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438 results on '"Schnabel, Robert D."'

1. The Ruminant Telomere-to-Telomere (RT2T) Consortium

Author

Kalbfleisch, Theodore S., McKay, Stephanie D., Murdoch, Brenda M., Adelson, David L., Almansa-Villa, Diego, Becker, Gabrielle, Beckett, Linda M., Benítez-Galeano, María José, Biase, Fernando, Casey, Theresa, Chuong, Edward, Clark, Emily, Clarke, Shannon, Cockett, Noelle, Couldrey, Christine, Davis, Brian W., Elsik, Christine G., Faraut, Thomas, Gao, Yahui, Genet, Carine, Grady, Patrick, Green, Jonathan, Green, Richard, Guan, Dailu, Hagen, Darren, Hartley, Gabrielle A., Heaton, Mike, Hoyt, Savannah J., Huang, Wen, Jarvis, Erich, Kalleberg, Jenna, Khatib, Hasan, Koepfi, Klaus-Peter, Koltes, James, Koren, Sergey, Kuehn, Christa, Leeb, Tosso, Leonard, Alexander, Liu, George E., Low, Wai Yee, McConnell, Hunter, McRae, Kathryn, Miga, Karen, Mousel, Michelle, Neibergs, Holly, Olagunju, Temitayo, Pennell, Matt, Petry, Bruna, Pewsner, Mirjam, Phillippy, Adam M., Pickett, Brandon D., Pineda, Paulene, Potapova, Tamara, Rachagani, Satyanarayana, Rhie, Arang, Rijnkels, Monique, Robic, Annie, Rodriguez Osorio, Nelida, Safonova, Yana, Schettini, Gustavo, Schnabel, Robert D., Sirpu Natesh, Nagabhishek, Stegemiller, Morgan, Storer, Jessica, Stothard, Paul, Stull, Caleb, Tosser-Klopp, Gwenola, Traglia, Germán M., Tuggle, Christopher K., Van Tassell, Curtis P., Watson, Corey, Weikard, Rosemarie, Wimmers, Klaus, Xie, Shangqian, Yang, Liu, Smith, Timothy P. L., O’Neill, Rachel J., and Rosen, Benjamin D.

Published
2024
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3. De novo assembly of the cattle reference genome with single-molecule sequencing.

Author

Rosen, Benjamin D, Bickhart, Derek M, Schnabel, Robert D, Koren, Sergey, Elsik, Christine G, Tseng, Elizabeth, Rowan, Troy N, Low, Wai Y, Zimin, Aleksey, Couldrey, Christine, Hall, Richard, Li, Wenli, Rhie, Arang, Ghurye, Jay, McKay, Stephanie D, Thibaud-Nissen, Françoise, Hoffman, Jinna, Murdoch, Brenda M, Snelling, Warren M, McDaneld, Tara G, Hammond, John A, Schwartz, John C, Nandolo, Wilson, Hagen, Darren E, Dreischer, Christian, Schultheiss, Sebastian J, Schroeder, Steven G, Phillippy, Adam M, Cole, John B, Van Tassell, Curtis P, Liu, George, Smith, Timothy PL, and Medrano, Juan F

Subjects
Animals, Cattle, Sequence Analysis, DNA, Breeding, Genomics, Polymorphism, Genetic, Genome, Reference Standards, RNA-Seq, Hereford, bovine genome, cattle, reference assembly, Human Genome, Biotechnology, Genetics
Abstract

BackgroundMajor advances in selection progress for cattle have been made following the introduction of genomic tools over the past 10-12 years. These tools depend upon the Bos taurus reference genome (UMD3.1.1), which was created using now-outdated technologies and is hindered by a variety of deficiencies and inaccuracies.ResultsWe present the new reference genome for cattle, ARS-UCD1.2, based on the same animal as the original to facilitate transfer and interpretation of results obtained from the earlier version, but applying a combination of modern technologies in a de novo assembly to increase continuity, accuracy, and completeness. The assembly includes 2.7 Gb and is >250× more continuous than the original assembly, with contig N50 >25 Mb and L50 of 32. We also greatly expanded supporting RNA-based data for annotation that identifies 30,396 total genes (21,039 protein coding). The new reference assembly is accessible in annotated form for public use.ConclusionsWe demonstrate that improved continuity of assembled sequence warrants the adoption of ARS-UCD1.2 as the new cattle reference genome and that increased assembly accuracy will benefit future research on this species.

Published
2020

6. Tissue Tropism in Host Transcriptional Response to Members of the Bovine Respiratory Disease Complex.

Author

Behura, Susanta K, Tizioto, Polyana C, Kim, JaeWoo, Grupioni, Natalia V, Seabury, Christopher M, Schnabel, Robert D, Gershwin, Laurel J, Van Eenennaam, Alison L, Toaff-Rosenstein, Rachel, Neibergs, Holly L, Regitano, Luciana CA, and Taylor, Jeremy F

Subjects
Lung, Animals, Cattle, Mannheimia haemolytica, Mycoplasma bovis, Herpesvirus 1, Bovine, Diarrhea Viruses, Bovine Viral, Respiratory Syncytial Virus, Bovine, Bovine Respiratory Disease Complex, Transcription, Genetic, Male, Host-Pathogen Interactions, Viral Tropism, Transcriptome, Diarrhea Viruses, Bovine Viral, Herpesvirus 1, Bovine, Respiratory Syncytial Virus, Transcription, Genetic
Abstract

Bovine respiratory disease (BRD) is the most common infectious disease of beef and dairy cattle and is characterized by a complex infectious etiology that includes a variety of viral and bacterial pathogens. We examined the global changes in mRNA abundance in healthy lung and lung lesions and in the lymphoid tissues bronchial lymph node, retropharyngeal lymph node, nasopharyngeal lymph node and pharyngeal tonsil collected at the peak of clinical disease from beef cattle experimentally challenged with either bovine respiratory syncytial virus, infectious bovine rhinotracheitis, bovine viral diarrhea virus, Mannheimia haemolytica or Mycoplasma bovis. We identified signatures of tissue-specific transcriptional responses indicative of tropism in the coordination of host's immune tissue responses to infection by viral or bacterial infections. Furthermore, our study shows that this tissue tropism in host transcriptional response to BRD pathogens results in the activation of different networks of response genes. The differential crosstalk among genes expressed in lymphoid tissues was predicted to be orchestrated by specific immune genes that act as 'key players' within expression networks. The results of this study serve as a basis for the development of innovative therapeutic strategies and for the selection of cattle with enhanced resistance to BRD.

Published
2017

7. RT2T: A Global Collaborative Project to Study Chromosomal Evolution in the Suborder Ruminantia

Author

Kalbfleisch, Ted, primary, McKay, Stephanie, additional, Murdoch, Brenda, additional, Adelson, David L., additional, Almansa, Diego, additional, Becker, Gabrielle, additional, Beckett, Linda M., additional, Benítez-Galeano, María José, additional, Biase, Fernando, additional, Casey, Theresa, additional, Chuong, Edward, additional, Clark, Emily, additional, Clarke, Shannon, additional, Cockett, Noelle, additional, Couldrey, Christine, additional, Davis, Brian W., additional, Elsik, Christine G., additional, Faraut, Thomas, additional, Gao, Yahui, additional, Genet, Carine, additional, Grady, Patrick, additional, Green, Jonathan, additional, Green, Richard, additional, Guan, Dailu, additional, Hagen, Darren, additional, Hartley, Gabrielle A., additional, Heaton, Mike, additional, Hoyt, Savannah J., additional, Huang, Wen, additional, Jarvis, Erich, additional, Kalleberg, Jenna, additional, Khatib, Hasan, additional, Koepfi, Klaus-Peter, additional, Koltes, James, additional, Koren, Sergey, additional, Kuehn, Christa, additional, Leeb, Tosso, additional, Leonard, Alexander, additional, Liu, George E., additional, Low, Wai Yee, additional, McConnell, Hunter, additional, McRae, Kathryn, additional, Miga, Karen, additional, Mousel, Michelle, additional, Neibergs, Holly, additional, O'Neill, Rachel, additional, Olagunju, Temitayo, additional, Pennell, Matt, additional, Petry, Bruna, additional, Pewsner, Mirjam, additional, Phillippy, Adam M., additional, Pickett, Brandon D., additional, Pineda, Paulene, additional, Potapova, Tamara, additional, Rachagani, Satyanarayana, additional, Rhie, Arang, additional, Rijnkels, Monique, additional, Robic, Annie, additional, Osorio, Nelida Rodriguez, additional, Safonova, Yana, additional, Schettini, Gustavo, additional, Schnabel, Robert D., additional, Natesh, Nagabhishek Sirpu, additional, Stegemiller, Morgan, additional, Storer, Jessica, additional, Stothard, Paul, additional, Stull, Caleb, additional, Tosser-Klopp, Gwenola, additional, Traglia, Germán M., additional, Tuggle, Chris, additional, Tassell, Curtis P. Van, additional, Watson, Corey, additional, Weikard, Rosemarie, additional, Wimmers, Klaus, additional, Xie, Shangqian, additional, Yang, Liu, additional, Smith, Tim, additional, and Rosen, Ben, additional

Published
2024
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9. Early cave art and ancient DNA record the origin of European bison.

Author

Soubrier, Julien, Gower, Graham, Chen, Kefei, Richards, Stephen M, Llamas, Bastien, Mitchell, Kieren J, Ho, Simon YW, Kosintsev, Pavel, Lee, Michael SY, Baryshnikov, Gennady, Bollongino, Ruth, Bover, Pere, Burger, Joachim, Chivall, David, Crégut-Bonnoure, Evelyne, Decker, Jared E, Doronichev, Vladimir B, Douka, Katerina, Fordham, Damien A, Fontana, Federica, Fritz, Carole, Glimmerveen, Jan, Golovanova, Liubov V, Groves, Colin, Guerreschi, Antonio, Haak, Wolfgang, Higham, Tom, Hofman-Kamińska, Emilia, Immel, Alexander, Julien, Marie-Anne, Krause, Johannes, Krotova, Oleksandra, Langbein, Frauke, Larson, Greger, Rohrlach, Adam, Scheu, Amelie, Schnabel, Robert D, Taylor, Jeremy F, Tokarska, Małgorzata, Tosello, Gilles, van der Plicht, Johannes, van Loenen, Ayla, Vigne, Jean-Denis, Wooley, Oliver, Orlando, Ludovic, Kowalczyk, Rafał, Shapiro, Beth, and Cooper, Alan

Subjects
Cell Nucleus, Animals, Bison, Cattle, DNA, Mitochondrial, Sequence Analysis, DNA, Evolution, Molecular, Phylogeny, Fossils, Paintings, Europe, Genome, Mitochondrial, Caves, DNA, Ancient, Human Genome, Genetics, DNA, Mitochondrial, Sequence Analysis, Evolution, Molecular, Genome, Ancient
Abstract

The two living species of bison (European and American) are among the few terrestrial megafauna to have survived the late Pleistocene extinctions. Despite the extensive bovid fossil record in Eurasia, the evolutionary history of the European bison (or wisent, Bison bonasus) before the Holocene (

Published
2016

10. Diversity and population-genetic properties of copy number variations and multicopy genes in cattle

Author

Bickhart, Derek M, Xu, Lingyang, Hutchison, Jana L, Cole, John B, Null, Daniel J, Schroeder, Steven G, Song, Jiuzhou, Garcia, Jose Fernando, Sonstegard, Tad S, Van Tassell, Curtis P, Schnabel, Robert D, Taylor, Jeremy F, Lewin, Harris A, and Liu, George E

Subjects
Biological Sciences, Genetics, Human Genome, Biotechnology, Animals, Breeding, Cattle, DNA Copy Number Variations, Gene Duplication, Genome, Multigene Family, Polymorphism, Genetic, cattle genome, population sequencing, copy number variation, taurine, indicine, Plant Biology & Botany
Abstract

The diversity and population genetics of copy number variation (CNV) in domesticated animals are not well understood. In this study, we analysed 75 genomes of major taurine and indicine cattle breeds (including Angus, Brahman, Gir, Holstein, Jersey, Limousin, Nelore, and Romagnola), sequenced to 11-fold coverage to identify 1,853 non-redundant CNV regions. Supported by high validation rates in array comparative genomic hybridization (CGH) and qPCR experiments, these CNV regions accounted for 3.1% (87.5 Mb) of the cattle reference genome, representing a significant increase over previous estimates of the area of the genome that is copy number variable (∼2%). Further population genetics and evolutionary genomics analyses based on these CNVs revealed the population structures of the cattle taurine and indicine breeds and uncovered potential diversely selected CNVs near important functional genes, including AOX1, ASZ1, GAT, GLYAT, and KRTAP9-1 Additionally, 121 CNV gene regions were found to be either breed specific or differentially variable across breeds, such as RICTOR in dairy breeds and PNPLA3 in beef breeds. In contrast, clusters of the PRP and PAG genes were found to be duplicated in all sequenced animals, suggesting that subfunctionalization, neofunctionalization, or overdominance play roles in diversifying those fertility-related genes. These CNV results provide a new glimpse into the diverse selection histories of cattle breeds and a basis for correlating structural variation with complex traits in the future.

Published
2016

11. Bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs

Author

Marsden, Clare D, Vecchyo, Diego Ortega-Del, O’Brien, Dennis P, Taylor, Jeremy F, Ramirez, Oscar, Vilà, Carles, Marques-Bonet, Tomas, Schnabel, Robert D, Wayne, Robert K, and Lohmueller, Kirk E

Subjects
Biological Sciences, Genetics, Human Genome, Life on Land, Animals, Animals, Domestic, Datasets as Topic, Dog Diseases, Dogs, Endangered Species, Genetic Variation, Genome, Heterozygote, Inbreeding, Population Density, Selection, Genetic, Selective Breeding, Wolves, deleterious mutations, domestication, bottleneck, selective sweep
Abstract

Population bottlenecks, inbreeding, and artificial selection can all, in principle, influence levels of deleterious genetic variation. However, the relative importance of each of these effects on genome-wide patterns of deleterious variation remains controversial. Domestic and wild canids offer a powerful system to address the role of these factors in influencing deleterious variation because their history is dominated by known bottlenecks and intense artificial selection. Here, we assess genome-wide patterns of deleterious variation in 90 whole-genome sequences from breed dogs, village dogs, and gray wolves. We find that the ratio of amino acid changing heterozygosity to silent heterozygosity is higher in dogs than in wolves and, on average, dogs have 2-3% higher genetic load than gray wolves. Multiple lines of evidence indicate this pattern is driven by less efficient natural selection due to bottlenecks associated with domestication and breed formation, rather than recent inbreeding. Further, we find regions of the genome implicated in selective sweeps are enriched for amino acid changing variants and Mendelian disease genes. To our knowledge, these results provide the first quantitative estimates of the increased burden of deleterious variants directly associated with domestication and have important implications for selective breeding programs and the conservation of rare and endangered species. Specifically, they highlight the costs associated with selective breeding and question the practice favoring the breeding of individuals that best fit breed standards. Our results also suggest that maintaining a large population size, rather than just avoiding inbreeding, is a critical factor for preventing the accumulation of deleterious variants.

Published
2016

12. What's in your next-generation sequence data? An exploration of unmapped DNA and RNA sequence reads from the bovine reference individual.

Author

Whitacre, Lynsey K, Tizioto, Polyana C, Kim, JaeWoo, Sonstegard, Tad S, Schroeder, Steven G, Alexander, Leeson J, Medrano, Juan F, Schnabel, Robert D, Taylor, Jeremy F, and Decker, Jared E

Subjects
Animals, Cattle, DNA, RNA, Sequence Analysis, DNA, Algorithms, High-Throughput Nucleotide Sequencing, DNA sequencing, RNA sequencing, Unmapped reads, Sequence Analysis, Biological Sciences, Information and Computing Sciences, Medical and Health Sciences, Bioinformatics
Abstract

BackgroundNext-generation sequencing projects commonly commence by aligning reads to a reference genome assembly. While improvements in alignment algorithms and computational hardware have greatly enhanced the efficiency and accuracy of alignments, a significant percentage of reads often remain unmapped.ResultsWe generated de novo assemblies of unmapped reads from the DNA and RNA sequencing of the Bos taurus reference individual and identified the closest matching sequence to each contig by alignment to the NCBI non-redundant nucleotide database using BLAST. As expected, many of these contigs represent vertebrate sequence that is absent, incomplete, or misassembled in the UMD3.1 reference assembly. However, numerous additional contigs represent invertebrate species. Most prominent were several species of Spirurid nematodes and a blood-borne parasite, Babesia bigemina. These species are either not present in the US or are not known to infect taurine cattle and the reference animal appears to have been host to unsequenced sister species.ConclusionsWe demonstrate the importance of exploring unmapped reads to ascertain sequences that are either absent or misassembled in the reference assembly and for detecting sequences indicative of parasitic or commensal organisms.

Published
2015

13. Worldwide Patterns of Ancestry, Divergence, and Admixture in Domesticated Cattle

Author

Decker, Jared E., McKay, Stephanie D., Rolf, Megan M., Kim, JaeWoo, Alcalá, Antonio Molina, Sonstegard, Tad S., Hanotte, Olivier, Götherström, Anders, Seabury, Christopher M., Praharani, Lisa, Babar, Masroor Ellahi, Regitano, Luciana Correia de Almeida, Yildiz, Mehmet Ali, Heaton, Michael P., Lui, Wansheng, Lei, Chu-Zhao, Reecy, James M., Saif-Ur-Rehman, Muhammad, Schnabel, Robert D., and Taylor, Jeremy F.

Subjects
Quantitative Biology - Populations and Evolution, Quantitative Biology - Genomics
Abstract

The domestication and development of cattle has considerably impacted human societies, but the histories of cattle breeds have been poorly understood especially for African, Asian, and American breeds. Using genotypes from 43,043 autosomal single nucleotide polymorphism markers scored in 1,543 animals, we evaluate the population structure of 134 domesticated bovid breeds. Regardless of the analytical method or sample subset, the three major groups of Asian indicine, Eurasian taurine, and African taurine were consistently observed. Patterns of geographic dispersal resulting from co-migration with humans and exportation are recognizable in phylogenetic networks. All analytical methods reveal patterns of hybridization which occurred after divergence. Using 19 breeds, we map the cline of indicine introgression into Africa. We infer that African taurine possess a large portion of wild African auroch ancestry, causing their divergence from Eurasian taurine. We detect exportation patterns in Asia and identify a cline of Eurasian taurine/indicine hybridization in Asia. We also identify the influence of species other than Bos taurus in the formation of Asian breeds. We detect the pronounced influence of Shorthorn cattle in the formation of European breeds. Iberian and Italian cattle possess introgression from African taurine. American Criollo cattle are shown to be of Iberian, and not African, decent. Indicine introgression into American cattle occurred in the Americas, and not Europe. We argue that cattle migration, movement and trading followed by admixture have been important forces in shaping modern bovine genomic variation., Comment: 38 pages, 15 figures. Various changes made to respond to peer reviews. Mostly, arguments were clarified and additional f-statistics were added

Published
2013
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16. Detection of selective sweeps in cattle using genome-wide SNP data

Author

Ramey, Holly R., Decker, Jared E., McKay, Stephanie D., Rolf, Megan M., Schnabel, Robert D., and Taylor, Jeremy F.

Subjects
Quantitative Biology - Genomics, Quantitative Biology - Populations and Evolution
Abstract

The domestication and subsequent selection by humans to create breeds of cattle undoubtedly altered the patterning of variation within their genomes. Strong selection to fix advantageous large-effect mutations underlying domesticability, breed characteristics or productivity created selective sweeps in which variation was lost in the chromosomal region flanking the selected allele. Selective sweeps have been identified in the genomes of many species including humans, dogs, horses, and chickens. We attempt to identify regions of the bovine genome that have been subjected to selective sweeps. Two datasets were used for the discovery and validation of selective sweeps via the fixation of alleles at a series of contiguous SNP loci. BovineSNP50 data were used to identify 28 putative sweep regions among 14 cattle breeds. Affymetrix BOS 1 prescreening assay data for five breeds were used to identify 114 regions and validate 5 regions identified using the BovineSNP50 data. Many genes are located within these regions; however, phenotypes that we predict to have historically been under strong selection include horned-polled, coat color, stature, ear morphology, and behavior. The identified selective sweeps represent recent events associated with breed formation rather than ancient events associated with domestication. No sweep regions were shared between indicine and taurine breeds reflecting their divergent selection histories. A primary finding of this study is the sensitivity of results to assay resolution. Despite the bias towards common SNPs in the BovineSNP50 design, false positive sweep regions appear to be common due to the limited resolution of the assay. This assay design bias leads to the detection of breed-specific sweep regions, or regions shared by a small number of breeds, restricting the suite of selected phenotypes detected to primarily those associated with breed characteristics., Comment: 40 pages, 2 figures

Published
2012
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21. Meta-analysis of genome-wide association studies for cattle stature identifies common genes that regulate body size in mammals

Author

Bouwman, Aniek C., Daetwyler, Hans D., Chamberlain, Amanda J., Ponce, Carla Hurtado, Sargolzaei, Mehdi, Schenkel, Flavio S., Sahana, Goutam, Govignon-Gion, Armelle, Boitard, Simon, Dolezal, Marlies, Pausch, Hubert, Brøndum, Rasmus F., Bowman, Phil J., Thomsen, Bo, Guldbrandtsen, Bernt, Lund, Mogens S., Servin, Bertrand, Garrick, Dorian J., Reecy, James, Vilkki, Johanna, Bagnato, Alessandro, Wang, Min, Hoff, Jesse L., Schnabel, Robert D., Taylor, Jeremy F., Vinkhuyzen, Anna A. E., Panitz, Frank, Bendixen, Christian, Holm, Lars-Erik, Gredler, Birgit, Hozé, Chris, Boussaha, Mekki, Sanchez, Marie-Pierre, Rocha, Dominique, Capitan, Aurelien, Tribout, Thierry, Barbat, Anne, Croiseau, Pascal, Drögemüller, Cord, Jagannathan, Vidhya, Vander Jagt, Christy, Crowley, John J., Bieber, Anna, Purfield, Deirdre C., Berry, Donagh P., Emmerling, Reiner, Götz, Kay-Uwe, Frischknecht, Mirjam, Russ, Ingolf, Sölkner, Johann, Van Tassell, Curtis P., Fries, Ruedi, Stothard, Paul, Veerkamp, Roel F., Boichard, Didier, Goddard, Mike E., and Hayes, Ben J.

Published
2018
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26. Fourth Report on Chicken Genes and Chromosomes 2022

Author

Smith, Jacqueline, Alfieri, James M., Anthony, Nick, Arensburger, Peter, Athrey, Giridhar N., Balacco, Jennifer, Balic, Adam, Bardou, Philippe, Barela, Paul, Bigot, Yves, Blackmon, Heath, Borodin, Pavel M., Carroll, Rachel, Casono, Meya C., Charles, Mathieu, Cheng, Hans, Chiodi, Maddie, Cigan, Lacey, Coghill, Lyndon M., Crooijmans, Richard, Das, Neelabja, Davey, Sean, Davidian, Asya, Degalez, Fabien, Dekkers, Jack M., Derks, Martijn, Diack, Abigail B., Djikeng, Appolinaire, Drechsler, Yvonne, Dyomin, Alexander, Fedrigo, Olivier, Fiddaman, Steven R., Formenti, Giulio, Frantz, Laurent A.F., Fulton, Janet E., Gaginskaya, Elena, Galkina, Svetlana, Gallardo, Rodrigo A., Geibel, Johannes, Gheyas, Almas A., Godinez, Cyrill John P., Goodell, Ashton, Graves, Jennifer A.M., Griffin, Darren K., Haase, Bettina, Han, Jian Lin, Hanotte, Olivier, Henderson, Lindsay J., Hou, Zhuo Cheng, Howe, Kerstin, Huynh, Lan, Ilatsia, Evans, Jarvis, Erich D., Johnson, Sarah M., Kaufman, Jim, Kelly, Terra, Kemp, Steve, Kern, Colin, Keroack, Jacob H., Klopp, Christophe, Lagarrigue, Sandrine, Lamont, Susan J., Lange, Margaret, Lanke, Anika, Larkin, Denis M., Larson, Greger, Layos, John King N., Lebrasseur, Ophélie, Malinovskaya, Lyubov P., Martin, Rebecca J., Cerezo, Maria Luisa Martin, Mason, Andrew S., McCarthy, Fiona M., McGrew, Michael J., Mountcastle, Jacquelyn, Muhonja, Christine Kamidi, Muir, William, Muret, Kévin, Murphy, Terence D., Ng'ang'a, Ismael, Nishibori, Masahide, O'Connor, Rebecca E., Ogugo, Moses, Okimoto, Ron, Ouko, Ochieng, Patel, Hardip R., Perini, Francesco, Pigozzi, María Ines, Potter, Krista C., Price, Peter D., Reimer, Christian, Rice, Edward S., Rocos, Nicolas, Rogers, Thea F., Saelao, Perot, Schauer, Jens, Schnabel, Robert D., Schneider, Valerie A., Simianer, Henner, Smith, Adrian, Stevens, Mark P., Stiers, Kyle, Tiambo, Christian Keambou, Tixier-Boichard, Michele, Torgasheva, Anna A., Tracey, Alan, Tregaskes, Clive A., Vervelde, Lonneke, Wang, Ying, Warren, Wesley C., Waters, Paul D., Webb, David, Weigend, Steffen, Wolc, Anna, Wright, Alison E., Wright, Dominic, Wu, Zhou, Yamagata, Masahito, Yang, Chentao, Yin, Zhong Tao, Young, Michelle C., Zhang, Guojie, Zhao, Bingru, Zhou, Huaijun, Smith, Jacqueline, Alfieri, James M., Anthony, Nick, Arensburger, Peter, Athrey, Giridhar N., Balacco, Jennifer, Balic, Adam, Bardou, Philippe, Barela, Paul, Bigot, Yves, Blackmon, Heath, Borodin, Pavel M., Carroll, Rachel, Casono, Meya C., Charles, Mathieu, Cheng, Hans, Chiodi, Maddie, Cigan, Lacey, Coghill, Lyndon M., Crooijmans, Richard, Das, Neelabja, Davey, Sean, Davidian, Asya, Degalez, Fabien, Dekkers, Jack M., Derks, Martijn, Diack, Abigail B., Djikeng, Appolinaire, Drechsler, Yvonne, Dyomin, Alexander, Fedrigo, Olivier, Fiddaman, Steven R., Formenti, Giulio, Frantz, Laurent A.F., Fulton, Janet E., Gaginskaya, Elena, Galkina, Svetlana, Gallardo, Rodrigo A., Geibel, Johannes, Gheyas, Almas A., Godinez, Cyrill John P., Goodell, Ashton, Graves, Jennifer A.M., Griffin, Darren K., Haase, Bettina, Han, Jian Lin, Hanotte, Olivier, Henderson, Lindsay J., Hou, Zhuo Cheng, Howe, Kerstin, Huynh, Lan, Ilatsia, Evans, Jarvis, Erich D., Johnson, Sarah M., Kaufman, Jim, Kelly, Terra, Kemp, Steve, Kern, Colin, Keroack, Jacob H., Klopp, Christophe, Lagarrigue, Sandrine, Lamont, Susan J., Lange, Margaret, Lanke, Anika, Larkin, Denis M., Larson, Greger, Layos, John King N., Lebrasseur, Ophélie, Malinovskaya, Lyubov P., Martin, Rebecca J., Cerezo, Maria Luisa Martin, Mason, Andrew S., McCarthy, Fiona M., McGrew, Michael J., Mountcastle, Jacquelyn, Muhonja, Christine Kamidi, Muir, William, Muret, Kévin, Murphy, Terence D., Ng'ang'a, Ismael, Nishibori, Masahide, O'Connor, Rebecca E., Ogugo, Moses, Okimoto, Ron, Ouko, Ochieng, Patel, Hardip R., Perini, Francesco, Pigozzi, María Ines, Potter, Krista C., Price, Peter D., Reimer, Christian, Rice, Edward S., Rocos, Nicolas, Rogers, Thea F., Saelao, Perot, Schauer, Jens, Schnabel, Robert D., Schneider, Valerie A., Simianer, Henner, Smith, Adrian, Stevens, Mark P., Stiers, Kyle, Tiambo, Christian Keambou, Tixier-Boichard, Michele, Torgasheva, Anna A., Tracey, Alan, Tregaskes, Clive A., Vervelde, Lonneke, Wang, Ying, Warren, Wesley C., Waters, Paul D., Webb, David, Weigend, Steffen, Wolc, Anna, Wright, Alison E., Wright, Dominic, Wu, Zhou, Yamagata, Masahito, Yang, Chentao, Yin, Zhong Tao, Young, Michelle C., Zhang, Guojie, Zhao, Bingru, and Zhou, Huaijun

Abstract

Chicken Genomic Diversity consortium: large-scale genomics to unravel the origins and adaptations of chickens

Published
2023

35. Resolving the Evolution of Extant and Extinct Ruminants with High-Throughput Phylogenomics

Author

Decker, Jared E., Pires, J. Chris, Conant, Gavin C., McKay, Stephanie D., Heaton, Michael P., Chen, Kefei, Cooper, Alan, Vilkki, Johanna, Seabury, Christopher M., Caetano, Alexandre R., Johnson, Gary S., Brenneman, Rick A., Hanotte, Olivier, Eggert, Lori S., Wiener, Pamela, Kim, Jong-Joo, Kim, Kwan Suk, Sonstegard, Tad S., Van Tassell, Curt P., Neibergs, Holly L., McEwan, John C., Brauning, Rudiger, Coutinho, Luiz L., Babar, Masroor E., Wilson, Gregory A., McClure, Matthew C., Rolf, Megan M., Kim, JaeWoo, Schnabel, Robert D., and Taylor, Jeremy F.

Published
2009
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37. A Non-Synonymous Point Mutation in a WD-40 Domain Repeat of EML5 Leads to Decreased Bovine Sperm Quality and Fertility

Author

Nogueira, Eriklis, primary, Tirpák, Filip, additional, Hamilton, Lauren E., additional, Zigo, Michal, additional, Kerns, Karl, additional, Sutovsky, Miriam, additional, Kim, JaeWoo, additional, Volkmann, Dietrich, additional, Jovine, Luca, additional, Taylor, Jeremy F., additional, Schnabel, Robert D., additional, and Sutovsky, Peter, additional

Published
2022
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39. Additional file 2 of Genome-wide association and genotype by environment interactions for growth traits in U.S. Red Angus cattle

Author

Smith, Johanna L., Wilson, Miranda L., Nilson, Sara M., Rowan, Troy N., Schnabel, Robert D., Decker, Jared E., and Seabury, Christopher M.

Abstract

Additional file 2: Table S1. Summary of QTL supporting pleiotropy detected for birth weight, weaning weight, and yearling weight GWAA and GxE GWAA in U.S. Red Angus cattle. Table S2. Summary of QTL with 2 to 4 supporting SNPs detected for birth weight in U.S. Red Angus cattle. Table S3. Genomic inflation factors (λ) calculated using observed P-values and expected P-values for GWAA for growth traits in U.S. Red Angus beef cattle. Table S4. Summary of QTL with 2 to 4 supporting SNPs detected for weaning weight in U.S. Red Angus cattle. Table S5. Summary of QTL with 2 to 4 supporting SNPs detected for yearling weight in U.S. Red Angus cattle. Table S6. Summary of GxE interactions with 2 to 4 supporting SNPs detected for birth weight in U.S. Red Angus cattle. Table S7. Genomic inflation factors (λ) calculated using observed P-values and expected P-values for GxE GWAA for growth traits in U.S. Red Angus beef cattle. Table S8. Summary of GxE interactions with 2 to 4 supporting SNPs detected for weaning weight in U.S. Red Angus cattle. Table S9. Summary of GxE interactions with 2 to 4 supporting SNPs detected for yearling weight in U.S. Red Angus cattle.

Published
2022
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44. Genome-Wide Survey of SNP Variation Uncovers the Genetic Structure of Cattle Breeds

Author

Gibbs, Richard A., Taylor, Jeremy F., Van Tassell, Curtis P., Barendse, William, Eversole, Kellye A., Gibbs, Richard A., Gill, Clare A., Green, Ronnie D., Hamernik, Debora L., Kappes, Steven M., Lien, Sigbjørn, Matukumalli, Lakshmi K., McEwan, John C., Nazareth, Lynne V., Schnabel, Robert D., Taylor, Jeremy F., Van Tassell, Curtis P., Weinstock, George M., Wheeler, David A., Ajmone-Marsan, Paolo, Barendse, William, Boettcher, Paul J., Caetano, Alexandre R., Fernando Garcia, Jose, Gill, Clare A., Green, Ronnie D., Hanotte, Olivier, Lien, Sigbjørn, Mariani, Paola, McEwan, John C., Skow, Loren C., Sonstegard, Tad S., Van Tassell, Curtis P., Williams, John L., Caetano, Alexandre R., Diallo, Boubacar, Green, Ronnie D., Hailemariam, Lemecha, Hanotte, Olivier, Martinez, Mario L., Morris, Chris A., Silva, Luiz O. C., Spelman, Richard J., Taylor, Jeremy F., Van Tassell, Curtis P., Mulatu, Woudyalew, Zhao, Keyan, Abbey, Colette A., Agaba, Morris, Araujo, Flábio R., Bunch, Rowan J., Burton, James, Gill, Clare A, Gorni, Chiara, Green, Ronnie D., Olivier, Hanotte, Harrison, Blair E., Lien, Sigbjørn, Luff, Bill, Machado, Marco A., Mariani, Paola, McEwan, John C., Morris, Chris A., Mwakaya, Joel, Plastow, Graham, Sim, Warren, Skow, Loren C., Smith, Timothy, Sonstegard, Tad S., Spelman, Richard J., Taylor, Jeremy F., Thomas, Merle B., Valentini, Alessio, Van Tassell, Curtis P., Williams, Paul, Womack, James, Woolliams, John A., Liu, Yue, Qin, Xiang, Worley, Kim C., Gao, Chuan, Gill, Clare A., Jiang, Huaiyang, Liu, Yue, Moore, Stephen S., Nazareth, Lynne V., Ren, Yanru, Song, Xing-Zhi, Wheeler, David A., Worley, Kim C., Bustamante, Carlos D., Hernandez, Ryan D., Muzny, Donna M., Nazareth, Lynne V., Patil, Shobha, Ren, Yanru, San Lucas, Anthony, Wheeler, David A., Fu, Qing, Kent, Matthew P., Lien, Sigbjørn, Moore, Stephen S., Nazareth, Lynne V., Vega, Richard, Wheeler, David A., Abbey, Colette A., Gao, Chuan, Gill, Clare A., Green, Ronnie D., Matukumalli, Lakshmi K., Matukumalli, Aruna, McWilliam, Sean, Van Tassell, Curtis P., Abbey, Colette A., Gill, Clare A., Kent, Matthew P., Lien, Sigbjørn, Matukumalli, Lakshmi K., Schnabel, Robert D., Sclep, Gert, Taylor, Jeremy F., Ajmone-Marsan, Paolo, Bryc, Katarzyna, Bustamante, Carlos D., Choi, Jungwoo, Gao, Hong, Grefenstette, John J., Matukumalli, Lakshmi K., Murdoch, Brenda, Moore, Stephen S., Nazareth, Lynne V., Stella, Alessandra, Van Tassell, Curtis P., Villa-Angulo, Rafael, Wheeler, David A., Wright, Mark, Aerts, Jan, Jann, Oliver, Matukumalli, Lakshmi K., Negrini, Riccardo, Sonstegard, Tad S., Williams, John L., Ajmone-Marsan, Paolo, Grefenstette, John J., Matukumalli, Lakshmi K., Negrini, Riccardo, Schnabel, Robert D., Taylor, Jeremy F., Villa-Angulo, Rafael, Grefenstette, John J., Matukumalli, Lakshmi K., Van Tassell, Curtis P., Villa-Angulo, Rafael, Goddard, Mike E., Hayes, Ben J., Barendse, William, Bradley, Daniel G., Boettcher, Paul J., Bustamante, Carlos D., Choi, Jungwoo, Barbosa da Silva, Marcos, Gill, Clare A., Lau, Lilian P. L., Liu, George E., Lynn, David J., Panzitta, Francesca, Sclep, Gert, Wright, Mark, Bustamante, Carlos D., Dodds, Ken G., McEwan, John C., Taylor, Jeremy F., and Van Tassell, Curtis P.

Published
2009

47. Powerful detection of polygenic selection and environmental adaptation in US beef cattle populations

Author

Rowan, Troy N, Durbin, Harly J, Nilson, Sara M, Seabury, Christopher M., Schnabel, Robert D, and Decker, Jared E.

Abstract

Selection is a basic principle of evolution. Many approaches and studies have identified DNA mutations rapidly selected to high frequencies, which leave pronounced signatures on the surrounding sequence (selective sweeps). However, for many important complex, quantitative traits, selection does not leave these intense signatures. Instead, hundreds or thousands of loci experience small changes in allele frequencies, a process called polygenic selection. We know that directional selection and local adaptation are actively changing genomes; however we have been unable to identify the genomic loci responding to this polygenic, complex selection. Here we show that the use of novel dependent variables in linear mixed models (which allow us to account for population structure, relatedness, inbreeding) identify complex, polygenic selection and local adaptation. Thousands of loci are responding to artificial directional selection and hundreds of loci have evidence of local adaptation. While advanced reproduction and genomic technologies are increasing the rate of directional selection, local adaptation is being lost. In a changing climate, the loss of local adaptation may be especially problematic. These selection mapping approaches can be used in evolutionary, model, and agriculture contexts.

Published
2020
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