☆ 4.6 Review

Progress and opportunities through use of genomics in animal production

TRENDS IN GENETICS (2022)

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Review Agriculture, Dairy & Animal Science

Invited review: A quarter of a century-International genetic evaluation of dairy sires using MACE methodology

M. A. Nilforooshan et al.

Summary: The international exchange of genetic materials has accelerated in recent decades, particularly in dairy cattle. The Multiple Across Country Evaluation (MACE) method, rooted in mixed-model theory, has been prominent in international genetic evaluation, handling genotype by environment interaction between countries. Future methods will need to utilize genomic information effectively and address genomic preselection bias to ensure accuracy in genetic evaluations.

JOURNAL OF DAIRY SCIENCE (2022)

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Article Veterinary Sciences

Genome editing of avian species: implications for animal use and welfare

Sudeepta K. Panda et al.

Summary: Avian species, especially chickens, play crucial roles in research and agriculture, with genome editing methods like CRISPR/Cas9 holding promise for enhancing avian health and productivity. These tools have diverse applications in biomedical, agricultural, and biotechnological activities, with a focus on identifying beneficial genetic variants and addressing animal welfare concerns.

LABORATORY ANIMALS (2022)

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Review Biochemical Research Methods

Towards progressive regulatory approaches for agricultural applications of animal biotechnology

Eric M. Hallerman et al.

Summary: Traditional breeding techniques have greatly benefited agricultural animals, but genome editing techniques now offer new opportunities for targeted genetic alterations. Regulatory approaches are being defined, and an international community is actively discussing and sharing information on animal biotechnology.

TRANSGENIC RESEARCH (2022)

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Review Genetics & Heredity

Practical guide for managing large-scale human genome data in research

Tomoya Tanjo et al.

Summary: Studies in human genetics involve dealing with a large amount of genomic sequencing data, providing guidance on how to process and analyze data for researchers. Key points include integrating global genome projects for improved analysis results, and developing computational platforms and workflow engines.

JOURNAL OF HUMAN GENETICS (2021)

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Article Agriculture, Dairy & Animal Science

Genetic parameters for carcase measurements and age at slaughter in commercial cattle

T. C. Pritchard et al.

Summary: Genetic parameters were estimated for five traits in cattle, with correlations indicating that selection for increased carcase weight should improve growth rate, conformation, and reduce fatness. Results show genetic variation in traits suitable for genetic improvement, with apparent breed differences.

ANIMAL (2021)

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Article Agriculture, Dairy & Animal Science

Predicting pregnancy status from mid-infrared spectroscopy in dairy cow milk using deep learning

W. Brand et al.

Summary: Accurately determining pregnancy status is crucial for dairy enterprises. This study utilized deep learning to identify features related to pregnancy status and metabolic changes in dairy cows from milk MIR spectral data. Results suggest that trained models can be used to alert farmers of nonviable pregnancies and verify conception dates.

JOURNAL OF DAIRY SCIENCE (2021)

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Article Evolutionary Biology

A Reference Genome Assembly of Simmental Cattle, Bos taurus taurus

Michael P. Heaton et al.

Summary: Genomics research has increasingly acknowledged the limitation of single reference genomes and turned to pangenome representations, with the Bovine Pangenome Consortium aiming to assemble genomes from over 600 recognized cattle breeds to capture the broadest genetic diversity. This study presents a complete single haplotype assembly for a Simmental cow, a triple-purpose breed known for its fast growth and beef yields, suggesting promising continuity and completeness comparable to the best Bos taurus reference assemblies.

JOURNAL OF HEREDITY (2021)

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Article Multidisciplinary Sciences

Metagenomic analysis of the cow, sheep, reindeer and red deer rumen

Laura Glendinning et al.

Summary: The rumen microbiota in ruminants play a vital role in nutrition and offer potential for industrial applications. Variations were found in microbial taxonomy, enzyme genes, and KEGG orthologs among different ruminant species, highlighting the diversity of rumen microbiomes.

SCIENTIFIC REPORTS (2021)

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Review Genetics & Heredity

Improvements in Gene Editing Technology Boost Its Applications in Livestock

Iuri Viotti Perisse et al.

Summary: Accelerated development of novel CRISPR/Cas9-based genome editing techniques allows for precise modifications in the mammalian genome, making it the preferred method for introducing gene alterations in livestock species. The expanding list of new CRISPR/Cas9-based genome editing tools includes methods to improve efficiency and specificity, gene regulation, base editing, and epigenetic modifications. Additionally, the advantages and disadvantages of two primary methods for producing gene-edited farm animals, as well as the agricultural and biomedical applications of gene editing technology, are discussed.

FRONTIERS IN GENETICS (2021)

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Article Biochemistry & Molecular Biology

Low-pass sequencing increases the power of GWAS and decreases measurement error of polygenic risk scores compared to genotyping arrays

Jeremiah H. Li et al.

Summary: The study found that low-pass sequencing combined with genotype imputation not only significantly increases the statistical power for genome-wide association studies but also provides increased accuracy for polygenic risk prediction compared to genotyping arrays.

GENOME RESEARCH (2021)

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Article Biochemistry & Molecular Biology

One-Step Generation of Multiple Gene-Edited Pigs by Electroporation of the CRISPR/Cas9 System into Zygotes to Reduce Xenoantigen Biosynthesis

Fuminori Tanihara et al.

Summary: The study successfully utilized a CRISPR/Cas9 system to simultaneously target GGTA1, CMAH, and B4GALNT2 in in vitro-fertilized zygotes, achieving the one-step generation of multiple gene-edited pigs without xenoantigens. Although the experiments resulted in the generation of GGTA1/CMAH double-edited pigs and GGTA1/CMAH/B4GALNT2 triple-edited pigs, these gene-edited pigs were genetic mosaics, indicating further refinement is needed to completely knock out all xenoantigens.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)

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Article Agriculture, Dairy & Animal Science

Genomic predictions for yield traits in US Holsteins with unknown parent groups

A. Cesarani et al.

Summary: The study aimed to assess the reliability and bias of estimated breeding values (EBV) from traditional BLUP, genomic EBV (GEBV) from single-step genomic BLUP (ssGBLUP) with unknown parent groups (UPG). Results showed that ssGBLUP with UPG for both A and the relationship matrix among genotyped animals provided the most accurate and least biased evaluations.

JOURNAL OF DAIRY SCIENCE (2021)

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Article Multidisciplinary Sciences

Direct allele introgression into pure chicken breeds using Sire Dam Surrogate (SDS) mating

Maeve Ballantyne et al.

Summary: The article introduces a novel inducibly sterile surrogate host chicken, which can produce pure breed chickens carrying donor genome edited genes through direct mating. The researchers demonstrate the successful introgression of two feather trait alleles into two pure chicken breeds using this method.

NATURE COMMUNICATIONS (2021)

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Article Multidisciplinary Sciences

Expanded catalog of microbial genes and metagenome-assembled genomes from the pig gut microbiome

Congying Chen et al.

Summary: The study conducted a comprehensive survey of the swine gut microbiome, resulting in the creation of a pig integrated gene catalog (PIGC) and metagenome-assembled genomes (MAGs). Through deep metagenomic sequencing, the researchers identified strain-level differences in the gut microbiome of wild boars and commercial Duroc pigs, providing expanded resources for pig microbiome-related research.

NATURE COMMUNICATIONS (2021)

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Article Evolutionary Biology

Genetic Engineering of Livestock: The Opportunity Cost of Regulatory Delay

Alison L. Van Eenennaam et al.

Summary: The slow progress in the commercialization of genetically engineered livestock is mainly due to technical issues, the structure of livestock industries, lack of public research funding and investment, regulatory obstacles, and concern about public opinion. Researchers and developers have encountered difficulties in producing genetically engineered livestock. Delays in commercializing GE livestock beyond the normative 10-year evaluation period are associated with billions of dollars in opportunity costs and reduced global food security.

ANNUAL REVIEW OF ANIMAL BIOSCIENCES, VOL 9, 2021 (2021)

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Article Multidisciplinary Sciences

Local adaptations of Mediterranean sheep and goats through an integrative approach

Bruno Serranito et al.

Summary: This study focused on local Mediterranean breeds of goats and sheep, using historical archives and statistical programs to identify adaptive genes, revealing their potential key roles in arid and altitude gradients.

SCIENTIFIC REPORTS (2021)

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Article Biotechnology & Applied Microbiology

Characterization of a haplotype-reference panel for genotyping by low-pass sequencing in Swiss Large White pigs

Adela Noskova et al.

Summary: The key-ancestor approach was used to prioritize individuals for whole-genome sequencing in Swiss Large White pigs, revealing significant genetic differentiation between two divergently selected lines, despite a recent split. Low-pass sequencing based genotyping showed high concordance with microarray genotyping.

BMC GENOMICS (2021)

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Meeting Abstract Agriculture, Dairy & Animal Science

Multi-omics Approaches to Improve Animal Production

Wellison Jarles Da Silva Diniz et al.

JOURNAL OF ANIMAL SCIENCE (2021)

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Article Agriculture, Dairy & Animal Science

A dimensional reduction approach to modulate the core ruminal microbiome associated with methane emissions via selective breeding

Alejandro Saborio-Montero et al.

Summary: The study proposes combining metagenomic and host genomic data for selective breeding of the cow hologenome towards reduced methane emissions. Through principal component analysis, the complex information of the rumen microbiota was condensed into a few principal components that could be used in animal breeding programs. The study found that genetic correlations between certain principal components and methane production were high, offering potential for reducing methane emissions in future generations through selective breeding programs.

JOURNAL OF DAIRY SCIENCE (2021)

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Article Agriculture, Dairy & Animal Science

Holobiont effect accounts for more methane emission variance than the additive and microbiome effects on dairy cattle

Alejandro Saborio-Montero et al.

Summary: The rumen microbiota is related to key traits in dairy cattle, and joint analysis of the host's genetic background and microbiota can be modeled using similarity matrices. This study compared the performance of different microbiome distance metrics in variance component estimation, finding that Ks with flattened off-diagonal elements were more accurate.

LIVESTOCK SCIENCE (2021)

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Article Biology

Metagenome-assembled genomes and gene catalog from the chicken gut microbiome aid in deciphering antibiotic resistomes

Yuqing Feng et al.

Summary: This study generated a large dataset by integrating microbial genomes from chicken gut samples across ten countries, identifying novel species and genera, common microbial populations, and abundant enzymes in the chicken gut. It also highlighted the effects of geography and host species on antibiotic resistance genes, with Chinese chicken samples showing higher relative abundance but lower diversity of ARGs compared to European samples. The study emphasizes the importance of understanding the chicken gut microbiome for potential applications in agriculture and health.

COMMUNICATIONS BIOLOGY (2021)

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Article Multidisciplinary Sciences

Novel functional sequences uncovered through a bovine multiassembly graph

Danang Crysnanto et al.

Summary: This study builds a diverse pangenome from multiple cattle assemblies, revealing genetic differences between different breeds and capturing previously undetected genetic variations. By utilizing whole-genome sequencing and transcriptome data, the research uncovers genes and transcripts that were previously unseen in the traditional reference genome, opening up new avenues for genetic investigations.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)

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Article Microbiology

Integrative Transkingdom Analysis of the Gut Microbiome in Antibiotic Perturbation and Critical Illness

Bastiaan W. Haak et al.

Summary: This study used multi-omics factor analysis to integrate bacterial, fungal, and viral components of the intestinal microbiota in critically ill patients, revealing a loss of anaerobic environment correlated with overgrowth of pathogenic bacteria, yeast, and depletion of short-chain fatty acids. The findings highlight the complexity of transkingdom changes following disruption of the intestinal bacterial microbiome, emphasizing the importance of further studying potential adjunctive therapies using anaerobic bacteria or SCFAs to reduce fungal expansion after antibiotic exposure.

MSYSTEMS (2021)

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Article Veterinary Sciences

Reducing Antimicrobial Use and Dependence in Livestock Production Systems: A Social and Economic Sciences Perspective on an Interdisciplinary Approach

Fanny Baudoin et al.

Summary: By utilizing an interdisciplinary approach, we have presented a comprehensive method to develop strategies and policies for addressing antimicrobial resistance in livestock production, ensuring the technical, economic, behavioral, and political feasibility of the measures.

FRONTIERS IN VETERINARY SCIENCE (2021)

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Review Biotechnology & Applied Microbiology

Surrogate broodstock to enhance biotechnology research and applications in aquaculture

Ye Hwa Jin et al.

Summary: The use of surrogate broodstock technology provides new opportunities for improving genome editing, preserving aquatic genetic resources, and reducing generation intervals in aquaculture breeding, ultimately expediting genetic gain and dissemination of high quality production animals.

BIOTECHNOLOGY ADVANCES (2021)

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Article Biochemistry & Molecular Biology

Integrated Environmental and Genomic Analysis Reveals the Drivers of Local Adaptation in African Indigenous Chickens

Almas A. Gheyas et al.

Summary: Breeding for climate resilience in livestock production is a crucial goal, with indigenous livestock showing local adaptations that allow for genetic studies on resilience control. Using ecological niche modeling and genome-wide selection signature analyses, key environmental drivers were identified in African village chickens, pointing towards a predominantly oligogenic control of adaptation. This study highlights the importance of pre-identifying environmental factors and genomic investigations in understanding adaptation in domestic animals.

MOLECULAR BIOLOGY AND EVOLUTION (2021)

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Editorial Material Developmental Biology

Dolly at 25 ... is she '... still goin' strong?'

Kevin D. Sinclair

REPRODUCTION (2021)

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Review Veterinary Sciences

Enhanced Detection of Major Pathogens and Toxins in Poultry and Livestock With Zoonotic Risks Using Nanomaterials-Based Diagnostics

Priya K. Manhas et al.

Summary: Nanotechnology plays a crucial role in enhancing the sensitivity and specificity of diagnostic tools for animal diseases, but challenges remain in achieving a balance between sensitivity, specificity, reproducibility, and cost-effectiveness.

FRONTIERS IN VETERINARY SCIENCE (2021)

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Article Agriculture, Dairy & Animal Science

Phenomes: the current frontier in animal breeding

Miguel Perez-Enciso et al.

Summary: Advancements in genomic technologies have allowed for industry-scale application of genomic selection, but increasing marker density up to sequence may not significantly improve genetic prediction accuracy unless causative mutations are identified. The challenges in the industry are shifting towards 'phenomics' instead of 'genomics', and developments in sensor technology and artificial intelligence are offering a wide range of analytical tools to address pressing societal demands.

GENETICS SELECTION EVOLUTION (2021)

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Article Agriculture, Dairy & Animal Science

On the use of whole-genome sequence data for across-breed genomic prediction and fine-scale mapping of QTL

Theo Meuwissen et al.

Summary: In this study, a computationally fast implementation of variable selection genomic prediction method was presented, showing its accuracy for across-breed predictions and QTL mapping precision. The results demonstrated that the combination of across-breed WGS data and Bayesian genomic prediction was remarkably effective for fine-mapping of QTL, improving prediction accuracies and discovering new SNPs affecting milk production.

GENETICS SELECTION EVOLUTION (2021)

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Review Biotechnology & Applied Microbiology

How the pan-genome is changing crop genomics and improvement

Rafael Della Coletta et al.

Summary: Crop genomics has advanced significantly in recent years thanks to improvements in sequencing technology, assembly methods, and computational resources. The study of structural variation within species and the characterization of pan-genomes have revealed extensive genome content variation among individuals within a species, which is revolutionizing crop genomics and improvement.

GENOME BIOLOGY (2021)

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Article Multidisciplinary Sciences

CRISPR, animals, and FDA oversight: Building a path to success

Laura R. Epstein et al.

Summary: The Food and Drug Administration recognizes the importance of innovative solutions and plays a key role in bringing safe and effective animal biotechnology products to the market. They emphasize a risk-based approach and efforts to improve transparency, predictability, and efficiency, believing that working together is the foundation for success.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)

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Article Ecology

Host genetic effects upon the early gut microbiota in a bovine model with graduated spectrum of genetic variation

Peixin Fan et al.

ISME JOURNAL (2020)

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Article Biotechnology & Applied Microbiology

Genomic and phenotypic analyses of six offspring of a genome-edited hornless bull

Amy E. Young et al.

NATURE BIOTECHNOLOGY (2020)

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Review Biology

Genome editing approaches to augment livestock breeding programs

Thomas Frederick Bishop et al.

JOURNAL OF EXPERIMENTAL BIOLOGY (2020)

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Letter Biotechnology & Applied Microbiology

Genome editing in animals: why FDA regulation matters

Steven M. Solomon

NATURE BIOTECHNOLOGY (2020)

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Editorial Material Biotechnology & Applied Microbiology

Template plasmid integration in germline genome-edited cattle

Alexis L. Norris et al.

NATURE BIOTECHNOLOGY (2020)

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Article Multidisciplinary Sciences

Precise CRISPR/Cas9 editing of the NHE1 gene renders chickens resistant to the J subgroup of avian leukosis virus

Anna Koslova et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

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Review Genetics & Heredity

Pangenomics Comes of Age: From Bacteria to Plant and Animal Applications

Agnieszka A. Golicz et al.

TRENDS IN GENETICS (2020)

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Editorial Material Public, Environmental & Occupational Health

Reducing antibiotic use in livestock, China

Yanhong Jessika Hu et al.

BULLETIN OF THE WORLD HEALTH ORGANIZATION (2020)

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Article Microbiology

Metagenomic Characterization of Intestinal Regions in Pigs With Contrasting Feed Efficiency

Jianping Quan et al.

FRONTIERS IN MICROBIOLOGY (2020)

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Article Biochemistry & Molecular Biology

Comprehensive analyses of 723 transcriptomes enhance genetic and biological interpretations for complex traits in cattle

Lingzhao Fang et al.

GENOME RESEARCH (2020)

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Article Multidisciplinary Sciences

Substitution of warthog NF-κB motifs into RELA of domestic pigs is not sufficient to confer resilience to African swine fever virus

Stephen McCleary et al.

SCIENTIFIC REPORTS (2020)

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Review Genetics & Heredity

Harnessing genomics to fast-track genetic improvement in aquaculture

Ross D. Houston et al.

NATURE REVIEWS GENETICS (2020)

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Review Biotechnology & Applied Microbiology

Gene Editing Regulation and Innovation Economics

Agustina I. Whelan et al.

FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY (2020)

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Article Agriculture, Dairy & Animal Science

The future of phenomics in dairy cattle breeding

John B. Cole et al.

ANIMAL FRONTIERS (2020)

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Article Genetics & Heredity

Gene Networks Driving Genetic Variation in Milk and Cheese-Making Traits of Spanish Assaf Sheep

Hector Marina et al.

GENES (2020)

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Review Agriculture, Dairy & Animal Science

Symposium review: Genomic selection for reducing environmental impact and adapting to climate change

Jennie E. Pryce et al.

JOURNAL OF DAIRY SCIENCE (2020)

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Review Agriculture, Dairy & Animal Science

Symposium review: Advances in sequencing technology herald a new frontier in cattle genomics and genome-enabled selection

D. M. Bickhart et al.

JOURNAL OF DAIRY SCIENCE (2020)

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Article Agriculture, Dairy & Animal Science

Predicting bovine tuberculosis status of dairy cows from mid-infrared spectral data of milk using deep learning

S. J. Denholm et al.

JOURNAL OF DAIRY SCIENCE (2020)

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Article Multidisciplinary Sciences

Donor-derived spermatogenesis following stem cell transplantation in sterile NANOS2 knockout males

Michela Ciccarelli et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

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Article Multidisciplinary Sciences

Rescue of germ cells in dnd crispant embryos opens the possibility to produce inherited sterility in Atlantic salmon

Hilal Guralp et al.

SCIENTIFIC REPORTS (2020)

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Article Microbiology

Rumen Microbiome Composition Is Altered in Sheep Divergent in Feed Efficiency

Steven McLoughlin et al.

FRONTIERS IN MICROBIOLOGY (2020)

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Review Veterinary Sciences

Image Analysis and Computer Vision Applications in Animal Sciences: An Overview

Arthur Francisco Araujo Fernandes et al.

FRONTIERS IN VETERINARY SCIENCE (2020)

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Article Genetics & Heredity

Improving Genomic Prediction of Crossbred and Purebred Dairy Cattle

Majid Khansefid et al.

FRONTIERS IN GENETICS (2020)

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Review Biotechnology & Applied Microbiology

From FAANG to fork: application of highly annotated genomes to improve farmed animal production

Emily L. Clark et al.

GENOME BIOLOGY (2020)

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Article Genetics & Heredity

Assessment of Imputation from Low-Pass Sequencing to Predict Merit of Beef Steers

Warren M. Snelling et al.

GENES (2020)

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Article Agriculture, Dairy & Animal Science

Optimizing genomic reference populations to improve crossbred performance

Yvonne C. J. Wientjes et al.

GENETICS SELECTION EVOLUTION (2020)

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Article Biotechnology & Applied Microbiology

Bovine breed-specific augmented reference graphs facilitate accurate sequence read mapping and unbiased variant discovery

Danang Crysnanto et al.

GENOME BIOLOGY (2020)

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Article Biotechnology & Applied Microbiology

Assembly of hundreds of novel bacterial genomes from the chicken caecum

Laura Glendinning et al.

GENOME BIOLOGY (2020)

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Review Computer Science, Information Systems

Blockchain Technology for Agriculture: Applications and Rationale

Hang Xiong et al.

FRONTIERS IN BLOCKCHAIN (2020)

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Article Agriculture, Dairy & Animal Science

Spermatogonial Stem Cell Transplantation: Insights and Outlook for Domestic Animals

Mariana I. Giassetti et al.

ANNUAL REVIEW OF ANIMAL BIOSCIENCES, VOL 7 (2019)

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Article Agriculture, Dairy & Animal Science

Predicting the effect of reference population on the accuracy of within, across, and multibreed genomic prediction

I van den Berg et al.

JOURNAL OF DAIRY SCIENCE (2019)

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Article Multidisciplinary Sciences

Australian gene-editing rules adopt ‘middle ground’

Smriti Mallapaty

NATURE (2019)

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Review Genetics & Heredity

Genome to Phenome: Improving Animal Health, Production, and Well-Being - A New USDA Blueprint for Animal Genome Research 2018-2027

Caird Rexroad et al.

FRONTIERS IN GENETICS (2019)

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Article Genetics & Heredity

Genomic Evaluation for a Crossbreeding System Implementing Breed-of-Origin for Targeted Markers

Claudia A. Sevillano et al.

FRONTIERS IN GENETICS (2019)

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Review Genetics & Heredity

Potential of Genome Editing to Improve Aquaculture Breeding and Production

Remi L. Gratacap et al.

TRENDS IN GENETICS (2019)

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Article Agriculture, Dairy & Animal Science

Genome editing for disease resistance in pigs and chickens

Chris Proudfoot et al.

ANIMAL FRONTIERS (2019)

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Review Biochemical Research Methods

Recent progress in electrochemical biosensors as point of care diagnostics in livestock health

Anil Gattani et al.

ANALYTICAL BIOCHEMISTRY (2019)

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Article Multidisciplinary Sciences

Reviving rare chicken breeds using genetically engineered sterility in surrogate host birds

Mark E. Woodcock et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

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Editorial Material Agriculture, Dairy & Animal Science

At the Intersection of Industry, Academia, and Government: How Do We Facilitate Productive Precision Livestock Farming in Practice?

Brett C. Ramirez et al.

ANIMALS (2019)

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Review Biochemistry & Molecular Biology

The Ecology and Evolution of Pangenomes

Michael A. Brockhurst et al.

CURRENT BIOLOGY (2019)

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Article Reproductive Biology

Pig in vitro fertilization: Where are we and where do we go?

Raquel Romar et al.

THERIOGENOLOGY (2019)

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Article Biochemistry & Molecular Biology

A genomic map of climate adaptation in Mediterranean cattle breeds

Laurence Flori et al.

MOLECULAR ECOLOGY (2019)

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Review Genetics & Heredity

Harnessing genomic information for livestock improvement

Michel Georges et al.

NATURE REVIEWS GENETICS (2019)

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Editorial Material Medicine, General & Internal

After the Storm - A Responsible Path for Genome Editing

George Q. Daley et al.

NEW ENGLAND JOURNAL OF MEDICINE (2019)

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Article Biotechnology & Applied Microbiology

Regulatory Status of Genome-Edited Organisms Under the Japanese Cartagena Act

Mai Tsuda et al.

FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY (2019)

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Review Genetics & Heredity

A Vision for Development and Utilization of High-Throughput Phenotyping and Big Data Analytics in Livestock

James E. Koltes et al.

FRONTIERS IN GENETICS (2019)

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Article Genetics & Heredity

High-Dimensional Bayesian Network Inference From Systems Genetics Data Using Genetic Node Ordering

Lingfei Wang et al.

FRONTIERS IN GENETICS (2019)

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Article Food Science & Technology

On-Farm Livestock Genome Editing Using Cutting Edge Reproductive Technologies

Gus R. McFarlane et al.

FRONTIERS IN SUSTAINABLE FOOD SYSTEMS (2019)

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Article Agriculture, Dairy & Animal Science

A multi-breed reference panel and additional rare variants maximize imputation accuracy in cattle

Troy N. Rowan et al.

GENETICS SELECTION EVOLUTION (2019)

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Article Agriculture, Dairy & Animal Science

Genomic prediction based on selected variants from imputed whole-genome sequence data in Australian sheep populations

Nasir Moghaddar et al.

GENETICS SELECTION EVOLUTION (2019)

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Article Biotechnology & Applied Microbiology

HUPAN: a pan-genome analysis pipeline for human genomes

Zhongqu Duan et al.

GENOME BIOLOGY (2019)

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Review Genetics & Heredity

APPLICATIONS OF NEXT-GENERATION SEQUENCING Towards a genomics-informed, real-time, global pathogen surveillance system

Jennifer L. Gardy et al.

NATURE REVIEWS GENETICS (2018)

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Article Agriculture, Dairy & Animal Science

Review: Semen sexing - current state of the art with emphasis on bovine species

R. Vishwanath et al.

ANIMAL (2018)

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Article Agriculture, Dairy & Animal Science

BIG DATA ANALYTICS AND PRECISION ANIMAL AGRICULTURE SYMPOSIUM: Machine learning and data mining advance predictive big data analysis in precision animal agriculture

Gota Morota et al.

JOURNAL OF ANIMAL SCIENCE (2018)

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Review Agriculture, Dairy & Animal Science

Novel strategies to genetically improve mastitis resistance in dairy cattle

P. Martin et al.

JOURNAL OF DAIRY SCIENCE (2018)

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Review Genetics & Heredity

Non-additive Effects in Genomic Selection

Luis Varona et al.

FRONTIERS IN GENETICS (2018)

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Article Agriculture, Dairy & Animal Science

The feasibility of using low-density marker panels for genotype imputation and genomic prediction of crossbred dairy cattle of East Africa

H. Aliloo et al.

JOURNAL OF DAIRY SCIENCE (2018)

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Article Biotechnology & Applied Microbiology

Variation graph toolkit improves read mapping by representing genetic variation in the reference

Erik Garrison et al.

NATURE BIOTECHNOLOGY (2018)

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Article Agriculture, Dairy & Animal Science

Functional Annotation of Animal Genomes (FAANG): Current Achievements and Roadmap

Elisabetta Giuffra et al.

Annual Review of Animal Biosciences (2018)

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Article Agriculture, Dairy & Animal Science

1000 Bull Genomes Project to Map Simple and Complex Genetic Traits in Cattle: Applications and Outcomes

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Gene-edited pigs are protected from porcine reproductive and respiratory syndrome virus

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Exploiting biological priors and sequence variants enhances QTL discovery and genomic prediction of complex traits

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Sequence variants selected from a multi-breed GWAS can improve the reliability of genomic predictions in dairy cattle

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Quantitative trait loci markers derived from whole genome sequence data increases the reliability of genomic prediction

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A crossbred reference population can improve the response to genomic selection for crossbred performance

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Improved precision of QTL mapping using a nonlinear Bayesian method in a multi-breed population leads to greater accuracy of across-breed genomic predictions

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Efficiency of multi-breed genomic selection for dairy cattle breeds with different sizes of reference population

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The sheep genome illuminates biology of the rumen and lipid metabolism

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Quantitative Genetic Background of the Host Influences Gut Microbiomes in Chickens

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Strategies and utility of imputed SNP genotypes for genomic analysis in dairy cattle

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Components of the accuracy of genomic prediction in a multi-breed sheep population

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Improving accuracy of genomic predictions within and between dairy cattle breeds with imputed high-density single nucleotide polymorphism panels

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Analyses of pig genomes provide insight into porcine demography and evolution

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A Review of Antibiotic Use in Food Animals: Perspective, Policy, and Potential

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A phasing and imputation method for pedigreed populations that results in a single-stage genomic evaluation

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Improved Lasso for genomic selection

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Species-Specific Variation in RELA Underlies Differences in NF-κB Activity: a Potential Role in African Swine Fever Pathogenesis

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Persistence of accuracy of genomic estimated breeding values over generations in layer chickens

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Understanding and using quantitative genetic variation

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Design of a High Density SNP Genotyping Assay in the Pig Using SNPs Identified and Characterized by Next Generation Sequencing Technology

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The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution

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Persistence of accuracy of genome-wide breeding values over generations when including a polygenic effect

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Testing strategies for genomic selection in aquaculture breeding programs

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Linkage disequilibrium and persistence of phase in Holstein-Friesian, Jersey and Angus cattle

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Data and theory point to mainly additive genetic variance for complex traits

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Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering

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Genetic parameters for EUROP carcass traits within different groups of cattle in Ireland

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Statistical epistasis is a generic feature of gene regulatory networks

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Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution

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