Open Access. Powered by Scholars. Published by Universities.®

Life Sciences Commons

Open Access. Powered by Scholars. Published by Universities.®

Articles 1 - 30 of 271

Full-Text Articles in Life Sciences

Genome-Wide Scans Identify Known And Novel Regions Associated With Prolificacy And Reproduction Traits In A Sub-Saharan African Indigenous Sheep (Ovis Aries), Asrat Tera Dolebo, Negar Khayatzadeh, Aberra Melesse, David Wragg, Mourad Rekik, Aynalem Haile, Barbara Rischkowsky, Max F. Rothschild, Joram M. Mwacharo Dec 2019

Genome-Wide Scans Identify Known And Novel Regions Associated With Prolificacy And Reproduction Traits In A Sub-Saharan African Indigenous Sheep (Ovis Aries), Asrat Tera Dolebo, Negar Khayatzadeh, Aberra Melesse, David Wragg, Mourad Rekik, Aynalem Haile, Barbara Rischkowsky, Max F. Rothschild, Joram M. Mwacharo

Animal Science Publications

Maximizing the number of offspring born per female is a key functionality trait in commercial- and/or subsistence-oriented livestock enterprises. Although the number of offspring born is closely associated with female fertility and reproductive success, the genetic control of these traits remains poorly understood in sub-Saharan Africa livestock. Using selection signature analysis performed on Ovine HD BeadChip data from the prolific Bonga sheep in Ethiopia, 41 candidate regions under selection were identified. The analysis revealed one strong selection signature on a candidate region on chromosome X spanning BMP15, suggesting this to be the primary candidate prolificacy gene in the breed ...


A Vision For Development And Utilization Of High-Throughput Phenotyping And Big Data Analytics In Livestock, James E. Koltes, John B. Cole, Roxanne Clemmens, Ryan N. Dilger, Luke M. Kramer, Joan K. Lunney, Molly E. Mccue, Stephanie D. Mckay, Raluca G. Mateescu, Brenda M. Murdoch, Ryan Reuter, Caird E. Rexroad, Guilherme J. M. Rosa, Nick V. L. Serão, Stephen N. White, M. Jennifer Woodward-Greene, Millie Worku, Hongwei Zhang, James M. Reecy Dec 2019

A Vision For Development And Utilization Of High-Throughput Phenotyping And Big Data Analytics In Livestock, James E. Koltes, John B. Cole, Roxanne Clemmens, Ryan N. Dilger, Luke M. Kramer, Joan K. Lunney, Molly E. Mccue, Stephanie D. Mckay, Raluca G. Mateescu, Brenda M. Murdoch, Ryan Reuter, Caird E. Rexroad, Guilherme J. M. Rosa, Nick V. L. Serão, Stephen N. White, M. Jennifer Woodward-Greene, Millie Worku, Hongwei Zhang, James M. Reecy

Animal Science Publications

Automated high-throughput phenotyping with sensors, imaging, and other on-farm technologies has resulted in a flood of data that are largely under-utilized. Drastic cost reductions in sequencing and other omics technology have also facilitated the ability for deep phenotyping of livestock at the molecular level. These advances have brought the animal sciences to a cross-roads in data science where increased training is needed to manage, record, and analyze data to generate knowledge and advances in Agriscience related disciplines. This paper describes the opportunities and challenges in using high-throughput phenotyping, “big data,” analytics, and related technologies in the livestock industry based on ...


Co-Expression Networks Reveal Potential Regulatory Roles Of Mirnas In Fatty Acid Composition Of Nelore Cattle, Priscila S. N. De Oliveira, Luiz L. Coutinho, Aline S. M. Cesar, Wellison J. Da Silva Diniz, Marcela M. De Souza, Bruno G. Andrade, James E. Koltes, Gerson B. Mourão, Adhemar Zerlotini, James M. Reecy, Luciana C. A. Regitano Jul 2019

Co-Expression Networks Reveal Potential Regulatory Roles Of Mirnas In Fatty Acid Composition Of Nelore Cattle, Priscila S. N. De Oliveira, Luiz L. Coutinho, Aline S. M. Cesar, Wellison J. Da Silva Diniz, Marcela M. De Souza, Bruno G. Andrade, James E. Koltes, Gerson B. Mourão, Adhemar Zerlotini, James M. Reecy, Luciana C. A. Regitano

Animal Science Publications

Fatty acid (FA) content affects the sensorial and nutritional value of meat and plays a significant role in biological processes such as adipogenesis and immune response. It is well known that, in beef, the main FAs associated with these biological processes are oleic acid (C18:1 cis9, OA) and conjugated linoleic acid (CLA-c9t11), which may have beneficial effects on metabolic diseases such as type 2 diabetes and obesity. Here, we performed differential expression and co-expression analyses, weighted gene co-expression network analysis (WGCNA) and partial correlation with information theory (PCIT), to uncover the complex interactions between miRNAs and mRNAs expressed in ...


Natural Selection Footprints Among African Chicken Breeds And Village Ecotypes, Ahmed R. Elbeltagy, Francesca Bertolini, Damarius S. Fleming, Angelica Van Goor, Chirs M. Ashwell, Carl J. Schmidt, Donald R. Kugonza, Susan J. Lamont, Max F. Rothschild May 2019

Natural Selection Footprints Among African Chicken Breeds And Village Ecotypes, Ahmed R. Elbeltagy, Francesca Bertolini, Damarius S. Fleming, Angelica Van Goor, Chirs M. Ashwell, Carl J. Schmidt, Donald R. Kugonza, Susan J. Lamont, Max F. Rothschild

Animal Science Publications

Natural selection is likely a major factor in shaping genomic variation of the African indigenous rural chicken, driving the development of genetic footprints. Selection footprints are expected to be associated with adaptation to locally prevailing environmental stressors, which may include diverse factors as high altitude, disease resistance, poor nutrition, oxidative and heat stresses. To determine the existence of a selection footprint, 268 birds were randomly sampled from three indigenous ecotypes from East Africa (Rwanda and Uganda) and North Africa (Baladi), and two registered Egyptian breeds (Dandarawi and Fayoumi). Samples were genotyped using the chicken Affymetrix 600K Axiom® Array. A total ...


Evaluation Of Snp Genotyping In Alpacas Using The Bovine Hd Genotyping Beadchip, Manuel More, Gustavo Gutierrez, Max Rothschild, Francesca Bertolini, F. Abel Ponce De Leon Apr 2019

Evaluation Of Snp Genotyping In Alpacas Using The Bovine Hd Genotyping Beadchip, Manuel More, Gustavo Gutierrez, Max Rothschild, Francesca Bertolini, F. Abel Ponce De Leon

Animal Science Publications

Alpacas are one of four South American Camelid species living in the highlands of the Andes. Production of alpaca fiber contributes to the economy of the region and the livelihood of many rural families. Fiber quantity and quality are important and in need of a modern breeding program based on genomic selection to accelerate genetic gain. To achieve this is necessary to discover enough molecular markers, single nucleotide polymorphisms (SNPs) in particular, to provide genome coverage and facilitate genome wide association studies to fiber production characteristics. The aim of this study was to discover alpaca SNPs by genotyping forty alpaca ...


Fluoxetine-Induced Alteration Of Murine Gut Microbial Community Structure: Evidence For A Microbial Endocrinology-Based Mechanism Of Action Responsible For Fluoxetine-Induced Side Effects, Mark Lyte, Karrie M. Daniels, Stephan Schmitz-Esser Jan 2019

Fluoxetine-Induced Alteration Of Murine Gut Microbial Community Structure: Evidence For A Microbial Endocrinology-Based Mechanism Of Action Responsible For Fluoxetine-Induced Side Effects, Mark Lyte, Karrie M. Daniels, Stephan Schmitz-Esser

Animal Science Publications

Background. Depression and major depressive disorder affect 25% of the population. First line treatment utilizing selective serotonin reuptake inhibitors (SSRIs) have met with limited success due to well-recognized negative side effects which include weight gain or loss. This inability to control unwanted side effects often result in patients stopping their antidepressant medications. The mechanisms underlying the failure of SSRIs are incompletely understood.

Methods. Male CF-1 mice (5 weeks of age, N D 10 per group) were per orally administered fluoxetine (20 mg per kg body weight) or diluent daily for 29 days. During this time fecal specimens were collected at ...


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 Jan 2019

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

Animal Science Publications

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 ...


Genetic Lines Respond Uniquely Within The Chicken Thymic Transcriptome To Acute Heat Stress And Low Dose Lipopolysaccharide, Melissa S. Monson, Angelica G. Van Goor, Michael E. Persia, Max F. Rothschild, Carl J. Schmidt, Susan J. Lamont Jan 2019

Genetic Lines Respond Uniquely Within The Chicken Thymic Transcriptome To Acute Heat Stress And Low Dose Lipopolysaccharide, Melissa S. Monson, Angelica G. Van Goor, Michael E. Persia, Max F. Rothschild, Carl J. Schmidt, Susan J. Lamont

Animal Science Publications

Exposure to high temperatures is known to impair immune functions and disease resistance of poultry. Characterizing changes in the transcriptome can help identify mechanisms by which immune tissues, such as the thymus, respond to heat stress. In this study, 22-day-old chickens from two genetic lines (a relatively resistant Fayoumi line and a more susceptible broiler line) were exposed to acute heat stress (35 °C) and/or immune simulation with lipopolysaccharide (LPS; 100 µg/kg). Transcriptome responses in the thymus were identified by RNA-sequencing (RNA-seq). Expression of most genes was unaffected by heat and/or LPS in the Fayoumi line, whereas ...


Venous Blood Gas And Chemistry Components Are Moderately Heritable In Commercial White Egg-Laying Hens Under Acute Or Chronic Heat Exposure, Kaylee Rowland, Michael E. Persia, Max F. Rothschild, Carl Schmidt, Susan J. Lamont Jan 2019

Venous Blood Gas And Chemistry Components Are Moderately Heritable In Commercial White Egg-Laying Hens Under Acute Or Chronic Heat Exposure, Kaylee Rowland, Michael E. Persia, Max F. Rothschild, Carl Schmidt, Susan J. Lamont

Animal Science Publications

Heat stress has a large negative impact on poultry around the world in both intensive and small-scale production systems. Better understanding of genetic factors contributing to response to high ambient temperatures would provide a basis to develop strategies for alleviating negative impacts of heat on poultry production. The objective of this work was to characterize the genetic control (heritability estimate and quantitative trait loci (QTL)) of blood chemistry components before and after exposure to acute and chronic high ambient temperature in a commercial egg laying line Hy-Line W-36 female parent line mature hens were exposed to 4 wk of daily ...


Genetic Analyses Of Tanzanian Local Chicken Ecotypes Challenged With Newcastle Disease Virus, Muhammed Walugembe, James R. Mushi, Esinam N. Amuzu-Aweh, Gaspar H. Chiwanga, Peter L. Msoffe, Ying Wang, Perot Saelao, Terra Kelly, Rodrigo A. Gallardo, Huaijun Zhou, Susan J. Lamont, Amandus P. Muhairwa, Jack C. M. Dekkers Jan 2019

Genetic Analyses Of Tanzanian Local Chicken Ecotypes Challenged With Newcastle Disease Virus, Muhammed Walugembe, James R. Mushi, Esinam N. Amuzu-Aweh, Gaspar H. Chiwanga, Peter L. Msoffe, Ying Wang, Perot Saelao, Terra Kelly, Rodrigo A. Gallardo, Huaijun Zhou, Susan J. Lamont, Amandus P. Muhairwa, Jack C. M. Dekkers

Animal Science Publications

Newcastle Disease (ND) is a continuing global threat to domestic poultry, especially in developing countries, where severe outbreaks of velogenic ND virus (NDV) often cause major economic losses to households. Local chickens are of great importance to rural family livelihoods through provision of high-quality protein. To investigate the genetic basis of host response to NDV, three popular Tanzanian chicken ecotypes (regional populations) were challenged with a lentogenic (vaccine) strain of NDV at 28 days of age. Various host response phenotypes, including anti-NDV antibody levels (pre-infection and 10 days post-infection, dpi), and viral load (2 and 6 dpi) were measured, in ...


Genome-Wide Association Study For Response To Vaccination In Angus Calves, L. M. Kramer, M. S. Mayes, E. D. Downey, R. G. Tait Jr., A. Woolums, C. Chase, J. M. Reecy Jan 2019

Genome-Wide Association Study For Response To Vaccination In Angus Calves, L. M. Kramer, M. S. Mayes, E. D. Downey, R. G. Tait Jr., A. Woolums, C. Chase, J. M. Reecy

Animal Science Publications

Background: Bovine respiratory disease complex (BRDC) is one of the most important sources of loss within the beef cattle industry in the USA. Steps have been taken to reduce the incidence of BRDC through vaccination. Despite the effectiveness of vaccines, large proportions of cattle still experience morbidity and mortality. Identification of genomic regions that are associated with variation in response to vaccination would allow for the selection of individuals genetically predisposed to respond to vaccination based on specific markers, while heritability and accuracy estimates would help facilitate genomic selection. This in turn may lead to selection for beef cattle herds ...


Detection Of Selection Signatures Among Brazilian, Sri Lankan, And Egyptian Chicken Populations Under Different Environmental Conditions, Muhammed Walugembe, Francesca Bertolini, Chandraratne Mahinda B. Dematawewa, Matheus P. Reis, Ahmed R. Elbeltagy, Carl J. Schmidt, Susan J. Lamont, Max F. Rothschild Jan 2019

Detection Of Selection Signatures Among Brazilian, Sri Lankan, And Egyptian Chicken Populations Under Different Environmental Conditions, Muhammed Walugembe, Francesca Bertolini, Chandraratne Mahinda B. Dematawewa, Matheus P. Reis, Ahmed R. Elbeltagy, Carl J. Schmidt, Susan J. Lamont, Max F. Rothschild

Animal Science Publications

Extreme environmental conditions are a major challenge in livestock production. Changes in climate, particularly those that contribute to weather extremes like drought or excessive humidity, may result in reduced performance and reproduction and could compromise the animal’s immune function. Animal survival within extreme environmental conditions could be in response to natural selection and to artificial selection for production traits that over time together may leave selection signatures in the genome. The aim of this study was to identify selection signatures that may be involved in the adaptation of indigenous chickens from two different climatic regions (Sri Lanka = Tropical; Egypt ...


Conserved, Breed-Dependent, And Subline-Dependent Innate Immune Responses Of Fayoumi And Leghorn Chicken Embryos To Newcastle Disease Virus Infection, Megan A. Schilling, Sahar Memari, Meredith Cavanaugh, Robab Katani, Melissa S. Deist, Jessica Radzio-Basu, Susan J. Lamont, Joram J. Buza, Vivek Kapur Jan 2019

Conserved, Breed-Dependent, And Subline-Dependent Innate Immune Responses Of Fayoumi And Leghorn Chicken Embryos To Newcastle Disease Virus Infection, Megan A. Schilling, Sahar Memari, Meredith Cavanaugh, Robab Katani, Melissa S. Deist, Jessica Radzio-Basu, Susan J. Lamont, Joram J. Buza, Vivek Kapur

Animal Science Publications

Newcastle disease virus (NDV) is a threat to the global poultry industry, but particularly for smallholder farmers in low- and middle-income countries. Previous reports suggest that some breeds of chickens are less susceptible to NDV infection, however, the mechanisms contributing to this are unknown. We here examined the comparative transcriptional responses of innate immune genes to NDV infection in inbred sublines of the Fayoumi and Leghorn breeds known to differ in their relative susceptibility to infection as well as at the microchromosome bearing the major histocompatability complex (MHC) locus. The analysis identified a set of five core genes, Mx1, IRF1 ...


Genome-Wide Association Scan For Qtl And Their Positional Candidate Genes Associated With Internal Organ Traits In Chickens, Gabriel Costa Monteiro Moreira, Mayara Salvian, Clarissa Boschiero, Aline Silva Mello Cesar, James M. Reecy, Thaís Fernanda Godoy, Mônica Corrêa Ledur, Dorian Garrick, Gerson Barreto Mourão, Luiz L. Coutinho Jan 2019

Genome-Wide Association Scan For Qtl And Their Positional Candidate Genes Associated With Internal Organ Traits In Chickens, Gabriel Costa Monteiro Moreira, Mayara Salvian, Clarissa Boschiero, Aline Silva Mello Cesar, James M. Reecy, Thaís Fernanda Godoy, Mônica Corrêa Ledur, Dorian Garrick, Gerson Barreto Mourão, Luiz L. Coutinho

Animal Science Publications

Background: Poultry breeding programs have been focused on improvement of growth and carcass traits, however, this has resulted in correlated changes in internal organ weights and increased incidence of metabolic disorders. These disorders can affect feed efficiency or even cause death. We used a high density SNP array (600 K, Affymetrix) to estimate genomic heritability, perform genome-wide association analysis, and identify genomic regions and positional candidate genes (PCGs) associated with internal organ traits in an F2 chicken population. We integrated knowledge of haplotype blocks, selection signature regions and sequencing data to refine the list of PCGs.

Results: Estimated genomic heritability ...


Unraveling Genomic Associations With Feed Efficiency And Body Weight Traits In Chickens Through An Integrative Approach, Gabriel Costa Monteiro Moreira, Mirele Daiana Poleti, Fábio Pértille, Clarissa Boschiero, Aline Silva Mello Cesar, Thaís Fernanda Godoy, Mônica Corrêa Ledur, James M. Reecy, Dorian J. Garrick, Luiz Lehmann Coutinho Jan 2019

Unraveling Genomic Associations With Feed Efficiency And Body Weight Traits In Chickens Through An Integrative Approach, Gabriel Costa Monteiro Moreira, Mirele Daiana Poleti, Fábio Pértille, Clarissa Boschiero, Aline Silva Mello Cesar, Thaís Fernanda Godoy, Mônica Corrêa Ledur, James M. Reecy, Dorian J. Garrick, Luiz Lehmann Coutinho

Animal Science Publications

Background: Feed efficiency and growth rate have been targets for selection to improve chicken production. The incorporation of genomic tools may help to accelerate selection. We genotyped 529 individuals using a high-density SNP chip (600 K, Affymetrix®) to estimate genomic heritability of performance traits and to identify genomic regions and their positional candidate genes associated with performance traits in a Brazilian F2 Chicken Resource population. Regions exhibiting selection signatures and a SNP dataset from resequencing were integrated with the genomic regions identified using the chip to refine the list of positional candidate genes and identify potential causative mutations.

Results: Feed ...


Brevibacterium From Austrian Hard Cheese Harbor A Putative Histamine Catabolism Pathway And A Plasmid For Adaptation To The Cheese Environment, Justin M. Anast, Monika Dzieciol, Dylan L. Schultz, Martin Wagner, Evelyne Mann, Stephan Schmitz-Esser Jan 2019

Brevibacterium From Austrian Hard Cheese Harbor A Putative Histamine Catabolism Pathway And A Plasmid For Adaptation To The Cheese Environment, Justin M. Anast, Monika Dzieciol, Dylan L. Schultz, Martin Wagner, Evelyne Mann, Stephan Schmitz-Esser

Animal Science Publications

The genus Brevibacterium harbors many members important for cheese ripening. We performed real-time quantitative PCR (qPCR) to determine the abundance of Brevibacterium on rinds of Vorarlberger Bergkäse, an Austrian artisanal washed-rind hard cheese, over 160 days of ripening. Our results show that Brevibacterium are abundant on Vorarlberger Bergkäse rinds throughout the ripening time. To elucidate the impact of Brevibacterium on cheese production, we analysed the genomes of three cheese rind isolates, L261, S111, and S22. L261 belongs to Brevibacterium aurantiacum, whereas S111 and S22 represent novel species within the genus Brevibacterium based on 16S rRNA gene similarity and average nucleotide ...


Signatures Of Selection And Environmental Adaptation Across The Goat Genome Post-Domestication, Francesca Bertolini, Bertrand Servin, Andrea Talenti, Estelle Rochat, Eui Soo Kim, Claire Oget, Isabelle Palhière, Alessandra Crisà, Gennaro Catillo, Roberto Steri, Marcel Amills, Licia Colli, Gabriele Marras, Marco Milanesi, Ezequiel Nicolazzi, Benjamin D. Rosen, Curtis P. Van Tassell, Brent Guldbrandtsen, Tad S. Sonstegard, Gwenola Tosser‑Klopp, Alessandra Stella, Max F. Rothschild, Stéphane Joost, Paola Crepaldi, Adaptmap Consortium Nov 2018

Signatures Of Selection And Environmental Adaptation Across The Goat Genome Post-Domestication, Francesca Bertolini, Bertrand Servin, Andrea Talenti, Estelle Rochat, Eui Soo Kim, Claire Oget, Isabelle Palhière, Alessandra Crisà, Gennaro Catillo, Roberto Steri, Marcel Amills, Licia Colli, Gabriele Marras, Marco Milanesi, Ezequiel Nicolazzi, Benjamin D. Rosen, Curtis P. Van Tassell, Brent Guldbrandtsen, Tad S. Sonstegard, Gwenola Tosser‑Klopp, Alessandra Stella, Max F. Rothschild, Stéphane Joost, Paola Crepaldi, Adaptmap Consortium

Animal Science Publications

Background: Since goat was domesticated 10,000 years ago, many factors have contributed to the differentiation of goat breeds and these are classified mainly into two types: (i) adaptation to different breeding systems and/or purposes and (ii) adaptation to different environments. As a result, approximately 600 goat breeds have developed worldwide; they differ considerably from one another in terms of phenotypic characteristics and are adapted to a wide range of climatic conditions. In this work, we analyzed the AdaptMap goat dataset, which is composed of data from more than 3000 animals collected worldwide and genotyped with the CaprineSNP50 BeadChip ...


Patterns Of Homozygosity In Insular And Continental Goat Breeds, Taina F. Cardoso, Marcel Amills, Francesca Bertolini, Max Rothschild, Gabriele Marras, Geert Boink, Jordi Jordana, Juan Capote, Sean Carolan, Jón H. Hallsson, Juha Kantanen, Agueda Pons, Johannes A. Lenstra, The Adaptmap Consortium Nov 2018

Patterns Of Homozygosity In Insular And Continental Goat Breeds, Taina F. Cardoso, Marcel Amills, Francesca Bertolini, Max Rothschild, Gabriele Marras, Geert Boink, Jordi Jordana, Juan Capote, Sean Carolan, Jón H. Hallsson, Juha Kantanen, Agueda Pons, Johannes A. Lenstra, The Adaptmap Consortium

Animal Science Publications

Background: Genetic isolation of breeds may result in a significant loss of diversity and have consequences on health and performance. In this study, we examined the effect of geographic isolation on caprine genetic diversity patterns by genotyping 480 individuals from 25 European and African breeds with the Goat SNP50 BeadChip and comparing patterns of homozygosity of insular and nearby continental breeds.

Results: Among the breeds analysed, number and total length of ROH varied considerably and depending on breeds, ROH could cover a substantial fraction of the genome (up to 1.6 Gb in Icelandic goats). When compared with their continental ...


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, Adaptmap Consortium Nov 2018

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, Adaptmap Consortium

Animal Science Publications

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.


Genome-Wide Snp Profiling Of Worldwide Goat Populations Reveals Strong Partitioning Of Diversity And Highlights Post-Domestication Migration Routes, Licia Colli, Marco Milanesi, Andrea Talenti, Francesca Bertolini, Minhui Chen, Alessandra Crisà, Kevin Gerard Daly, Marcello Del Corvo, Bernt Guldbrandtsen, Johannes A. Lenstra, Benjamin D. Rosen, Elia Vajana, Gennaro Catillo, Stéphane Joost, Ezequiel Luis Nicolazzi, Estelle Rochat, Max F. Rothschild, Bertrand Servin, Tad S. Sonstegard, Roberto Steri, Curtis P. Van Tassell, Paolo Ajmone‑Marsan, Paola Crepaldi, Alessandra Stella, Adaptmap Consortium Nov 2018

Genome-Wide Snp Profiling Of Worldwide Goat Populations Reveals Strong Partitioning Of Diversity And Highlights Post-Domestication Migration Routes, Licia Colli, Marco Milanesi, Andrea Talenti, Francesca Bertolini, Minhui Chen, Alessandra Crisà, Kevin Gerard Daly, Marcello Del Corvo, Bernt Guldbrandtsen, Johannes A. Lenstra, Benjamin D. Rosen, Elia Vajana, Gennaro Catillo, Stéphane Joost, Ezequiel Luis Nicolazzi, Estelle Rochat, Max F. Rothschild, Bertrand Servin, Tad S. Sonstegard, Roberto Steri, Curtis P. Van Tassell, Paolo Ajmone‑Marsan, Paola Crepaldi, Alessandra Stella, Adaptmap Consortium

Animal Science Publications

Background: Goat populations that are characterized within the AdaptMap project cover a large part of the worldwide distribution of this species and provide the opportunity to assess their diversity at a global scale. We analysed genome-wide 50 K single nucleotide polymorphism (SNP) data from 144 populations to describe the global patterns of molecular variation, compare them to those observed in other livestock species, and identify the drivers that led to the current distribution of goats.

Results: A high degree of genetic variability exists among the goat populations studied. Our results highlight a strong partitioning of molecular diversity between and within ...


Genome-Wide Patterns Of Homozygosity Provide Clues About The Population History And Adaptation Of Goats, Francesca Bertolini, Tainã Figueiredo Cardoso, Gabriele Marras, Ezequiel L. Nicolazzi, Max F. Rothschild, Marcel Amills, Adaptmap Consortium Nov 2018

Genome-Wide Patterns Of Homozygosity Provide Clues About The Population History And Adaptation Of Goats, Francesca Bertolini, Tainã Figueiredo Cardoso, Gabriele Marras, Ezequiel L. Nicolazzi, Max F. Rothschild, Marcel Amills, Adaptmap Consortium

Animal Science Publications

Background: Patterns of homozygosity can be influenced by several factors, such as demography, recombination, and selection. Using the goat SNP50 BeadChip, we genotyped 3171 goats belonging to 117 populations with a worldwide distribution. Our objectives were to characterize the number and length of runs of homozygosity (ROH) and to detect ROH hotspots in order to gain new insights into the consequences of neutral and selection processes on the genome-wide homozygosity patterns of goats.

Results: The proportion of the goat genome covered by ROH is, in general, less than 15% with an inverse relationship between ROH length and frequency i.e ...


Integration Of Genome Wide Association Studies And Whole Genome Sequencing Provides Novel Insights Into Fat Deposition In Chicken, Gabriel Costa Monteiro Moreira, Clarissa Boschiero, Aline Silva Mello Cesar, James M. Reecy, Thaís Fernanda Godoy, Fábio Pértille, Mônica Corrêa Ledur, Ana Silvia Alves Meira Tavares Moura, Dorian J. Garrick, Luiz Lehmann Coutinho Nov 2018

Integration Of Genome Wide Association Studies And Whole Genome Sequencing Provides Novel Insights Into Fat Deposition In Chicken, Gabriel Costa Monteiro Moreira, Clarissa Boschiero, Aline Silva Mello Cesar, James M. Reecy, Thaís Fernanda Godoy, Fábio Pértille, Mônica Corrêa Ledur, Ana Silvia Alves Meira Tavares Moura, Dorian J. Garrick, Luiz Lehmann Coutinho

Animal Science Publications

Excessive fat deposition is a negative factor for poultry production because it reduces feed efficiency, increases the cost of meat production and is a health concern for consumers. We genotyped 497 birds from a Brazilian F2 Chicken Resource Population, using a high-density SNP array (600 K), to estimate the genomic heritability of fat deposition related traits and to identify genomic regions and positional candidate genes (PCGs) associated with these traits. Selection signature regions, haplotype blocks and SNP data from a previous whole genome sequencing study in the founders of this chicken F2 population were used to refine the list of ...


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 Oct 2018

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

Animal Science Publications

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 ...


A Polymorphism In The Fatty Acid Desaturase-2 Gene Is Associated With The Arachidonic Acid Metabolism In Pigs, Sofia Gol, Ramona N. Pena, Max F. Rothschild, Marc Tor, Joan Estany Sep 2018

A Polymorphism In The Fatty Acid Desaturase-2 Gene Is Associated With The Arachidonic Acid Metabolism In Pigs, Sofia Gol, Ramona N. Pena, Max F. Rothschild, Marc Tor, Joan Estany

Animal Science Publications

Arachidonic acid (C20:4) is related to a wide range of biological effects including lipid homeostasis. The fatty acid desaturase-2 (FADS2) gene encodes for the delta-6-desaturase, which is involved in the biosynthesis of C20:4 from linoleic acid (C18:2). The purpose of this study was to characterise mutations in the promoter of the porcine FADS2, evaluating in particular the effect of one haplotype tagging polymorphism (rs321384923A > G) on the biosynthesis pathway of C20:4. A total of 1,192 Duroc barrows with records on fatty acid composition in muscle and subcutaneous fat were genotyped. Pigs carrying the A allele ...


Immunomodulatory Effects Of Heat Stress And Lipopolysaccharide On The Bursal Transcriptome In Two Distinct Chicken Lines, Melissa S. Monson, Angelica Van Goor, Christopher M. Ashwell, Michael E. Persia, Max F. Rothschild, Carl J. Schmidt, Susan J. Lamont Aug 2018

Immunomodulatory Effects Of Heat Stress And Lipopolysaccharide On The Bursal Transcriptome In Two Distinct Chicken Lines, Melissa S. Monson, Angelica Van Goor, Christopher M. Ashwell, Michael E. Persia, Max F. Rothschild, Carl J. Schmidt, Susan J. Lamont

Animal Science Publications

Background: Exposure to heat stress suppresses poultry immune responses, which can increase susceptibility to infectious diseases and, thereby, intensify the negative effects of heat on poultry welfare and performance. Identifying genes and pathways that are affected by high temperatures, especially heat-induced changes in immune responses, could provide targets to improve disease resistance in chickens. This study utilized RNAsequencing (RNA-seq) to investigate transcriptome responses in the bursa of Fabricius, a primary immune tissue, after exposure to acute heat stress and/or subcutaneous immune stimulation with lipopolysaccharide (LPS) in a 2 × 2 factorial design: Thermoneutral + Saline, Heat + Saline, Thermoneutral + LPS and Heat ...


Genome-Wide Association Studies Of Inflammatory Bowel Disease In German Shepherd Dogs, Atiyeh Peiravan, Francesca Bertolini, Max Rothschild, Kenneth W. Simpson, Albert E. Jergens, Karin Allenspach, Dirk Werling Jul 2018

Genome-Wide Association Studies Of Inflammatory Bowel Disease In German Shepherd Dogs, Atiyeh Peiravan, Francesca Bertolini, Max Rothschild, Kenneth W. Simpson, Albert E. Jergens, Karin Allenspach, Dirk Werling

Animal Science Publications

Canine Inflammatory Bowel Disease (IBD) is considered a multifactorial disease caused by complex interactions between the intestinal immune system, intestinal microbiota and environmental factors in genetically susceptible individuals. Although IBD can affect any breed, German shepherd dogs (GSD) in the UK are at increased risk of developing the disease. Based on previous evidence, the aim of the present study was to identify single nucleotide polymorphisms (SNPs), which may confer genetic susceptibility or resistance to IBD using a genome-wide association study (GWAS). Genomic DNA was extracted from EDTA blood or saliva samples of 96 cases and 98 controls. Genotyping of cases ...


Identification Of Putative Regulatory Regions And Transcription Factors Associated With Intramuscular Fat Content Traits, Aline S. M. Cesar, Luciana C. A. Regitano, James M. Reecy, Mirele D. Poleti, Priscila S. N. Oliveira, Gabriella B. De Oliveira, Gabriel C. M. Moreira, Maurício A. Mudadu, Polyana C. Tizioto, James E. Koltes, Elyn Fritz-Waters, Luke Kramer, Dorian Garrick, Hamid Beiki, Ludwig Geistlinger, Gerson B. Mourão, Adhemar Zerlotini, Luiz L. Coutinho Jun 2018

Identification Of Putative Regulatory Regions And Transcription Factors Associated With Intramuscular Fat Content Traits, Aline S. M. Cesar, Luciana C. A. Regitano, James M. Reecy, Mirele D. Poleti, Priscila S. N. Oliveira, Gabriella B. De Oliveira, Gabriel C. M. Moreira, Maurício A. Mudadu, Polyana C. Tizioto, James E. Koltes, Elyn Fritz-Waters, Luke Kramer, Dorian Garrick, Hamid Beiki, Ludwig Geistlinger, Gerson B. Mourão, Adhemar Zerlotini, Luiz L. Coutinho

Animal Science Publications

Background: Integration of high throughput DNA genotyping and RNA-sequencing data allows for the identification of genomic regions that control gene expression, known as expression quantitative trait loci (eQTL), on a whole genome scale. Intramuscular fat (IMF) content and carcass composition play important roles in metabolic and physiological processes in mammals because they influence insulin sensitivity and consequently prevalence of metabolic diseases such as obesity and type 2 diabetes. However, limited information is available on the genetic variants and mechanisms associated with IMF deposition in mammals. Thus, our hypothesis was that eQTL analyses could identify putative regulatory regions and transcription factors ...


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 May 2018

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

Animal Science Publications

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 ...


Age-Associated Microbiome Shows The Giant Panda Lives On Hemicelluloses, Not On Cellulose, Wenping Zhang, Wenbin Liu, Rong Hu, Liang Zhang, Stephan Schmitz-Esser, Huaibo Sun, Junjin Xie, Yunfei Zhang, Chengdong Wang, Lifeng Li, Bisong Yue, He Huang, Hairui Wang, Fujun Shen, Zhihe Zhang May 2018

Age-Associated Microbiome Shows The Giant Panda Lives On Hemicelluloses, Not On Cellulose, Wenping Zhang, Wenbin Liu, Rong Hu, Liang Zhang, Stephan Schmitz-Esser, Huaibo Sun, Junjin Xie, Yunfei Zhang, Chengdong Wang, Lifeng Li, Bisong Yue, He Huang, Hairui Wang, Fujun Shen, Zhihe Zhang

Animal Science Publications

The giant panda feeds almost exclusively on bamboo, a diet highly enriched in lignin and cellulose, but is characterized by a digestive tract similar to carnivores. It is still large unknown if and how the giant panda gut microbiota contributes to lignin and cellulose degradation. Here we show the giant pandas’ gut microbiota does not significantly contribute to cellulose and lignin degradation. We found that no operational taxonomic unit had a nearest neighbor identified as a cellulolytic species or strain with a significant higher abundance in juvenile than cubs, a very low abundance of putative lignin and cellulose genes existed ...


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, Et Al. Mar 2018

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, Et Al.

Animal Science Publications

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 ...