De novo assembly of the cattle reference genome with single-molecule sequencing

Rosen, Benjamin D, Bickhart, Derek M, Schnabel, Robert D, Koren, Sergey, Elsik, Christine G, Tseng, Elizabeth, Rowan, Troy N, Low, Wai Y +25 more·2020·GigaScience

DOI 10.1093/gigascience/giaa021

Cited by (858)

Items 101–200 of 858

Copy number variations in BOLA‐DQA2 , BOLA‐DQB , and BOLA‐DQA5 show the genomic architecture and haplotype frequency of major histocompatibility complex class II genes in Holstein cows
Koya Fukunaga, Yusuke Yamashita, Takuya Yagisawa · 2020 · HLA
Male recombination map of the autosomal genome in German Holstein
Saber Qanbari, Dörte Wittenburg · 2020 · Genetics Selection Evolution
The genetic history of Mayotte and Madagascar cattle breeds mirrors the complex pattern of human exchanges in Western Indian Ocean
Jessica Magnier, Tom Druet, Michel Navès, Mélissa Ouvrard, Solène Raoul, Jérôme Janelle, Katayoun Moazami‐Goudarzi, Matthieu Lesnoff, Emmanuel Tillard, Mathieu Gautier et al. · 2022 · G3 Genes Genomes Genetics
Periconceptual Maternal Nutrition Affects Fetal Liver Programming of Energy- and Lipid-Related Genes
Wellison J. S. Diniz, Alison K K Ward, Kacie L McCarthy, Cierrah J J Kassetas, Friederike Baumgaertner, Lawrence P. Reynolds, Pawel P P Borowicz, Kevin K K Sedivec, James D Kirsch, Sheri T. Dorsam et al. · 2023 · Animals
High-resolution structural variants catalogue in a large-scale whole genome sequenced bovine family cohort data
Young-Lim Lee, Mirte Bosse, Haruko Takeda, Gabriel Costa Monteiro Moreira, Latifa Karim, Tom Druet, Claire Oget, Wouter R. Coppieters, Roel F. Veerkamp, Martien A. M. Groenen et al. · 2023 · BMC Genomics
Genetic architecture of individual variation in recombination rate on the X chromosome in cattle
Junjie Zhang, Naveen Kumar Kadri, Erik Mullaart, Richard J. Spelman, Sébastien Fritz, Didier Boichard, Carole Charlier, Michel Georges, Tom Druet · 2020 · Heredity
Pan-genomics: Insight into the Functional Genome, Applications, Advancements, and Challenges
Akansha Sarawad, Spoorti Hosagoudar, Prachi Parvatikar · 2024 · Current Genomics
Uncovering Sub-Structure and Genomic Profiles in Across-Countries Subpopulations of Angus Cattle
Diercles Francisco Cardoso, Gerardo Alves Fernandes Júnior, Daiane Cristina Becker Scalez, Anderson Antônio Carvalho Alves, Ana Fabrícia Braga Magalhães, Tiago Bresolin, Ricardo Vieira Ventura, Changxi Li, M. C. de S. Oliveira, Laércio R. Porto-Neto et al. · 2020 · Scientific Reports
Investigation of ancestral alleles in the Bovinae subfamily
Maulana M. Naji, Yuri Tani Utsunomiya, Johann Sölkner, Benjamin D. Rosen, Gábor Mészáros · 2021 · BMC Genomics
Mining massive genomic data of two Swiss Braunvieh cattle populations reveals six novel candidate variants that impair reproductive success
Irene M. Häfliger, Franz R. Seefried, Mirjam Spengeler, Cord Drögemüller · 2021 · Genetics Selection Evolution
Spontaneous and ART-induced large offspring syndrome: similarities and differences in DNA methylome
Yahan Li, Jordana S. Lopes, Pilar Coy, Rocío Melissa Rivera · 2022 · Epigenetics
Identification of large offspring syndrome during pregnancy through ultrasonography and maternal blood transcriptome analyses
Rocío Melissa Rivera, Anna K. Goldkamp, Bhaumik Narendrabhai Patel, Darren E. Hagen, Edgar Joel Soto‐Moreno, Yahan Li, Chris Nayoon Kim, Cliff Miller, Fred E. Williams, Elizabeth A. Jannaman et al. · 2022 · Scientific Reports
The Future of Livestock Management: A Review of Real-Time Portable Sequencing Applied to Livestock
Harrison J. Lamb, Ben J. Hayes, Loan T Nguyen, Elizabeth M. Ross · 2020 · Genes
Long-range linkage disequilibrium in French beef cattle breeds
Abdelmajid El Hou, Dominique Rocha, Éric Venot, Véronique Blanquet, Romain Philippe · 2021 · Genetics Selection Evolution
Transcription initiation mapping in 31 bovine tissues reveals complex promoter activity, pervasive transcription, and tissue-specific promoter usage
Daniel Estanislao Goszczynski, Michelle M. Halstead, Alma Islas‐Trejo, Huaijun Zhou, Pablo J. Ross · 2021 · Genome Research
Sequence-based GWAS in 180,000 German Holstein cattle reveals new candidate variants for milk production traits
A. Križanac, C. Reimer, J. Heise, Zeng-Ting Liu, J. Pryce, J. Bennewitz, G. Thaller, C. Falker-Gieske, J. Tetens · 2025 · Genetics Selection Evolution
Whole-Genome Resequencing Reveals Adaptation Prior to the Divergence of Buffalo Subspecies
Mostafa Rafiepour, Esmaeil Ebrahimie, Mohammad Farhad Vahidi, Ghasem Hosseini Salekdeh, Ali Niazi‎, Mohammad Dadpasand, Dong Liang, Jingfang Si, Xiangdong Ding, Jianlin Han et al. · 2020 · Genome Biology and Evolution
Genetic and Genomic Characterization of a New Beef Cattle Composite Breed (Purunã) Developed for Production in Pasture-Based Systems
Henrique A. Mulim, Luiz F. Brito, Luís Fernando Batista Pinto, José Luís Moletta, Lilian Regina da Silva, Victor Breno Pedrosa · 2022 · Frontiers in Genetics
Vetinformatics from functional genomics to drug discovery: Insights into decoding complex molecular mechanisms of livestock systems in veterinary science
Rajesh Kumar Pathak, Jun‐Mo Kim · 2022 · Frontiers in Veterinary Science
Whole blood transcriptome analysis in dairy calves experimentally challenged with bovine herpesvirus 1 (BoHV-1) and comparison to a bovine respiratory syncytial virus (BRSV) challenge
Stephanie O’Donoghue, Bernadette Earley, Dayle Johnston, Matthew Sean McCabe, Jae Woo Kim, Jeremy F. Taylor, Catherine M. Duffy, Ken Lemon, Michael J. McMenamy, Sara Louise Cosby et al. · 2023 · Frontiers in Genetics
Bacterial enrichment prior to third-generation metagenomic sequencing improves detection of BRD pathogens and genetic determinants of antimicrobial resistance in feedlot cattle
Emily K. Herman, Stacey R. Lacoste, Claire N. Freeman, Simon J. G. Otto, E. Luke McCarthy, Matthew G. Links, Paul Stothard, Cheryl Waldner · 2024 · Frontiers in Microbiology
Invited review: Management of genetic defects in dairy cattle populations
John B. Cole, Christine F. Baes, Sophie Eaglen, Thomas J. Lawlor, Christian Maltecca, Martha Sofia Ortega, Paul Michael VanRaden · 2025 · Journal of Dairy Science
Kouprey (Bos sauveli) genomes unveil polytomic origin of wild Asian Bos
Mikkel‐Holger S. Sinding, Marta Maria Ciucani, Jazmín Ramos‐Madrigal, Alberto Carmagnini, Jacob Agerbo Rasmussen, Shaohong Feng, Guangji Chen, Filipe Garrett Vieira, Valeria Mattiangeli, R. K. Ganjoo et al. · 2021 · iScience
Genomic prediction using low-coverage portable Nanopore sequencing
Harrison J. Lamb, Ben J. Hayes, Imtiaz A. S. Randhawa, Loan T Nguyen, Elizabeth M. Ross · 2021 · PLoS ONE
Recovery of mitogenomes from whole genome sequences to infer maternal diversity in 1883 modern taurine and indicine cattle
Jigme Dorji, Christy J. Vander Jagt, Amanda Jane Chamberlain, Benjamin G. Cocks, Iona M. MacLeod, Hans D. Daetwyler · 2022 · Scientific Reports
Whole-Genome Resequencing Reveals Selection Signatures of Abigar Cattle for Local Adaptation
Wondossen Ayalew, Xiaoyun Wu, Getinet Mekuriaw Tarekegn, Tesfaye Sisay Tessema, Rakan Naboulsi, Renaud Van Damme, Erik Bongcam‐Rudloff, Zewdu Edea, Solomon Enquahone, Ping Yan · 2023 · Animals
Preferential differential gene expression within the WC1.1+ γδ T cell compartment in cattle naturally infected with Mycobacterium bovis
Sajad Ahmad Bhat, Mahmoud M. Elnaggar, Thomas Jonathan Hall, Gillian P. McHugo, Cian Reid, David Evan MacHugh, Kieran G. Meade · 2023 · Frontiers in Immunology
PacBio Single-Molecule Long-Read Sequencing Provides New Light on the Complexity of Full-Length Transcripts in Cattle
Tianpeng Chang, Bingxing An, Mang Liang, Xinghai Duan, Lili Du, Wentao Cai, Bo Zhu, Xue Gao, Yan Chen, Lingyang Xu et al. · 2021 · Frontiers in Genetics
African Suid Genomes Provide Insights into the Local Adaptation to Diverse African Environments
Hai‐Bing Xie, Yan Chen, Adeniyi C. Adeola, Kun Wang, Cuiping Huang, Mingmin Xu, Qiang Qiu, Xue Yin, Chen-Yu Fan, Yunfei Ma et al. · 2022 · Molecular Biology and Evolution
Optical mapping compendium of structural variants across global cattle breeds
Andrea Talenti, Jessica Powell, David Wragg, Maurine C. Chepkwony, Andressa Fisch, Beatriz Rossetti Ferreira, Maria Eugênia Zerlotti Mercadante, Isabel Kinney Ferreira de Miranda Santos, Chukwunonso Ezeasor, Emmanuel Obishakin et al. · 2022 · Scientific Data
Genomic Insights into the Population History and Adaptive Traits of Latin American Criollo Cattle
Ward, James A., Ng'ang'a, Said I., Randhawa, Imtiaz A. S., McHugo, Gillian P., O'Grady, John F., Flórez, Julio M., Browne, John A., Pérez O’Brien, Ana M., Landaeta-Hernández, Antonio J., Garcia, Jóse F. et al. · 2024 · Royal Society Open Science
Genomic prediction in Nordic Red dairy cattle considering breed origin of alleles
Ana Guillenea, Guosheng Su, Mogens Sand⊘ Lund, Emre Karaman · 2022 · Journal of Dairy Science
Identification of Key Pathways Associated With Residual Feed Intake of Beef Cattle Based on Whole Blood Transcriptome Data Analyzed Using Gene Set Enrichment Analysis
Godstime Ayobami Taiwo, Modoluwamu D. Idowu, James Denvir, Andres Alfredo Pech-Cervantes, Ibukun Michael Ogunade · 2022 · Frontiers in Veterinary Science
OCT4/POU5F1 is indispensable for the lineage differentiation of the inner cell mass in bovine embryos
Kilian Simmet, Mayuko Kurome, Valeri Zakhartchenko, Horst‐Dieter Reichenbach, Claudia Springer, Andrea Bähr, Helmut Blum, Julia Philippou‐Massier, Eckhard Wolf · 2022 · The FASEB Journal
Beef Cattle Genome Project: Advances in Genome Sequencing, Assembly, and Functional Genes Discovery
Zhendong Gao, Ying Lu, Yuqing Chong, Mengfei Li, Jieyun Hong, Jiao Wu, Dongwang Wu, Dongmei Xi, Weidong Deng · 2024 · International Journal of Molecular Sciences
Candidate Genes, Markers, Signatures of Selection, and Quantitative Trait Loci (QTLs) and Their Association with Economic Traits in Livestock: Genomic Insights and Selection
Nada N. A. M. Hassanine, Ahmed A. Saleh, Mohamed Osman Abdalrahem Essa, Saber Y. Adam, Raza Mohai Ud Din, Shahab Ur Rehman, Rahmat Ali, Hosameldeen Mohamed Husien, Mengzhi Wang · 2025 · International Journal of Molecular Sciences
Cross-population selection signatures in Canchim composite beef cattle
Igor Nelson Herculano Duarte, Ayrton Fernandes de Oliveira Bessa, Luciana Diniz Rola, Maria Victória Henrique Genuíno, Iasmin Marques Rocha, C. R. Marcondes, Luciana Correia de Almeida Regitano, Danísio Prado Munari, Donagh Pearse Berry, Marcos Eli Buzanskas · 2022 · PLoS ONE
Progress and future perspectives of livestock genomics in India: a mini review
K.A. Saravanan, Manjit Panigrahi, Harshit Kumar, Sonali Sonejita Nayak, Divya Rajawat, Bharat Bhushan, Triveni Dutt · 2022 · Animal Biotechnology
Assessment of genotyping array performance for genome-wide association studies and imputation in African cattle
Valentina Riggio, Abdulfatai Tijjani, Rebecca Callaby, Andrea Talenti, David Wragg, Emmanuel Obishakin, Chukwunonso Ezeasor, Frans Jongejan, Ndudim Isaac Ogo, Fred Aboagye‐Antwi et al. · 2022 · Genetics Selection Evolution
Single-step genome-wide association analyses of claw horn lesions in Holstein cattle using linear and threshold models
Bingjie Li, Matthew Barden, Vanessa Varvara Kapsona, Enrique Sánchez-Molano, Alkiviadis Anagnostopoulos, Bethany Eloise Griffiths, Cherril Bedford, Xiaoxia Dai, Mike P. Coffey, Androniki Psifidi et al. · 2023 · Genetics Selection Evolution
Systems biology under heat stress in Indian cattle
Raja Ishaq Nabi Khan, Amit Ranjan Sahu, Waseem Akram Malla, Manas Ranjan Praharaj, Neelima Hosamani, Shakti Kumar, Smita Gupta, Shweta Sharma, Archana Saxena, Anshul Varshney et al. · 2021 · Gene
A Non-Synonymous Point Mutation in a WD-40 Domain Repeat of EML5 Leads to Decreased Bovine Sperm Quality and Fertility
Ériklis Nogueira, Filip Tirpák, Lauren E Hamilton, Michal Zigo, Karl C. Kerns, Miriam Sutovsky, JaeWoo Kim, Dietrich H. Volkmann, Luca Jovine, Jeremy F. Taylor et al. · 2022 · Frontiers in Cell and Developmental Biology
Biases from Oxford Nanopore library preparation kits and their effects on microbiome and genome analysis
Ziming Chen, Chian Teng Ong, Loan T Nguyen, Harrison J. Lamb, Óscar González-Recio, Mónica Gutiérrez‐Rivas, Sarah J. Meale, Elizabeth M. Ross · 2025 · BMC Genomics
Reverse Genetic Screen for Deleterious Recessive Variants in the Local Simmental Cattle Population of Switzerland
Irene M. Häfliger, Franz R. Seefried, Cord Drögemüller · 2021 · Animals
Cross-species enhancer prediction using machine learning
Callum MacPhillamy, Hamid Alinejad‐Rokny, Wayne S. Pitchford, Wai Yee Low · 2022 · Genomics
Genome-wide association analysis of heifer livability and early first calving in Holstein cattle
Yahui Gao, Alexis Marceau, Victoria Iqbal, José Antonio Torres‐Vázquez, Mahesh Neupane, Jicai Jiang, George E. Liu, Li Ma · 2023 · BMC Genomics
Multiple independent de novo mutations are associated with the development of schistosoma reflexum, a lethal syndrome in cattle
Joana G. P. Jacinto, Irene M. Häfliger, Anna Letko, Jim Weber, Markus Freick, Arcangelo Gentile, Cord Drögemüller, Jørgen Steen Agerholm · 2024 · The Veterinary Journal
Analyzing the relationship of RNA and DNA methylation with gene expression
Shuang Xie, Darren E. Hagen, Gabrielle M. Becker, Kimberly M Davenport, Katie A Shira, Morgan R Stegemiller, Jacob W Thorne, Sarem F. Khilji, Denise E. Konetchy, Patricia Villamediana et al. · 2025 · Genome biology
Major quantitative trait loci influencing milk production and conformation traits in Guernsey dairy cattle detected on Bos taurus autosome 19
Bingjie Li, Paul Michael VanRaden, D.J. Null, Jeffery R. O’Connell, John B. Cole · 2020 · Journal of Dairy Science
Introgression contributes to distribution of structural variations in cattle
Maulik R. Upadhyay, Martijn F. L. Derks, Göran Andersson, Ivica Međugorac, Martien A. M. Groenen, Richard P. M. A. Crooijmans · 2021 · Genomics
KCNG1-Related Syndromic Form of Congenital Neuromuscular Channelopathy in a Crossbred Calf
Joana G. P. Jacinto, Irene M. Häfliger, Eylem Emek Akyürek, Roberta Sacchetto, Cinzia Benazzi, Arcangelo Gentile, Cord Drögemüller · 2021 · Genes
Supranutritional Maternal Organic Selenium Supplementation during Different Trimesters of Pregnancy Affects the Muscle Gene Transcriptome of Newborn Beef Calves in a Time-Dependent Manner
Wellison J. S. Diniz, Gerd Bobe, Joseph J. Klopfenstein, Yunus Gultekin, T. Zane Davis, Alison K K Ward, Jean A. Hall · 2021 · Genes
Taurine pangenome uncovers a segmental duplication upstream of <i>KIT</i> associated with depigmentation in white-headed cattle
Milia, Sotiria, Leonard, Alexander S., Mapel, Xena Marie, Bernal Ulloa, Sandra Milena, Drögemüller, Cord, Pausch, Hubert · 2025 · Genome Research
Global Pangenome Analysis Highlights the Critical Role of Structural Variants in Cattle Improvement and Identifies a Unique Event as a Novel Enhancer in IGFBP7+ Cells
Shoulu Dai, Pengju Zhao, Wenhao Li, Lingwei Peng, Enhui Jiang, Yuqin Du, Wengang Zhang, Xuelei Dai, Liu Yang, Zhiqiang Li et al. · 2025 · Molecular Biology and Evolution
Raw transcriptomics data to gene specific SSRs: a validated free bioinformatics workflow for biologists
Nathasha Naranpanawa, C. H. W. M. R. B. Chandrasekara, P. C. G. Bandaranayake, Asitha Bandaranayake · 2020 · Scientific Reports
Highly‐contiguous bovine genomes underpin accurate functional analyses and updated nomenclature of MHC class I
John C. Schwartz, Giuseppe Maccari, Dorothea Heimeier, John A. Hammond · 2021 · HLA
Discovering Copy Number Variation in Dual-Purpose XinJiang Brown Cattle
Jinghang Zhou, Liyuan Liu, Edwardo Reynolds, Xixia Huang, Dorian J. Garrick, Yuangang Shi · 2022 · Frontiers in Genetics
Chromosome‐level genome assembly for takin (Budorcas taxicolor) provides insights into its taxonomic status and genetic diversity
Anning Li, Qimeng Yang, Ran Li, Xuelei Dai, Keli Cai, Yinghu Lei, Kangsheng Jia, Yu Jiang, Linsen Zan · 2022 · Molecular Ecology
Genetic parameter estimates for male and female fertility traits using genomic data to improve fertility in Australian beef cattle
Babatunde Shittu Olasege, Muhammad S. Tahir, Gabriela Canabrava Gouveia, Jagish Kour, Laercio R. Porto Neto, Ben J. Hayes, Marina R. S. Fortes · 2021 · Animal Production Science
Whole Genome DNA Methylation Variations in Mammary Gland Tissues from Holstein Cattle Producing Milk with Various Fat and Protein Contents
Mengqi Wang, Nathalie Bissonnette, Pier-Luc Dudemaine, Xin Zhao, Eveline Mengwi Ibeagha-Awemu · 2021 · Genes
Unrevealing functional candidate genes for bovine fertility through RNA sequencing meta-analysis and regulatory elements networks of co-expressed genes and lncRNAs
Pablo Augusto de Souza Fonseca, Aroa Suárez‐Vega, Ángela Cánovas · 2022 · Functional & Integrative Genomics
Genomic inbreeding and selection signatures in the local dairy breed Icelandic Cattle
Egill Gautason, Anna A. Schönherz, Goutam Sahana, Bernt Guldbrandtsen · 2021 · Animal Genetics
The genome of the lowland anoa (Bubalus depressicornis) illuminates the origin of river and swamp buffalo
Manon Curaudeau, Roberto Rozzi, Alexandre Hassanin · 2021 · Molecular Phylogenetics and Evolution
A 1-bp deletion in bovine QRICH2 causes low sperm count and immotile sperm with multiple morphological abnormalities
Maya Hiltpold, Fredi Janett, Xena Marie Mapel, Naveen Kumar Kadri, Zih‐Hua Fang, Hermann Schwarzenbacher, Franz R. Seefried, Mirjam Spengeler, Ulrich Witschi, Hubert Pausch · 2022 · Genetics Selection Evolution
Chromosome-level assembly of the Rangifer tarandus genome and validation of cervid and bovid evolution insights
William Poisson, Julien Prunier, Alexandra Carrier, Isabelle Gilbert, Gabriela F. Mastromonaco, Vicky Albert, Joëlle Taillon, Vincent Bourret, Arnaud Droit, Steeve D. Côté et al. · 2023 · BMC Genomics
Assessing different metrics of pedigree and genomic inbreeding and inbreeding effect on growth, fertility, and feed efficiency traits in a closed-herd Nellore cattle population
Ricardo Dutra do Bem, Lorena Ferreira Benfica, D.A. Silva, Eula Regina Carrara, Luiz F. Brito, Henrique A. Mulim, Marcelo Sant’Ana Borges, Joslaine Noely dos Santos Gonçalves Cyrillo, Roberta Carrilho Canesin, Sarah Figueiredo Martins Bonilha et al. · 2024 · BMC Genomics
Analyzing Runs of Homozygosity Reveals Patterns of Selection in German Brown Cattle
Anna Wirth, Jürgen Duda, Reiner Emmerling, Kay‐Uwe Götz, Franz Birkenmaier, O. Distl · 2024 · Genes
Genetic Regulation of Biomarkers as Stress Proxies in Dairy Cows
Marco Milanesi, Matilde Maria Passamonti, Katia Cappelli, Andrea Minuti, Valentino Palombo, Sandy Sgorlon, Stefano Capomaccio, Mariasilvia D’Andrea, Erminio Trevisi, Bruno Stefanon et al. · 2021 · Genes
Multi-breed genomic predictions and functional variants for fertility of tropical bulls
Laercio R. Porto Neto, Pâmela A. Alexandre, Nicholas James Hudson, John Bertram, Sean M. McWilliam, Wei Liang Andre Tan, Marina R. S. Fortes, Michael McGowan, Ben J. Hayes, Antônio Reverter · 2023 · PLoS ONE
Weighted single-step genome-wide association analyses for milk traits in Holstein and Holstein x Jersey crossbred dairy cattle.
Maria Agustina Raschia, Juan Pablo Nani, Hugo Adrián Carignano, Ariel Amadío, Daniel Omar Maizon, M. A. Poli · 2020 · Livestock Science
Whole-Genome SNP Characterisation Provides Insight for Sustainable Use of Local South African Livestock Populations
Este van Marle-Köster, Simon Frederick Lashmar, Anel Retief, Carina Visser · 2021 · Frontiers in Genetics
CNVs with adaptive potential in Rangifer tarandus: genome architecture and new annotated assembly
Julien Prunier, Alexandra Carrier, Isabelle Gilbert, William Poisson, Vicky Albert, Joëlle Taillon, Vincent Bourret, Steeve D. Côté, Arnaud Droit, Claude Robert · 2021 · Life Science Alliance
Quantitative trait locus for calving traits on Bos taurus autosome 18 in Holstein cattle is embedded in a complex genomic region
Nina Dachs, Maulik R. Upadhyay, Elisabeth Hannemann, Andreas Hauser, Stefan Krebs, Doris Seichter, Ingolf Ruß, Lilian Johanna Gehrke, Georg Erwin Thaller, Ivica Međugorac · 2023 · Journal of Dairy Science
Metagenomic and Meta-Transcriptomic Analysis Reveal the Colonization and Expression Profile of Probiotic Strains in Humans and Animals
Yunjuan Peng, Routing Chen, Zhihao Zhang, Rui Jin, Ting Xie, Xinting Liu, Jianmin Chai, Samantha M Howe, Jiangchao Zhao, Ying Li et al. · 2023 · Fermentation
Transcriptomics analysis of the bovine endometrium during the perioestrus period
Mohammed Abdulaziz Alfattah, Carolina N. Correia, John Arthur Browne, Paul McGettigan, Katarzyna Pluta, Stephen D. Carrington, David Evan MacHugh, Jane Ann Irwin · 2024 · PLoS ONE
Disentangling river and swamp buffalo genetic diversity: initial insights from the 1000 Buffalo Genomes Project
Paulene S Pineda, Ester B. Flores, Lilian Pagaduan Villamor, Connie Joyce M Parac, Mehar Singh Khatkar, Thu‐Hien To, Timothy P. L. Smith, Benjamin D. Rosen, Paolo Ajmone‐Marsan, Licia Colli et al. · 2024 · GigaScience
Empirical versus estimated accuracy of imputation: optimising filtering thresholds for sequence imputation
Tuan Viet Nguyen, Sunduimijid Bolormaa, Coralie M. Reich, Amanda Jane Chamberlain, Christy J. Vander Jagt, Hans D. Daetwyler, Iona M. MacLeod · 2024 · Genetics Selection Evolution
Genome-Wide Association Studies Reveal Susceptibility Loci for Noninfectious Claw Lesions in Holstein Dairy Cattle
Ellen Lai, Alexa L. Danner, Thomas R. Famula, Anita M. Oberbauer · 2021 · Frontiers in Genetics
A frameshift insertion in FA2H causes a recessively inherited form of ichthyosis congenita in Chianina cattle
Joana G. P. Jacinto, Irene M. Häfliger, Inês Berenguer Veiga, Anna Letko, Arcangelo Gentile, Cord Drögemüller · 2021 · Molecular Genetics and Genomics
Allele-specific aberration of imprinted domain chromosome architecture associates with large offspring syndrome
Yahan Li, Frimpong Boadu, Max R. Highsmith, Darren E. Hagen, Jianlin Jack Cheng, Rocío Melissa Rivera · 2022 · iScience
Single-cell insights into development of the bovine placenta
Kimberly M Davenport, Eleanore V. O’Neil, Martha Sofia Ortega, Amanda L. Patterson, Andrew M. Kelleher, Wesley C. Warren, Thomas E. Spencer · 2023 · Biology of Reproduction
Chromosome-level genome assembly of Korean native cattle and pangenome graph of 14 Bos taurus assemblies
Jisung Jang, Jaehoon Jung, Young Ho Lee, Sanghyun Lee, Myunggi Baik, Heebal Kim · 2023 · Scientific Data
Evaluating the potential impact of selection for the A2 milk allele on inbreeding and performance in Australian Holstein cattle
B.A. Scott, M. Haile‐Mariam, Iona M. MacLeod, Ruidong Xiang, J.E. Pryce · 2023 · Frontiers in Animal Science
Genome-wide association study between copy number variation and feeding behavior, feed efficiency, and growth traits in Nellore cattle
Lorena Ferreira Benfica, Luiz F. Brito, Ricardo Dutra do Bem, Henrique A. Mulim, Joseph Glessner, Larissa Graciano Braga, Leonardo Siqueira Glória, Joslaine Noely dos Santos Gonçalves Cyrillo, Sarah Figueiredo Martins Bonilha, Maria Eugênia Zerlotti Mercadante · 2024 · BMC Genomics
New mutation within a common haplotype is associated with calf muscle weakness in Holsteins
Ahmed Al-Khudhair, Paul Michael VanRaden, D.J. Null, Mahesh Neupane, Matthew Charles McClure, C.D. Dechow · 2024 · Journal of Dairy Science
Genetic diversity and recent ancestry based on whole-genome sequencing of endangered Swedish cattle breeds
Ajith Harish, Fernando A. Lopes Pinto, S. Eriksson, Anna M. Johansson · 2024 · BMC Genomics
Genome-wide association analyses reveal copy number variant regions associated with reproduction and disease traits in Canadian Holstein cattle
Hinayah Rojas de Oliveira, T.C.S. Chud, Gerson A. Oliveira Júnior, Ísis da Costa Hermisdorff, Saranya G. Narayana, Christina Marie Rochus, Adrien M. Butty, F. Malchiodi, Paul Stothard, F. Miglior et al. · 2024 · Journal of Dairy Science
Whole Genome Scan Uncovers Candidate Genes Related to Milk Production Traits in Barka Cattle
Wondossen Ayalew, Xiaoyun Wu, Getinet Mekuriaw Tarekegn, Tesfaye Sisay Tessema, Rakan Naboulsi, Renaud Van Damme, Erik Bongcam‐Rudloff, Zewdu Edea, Min Chu, Solomon Enquahone et al. · 2024 · International Journal of Molecular Sciences
Imputation accuracy and carrier frequency of deleterious recessive defects in Australian dairy cattle
Irene van den Berg, T.V. Nguyen, T.T.T. Nguyen, J.E. Pryce, G.J. Nieuwhof, I M MacLeod · 2024 · Journal of Dairy Science
Tailoring Genomic Selection for Bos taurus indicus: A Comprehensive Review of SNP Arrays and Reference Genomes
Adebisi R. Ogunbawo, Henrique A. Mulim, Gabriel Soares Campos, Allan Paul Schinckel, Hinayah Rojas de Oliveira · 2024 · Genes
Selection Increases Mitonuclear DNA Discordance but Reconciles Incompatibility in African Cattle
Xian Shi, Cheng Ma, Ningbo Chen, Mingmin Xu, Sumaya Kambal, Zheng‐Fei Cai, Qiwen Yang, Adeniyi C. Adeola, Li-Sheng Liu, Jun Wang et al. · 2025 · Molecular Biology and Evolution
Bayesian genome-wide analysis of cattle traits using variants with functional and evolutionary significance
Ruidong Xiang, Ed J. Breen, Claire Prowse-Wilkins, Amanda Jane Chamberlain, Michael Edward Goddard · 2021 · Animal Production Science
Adaptive selection signatures in river buffalo with emphasis on immune and major histocompatibility complex genes
Yan Xin Ren, Callum MacPhillamy, Thu‐Hien To, Timothy P. L. Smith, John Lewis Williams, Wai Yee Low · 2021 · Genomics
Genome-wide association analyses of carcass traits using copy number variants and raw intensity values of single nucleotide polymorphisms in cattle
Pierce Rafter, Isobel Claire Gormley, Deirdre C. Purfield, Andrew C. Parnell, Saeid Naderi, Donagh Pearse Berry · 2021 · BMC Genomics
Mutant alleles differentially shape fitness and other complex traits in cattle
Ruidong Xiang, Ed J. Breen, Sunduimijid Bolormaa, Christy J. Vander Jagt, Amanda Jane Chamberlain, Iona M. MacLeod, Michael Edward Goddard · 2021 · Communications Biology
Identification of Alternative Splicing Events Associated with Paratuberculosis in Dairy Cattle Using Multi-Tissue RNA Sequencing Data
Houcheng Li, Jinfeng Huang, Junnan Zhang, Yahui Gao, Bo Han, Dongxiao Sun · 2022 · Genes
Evaluation of Host Depletion and Extraction Methods for Shotgun Metagenomic Analysis of Bovine Vaginal Samples
Chian Teng Ong, Gry Brandt Boe-Hansen, Elizabeth M. Ross, Patrick Joseph Blackall, Conny Turni, Ben J. Hayes, Ala E. Tabor · 2022 · Microbiology Spectrum
Benchmarking phasing software with a whole-genome sequenced cattle pedigree
Claire Oget, Naveen Kumar Kadri, Gabriel Costa Monteiro Moreira, Latifa Karim, Wouter R. Coppieters, Michel Georges, Tom Druet · 2022 · BMC Genomics
Identification and Annotation of Potential Function of Regulatory Antisense Long Non-Coding RNAs Related to Feed Efficiency in Bos taurus Bulls
Wietje Nolte, Rosemarie Weikard, Ronald M. Brunner, Elke Albrecht, Harald Michael Hammon, Antônio Reverter, Christa Kühn · 2020 · International Journal of Molecular Sciences
Powerful detection of polygenic selection and evidence of environmental adaptation in US beef cattle
Troy N. Rowan, Harly J. Durbin, Christopher M. Seabury, Robert D. Schnabel, Jared E. Decker · 2020 · bioRxiv (Cold Spring Harbor Laboratory)