Animal Sciences Commons^™

Adaptmap: Exploring Goat Diversity And Adaptation, Alessandra Stella, Ezequiel Luis Nicolazzi, Curtis P. Van Tassell, Max F. Rothschild, Licia Colli, Benjamin D. Rosen, Tad S. Sonstegard, Paola Crepaldi, Gwenola Tosser-Klopp, Stephane Joost, Francesca Bertolini, Jim Reecy

James M Reecy

International initiatives on goat genetics and genomics

Goats are bred worldwide and present in a wide variety of production environments. Local breeds, which are well adapted to a range of agro-ecological conditions, contribute to ensuring the sustainability of livestock farming in marginal and difficult areas in both developed and developing countries. Compared to other livestock species, goats have been domesticated in a single region and subject to a limited amount of hybridization between breeds, thus they represent one of the best species for the study of genetic diversity and adaptation.

Building A Livestock Genetic And Genomic Information Knowledgebase Through Integrative Developments Of Animal Qtldb And Corrdb, Zhi-Liang Hu, Carissa A. Park, James M. Reecy

James M Reecy

Successful development of biological databases requires accommodation of the burgeoning amounts of data from high-throughput genomics pipelines. As the volume of curated data in Animal QTLdb (https://www.animalgenome.org/QTLdb) increases exponentially, the resulting challenges must be met with rapid infrastructure development to effectively accommodate abundant data curation and make metadata analysis more powerful. The development of Animal QTLdb and CorrDB for the past 15 years has provided valuable tools for researchers to utilize a wealth of phenotype/genotype data to study the genetic architecture of livestock traits. We have focused our efforts on data curation, improved data quality ...

An Integrative Transcriptome Analysis Indicates Regulatory Mrna-Mirna Networks For Residual Feed Intake In Nelore Cattle, Priscila S.N. De Oliveira, Luiz L. Coutinho, Polyana C. Tizioto, Aline S. M. Cesar, Gabriella B. De Oliveira, Wellison J. Da S. Diniz, Andressa O. De Lima, James M. Reecy, Gerson B. Mourão, Adhemar Zerlotini, Luciana C. A. Regitano

James M Reecy

Residual Feed Intake (RFI) is an economically relevant trait in beef cattle. Among the molecular regulatory mechanisms, microRNAs (miRNAs) are an important dimension in post-transcriptional regulation and have been associated with different biological pathways. Here, we performed differential miRNAs expression and weighted gene co-expression network analyses (WGCNA) to better understand the complex interactions between miRNAs and mRNAs expressed in bovine skeletal muscle and liver. MiRNA and mRNA expression data were obtained from Nelore steers that were genetically divergent for RFI (N = 10 [low RFI or feed efficient]; N = 10 [high RFI or feed inefficient]). Differentially expressed and hub miRNAs such ...

Integrative Analysis Of Micrornas And Mrnas Revealed Regulation Of Composition And Metabolism In Nelore Cattle, Gabriella B. Oliveira, Luciana C. A. Regitano, Aline S.M. Cesar, James M. Reecy, Karina Y. Degaki, Mirele D. Poleti, Andrezza M. Felício, James E. Koltes, Luiz L. Coutinho

James M Reecy

Background: The amount of intramuscular fat can influence the sensory characteristics and nutritional value of beef, thus the selection of animals with adequate fat deposition is important to the consumer. There is growing knowledge about the genes and pathways that control the biological processes involved in fat deposition in muscle. MicroRNAs (miRNAs) belong to a well-conserved class of non-coding small RNAs that modulate gene expression across a range of biological functions in animal development and physiology. The aim of this study was to identify differentially expressed (DE) miRNAs, regulatory candidate genes and co-expression networks related to intramuscular fat (IMF) deposition ...

Meta-Analysis Of Genome-Wide Association Studies For Cattle Stature Identifies Common Genes That Regulate Body Size In Mammals, Aniek C. Bouwman, Dorian J. Garrick, James Reecy, Curtis P. Van Tassell

James M Reecy

Stature is affected by many polymorphisms of small effect in humans1. In contrast, variation in dogs, even within breeds, has been suggested to be largely due to variants in a small number of genes2,3. Here we use data from cattle to compare the genetic architecture of stature to those in humans and dogs. We conducted a meta-analysis for stature using 58,265 cattle from 17 populations with 25.4 million imputed whole-genome sequence variants. Results showed that the genetic architecture of stature in cattle is similar to that in humans, as the lead variants in 163 significantly ...

Agbiodata Consortium Recommendations For Sustainable Genomics And Genetics Databases For Agriculture, Lisa Harper, Jacqueline Campbell, Ethalinda K. S. Cannon, Monica Poelchau, Carson Andorf, Clayton Birkett, Steve Cannon, David Grant, Zhi-Liang Hu, Gerard Lazo, Rex Nelson, Carissa Park, James Reecy, Taner Z. Sen, Doreen Ware, Margaret Woodhouse

James M Reecy

The future of agricultural research depends on data. The sheer volume of agricultural biological data being produced today makes excellent data management essential. Governmental agencies, publishers and science funders require data management plans for publicly funded research. Furthermore, the value of data increases exponentially when they are properly stored, described, integrated and shared, so that they can be easily utilized in future analyses. AgBioData (https://www.agbiodata.org) is a consortium of people working at agricultural biological databases, data archives and knowledgbases who strive to identify common issues in database development, curation and management, with the goal of creating database ...

Integration Of Machine Learning And Meta-Analysis Identifies The Transcriptomic Bio-Signature Of Mastitis Disease In Cattle, Somayeh Sharifi, Abbas Pakdel, Mansour Ebrahim, James M. Reecy, Samaneh Fazeli Farsani, Esmaeil Ebrahimie

James M Reecy

Gram-negative bacteria such as Escherichia coli (E. coli) are assumed to be among the main agents that cause severe mastitis disease with clinical signs in dairy cattle. Rapid detection of this disease is so important in order to prevent transmission to other cows and helps to reduce inappropriate use of antibiotics. With the rapid progress in high-throughput technologies, and accumulation of various kinds of ‘-omics’ data in public repositories, there is an opportunity to retrieve, integrate, and reanalyze these resources to improve the diagnosis and treatment of different diseases and to provide mechanistic insights into host resistance in an efficient ...

Identification Of Genome-Wide Snp-Snp Interactions Associated With Important Traits In Chicken, Hui Zhang, Jia-Qiang Yu, Li-Li Yang, Luke M. Kramer, Xin-Yang Zhang, Wei Na, James M. Reecy, Hui Li

James M Reecy

Background: In addition to additive genetic effects, epistatic interactions can play key roles in the control of phenotypic variation of traits of interest. In the current study, 475 male birds from lean and fat chicken lines were utilized as a resource population to detect significant epistatic effects associated with growth and carcass traits.

Results: A total of 421 significant epistatic effects were associated with testis weight (TeW), from which 11 sub-networks (Sub-network1 to Sub-network11) were constructed. In Sub-network1, which was the biggest network, there was an interaction between GGA21 and GGAZ. Three genes on GGA21 (SDHB, PARK7 and VAMP3) and ...

A Genome-Wide Association Study Reveals Novel Genomic Regions And Positional Candidate Genes For Fat Deposition In Broiler Chickens, Gabriel Costa Monteiro Moreira, Clarissa Boschiero, Aline Silva Mello Cesar, James M. Reecy, Thaís Fernanda Godoy, Priscila Anchieta Trevisoli, Maurício E. Cantão, Mônica Corrêa Ledur, Adriana Mércia Guaratini Ibelli, Jane De Oliveira Peixoto, Ana Silvia Alves Meira Tavares Moura, Dorian Garrick, Luiz Lehmann Coutinho

James M Reecy

Background: Excess fat content in chickens has a negative impact on poultry production. The discovery of QTL associated with fat deposition in the carcass allows the identification of positional candidate genes (PCGs) that might regulate fat deposition and be useful for selection against excess fat content in chicken’s carcass. This study aimed to estimate genomic heritability coefficients and to identify QTLs and PCGs for abdominal fat (ABF) and skin (SKIN) traits in a broiler chicken population, originated from the White Plymouth Rock and White Cornish breeds.

Results: ABF and SKIN are moderately heritable traits in our broiler population with ...

Gene Co-Expression Analysis Indicates Potential Pathways And Regulators Of Beef Tenderness In Nellore Cattle, Tassia Mangetti, Luciana Correia De Almeida Regitano, James E. Koltes, Aline Silva Mello Cesar, Sonia Cristina Da Silva Andrade, Gerson Barreto Mourao, Gustavo Gasparin, Gabriel Costa Monteiro Moreira, Elyn Fritz-Waters, James M. Reecy, Luiz Lehmann Coutinho

James M Reecy

Beef tenderness, a complex trait affected by many factors, is economically important to beef quality, industry, and consumer’s palatability. In this study, RNA-Seq was used in network analysis to better understand the biological processes that lead to differences in beef tenderness. Skeletal muscle transcriptional profiles from 24 Nellore steers, selected by extreme estimated breeding values (EBVs) for shear force after 14 days of aging, were analyzed and 22 differentially expressed transcripts were identified. Among these were genes encoding ribosomal proteins, glutathione transporter ATP-binding cassette, sub-family C (CFTR/MRP), member 4 (ABCC4), and synaptotagmin IV (SYT4). Complementary co-expression analyses using ...

Large-Scale Gene Co-Expression Network As A Source Of Functional Annotation For Cattle Genes, Hamid Beiki, Ardeshir Nejati-Javaremi, Abbas Pakdel, Ali Masoudi-Nejad, Zhi-Liang Hu, James M. Reecy

James M Reecy

Background: Genome sequencing and subsequent gene annotation of genomes has led to the elucidation of many genes, but in vertebrates the actual number of protein coding genes are very consistent across species (~20,000). Seven years after sequencing the cattle genome, there are still genes that have limited annotation and the function of many genes are still not understood, or partly understood at best. Based on the assumption that genes with similar patterns of expression across a vast array of tissues and experimental conditions are likely to encode proteins with related functions or participate within a given pathway, we constructed ...

Network Analysis Reveals Putative Genes Affecting Meat Quality In Angus Cattle, Raluca G. Mateescu, Dorian J. Garrick, James M. Reecy

James M Reecy

Improvements in eating satisfaction will benefit consumers and should increase beef demand which is of interest to the beef industry. Tenderness, juiciness, and flavor are major determinants of the palatability of beef and are often used to reflect eating satisfaction. Carcass qualities are used as indicator traits for meat quality, with higher quality grade carcasses expected to relate to more tender and palatable meat. However, meat quality is a complex concept determined by many component traits making interpretation of genome-wide association studies (GWAS) on any one component challenging to interpret. Recent approaches combining traditional GWAS with gene network interactions theory ...

Differences In The Skeletal Muscle Transcriptome Profile Associated With Extreme Values Of Fatty Acids Content, Aline S. M. Cesar, Luciana C. A. Regitano, Mirele D. Poleti, Sónia C. S. Andrade, Polyana C. Tizioto, Priscila S. N. Oliveira, Andrezza M. Felício, Michele L. Do Nascimento, Amália S. Chaves, Dante P. D. Lanna, Rymer R. Tullio, Renata T. Nassu, James E. Koltes, Eric Frtiz-Waters, Gerson B. Mourão, Adhemar Zerlotini-Neto, James M. Reecy, Luiz L. Coutinho

James M Reecy

Background: Lipids are a class of molecules that play an important role in cellular structure and metabolism in all cell types. In the last few decades, it has been reported that long-chain fatty acids (FAs) are involved in several biological functions from transcriptional regulation to physiological processes. Several fatty acids have been both positively and negatively implicated in different biological processes in skeletal muscle and other tissues. To gain insight into biological processes associated with fatty acid content in skeletal muscle, the aim of the present study was to identify differentially expressed genes (DEGs) and functional pathways related to gene ...

Go‐Faang Meeting: A Gathering On Functional Annotation Of Animal Genomes, Christopher K. Tuggle, Elisabetta Giuffra, Stephen N. White, Laura Clarke, Huaijun Zhou, Pablo J. Ross, Herve Acloque, James M. Reecy, Alan Archibald, Rebecca R. Bellone, Michele Boichard, Amanda Chamberlain, Hans Cheng, Richard P. M. A. Crooijmans, Mary E. Delany, Carrie J. Finno, Martien A. M. Groenen, Ben Hayes, Joan K. Lunney, Jessica L. Petersen, Graham S. Plastow, Carl J. Schmidt, Jiuzhou Song, Mick Watson

James M Reecy

The Functional Annotation of Animal Genomes (FAANG) Consortium recently held a Gathering On FAANG (GO‐FAANG) Workshop in Washington, DC on October 7–8, 2015. This consortium is a grass‐roots organization formed to advance the annotation of newly assembled genomes of domesticated and non‐model organisms (www.faang.org). The workshop gathered together from around the world a group of 100+ genome scientists, administrators, representatives of funding agencies and commodity groups to discuss the latest advancements of the consortium, new perspectives, next steps and implementation plans. The workshop was streamed live and recorded, and all talks, along with speaker ...

Deriving Gene Networks From Snp Associated With Triacylglycerol And Phospholipid Fatty Acid Fractions From Ribeyes Of Angus Cattle, Justin W. Buchanan, James M. Reecy, Dorian J. Garrick, Qing Duan, Donald C. Beitz, James E. Koltes, Mahdi Saatchi, Lars Koesterke, Raluca G. Mateescu

James M Reecy

The fatty acid profile of beef is a complex trait that can benefit from gene-interaction network analysis to understand relationships among loci that contribute to phenotypic variation. Phenotypic measures of fatty acid profile from triacylglycerol and phospholipid fractions of longissimus muscle, pedigree information, and Illumina 54 k bovine SNP genotypes were utilized to derive an annotated gene network associated with fatty acid composition in 1,833 Angus beef cattle. The Bayes-B statistical model was utilized to perform a genome wide association study to estimate associations between 54 k SNP genotypes and 39 individual fatty acid phenotypes within each fraction. Posterior ...

Genetic Architecture Of Gene Expression Underlying Variation In Host Response To Porcine Reproductive And Respiratory Syndrome Virus Infection, Arun Kommadath, Hua Bao, Igseo Choi, James M. Reecy, James E. Koltes, Elyn Fritz-Waters, Chris J. Eisley, Jason R. Grant, Robert R. R. Rowland, Christopher K. Tuggle, Jack C. M. Dekkers, Joan K. Lunney, Le Luo Guan, Paul Stothard, Graham S. Plastow

James M Reecy

It has been shown that inter-individual variation in host response to porcine reproductive and respiratory syndrome (PRRS) has a heritable component, yet little is known about the underlying genetic architecture of gene expression in response to PRRS virus (PRRSV) infection. Here, we integrated genome-wide genotype, gene expression, viremia level, and weight gain data to identify genetic polymorphisms that are associated with variation in inter-individual gene expression and response to PRRSV infection in pigs. RNA-seq analysis of peripheral blood samples collected just prior to experimental challenge (day 0) and at 4, 7, 11 and 14 days post infection from 44 pigs ...

Design And Validation Of A 90k Snp Genotyping Assay For The Water Buffalo (Bubalus Bubalis), Daniela Iamartino, Ezequiel L. Nicolazzi, Curtis P. Van Tassell, James M. Reecy, Eric R. Fritz-Waters, James E. Koltes, Stefano Biffani, Tad S. Sonstegard, Steven G. Schroeder, Paolo Ajmone-Marsan, Riccardo Negrini, Rolando Pasquariello, Paola Ramell, Angelo Coletta, Jose F. Garcia, Ahmad Ali, Luigi Ramunno, Gianfranco Cosenza, Denise A. A. De Oliveira, Marcela G. Drummond, Eduardo Bastianetto, Alessandro Davassi, Ali Pirani, Fiona Brew, John L. Williams

James M Reecy

Background The availability of the bovine genome sequence and SNP panels has improved various genomic analyses, from exploring genetic diversity to aiding genetic selection. However, few of the SNP on the bovine chips are polymorphic in buffalo, therefore a panel of single nucleotide DNA markers exclusive for buffalo was necessary for molecular genetic analyses and to develop genomic selection approaches for water buffalo. The creation of a 90K SNP panel for river buffalo and testing in a genome wide association study for milk production is described here.

Methods The genomes of 73 buffaloes of 4 different breeds were sequenced and ...

Bioinformatic Analyses In Early Host Response To Porcine Reproductive And Respiratory Syndrome Virus (Prrsv) Reveals Pathway Differences Between Pigs With Alternate Genotypes For A Major Host Response Qtl, Martine Schroyen, Christopher Eisley, James E. Koltes, Eric Fritz-Waters, Igseo Choi, Graham S. Plastow, Leluo Guan, Paul Stothard, Hua Bao, Arun Kommadath, James M. Reecy, Joan K. Lunney, Robert R. R. Rowland, Jack C. M. Dekkers, Christopher K. Tuggle

James M Reecy

Background: A region on Sus scrofa chromosome 4 (SSC4) surrounding single nucleotide polymorphism (SNP) marker WUR10000125 (WUR) has been reported to be strongly associated with both weight gain and serum viremia in pigs after infection with PRRS virus (PRRSV). A proposed causal mutation in the guanylate binding protein 5 gene (GBP5) is predicted to truncate the encoded protein. To investigate transcriptional differences between WUR genotypes in early host response to PRRSV infection, an RNA-seq experiment was performed on globin depleted whole blood RNA collected on 0, 4, 7, 10 and 14 days post-infection (dpi) from eight littermate pairs with one ...

Developmental Progress And Current Status Of The Animal Qtldb, Zhi-Liang Hu, Carissa A. Park, James M. Reecy

James M Reecy

The Animal QTL Database (QTLdb; http://www.animalgenome.org/QTLdb) has undergone dramatic growth in recent years in terms of new data curated, data downloads and new functions and tools. We have focused our development efforts to cope with challenges arising from rapid growth of newly published data and end users’ data demands, and to optimize data retrieval and analysis to facilitate users’ research. Evidenced by the 27 releases in the past 11 years, the growth of the QTLdb has been phenomenal. Here we report our recent progress which is highlighted by addition of one new species, four new data ...

Ecological Factors Influencing Plant Distribution In The Shadscale Zone Of Southeastern Utah, Kamal M. Ibrahim

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The intimate relationship between vegetation and soil has long been a subject of interest. Ecologists, soil surveyors, and ranchers have recognized that vegetation differences are often accompanied by variation in soil types.