment for important production phenotypes in Angus cattle.
• 2016-2019: NIH 1R01HD084353. “Linking Fertility-Associated Gene Polymorphisms to Aberrant Sperm Phenotypes.” Sutovsky P, RD Schnabel, JF Taylor. 7/1/2016-6/30/21. $2,149,000. This grant has just started but plans to sequence 100 bulls with either sperm abnormalities or with extreme differences for conception rate to identify mutations in genes known to be expressed in sperm that are responsible for the defects and variants that are candidates for genetic variation in male fertility. We have begun the collection of sperm samples from US and Canadian AI companies. Impact(s): The project is expected to identify and validate sperm phenotype biomarkers encoded by fertility associated polymorphic genes, and to improve sire management by genetic selection and automated semen evaluation. This project will also yield new methods and potentially new treatments for human male and idiopathic infertility.
• Gene Seek and Zoetis provided industry funds and support to leverage the cost of developing the new bovine genome assembly, $73,000.

Travel support and opportunities for trainings:

• Funding was used to bring students to the annual PAG meeting based on a competitive travel award. Coordinator funds were also used on several occasions to help support the NRSP8 speaker at PAG.

Major impact products (could be potential impact):

• Genomic selection has dramatically improved the rate of genetic progress within the US dairy industry. The dairy industry has used SNP-chips to genotype over 1 million dairy cattle. Application of GS reduced animal selection generation interval (from 5 years to less than one year) and has increased prediction accuracy by more than 30 percent for an estimated annual benefits of $100 million per year.
• Genomic selection is starting to be implemented in the US beef industry.
• Development of a 173,609 SNP functional variant assay containing variants highly enriched for rare functional variation within the bovine genome and including 82,979 variants that alter amino acids within gene products, 665 Indels that either alter frame or add/delete amino acids, and 2017 splice site variants. The assay is currently publicly available through GeneSeek.

HORSE

http://www.uky.edu/Ag/Horsemap/

Direct contributions to Objective 1:

• A new reference genome build (EqCab 3.0) was created for the horse and shared among workshop participants. Public release and publication is expected in late 2017. Morris Animal Foundation, NRSP-8 coordinator and other federal funds supported this work. Impact(s): The new assembly improved gene annotation, increased contig N50 from 112 Kb to 1.4 Mb, and eliminated most of the regions with ambiguous sequence (“Ns”). The improved reference will increase the power and efficacy of genomics research to discover the genes and alleles underlying disease and economically important performance traits in the horse.
• The annotation of the horse genome was improved through investigations of gene expression and splice variation that occurs among diverse tissues. Data supporting wide- scale annotations of the horse genome were published in several reports (2013-2016). Impact(s): Improved annotation provides context for the discoveries by making it possible to identify the functional aspects of genetic variation.
• SNP and insertion-deletion polymorphism discovery was performed using whole genome sequence from 153 horses as part of an effort to design 2M and 670K SNP Affymetrix SNP arrays. Impact(s): This work documents the extent of variation that exists among 24 horse breeds and made genotypes from 485 horses across 2M SNPs publically available providing raw material for use in developing research tools. (Schaefer RJ, et al. Developing a 670k genotyping array to tag~ 2M SNPs across 24 horse breeds. BMC Genomics 18.1 (2017): 565).

Direct contributions to Objective 2:

• An assay tool to assay ~65K SNPs (SNP70) was developed to replace the ~54K SNP (SNP50) tool in 2013. The development of this tool was a collaborative activity of the NRSP-8 community and made publicly available. An imputation pipeline between these two moderate-density arrays was developed. (McCoy AM, McCue ME. Validation of imputation between equine genotyping arrays. Animal Genetics 45:153, 2014. PMCID: PMC4000747.) Impact(s): Developing this tool and imputation pipeline made it possible to continue to perform genome-wide analyses that impact the health and welfare of horses.
• SNP discovery based on whole genome sequence from 153 horses was used to construct the next generation 2M and 670K SNP Affymetrix SNP arrays for equine whole genome analyses. The 670K array is designed for imputation and enables data from prior lower density SNP arrays to be imputed up to ~1.8M SNPs. The equine 670K SNP chip was made available in 2015. (Schaefer RJ, et al. Developing a 670K genotyping array to tag~ 2M SNPs across 24 horse breeds. BMC Genomics 18.1 (2017): 565.). Impact(s): This 670K array and imputation resource improves genome coverage more than 30-fold over the medium density (54K and 65K) SNP arrays. More than 20,000 670K genotyping arrays have been used to date. This increase in SNP density will allow for GWAS in genetic diverse breeds of economic importance such as the American Quarter Horse (~4 million registered individuals).
• Because of the closing of the commercial operation of the BAC library, the primary CHORI 241 BAC library was moved from the Children’s' Hospital of Oakland to the laboratory of Samantha Brooks (co-coordinator) at the University of Florida. Impact(s): This will ensure continued access to the library for equine researchers. This resource is key for investigating the broader aspects of structure and organization of the horse genome.

Direct contributions to Objective 3:

• Horse technical committee members joined the FAANG initiative to generate gene expression data for 38 of tissues from two horses. In connection, competitive, extramural industry funding was obtained to further develop this dataset. Impact(s): This resource will empower research in the area of functional genomics.
• The horse genomics community actively utilized the collaborative resources provided in the AnimalGenome.org Data Repository. The site hosts large shared files, prepublication works and polymorphism data.
• Horse specific transcriptome assemblies not yet curated by NCBI were made available at AnimalGenome.org and through GitHub (https://github.com/drtamermansour/horse_trans). Impact(s): This resource increases the publically availability of equine transcriptional data and will improve genome annotation.
• With the assistance of horse genome researchers, the AnimalQTL database added horse to the species list. Impact(s): This resource provides rapid access to 1,245 equine QTL and associated metadata.
• Horse genome workshop members deposited 1,524 genomic SRA archives for the horse. These accessions contain many fully re-sequenced genomes, as well as targeted datasets generated by diverse NGS platforms. Impact(s): This resource increases the publically availability of equine whole genome sequence and transcriptomic data.

Communication: 

• Additional workshops were conducted for NRSP-8 participants in connection with the International Society of Animal Genetics ([ISAG] 2016 [Salt Lake City], ISAG 2014 [Xian, China], ISAG 2012 [Cairns, Australia], and ISAG 2017 [Dublin, Ireland]). Impact(s): These meetings facilitated communication and collaborations among international scientists working on all species and extended discussions conducted at the annual NRSP-8 workshops.
• Additional workshops were conducted with support of the Dorothy Russell Havemeyer Foundation that focused on issues related to horse genomics (2013 [Azores, Portugal], 2015 [Hannover, Germany], 2018 [planned, Pavia, Italy]). Impact(s): These workshops include the entire international horse genomics research community and facilitate exchange of information and collaboration between scientists.
• Following the identification of critical needs in coordinating collaborations across institutions for new and evolving projects, an initiative to provide a database of ongoing work is now hosted thorough collaboration with the Interbull.org service. Impact(s): This database currently provides a listing of projects recruiting samples, but may eventually expand to include file sharing for exchange of SNP and NGS datasets.

Research support mini-grants (coordinator grants):

• Matching funds provided to support development of the SNP70 SNP genotyping array (~65K SNPs) for discovery research on the genomics of horses.
• Matching Funds provided to support development of the 670K SNP genotyping array. Primary funding from USDA-NIFA ( Molly McCue PI) along with coordinator funds were used to develop a 2M test array. 670K SNPs were selected to tag ~1.8M SNPs across 24 horse breeds.
• Matching funds provided for EqCab 3.0. Primary funding from the Morris Animal Foundation. Improved predictions from assembly.
• Matching funds provided to develop FAANG resources for horse; primary funding came from Grayson-Jockey Club Research foundation project Developing resource for functional genomics research.

Leveraged funds and stakeholders’ use of project outputs:

From 2012-2017, the equine investigators leveraged the tools and resources generated through NRSP-8 to obtain $22,845,204 in additional funding. This included $14,605,017 in funding from federal sources, $4,799,843 in funding from private foundations and industry sources and $3,440,344 in intramural funding. Selected grants are highlighted below.

• “Genetic diversity and selection in the domestic horse.” Dr. Molly McCue PI, Dr. James Mickelson Co-I, and others $499,481 USDA-AFRI. Impact(s): This proposal quantified genetic diversity and to identify functional alleles that cause variation in size, locomotion and athletic phenotypes among 36 domestic horse breeds.
• “Tools to Link Genotype to Phenotype in the Horse.” Dr. Molly McCue PI, Dr. James Mickelson Co-I, and others. $499,727 USDA-NIFA. In this proposal builds upon the recent development of high-density SNP arrays to develop tools that further facilitate GWAS in the horse by: 1) enabling complementary GWAS approaches including gene, haplotype, and pathway-based analyses through SNP-to-gene mapping and the construction of a haplotype map; 2) increasing marker density by developing an imputation resource; and 3) constructing context-specific co-expression networks for integrated network-based association analysis.  Prioritization of candidate genes is assisted by: 4) refining the physical annotation of mRNAs, lncRNAs, and miRNAs; and 5) improving functional annotation of these loci through tissue-specific gene expression and gene co-expression networks. Finally, the identification of functional alleles will be accelerated by 6) developing a comprehensive catalog of genetic variants from WGS of >450 horses.
• “Functional Prioritization of Candidate Genes and Alleles for Equine Metabolic Syndrome.” Dr. Molly McCue PI, Dr. James Mickelson Co-I. $499,815 USDA-NIFA. Genome wide association in Welsh Ponies (WP) and Morgan horses has identified >180 chromosomal regions of interest (ROI) harboring >3,000 positional candidate genes associated with Equine Metabolic Syndrome (EMS) phenotypes. The objectives of this proposal are to 1) prioritize candidate genes using skeletal muscle and/or adipose tissue gene expression or alterations in serum metabolite abundance to support their role in EMS pathophysiology; and 2) identify the functional alleles underlying EMS phenotypes.
• “Discovering Causal Variants for Complex Disease Using Functional Networks in the Horse.” Dr. Rob Schaefer PI, Dr. Molly McCue mentor. $150,000 USDA-NIFA. The goals of this grant are to develop software tools to integrate available sources of genomic data and functional data (WGS, SNP, RNA-sequencing, proteomics and metabolomics) in agricultural species to better understand complex phenotypic traits using metabolic syndrome in the domestic horse as a test case.
• “Protein Networks Mediating Airway Hyper-Responsiveness In Equine Airways.” Dr. Chipper Swiderski $438,153 USDA-AFRI. This grant seeks to better understand the etiopathogenesis of Recurrent Airway Obstruction in the horse through proteomic studies and improved annotation of genes expressed during disease exacerbation.
• “Comparative Genomics in Qatar.” Dr. Doug Antczak and Dr. Samantha Brooks, $1,030,000 Qatar National Research Foundation- National Priorities Research Program. This project will document variation and signatures of selection in desert breeds of horse, as part of a larger effort to improve genomic resources in desert adapted hoof stock.
• “Identification of Genetic Factors Responsible for Establishment of Equine Arteritis Virus Carrier State in Stallions.” Dr. Uri Balasuriya PI, Dr. Ernie Bailey Co-PI and others. $2,930,000 USDA-AFRI.

Travel support and opportunities for training:

• Travel of 64 students/postdocs was funded to attend the Equine workshop at PAG meetings (2012-2016). The purpose of the travel award program is to help graduate students and postdocs to travel to the meeting to present their research.
• Support for five NRSP-8 members to attend GO-FAANG workshop in Washington DC to provide leadership horse group in connection with this initiative.
• Member sent to participate in Hack-a-thon in Europe 2016 in support of FAANG activities. Integration with international efforts to develop functional genomics databases for animal genomics.

Major impact products (could be potential impact):

• Development of 4 SNP genotyping arrays (54K, 65K, 670K and 2M). Impact(s): These arrays allow for efficient and economic performance of dozens of genome-wide analyses in the horse.
• Genomic diagnostics in the horse have now expanded to include commercially available tests over 100 markers contributing to more than 40 diverse traits. Impact(s): Costs per test are falling, and as adoption of genomic selection and mandatory genetic testing increases across the industry, translating in to reduced economic losses due to genetic disease.
• Diagnostic tests created for markers related to performance, disease and color, including DMRT3 and gait, TBX3 and dun color, SHOX and dwarfism, B4GALT7 and dwarfism, ACAN and dwarfism, RFWD3 and Appaloosa color pattern, SERPINB11 and hoof quality, KIT and spotting in donkeys, HOXD3 and occipitoalantoaxial malformation, CXCL16 and susceptibility to equine arteritis virus.
• Additional targets for investigation were identified through genome-wide analyses including signatures of selection in 38 horse breeds, genomic loci contributing to osteochondrosis, recurrent laryngeal neuropathy and others.
• Molecular tests to identify chromosome abnormalities were reported and additional test are being developed. Impact(s): Chromosome abnormalities are the most common genetic cause of infertility and disease amongst horses and molecular tests are much less expensive than conventional karyotyping.
• The major histocompatibility complex plays a major role in the occurrence and consequences of allergic and infectious diseases. Determinants playing a role in specific diseases were identified and methods were developed to improve our ability to identify yet other MHC determinants. Impact(s): MHC is a genetically complex region but plays a major role in immune responses.  Knowledge of the MHC remains incomplete for all species and but research is turning up applications, especially with respect to vaccine design and immune therapy.

POULTRY

https://www.animalgenome.org/poultry/

Direct contributions to Objective 1:

• The chicken genome build (Galllus_gallus-5.0) was released to the public in 2015. Impact(s): This improved build, which was aided by long single molecular sequencing and finished BACs, yielded a gain of 180 Mb in assembled bases and provided coverage to 3 previously missing autosomes. As the reference genome, this invaluable resource greatly enhances the ability to identify genes and genetic variations associated with traits of agronomic interest.
• A turkey draft genome was generated from next generation sequencing and a turkey BAC contig (physical) map.
• Guidelines for standardized gene nomenclature for chicken genes were developed to assign nomenclature to (1) MHC genes; (2) genes highly expressed in egg white, yolk and eggshell; (3) histone; and (4) myosin genes. Impact(s): This nomenclature was shared with NCBI and Ensembl.

Direct contributions to Objective 2:

• Very high-density SNP mapping (ca. 600K SNP) panels have been developed and along with 60K SNP chips. Impact(s): These genotyping arrays are being employed in genome-wide association studies (GWAS) and genomic selection (GS).
• Efforts have been initiated to annotate the chicken genome, especially with respect to regulatory elements. In brief, datasets for transcripts, histone marks, methylation and more have been integrated to identify promoters, enhancers, and silencers. Impact(s): This information is vital to help connect genotypic variation to phenotypic variation.
• Transcript and comparative genome hybridization arrays were developed and distributed.

Direct contributions to Objective 3:

• Over 40 unique chicken research lines and their derived materials have been shared with amongst investigators to expand studies on the chicken genome.
• DNA from the East Lansing international reference mapping population has been sent to many laboratories throughout the world. Similarly, DNA from the junglefowl used to generate the reference sequence assembly has been widely distributed.

Communication: 

• Provided support for members to attend GO-FAANG meeting and/or other multi-state research project meetings to enhance communications of activities, communicate about resources.

Research support mini-grants (coordinator grants):

• Provided $30,000 in funds towards the USDA AFRI Animal ENCODE proposal; Huaijun Zhou, UC Davis – PI.
• Financial support provided to W. Warren, Washington U., St Louis, for sequencing of microchromosomes, which has aided to fill in gaps in the genome assembly.
• Financial support provided to M. Delany, UC Davis, to create a capture arrays and sequence the wg-2 mutation in the Wingless-2.331 congenic inbred line.
• Financial support provided to H. Zhou, UC Davis, for challenge experiments involving highly pathogenic Newcastle Disease Virus (NDV) and the Fayoumi and Leghorn strains in order to characterize genetic resistance.
• Financial support provided to B. Muir, Purdue U. to create a synthetic resource population using 8 diverse genetic lines to fine map genetic resistance to Marek’s disease.
• Financial support provided to M. Miller, City of Hope, for further sequencing of microchromosome 16 BAC clones to improve understanding of the MHC/Rfp-Y complex.

Leveraged funds and stakeholders’ use of project outputs:

From 2013-2017, the investigators and stakeholders leveraged the tools and resources generated through NRSP-8 to obtain at least $18,675,963 additional funding from federal sources and $150,000 in funding from industry sources (Cobb Vantress supported efforts towards the improvement of the chicken genome assembly). Selected grants are highlighted below:

• 2013-2017: USDA NIFA 2013-67015-21357. “Improving the chicken genome assembly and annotation.” Warren W, CT Brown, H Cheng H, and J Dodgson. $485,690. This grant supported the improvement of the chicken genome assembly and annotation by filling in known gaps within and between existing scaffolds, and refining microchromosome linkage maps for localization of unplaced sequences. Impacts(s): With the biology becoming reliant on a genome assembly, the higher quality chicken assembly aided all efforts especially with respect to identifying genes and pathways of agronomic importance. Furthermore, other avian genomes were improved as they also rely on the chicken genome assembly as their reference as well.
• 2012-2017. USDA NIFA 2012-67015-19419. “Enhancing genetic resistance to Marek’s disease in chicken via allele-specific expression screens and genome-wide selection.” This grant supported the identification of genes and genetic markers associated with resistance to Marek’s disease (MD), a herpesvirus-induced lymphoma of chickens. Hypothesizing that differences in gene expression (when, where, and how much) are the major contributors of phenotypic variation for complex traits such as disease resistance, SNPs that exhibit allele-specific expression (ASE) in response to Marek’s disease virus infection were identified. These ASE SNPs were found to account for over 83% of the genetic variance and were 125% more accurate in genomic selection compared to pedigree evaluation (i.e., BLUP). Impact(s): These results support the hypothesis that phenotypic variation in traits is primarily due to changes in regulation of gene expression rather than other sources such as differences in protein composition. Furthermore, we have identified most of the genes that confer MD genetic resistance, which should help reduce the ~$1-2 billion in annual losses associated with MD.
• 2013-2018. USAID AID-OAA-A-13-00080 “Improving food security in Africa by enhancing resistance to disease and heat in chickens; Feed the future innovation lab for genomics to improve poultry” Zhou H. Bunn D, Gallardo G, Lamont S. Dekkers J. et al. $6,000,000. This grant uses contemporary high-throughput genetic technologies of SNP chips and functional genomics, along with targeted genome resequencing and extensive statistical and bioinformatic analyses to dissect and identify the genetic factors of the chicken that enhance its resistance against NDV and heat stress by assessing diverse populations of chickens, including well- characterized research lines and highly relevant local African ecotypes. Impact: The project has significantly improved institute capacity (infrastructure has developed in Africa) and human capacity building, including by training of students and scientists both on-site in Africa and in the US in essential skills that enable the African partners to sustain and disseminate the results of this project. Project outcomes are expected to reduce poverty, hunger, and malnutrition, and empower women through increased agricultural productivity achieved by decreasing the major losses that currently occur as a result of Newcastle disease and heat stress in African chickens.
• 2015-2017. USDA NIFA 2015-67015-22940 “Genome wide identification and annotation of functional regulatory regions in livestock species” H. Zhou, P. Ross, I. Korf. $500,000. This grant supported research effort in functionally annotating regulatory elements in the three major farm animal species by integrative bioinformatic analysis of RNA-seq, DNase-seq and ChIP-seq data from the eight most important tissues. Impact: This will generate first line of re-annotation of gene structure and landscape of functional regulatory elements in chicken, bovine, and swine genomes, and will develop a framework to continue a more in-depth functional annotation of these genomes and other agricultural animals.
• 2011-2016. USDA NIFA “System Biology Analysis & Modeling Of Complex “Omic” Data: A Service Center Approach”. Zhou H. Drake K. $750,000. This grant has supported an effort in collaboration with Seralogix, to provide sophisticated systems biology and modeling analysis with visualization for a total of 12 projects generating more than 100 data analysis module reports. These projects include microarray and RNA-seq data from cattle, sheep, chicken and mice in the areas of nutrition, reproduction, growth and disease. Impacts: Results have contributed greatly to our understanding and formulation of new hypotheses that are advancing the fields of animal infection, nutrition, reproduction, and physiology.
• 2015-2018. USDA NIFA 2015-67015-23093 and BBSRC BB/M028208/1. “US-UK Collaborative Research: Host Resistance to Avian Pathogenic E. coli” Lamont, S.J. (PD), Wolc, A; Kaiser, P. (dec.), Stevens, M., Vervelde, L. $499,999 (USDA). This grant supported the genomic, molecular and cellular characterization of the host-pathogen interactions between chickens and avian pathogenic E. coli (APEC), through the use of unique inbred chicken lines in both countries that differ in resistance to avian pathogenic E. coli (APEC), analysis of transgenic chickens in which all cells of the myeloid lineage express a fluorescent protein to aid the phenotyping of APEC-infected cells, definition of the transcriptome of infected cells, association of resistance with bird genetic variation (in structure and expression) through GWAS and RNA-seq analysis, and validation of selected research findings for translation into industry application. Impact(s): The impacts of this grant will be a reduction of the negative impact of respiratory APEC on the poultry industry, improved poultry health and vaccine strategies, and decreased use of antibiotics in food animals.

Travel support and opportunities for trainings:

• Provided financial support for over 40 students, postdocs, members, and speakers to attend the PAG Poultry Workshop (2013-2017).

Major impact products (could be potential impact):

• Genomic selection is now routinely implemented in both the meat (broiler) and egg (layer) breeding companies. This has greatly accelerated the genetic progress required by the industry to meet the growing consumer demand. Furthermore, poultry health and welfare have been enhanced.
• The chicken genome assembly reached the stage that scientists can confidently identify genes and genetic variations associated with biological traits, many of which are highly relevant to the poultry industry.
• The draft assembly of the turkey genome has been released, which affords the opportunity for efforts similar to those in the poultry industry, e.g., biological characterization, genomic selection.

SHEEP/GOAT

http://www.animalgenome.org/sheep/

Direct contributions to Objective 1:

• Reference genomes were published for goat in Nature Biotechnology in 2013 and for sheep in Science in 2014. An improved reference genome for the goat was published in Nature Genetics in 2017 that leveraged single molecule sequencing plus chromatin conformation capture to create a genome assembly with chromosome length scaffolds. Impact(s): The reference genomes advanced the status of mammal genome assembly and annotation technology at the time of publication. They also enabled comparative genomic insight into rumen biology, and expanded understanding of genes underlying numerous economically important traits. The improved goat genome reference elevated the standard for quality of mammal reference genome assemblies. Together, these results will underpin all future efforts to improve genetics of productive efficiency in sheep and goats.

Direct contributions to Objective 2:

• A sheep 600K SNP chip and a goat 52K SNP chip were both released for research in 2014. Impact(s): This dramatic increase in SNP density for sheep and the first genome-wide medium density panel for goat have enabled powerful new tools including genome-wide association and genomic selection to dissect and improve numerous traits in sheep and goats.

Direct contributions to Objective 3:

• A sheep genomes database has been assembled to provide a public, large-scale warehouse for global sheep genetic diversity. The database now includes re-sequencing data from almost 1,000 sheep genomes with an overall total of nearly 100 million identified sequence variants. Impact(s): This resource will accelerate the identification of causal variants for numerous traits and enable previously inconceivable analyses.

Communication: 

• Strategic planning conference calls with international attendance were held in 2015 and 2016, in addition to annual meetings at PAG and biennial meetings at International Society for Animal Genetics (ISAG). Impact(s): These contributed to the development and implementation of the Ovine FAANG Project tissue collection in the U.S. and recent successful leveraged grant funding.

Research support mini-grants (coordinator grants):

• Ovine FAANG (Functional Annotation of ANimal Genomes) Project tissue collection ($15,000 Coordinator funds). Sample collection of 100 tissues from a new reference genome sheep was conducted in 2016. Impact(s): Use of the reference genome anim

Aquaculture Publications -

Jin Y, Zhou T, Li N, Liu S, Xu X, Tan S, Shi H, Yang Y, Yuan Z, Wang W, Pan Y, Gao D, Dunham R, Liu ZJ. 2018. JAK and STAT members in channel catfish: Identification, phylogenetic analysis and expression profiling after bacterial infection. Developmental and Comparative Immunology, in press.

Yuan Z, Huang W, Liu S, Xu P, Dunham R, Liu ZJ. 2018. Historical demography of common carp estimated from individuals collected from various parts of the world using the pairwise sequentially Markovian coalescent approach. Genetica, in press.

Yang Y, Fu Q, Liu Y, Wang X, Dunham R, Liu S, Bao L, Zeng Q, Zhou T, Li N, Qin Z, Jiang C, Gao D, Liu ZJ. 2018. Comparative transcriptome analysis reveals conserved branching morphogenesis related genes involved in chamber formation of catfish swimbladder. Physiological Genomics, in press.

Fu Q, Yang Y, Li C, Zeng Q, Zhou T, Li N, Liu Y, Liu S, Li D, Liu ZJ. 2017. The CC and CXC chemokine receptors in channel catfish (Ictalurus punctatus) and their involvement in disease and hypoxia responses. Developmental and Comparative Immunology 77: 241-251.

Fu Q, Yang Y, Li C, Zeng Q, Zhou T, Li N, Liu Y, Li Y, Wang X, Liu S, Li D, Liu ZJ. 2017. The chemokinome superfamily: II. The 64 CC chemokines in channel catfish and their involvement in disease and hypoxia responses. Developmental and Comparative Immunology 73: 97-108.

Geng X, Liu S, Yuan Z, Jiang Y, Zhi D, and Liu ZJ. 2017. A genome wide association study reveals that genes with functions for bone development are associated with body conformation in catfish. Marine Biotechnology 19: 570-578.

Wang X, Liu S, Dunham R, Liu ZJ. 2017. Effects of strain and body weight on low-oxygen tolerance of channel catfish. Aquaculture International 25: 1645-1652. DOI: 10.1007/s10499-017-0125-2

The Aquaculture Genomics, Genetics and Breeding Workshop, Abdelrahman H, ElHady M, Alcivar-Warren A, Allen S, Al-Tobasei R, Bao L, Beck B, Blackburn H, Bosworth B, Buchanan J, Chappell J, Daniels W, Dong S, Dunham R, Durland E, Elaswad A, Gomez-Chiarri M, Gosh K, Guo X, Hackett P, Hanson T, Hedgecock D, Howard T, Holland L, Jackson M, Jin Y, Kahlil K, Kocher T, Leeds T, Li N, Lindsey L, Liu S, Liu ZJ*, Martin K, Novriadi R, Odin R, Palti Y, Peatman E, Proestou D, Qin G, Reading B, Rexroad C, Roberts S, Salem M, Severin A, Shi H, Shoemaker C, Stiles S, Tan S, Tang KFJ, Thongda W, Tiersch T, Tomasso J, Tri Prabowo W, Vallejo R, van der Steen H, Vo K, Waldbieser G, Wang H, Wang X, Xiang J, Yang Y, Yant R, Yuan Z, Zeng Q, and Zhou T. 2017. Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research. BMC Genomics 18: 191. DOI 10.1186/s12864-017-3557-1

Wang X, Liu S, Yang Y, Fu Q, Abebe A, Liu ZJ. 2017. Identification of NF-κB related genes in channel catfish and their expression profiles in mucosal tissues after columnaris bacterial infection. Developmental and Comparative Immunology 70: 27-38.

Li N, Zhou T, Geng X, Jin Y, Wang X, Liu S, Xu X, Gao D, Li Q, Liu ZJ. 2017. Identification of novel genes significantly affecting growth in catfish through GWAS analysis. Molecular Genetics and Genomics, in press. doi.org/10.1007/s00438-017-1406-1

Yuan Z, Liu S, Bao L, Zhou T, Liu ZJ. 2017. Comparative genome analysis of 52 fish species suggests differential associations of repetitive elements with their living aquatic environments. BMC Genomics, in press.

Zhong X, Wang X, Zhou T, Jin Y, Tan S, Jiang C, Geng X, Li N, Shi H, Zeng Q, Yang Y, Yuan Z, Bao L, Tian C, Liu S, Li Q, Liu ZJ. 2017. Genome-wide association study reveals multiple novel QTL associated with low-oxygen tolerance in hybrid catfish. Marine Biotechnology 19: 379-390. DOI: 10.1007/s10126-017-9757-5.

Li Y, Geng X, Bao L, Elaswad A, Huggins KW, Dunham R, Liu ZJ. 2017. A deletion in the Hermansky-Pudlak syndrome 4 (Hps4) gene appears to be responsible for albinism in channel catfish. Molecular Genetics and Genomics, in press. DOI 10.1007/s00438-017-1302-8

Nunes, José de Ribamar da Silva, Liu S, Pértille F, Perazza C, Vera Maria Fonseca de Almeida Val, Hilsdorf AWS, Liu ZJ, & Coutinho LL. 2017. Large-scale SNP discovery and construction of a high-density genetic map of tambaqui (Colossoma macropomum) through genotyping-by-sequencing. Scientific Report 7: 46112.

Zhou T, Liu S, Geng X, Jin Y, Jiang C, Bao L, Yao J, Zhang Y, Zhang J, Sun L, Wang X, Li N, Tan S, Liu ZJ. 2017. GWAS analysis of QTL for enteric septicemia of catfish and their involved genes suggest evolutionary conservation of a molecular mechanism of disease resistance. Molecular Genetics and Genomics 292: 231-242. DOI 10.1007/s00438-016-1269-x

Gao S, and Liu ZJ. 2017. Taste receptors and gustatory associated G proteins in channel catfish, Ictalurus punctatus. Comparative Biochemistry and Physiology, part D, Genomics and Proteomics 21: 1-9. doi.org/10.1016/j.cbd.2016.10.002.

Gao S, Liu S, Yao J, Li N, Yuan Z, Zhou T, Li Q, and Liu ZJ. 2017. Genomic organization and evolution of olfactory receptors and trace amine-associated receptors in channel catfish, Ictalurus punctatus. Biochimica et Biophysica Acta - General Subjects 1861 (2017): 644-651. Doi 10.1016/j.bbagen.2016.10.017.

Zeng Q, Fu Q, Li Y, Waldbieser G, Bosworth B, Liu S, Yang Y, Bao L, Yuan Z, Li N, and Liu ZJ. 2017. Development of a 690K SNP array in catfish and its application for genetic mapping of 250,000 markers and validation of the reference genome sequence.  Scientific Report 7: 40347 DOI:10.1038/srep40347.

Zhou T, Li N, Liu S, Jin Y, Fu Q, Gao S, Wang X, Liu ZJ. 2017. The NCK and ABI adaptor genes in catfish and their involvement in ESC disease responses. Developmental and Comparative Immunology 73: 119-123.

Tian C, Tan S, Bao L, Zeng Q, Liu S, Yang Y, Zhong X, Liu ZJ. 2017. DExD/H-box RNA helicase genes are differentially expressed between males and females during the critical period of male sex differentiation in channel catfish. Comparative Biochemistry and Physiology part D 22: 109-119.

Fu Q, Zeng Q, Li Y, Yang Y, Li C, Zhou T, Li N, Liu S, Yao J, Jiang C, Li D, Liu ZJ. 2017. The chemokinome superfamily in channel catfish: I. CXC subfamily and their involvement in disease defense and hypoxia responses. Fish and Shellfish Immunology 60: 380-390.

Puritz, J. B., & Lotterhos, K. E. (2017). Expressed Exome Capture Sequencing (EecSeq): a method for cost-effective exome sequencing for all organisms with or without genomic resources. bioRxiv, 223735.

Qi, H., Song, K., Li, C., Wang, W., Li, B., Li, L., Zhang, G. (2017) Construction and evaluation of a high-density SNP array for the Pacific oyster (Crassostrea gigas). PLoS One, 12(3), e0174007.

Bachère, E., Barranger, A., Bruno, R., Rouxel, J., Menard, D., Piquemal, D., & Akcha, F. (2017). Parental diuron-exposure alters offspring transcriptome and fitness in Pacific oyster Crassostrea gigas. Ecotoxicology and Environmental Safety, 142, 51-58.

Gutierrez, A. P., Turner, F., Gharbi, K., Talbot, R., Lowe, N. R., Peñaloza, C., ... & Houston, R. D. (2017). Development of a medium density combined-species SNP Array for Pacific and European oysters (Crassostrea gigas and Ostrea edulis). G3: Genes, Genomes, Genetics, 7(7), 2209-2218.

Gutierrez, A., Bean, T. P., Hooper, C., Stenton, C. A., Sanders, M. B., Paley, R. K., & Houston, R. D. (2017). A genome-wide association study for host resistance to Asteroid Herpesvirus in Pacific oysters (Crassostrea gigas). bioRxiv, 223032.

Song, K., Li, L., & Zhang, G. (2017). The association between DNA methylation and exon expression in the Pacific oyster Crassostrea gigas. PloS one, 12(9), e0185224.

Gonzalez-Romero, R., Suarez-Ulloa, V., Rodriguez-Casariego, J., Garcia-Souto, D., Diaz, G., Smith, A., ... & Eirin-Lopez, J. M. (2017). Effects of Florida Red Tides on histone variant expression and DNA methylation in the Eastern oyster Crassostrea virginica. Aquatic Toxicology, 186, 196-204.

Li, B., Song, K., Meng, J., Li, L., & Zhang, G. (2017). Integrated application of transcriptomics and metabolomics provides insights into glycogen content regulation in the Pacific oyster Crassostrea gigas. BMC genomics, 18(1), 713.

Gavery MR, Roberts SB. (2017) Epigenetic considerations in aquaculture PeerJ 5:e4147 doi: 10.7717/peerj.4147

Samuel J. White, Brent Vadopalas, Katherine Silliman & Steven B. Roberts (2017) Genotoype-by-sequencing of three geographically distinct populations of Olympia oysters, Ostrea lurida Scientific Data 4, Article number: 170130 doi: 10.1038/sdata.2017.130

Heare JE, White SJ, Vadopalas B, Roberts SB. (2018) Differential response to stress in Ostrea lurida as measured by gene expression PeerJ 6:e4261.

Emma B. Timmins-Schiffman, Grace A Crandall, Brent Vadopalas, Michael E. Riffle, Brook L. Nunn and Steven Roberts (2017) Integrating discovery-driven proteomics and selected reaction monitoring to develop a non-invasive assay for geoduck reproductive maturation Journal of Proteome Research doi: 10.1021/acs.jproteome.7b00288

Al-Tobasei, R., Ali, A., Leeds, T.D., Liu, S., Palti, Y., Kenney, B. & Salem, M. (2017). Identification of SNPs associated with muscle yield and quality traits using allelic-imbalance analyses of pooled RNA-Seq samples in rainbow trout. BMC Genomics, 18: 582

Campbell, N.R., C. Kamphaus, K. Murdoch, and S.R. Narum.  2017. Patterns of genomic variation in Coho salmon following reintroduction to the interior Columbia River. Ecology and Evolution 7:10350-10360.

Cleveland, B.M., Leeds, T.D., Rexroad III, C.E., Summerfelt, S., Good, C., Davidson, J., May, T., Wolters, W.R., Plemmons, B., Kenney, P. 2017. Genetic line by environment interaction on rainbow trout growth and processing traits. North American Journal of Aquaculture. 79:140-154.

Koganti, P., Wang, J., Cleveland, B., Ma, H., Weber, G., and Yao, J. 2017. Estradiol regulates expression of miRNAs associated with myogenesis in rainbow trout. Molecular and Cellular Endocrinology, 443, 1-14.

Koganti, P., Wang, J., Cleveland, B.M., and Yao, J. 2017. 17β-Estradiol increases non-CpG methylation in exon 1 of the rainbow trout (Oncorhynchus mykiss) MyoD gene.  Marine Biotechnology 19(4):321-327.

Leeds, T. D., R. L. Vallejo, G. M. Weber, D. Gonzalez-Pena, J. T. Silverstein. 2016. Response to five generations of selection for growth performance traits in rainbow trout (Oncorhynchus mykiss). Aquaculture 465:341-351.

Liu, S., Palti, Y., Martin, K.E., Parsons, J.E., Rexroad, III, C.E. 2017. Assessment of genetic differentiation and genetic assignment of commercial rainbow trout strains using a SNP panel. Aquaculture. 468(1): 120-125.

Ma, H., G. M. Weber, H. Wei, J. Yao. 2016. Identification of mitochondrial genome-encoded small RNAs related to egg deterioration caused by postovulatory aging in rainbow trout. Mar. Biotechnol. 18:584-597.

Macqueen, D.J., Primmer, C.R., Houston, R.D., Nowak, B.F., Bernatchez, L., Bergseth, S., Davidson, W.S., Gallardo-Escárate, C., Goldammer, T., Guiguen, Y., Iturra, P., Kijas, J.W., Koop, B.F., Lien, S., Maass, A., Martin, S.a.M., Mcginnity, P., Montecino, M., Naish, K.A., Nichols, K.M., Ólafsson, K., Omholt, S.W., Palti, Y., Plastow, G.S., Rexroad, C.E., Rise, M.L., Ritchie, R.J., Sandve, S.R., Schulte, P.M., Tello, A., Vidal, R., Vik, J.O., Wargelius, A. & Yáñez, J.M. (2017). Functional Annotation of All Salmonid Genomes (FAASG): an international initiative supporting future salmonid research, conservation and aquaculture. BMC Genomics, 18: 484.

Matala, A.P., B. Allen, S.R. Narum, and E. Harvey. 2017. Restricted gene flow between resident Oncorhynchus mykiss and an admixed population of anadromous steelhead. Ecology and Evolution 7:8349-8362.

Narum, S.R., P. Gallardo, C. Correa, A. Matala, D. Hasselman, B.J.G. Sutherland, and L. Bernatchez. 2017. Genomic patterns of diversity and divergence of two introduced species in Patagonia, South America. Evolutionary Applications 10:402-416.

Paneru, B.D., Al-Tobasei, R., Kenney, B., Leeds, T.D. & Salem, M. (2017). RNA-Seq reveals MicroRNA expression signature and genetic polymorphism associated with growth and muscle quality traits in rainbow trout. Scientific Reports, 7: 9078.

Vallejo, R.L., Leeds, T.D., Gao, G., Parsons, J.E., Martin, K.E., Evenhuis, J., Fragomeni, B.O., Wiens, G.D., Palti, Y. 2017. Genomic selection models double the accuracy of predicted breeding values for bacterial cold water disease resistance compared to a traditional pedigree-based model in rainbow trout aquaculture. Genetics Selection Evolution. 49(17):1-33.

Vallejo, R.L., Leeds, T.D., Gao, G., Parsons, J.E., Martin, K.E., Evenhuis, J.P., Fragomeni, B.O., Wiens, G.D. & Palti, Y. (2017). Genomic selection models double the accuracy of predicted breeding values for bacterial cold water disease resistance compared to a traditional pedigree-based model in rainbow trout aquaculture. Genetics Selection Evolution, 49: 17.

Salger, S.A., Reading, B.J., and Noga, E.J. 2017. Tissue Localization of Piscidin Host-Defense Peptides during Striped Bass (Morone saxatilis) Development. Fish and Shellfish Immunology 61: 173-180.

Fuller, S.A., Rawles, S.D., McEntire, M.E., Bader, T.J., Riche, M, Beck, B.H., and Webster, C.D. 2017. White bass (Morone chrysops) preferentially retain n‑3 PUFA in ova when fed prepared diets with varying FA content. Lipids 52: 823-836.

Fuller, S.A., Beck, B.H., Rawles, S.D., Green, B.W., Li, C., Peatman, E. Childress, C.J., Gaylord, T.G., Barrows, F.T., McEntire, M.E. 2017. Hybrid striped bass National Breeding Program:  Research towards genetic improvement of a non-model species. Bulletin of Japan Fisheries Research and Education Agency 45: 89-100.

Horse Publications -

Al Abri, M.A., König von Borstel, U., Strecker, V. and Brooks, S.A. (2017) 'Application of Genomic Estimation Methods of Inbreeding and Population Structure in an Arabian Horse Herd', Journal of Heredity, 108(4), 361-368, available: http://dx.doi.org/10.1093/jhered/esx025.

Aleman M, Finno CJ, Weich K, Penedo MCT. Investigation of known genetic mutations of Arabian horses in Egyptian Arabian foals with Juvenile Idiopathic Epilepsy. J Vet Intern Med 2017; doi: 10.1111/jvim.14873. [Epub ahead of print].

Balmer P, Bauer A, Pujar S, McGarvey KM, Welle M, Galichet A, Müller EJ, Pruitt KD, Leeb T, Jagannathan V. A curated catalog of canine and equine keratin genes. PLoS One. 2017 Aug 28;12(8):e0180359. doi: 10.1371/journal.pone.0180359. eCollection 2017. PMID: 28846680

Bauer A, Hiemesch T, Jagannathan V, Neuditschko M, Bachmann I, Rieder S, Mikko S, Penedo MC, Tarasova N, Vitková M, Sirtori N, Roccabianca P, Leeb T, Welle MM. A Nonsense Variant in the ST14 Gene in Akhal-Teke Horses with Naked Foal Syndrome.  G3 (Bethesda). 2017 Apr 3;7(4):1315-1321. doi: 10.1534/g3.117.039511.

Bellone, R.R., Liu, J., Petersen, J.L. Mack, M., Singer-Berk, M., Drögemüller, C., Malvick, J., Wallner, B., Brem, G., Penedo, M.C., & Lassaline, M. (2017) A missense mutation in damage-specific DNA binding protein 2 is a genetic risk factor for limbal squamous cell carcinoma in horses. International Journal of Cancer 141(2):342-353.

Bergmann T, Lindvall M, Moore E, Moore E, Sidney J, Miller D, Tallmadge RL, Myers PT, Malaker SA, Shabanowitz J, Osterrieder N, Peters B, Hunt DF, Antczak DF, Sette A. Peptide-binding motifs of two common equine class I MHC molecules in Thoroughbred horses. Immunogenetics. 2017 69 351-358.

Bordbari MH, Penedo MC, Aleman M, Mickelson JR, Valberg SJ, Finno CJ. Deletion of 2.7kb near HOX3 in an Arabian horse with occipitoatlantoaxial malformation. Anim Genet. 2017 Jun;48(3):287-294.

Brown J, Valberg SJ, Hogg M, Finno CJ. Effect of feeding two RRR-alpha-tocopherol formulations on serum, cerebrospinal fluid and muscle alpha-tocopherol concentrations in horses with subclinical vitamin E deficiency. Equine Vet J, 2017 Apr 22. doi: 10.1111/evj.12692. [Epub ahead of print]

Brunner MAT, Jagannathan V, Waluk DP, Roosje P, Linek M, Panakova L, Leeb T, Wiener DJ, Welle MM. Novel insights into the pathways regulating the canine hair cycle and their deregulation in alopecia X. PLoS One. 2017 Oct 24;12(10): e0186469. doi: 10.1371/journal.pone.0186469. eCollection 2017. PMID: 29065140

Bryan K, McGivney BA, Farries G, McGettigan PA, McGivney CL, Gough KF, MacHugh DE, Katz LM, Hill EW. Equine skeletal muscle adaptations to exercise and training: evidence of differential regulation of autophagosomal and mitochondrial components. BMC Genomics. 2017 Aug 9;18(1):595. doi: 10.1186/s12864-017-4007-9.

Burger D, Thomas S, Aepli H, Dreyer M, Fabre G, Marti E, Sieme H, Robinson MR, Wedekind C.Major histocompatibility complex-linked social signaling affects female fertility. Proc Biol Sci. 2017 Dec 6;284(1868). pii: 20171824. doi: 10.1098/rspb.2017.1824.PMID: 29212724

Canisso IF, Ball BA, Esteller-Vico A, Williams NM, Squires EL, Troedsson MH.  (2017) Changes in maternal androgens and oestrogens in mares with experimentally-induced ascending placentitis.  Equine Vet J.  49(2):244-249. 

Carossino M, Loynachan AT, Canisso IF, Cook RF, Campos JR, Nam B, Go YY, Squires EL, Troedsson MHT, Swerczek T, Del Piero F, Bailey E, Timoney PJ, Balasuriya UBR. (2017) Equine Arteritis Virus Has Specific Tropism for Stromal Cells and CD8(+) T and CD21(+) B Lymphocytes but Not for Glandular Epithelium at the Primary Site of Persistent Infection in the Stallion Reproductive Tract. J Virol.  91e00418-17.

Claes A, Ball BA, Scoggin KE, Roser JF, Woodward EM, Davolli GM, Squires EL, Ball BA.  (2017) The influence of age, antral follicle count and diestrous ovulations on estrous cycle characteristics of mares.  Theriogenology.  97:34-40. 

Dorado J., Anaya G., Bugno-Poniewierska M., Molina A., Mendez-Sanchez A., Ortiz I., Moreno-Millán M., Hidalgo M., Peral García P., Demyda-Peyrás S. 2017. First case of sterility associated with sex chromosomal abnormalities in a jenny. Reprod. Domest Anim. .52 (2) :227-234.

Dürig N, Jude R, Holl H, Brooks SA, Lafayette C, Jagannathan V, Leeb T. Whole genome sequencing reveals a novel deletion variant in the KIT gene in horses with white spotted coat colour phenotypes. Anim Genet. 2017 Aug;48(4):483-485. doi: 10.1111/age.12556. Epub 2017 Apr 26.PMID: 28444912

Dürig N, Jude R, Jagannathan V, Leeb T. A novel MITF variant in a white American Standardbred foal. Anim Genet. 2017 Feb;48(1):123-124. doi: 10.1111/age.12484. Epub 2016 Sep 5.

Durward-Akhurst S, Valberg SJ. Review of immune-mediated muscle diseases in the horse. Vet Path 2017 Jan 1:300985816688755. doi: 10.1177/0300985816688755

Esteller-Vico A, Ball BA, Troedsson MHT, Squires EL.  (2017) Endocrine changes, fetal growth, and uterine artery hemodynamics after chronic estrogen suppression during the last trimester of equine pregnancy.  Biol Reprod.  96(2): 197-210.

Farries G, McGettigan PA, Gough KF, McGivney BA, MacHugh DE, Katz LM, Hill EW. Genetic contributions to precocity traits in racing Thoroughbreds. Anim Genet.2017 Dec 12. doi: 10.1111/age.12622. [Epub ahead of print] PubMed PMID: 29230835.

Fedorka CE, Scoggin KE, Squires EL, Ball BA, Troedsson MHT.  (2017) Expression and localization of cysteine-rich secretory protein-3 (CRISP-3) in the prepubertal and postpubertal male horse.  Theriogenology.  87:187-192. 

Fedorka CE, Scoggin KE, Woodward EM, Squires EL, Ball BA, Troedsson M.  (2017) The effect of select seminal plasma proteins on endometrial mRNA cytokine expression in mares susceptible to persistent mating-induced endometritis.  Reprod Domest Anim.  52(1):89-96.

Fenn, DJ, T. Raudsepp, E. G. Cothran, N.A. Hamilton and B. Haase (2017) Validation of a candidate causative mutation for white spotting in donkeys. Anim Genet 48 (1): 124 – 125 

Fernandes CB, Loux SC, Scoggin KE, Squires EL, Troedsson MHT, Esteller-Vico A, Ball BA.  Sex Steroid Receptors, Prostaglandin E2 Receptors, and Cyclooxygenase in the Equine Cervix During Estrus, Diestrus and Pregnancy:  Gene Expression and Cellular Localization.  Animal Reproduction Science. 187:141-151.

Hamilton NA (2017). Gene doping detection: The past, present and future. Proc 21st Int Conf Racing Analysts Vets. (Accepted in press)

Hoban, R., K. Castle, N.A. Hamilton and B. Haase  (2017)  Novel KIT variants for Dominant White in the Australian horse population. Anim Genet doi: 10.1111/age.12627

Holl, H., Isaza, R., Mohamoud, Y., Ahmed, A., Almathen, F., Youcef, C., Gaouar, S., Antczak, D.F. and Brooks, S. (2017) 'A Frameshift Mutation in KIT is Associated with White Spotting in the Arabian Camel', Genes, 8(3), 102.

Holl, H., Vanhnasy, J., Everts, R., Hoefs-Martin, K., Cook, D., Brooks, S., Carpenter, M., Bustamante, C. and Lafayette, C. (2017) 'Single nucleotide polymorphisms for DNA typing in the domestic horse', Animal Genetics, 48(6), 669-676, available: http://dx.doi.org/10.1111/age.12608. (JIF= 1.973)

Holl, H.M., Brooks, S.A., Carpenter, M.L., Bustamante, C.D. and Lafayette, C. (2017) 'A novel splice mutation within equine KIT and the W15 allele in the homozygous state lead to all white coat color phenotypes', Animal Genetics, 48(4), 497-498, available: http://dx.doi.org/10.1111/age.12554.

Ishikawa S, Horinouchi C, Mizoguchi R, Senokuchi A, Kamikakimoto R, Murata D, Hatazoe T, Tozaki T, Misumi K, Hobo S. (2017) Isolation of equine peripheral blood stem cells from a Japanese native horse. J. Equine Sci.  28:153-158.

Jacob SI, Geor RJ, Weber PSD, Harris PA, McCue ME.  Effect of dietary carbohydrates and time of year on ACTH and cortisol concentrations in adult and aged horses.  Domest Anim Endocrinol. 2017 Nov 1;63:15-22. doi: 10.1016/j.domaniend.2017.10.005. [Epub ahead of print]

Jacob SI, Geor RJ, Weber PSD, Harris PA, McCue ME. Effect of age and dietary carbohydrate profiles on glucose and insulin dynamics in horses. Equine Veterinary Journal, manuscript online: 18 August 2017 DOI: 10.1111/evj.12745.

Klaudia Pawlina-Tyszko, Artur Gurgul, Tomasz Szmatoła, Katarzyna Ropka-Molik, Ewelina Semik-Gurgul, Jolanta Klukowska-Rotzler, Christoph Koch, Kathrin Mahlmann, Monika Bugno-Poniewierska. 2017. Genomic landscape of copy number variation and copy neutral loss of heterozygosity events in equine sarcoids reveals increased instability of the sarcoid genome. BIOCHIMIE, 140: 122-132.

Lewis SS, Nicholson AM, Williams Z, Valberg SJ. Warmblood horses with polysaccharide storage myopathy: Clinical characteristics and muscle glycogen concentrations. Am J Vet Res 2017: 78(11):1305-1312.

Lewis, S.L., Holl, H., Streeter, C., Posbergh, C., Schanbacher, B., Place, N., Mallicote, M., Long, M. and Brooks, S. (2017) 'Genomewide association study reveals a risk locus for equine metabolic syndrome in the Arabian horse', Journal of Animal Science, 95(3), 1071-1079.

Librado P, Gamba C, Gaunitz C, Der Sarkissian C, Pruvost M, Albrechtsen A, Fages A, Khan N, Schubert M, Jagannathan V, Serres-Armero A, Kuderna LFK, Povolotskaya IS, Seguin-Orlando A, Lepetz S, Neuditschko M, Thèves C, Alquraishi S, Alfarhan AH, Al-Rasheid K, Rieder S, Samashev Z, Francfort HP, Benecke N, Hofreiter M, Ludwig A, Keyser C, Marques-Bonet T, Ludes B, Crubézy E, Leeb T, Willerslev E, Orlando L. Ancient genomic changes associated with domestication of the horse. Science. 2017 Apr 28;356(6336):442-445. doi: 10.1126/science.aam5298. PMID: 28450643

Loux SC, Scoggin KE, Bruemmer J, Canisso I, Troedsson MHT, Squires EL, Ball BA. (2017) Evaluation of Circulating miRNAs During Late Pregnancy in the Mare.  PLOS ONE 12(4):e0175045. 

Loux SC, Scoggin KE, Troedsson MHT, Squires EL, Ball BA. (2017) Characterization of the Cervical Mucus Plug in Mares. Reproduction. 153(2): 197-210.  

Mack, M., Kowalski, E., Grahn, R., Bras, D., Penedo, M.C.T., & Bellone, R. (2017) Two variants in SLC24A5 are associated with “Tiger-Eye” iris pigmentation in Puerto Rican Paso Fino horses. G3: Genes|Genomes|Genetics 7(8):2799-2806. DOI:10.1534/g3.117.043786.

Maile CA, Hingst JR, Mahalingan KK, O'Reilly AO, Cleasby ME, Mickelson JR, McCue ME, Anderson SM, Hurley TD, Wojtaszewski JF, Piercy RJ.A highly prevalent equine glycogen storage disease is explained by constitutive activation of a mutant glycogen synthase. Biochimica et Biophysica Acta General Subjects, January 2017 Volume: 1861   Issue: 1   Pages: 3388-3398.

Mansour, T.A., Scott, E.Y.,  Finno,  C.J.,  Bellone,  R.R., Mienaltowski, M.J.,  Penedo, M.C., Ross, P.J., Valberg,  S.J., Murray, J.D., &  Brown, C.T.  (2017) Tissue resolved, gene structure refined equine transcriptome. BMC Genomics 18: 103. DOI: 10.1186/s12864-016-3451-2

McCue ME, McCoy AM.  The Scope of Big Data in One Medicine: Unprecedented Opportunities and Challenges.  Front Vet Sci. 2017 Nov 16;4:194. doi:  10.3389/fvets.2017.00194. eCollection 2017.

McGivney BA, Griffin ME, Gough KF, McGivney CL, Browne JA, Hill EW, Katz LM. Evaluation of microRNA expression in plasma and skeletal muscle of thoroughbred racehorses in training. BMC Vet Res. 2017 Nov 22;13(1):347. doi: 10.1186/s12917-017-1277-z. PubMed PMID: 29166903; PubMed Central PMCID:

McGivney CL, Sweeney J, David F, O'Leary JM, Hill EW, Katz LM. Intra- and interobserver reliability estimates for identification and grading of upper respiratory tract abnormalities recorded in horses at rest and during overground  endoscopy. Equine Vet J. 2017 Jul;49(4):433-437. doi: 10.1111/evj.12653.

Miller, D., Tallmadge, R.L., Binns, M., Zhu, B., Mohamoud, Y.A., Ahmed, A., Brooks, S.A. and Antczak, D.F. (2017) 'Polymorphism at expressed DQ and DR loci in five common equine MHC haplotypes', Immunogenetics, 69(3), 145-156, available: http://dx.doi.org/10.1007/s00251-016-0964-4.

Miyata H, Itoh R, Sato F, Takebe N, Hada T, Tozaki T. (2017) Effect of Myostatin SNP on muscle fiber properties in male Thoroughbred horses during training period. J. Physiol. Sci. doi: 10.1007/s12576-017-0575-3. [Epub ahead of print]

Pacholewska A, Kraft MF, Gerber V, Jagannathan V. Differential Expression of Serum MicroRNAs Supports CD4⁺ T Cell Differentiation into Th2/Th17 Cells in Severe Equine Asthma. Genes (Basel). 2017 Dec 12;8(12). pii: E383. doi: 10.3390/genes8120383.PMID: 29231896

Pacholewska A, Marti E, Leeb T, Jagannathan V, Gerber V. LPS-induced modules of co-expressed genes in equine peripheral blood mononuclear cells. BMC Genomics. 2017 Jan 5;18(1):34. doi: 10.1186/s12864-016-3390-y.  PMID: 28056766

Pawlina K., Gurgul A., Szmatoła T., Koch C., Mahlmann K, Witkowski M., Bugno-Poniewierska M. 2017. Comprehensive characteristics of microRNA expression profile of equine sarcoids. BIOCHIMI 137; 20-28.
Ropka-Molik K., Stefaniuk-Szmukier M., Żukowski K., Piórkowska K., GurgulA., Bugno-Poniewierska M. 2017. Transcriptome profiling of Arabian horse blood during training regimens. 2017. BMC Genetics. DOI 10.1186/s12863-017-0499-1

Pedersen PJ, Thomsen KB, Flak JB, Tejada MA, Hauser F, Trachsel D, Buhl R, Kalbfleisch T, DePriest MS, MacLeod JN, Calloe K, Klaerke DA,  Molecular cloning and functional expression of the K+ channel KV7.1 and the regulatory subunit KCNE1 from equine myocardium. Res Vet Sci. 2017;113:79-86. doi: 10.1016/j.rvsc.2017.09.010. PubMed PMID: 28917093.

Rooney MF, Porter RK, Katz LM, Hill EW. Skeletal muscle mitochondrial bioenergetics and associations with myostatin genotypes in the Thoroughbred horse. PLoS One. 2017 Nov 30;12(11):e0186247. doi: 10.1371/journal.pone.0186247. 

Ropka-Molik K., Stefaniuk-Szmukier M., Żukowski K., Piórkowska K., Bugno-Poniewierska M. Exercise-induced modification of the skeletal muscle transcriptome in Arabian horses. 2017. Physiol Genomics. doi: 10.1152/physiolgenomics.00130.2016.

Sadeghi R, Moradi-Shahrbabak M, Miraei Ashtiani SR, Miller DC, Antczak DF. MHC haplotype diversity in Persian Arabian horses determined using polymorphic microsatellites. Immunogenetics. 2017 Nov 23.

Schaefer RJ, Schubert M, Bailey E, Bannasch DL, Barrey E, Bar-Gal GK, Brem G, Brooks SA, Distl O, Fries R, Finno CJ, Gerber V, Haase B, Jagannathan V, Kalbfleisch T, Leeb T, Lindgren G, Lopes MS, Mach N, da Câmara Machado A, MacLeod JN, McCoy A, Metzger J, Penedo C, Polani S, Rieder S, Tammen I, Tetens J, Thaller G, Verini-Supplizi A, Wade CM, Wallner B, Orlando L, Mickelson JR, McCue ME. Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds. BMC Genomics. 2017 Jul 27;18(1):565. doi: 10.1186/s12864-017-3943-8. PMID: 28750625

Schnider D, Rieder S, Leeb T, Gerber V, Neuditschko M. A genome-wide association study for equine recurrent airway obstruction in European Warmblood horses reveals a suggestive new quantitative trait locus on chromosome 13. Anim Genet. 2017 Dec;48(6):691-693. doi: 10.1111/age.12583. Epub 2017 Jul 24.PMID: 28737212

Scott, E.Y., Mansour, T., Bellone, R.R., Brown, C.T., Mienaltowski, M.J., Penedo, M.C., Ross, P.J., Valberg, S.J., Murray, J.D., & Finno, C.J. Identification of long non-coding RNA in the horse transcriptome. BMC Genomics 18:511 DOI 10.1186/s12864-017-3884-2.

.1186/s12864-017-3884-2

Semik E., Ząbek T., Gurgul A., Fornal A., Szmatoła T., Pawlina K., Wnuk M., Klukowska-Rötzler J., Koch C., Mählmann K., Bugno-Poniewierska M. 2017. Comparative analysis of DNA methylation patterns of equine sarcoid and healthy skin samples. Veterinary and Comparative Oncology DOI 10.1111/vco.12308

Senju N, Tozaki T, Kakoi H, Almunia J, Maeda M, Matsuyama R, Takasu M. (2017) Genetic characterization of the Miyako horse based on polymorphisms of microsatellites and mitochondrial DNA. J. Vet. Med. Sci. 79:218-223.

Senju N, Tozaki T, Kakoi H, Shinjo A, Matsuyama R, Almunia J, Takasu M. (2017) Genetic diversity of the Yonaguni horse based on polymorphisms in microsatellites and mitochondrial DNA. J. Vet. Med. Sci. 79:425-431.

Staiger EA, Almén MS, Promerová M, Brooks S, Cothran EG, Imsland F, Jäderkvist Fegraeus K, Lindgren G, Mehrabani Yeganeh H, Mikko S, Vega-Pla JL, Tozaki T, Rubin CJ, Andersson L. (2017) The evolutionary history of the DMRT3 'Gait keeper' haplotype. Anim. Genet. 48:551-559.

Swiderski CE, Bowser JE, Costa LRR. Pasture associated asthma. Proceedings of the American College of Veterinary Internal Medicine, National Harbor, Maryland, USA, June 8-10, 2017.

Swiderski CE, Hunter CE, Bowser JE, Costa LR, Cooley JA, Claude AD, Eddy AL, Bright LA. Deciphering the role of airway hyper-responsiveness in equine pasture asthma. Journal of Equine Veterinary Science. 52:29-35, 2017.

Tamer TA, Erica Y Scott ET,  Finno CJ, Bellone RR, Mienaltowski MJ, Penedo MC, Ross PJ, Valberg SJ, Murray JD, Brown CT. Tissue Resolved, Gene Structure Refined Equine Transcriptome. BMC Genomics. BMC Genomics. 2017 Jan 20;18(1):103.

Tozaki T, Kikuchi M, Kakoi H, Hirota KI, Nagata SI. (2017) A genome-wide association study for body weight in Japanese Thoroughbred racehorses clarifies candidate regions on chromosomes 3, 9, 15, and 18. J. Equine Sci. 28:127-134.

Valberg SJ, Nicholson AM, Lewis SS, Reardon RA, Finno CJ. Clinical and histopathological features of myofibrillar myopathy in Warmblood horses. Equine Vet J 2017 May 22. doi: 10.1111/evj.12702. [Epub ahead of print].

Viluma A, Mikko S, Hahn D, Skow L, Andersson G, Bergström TF. Genomic structure of the horse major histocompatibility complex class II region resolved using PacBio long-read sequencing technology. Scientific Reports, 7:45518, doi:10.1038/srep45518, 2017

Wallner B, Palmieri N, Vogl C, Rigler D, Bozlak E, Druml T, Jagannathan V, Leeb T, Fries R, Tetens J, Thaller G, Metzger J, Distl O, Lindgren G, Rubin CJ, Andersson L, Schaefer RJ, McCue ME, Neuditschko M, Rieder S, Schlötterer C and Brem G. Y Chromosome Uncovers the Recent Oriental Origin of Modern Stallions. Current Biology, Volume 27, Issue 13, 10 July 2017, Pages 2029-2035.e5

Wilkin, T. A. Baoutina and N.A. Hamilton (2017) Equine performance genes and the future of doping in horse racing.  Drug Test Analysis  DOI 10.1002/dta.2198

Poultry Publications -

Baldwin, C.L et. al. (11 authors on committee) National Academies of Sciences, Engineering, and Medicine. 2017. Revisiting Brucellosis in the Greater Yellowstone Area. The National Academies Press: Washington, DC. 209 pgs; ISBN 978-0-309-45831-3 | DOI 10.17226/24750 [https://www.nap.edu/download/24750]

Cinar, M.U., Schneider, D.A., Waldron, D.F., O’Rourke, K.I., White, S.N. Goats singly heterozygous for PRNP S146 or K222 orally inoculated with classical scrapie at birth show no disease at ages well beyond six years. The Veterinary Journal. (in press)

Dechow, C.D., Liu, W.-S. (2017) Genome-wide DNA methylation patterns and differential methylation in leukocytes from Holstein cattle with variable milk yield. BMC Genomics (manuscript under revision).

Dechow, C., Liu, W.-S., Idun, J., Maness, W. (2017) Two dominant paternal lineages for North American Jersey artificial insemination sires. J. Dairy Sci. (In Press). Ghadikolaei, A.N., Yeganeh, H.M., Miarei-Aashtiani, S.R., Staiger, E.A., Huson, H.J., Genome-wide association studies identify candidate genes for coat color and mohair traits in the Iranian Markhoz goat, Frontiers in Genetics (under revision Jan 2018)

Kiser, J.N., Neupane, M., White, S.N., Neibergs, H.L. Identification of genes associated with susceptibility to Mycobacterium avium ssp. paratuberculosis (Map) tissue infection in Holstein cattle using gene set enrichment analysis-SNP. Mammalian Genome. (in press)

Kiser, J.N., White, S.N., Johnson, K.A., Hoff, J., Taylor, J.F., Neibergs, H.L. Identification of loci associated with susceptibility to Mycobacterium avium subspecies paratuberculosis (Map) tissue infection in cattle. Journal of Animal Science. 95(3):1080-1091. 2017.

Liu, W.-S., Zhao, Y.Q., Lu, C., Ning, G., Ma, Y., Diaz, F., O'Connor, M. (2017) A novel testis-specific protein, PRAMEY, is involved in spermatogenesis in cattle. Reproduction 153, 847–863.

Mason, K.L., Gonzalez, M.V., Chung, C., Mousel, M.R., White, S.N., Taylor, J.B., Scoles, G.A. Detection of Anaplasma ovis and validation of improved A. marginale cELISA kit for diagnostic use in domestic sheep. Journal of Veterinary Diagnostic Investigation. 29(5):763-766. 2017.

Noelle E. Cockett, Brian Dalrymple, James Kijas, Brenda Murdoch, Kim C. Worley. Mapping the sheep genome, Chapter 5, Achieving sustainable production of sheep Burleigh Dodds Series in Agricultural Science (Book 22), Edited by Prof J.P.C. Greyling, Burleigh Dodds Science Publishing September 15, 2017

Notter, D. R., Mousel, M. R., Lewis, G. S., Leymaster, K. A., and Taylor, J. B. Evaluation of Rambouillet, Polypay, and Romanove-White Dorper x Rambouillet ewes mated to terminal sires in an extensive rangeland production system: lamb production. J. Anim. Sci. 95:3851-3862. 2017.

Oliveira, R.D., Mousel, M.R., Pabilonia, K.L., Highland, M.A., Taylor, J.B., Knowles, D.P., White, S.N. Domestic sheep show average Coxiella burnetii seropositivity generations after a sheep-associated human Q fever outbreak but lack detectable shedding by placental, vaginal, and fecal routes. PLoS One 12(11): e0188054. 2017.

Posbergh, C.J. & Huson, H.J., (2018) Making Moorit: Mutations in TYRP1 are responsible for brown coat color in different United States sheep breeds, Proceedings 11^th World Congress of Genetics Applied to Livestock Production, (accepted, under revision Nov 2017).

Posbergh, C.J., Kalla, S.E., Sutter, N.B., Tennant, B.C., Huson, H.J., A mutation responsible for hyperbilirubinemia and photosensitivity in Southdown sheep similar to Rotor Syndrome American Journal of Veterinary Research (accepted July 2017, In Press

Posbergh, C.J., Thonney M.L., Huson H.J., The eyes have it: genomic approaches identify novel gene associations with aseasonality in sheep, BMC Genomics (submitted Jan 2018)

PrabhuDas M, Baldwin CL, Bollyky PL, Bowdish DME, Drickamer K, Febbraio M, Herz J, Kobzik L, Krieger M, Loike J, McVicker B, Means TK, Moestrup S, Post SR, Tatsuya Sawamura T, Silverstein S, Speth RC, Telfer JC, Thiele GM, Wang X-Y, Wright SD, El Khoury J. A Consensus Definitive Classification of Scavenger receptors. Journal of Immunology 2017; 198(10):3775-3789. doi: 10.4049/jimmunol.1700373. PMID: 28483986

Tezgel AÖ, Jacobs PT*, Backlund CM, Telfer JC, Tew GN Synthetic Protein Mimics for Functional Protein Delivery. Biomacromolecules 2017; 18(3):819-825. doi: 10.1021/acs.biomac.6b01685. Epub 2017 Feb 27. PMID: 28165726.

White, S.N., Oliveira, R.D., Mousel, M.R., Gonzalez, M.V., Highland, M.A., Herndon, M.K., Taylor, J.B., Knowles, D.P. Underdominant KCC3b R31I association with blood sodium concentration in domestic sheep suggests role in oligomer function. Animal Genetics 48(5):626-627. 2017.

Zhang, Y.Y., Deng, X.G., Liu, W.-S., Deng, X.M. (2017) Estimation of recombination rate and effective population size with ovine genome-wide SNP-chip. Sciencepaper Online 201704-232 

Swine Publications -

Bertolini F., J.C.S. Harding, B. Mote, A. Ladinig, G.S. Plastow and M.F. Rothschild. 2017. Genomic investigation of piglet resilience following porcine epidemic diarrhea outbreaks. Animal Genetics. 48(2):228-232. doi: 10.1111/age.12522.

Casiró S, D. Velez-Irizarry, C.W. Ernst, N.E. Raney, R.O. Bates, M.G. Charles and J.P. Steibel. 2017. Genome-wide association study in an F2 Duroc x Pietrain resource population for economically important meat quality and carcass traits. J. Anim. Sci. 95:545-558.

Choi, I., R.O. Bates, N.E. Raney and C.W. Ernst. 2017. Association of a corticotropin-releasing hormone receptor 2 (CRHR2) polymorphism with carcass merit, meat quality and stress response traits in pigs. Canadian J. Anim. Sci. 97:536-540.

Cole JB, Bormann JM, Gill CA, Khatib H, Koltes JE, Maltecca C, Miglior F. 2017. BREEDING AND GENETICS SYMPOSIUM: Resilience of livestock to changing environments. J Anim Sci. 95(4):1777-1779.

Daza, K.R., J.P. Steibel, D. Velez-Irizarry, N.E. Raney, R.O. Bates and C.W. Ernst. 2017. Profiling and characterization of a longissimus dorsi muscle microRNA dataset from an F2 Duroc x Pietrain pig resource population. Genom. Data. 13:50-53.

Funkhouser, S.A., R.O. Bates, C.W. Ernst, D. Newcom and J.P. Steibel. 2017. Estimation of genome-wide and locus-specific breed composition in pigs. Translational Anim. Sci. 1:36-44.


Funkhouser, S.A., J.P. Steibel, R.O. Bates, N.E. Raney and C.W. Ernst. 2017. Evidence for transcriptome-wide RNA editing among Sus scrofa PRE-1 SINE elements. BMC Genomics.18:360.
Garcia-Baccino, C.A., S. Munilla, A. Legarra, Z.G. Vitezica, N.S. Forneris, R.O. Bates, C.W. Ernst, N.E. Raney, J.P. Steibel and R.J. Cantet. 2017. Estimates of the actual relationship between half-sibs in a pig population. J. Anim. Breed. Genet. 134:109- 118.


Howard JT, Pryce JE, Baes C, Maltecca C. Invited review: Inbreeding in the genomics era: Inbreeding, inbreeding depression, and management of genomic variability. J Dairy Sci. 2017;100(8):6009-6024

Howard JT, Tiezzi F, Huang Y, Gray KA, Maltecca C. 2016. Characterization and management of long runs of homozygosity in parental nucleus lines and their associated crossbred progeny. Genet Sel Evol. 24;48(1):91.

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