Article
Agriculture, Dairy & Animal Science
C. Brekke, S. E. Johnston, A. B. Gjuvsland, P. Berg
Summary: This study investigates the variation in recombination rates between sexes and individual animals using pedigree information and genotype data in a large cattle population. The results show higher recombination rates in males compared to females, but little variation in recombination distribution between the sexes. Heritability analysis indicates a low but significant genetic contribution to recombination rates in both males and females. Additionally, two loci associated with individual recombination counts in females were identified.
JOURNAL OF DAIRY SCIENCE
(2023)
Article
Agriculture, Dairy & Animal Science
Ana Guillenea, Guosheng Su, Mogens Sandro Lund, Emre Karaman
Summary: This study investigated the reliability of genomic prediction using the breed origin of alleles approach in the Nordic Red population. The results showed that including whole-genome sequencing SNP and dividing the genome into fixed regions can improve the reliability of genomic prediction.
JOURNAL OF DAIRY SCIENCE
(2022)
Article
Agriculture, Dairy & Animal Science
Margot Slagboom, Viktor Milkevych, Huiming Liu, Jorn Rind Thomasen, Morten Kargo, Christin Schmidtmann
Summary: Red cattle breeds exist throughout Europe. Collaborating with mainstream breeds can increase local breed's genetic potential, but may result in decreased breed purity.
Article
Genetics & Heredity
Markus Schmid, Joana Stock, Joern Bennewitz, Robin Wellmann
Summary: This study proposes a method for computing genomic breeding values for small admixed breeds that incorporates phenotypic and genomic information from large introgressed breeds while considering the origin of alleles. The proposed method outperforms conventional within-breed and multi-breed genomic best linear unbiased prediction models in most cases, according to a simulation study.
FRONTIERS IN GENETICS
(2022)
Editorial Material
Biochemistry & Molecular Biology
Malgorzata Pilot
Summary: The study demonstrates that the true phylogenetic signal within a genome is concentrated in low-recombination regions, and information from these regions is essential for accurately inferring lineage splitting order. Their analytical approaches reveal the possibility of reconstructing complex intraspecific evolutionary relationships.
Article
Agronomy
Karima Ben Mansour, Adrian J. Gibbs, Marcela Kominkova, Petr Kominek, Jana Brozova, Jan Kazda, Miloslav Zouhar, Pavel Rysanek
Summary: Watermelon mosaic virus (WMV) is a potyvirus that infects cucurbits and is economically important worldwide. A study confirmed the presence of WMV in Czech Republic through sequencing and phylogenetic analysis, revealing that the Czech isolates are closely related to European isolates and exhibit a high rate of recombination. The complete WMV genomes form three phylogenetic clades, with basal Chinese isolates dating back at least 2000 years. WMV became a crop pathogen around 1000 years ago, coinciding with the introduction of watermelon cultivation in northern China.
Article
Agriculture, Dairy & Animal Science
H. Wilmot, T. Druet, I. Hulsegge, N. Gengler, M. P. L. Calus
Summary: Enhancing collaboration between related breeds is crucial for improving competitiveness and sustainability of local breeds. Developing an across-breed reference population can better manage local breeds, but how different red-pied cattle breeds collaborate in the Benelux region is unclear. This study aims to estimate inbreeding levels, determine genomic relatedness, and detect genomically close animals for building a reference population for two endangered breeds.
Article
Veterinary Sciences
Maien Munthe-Kaas, Guro Sveberg, Ingrid Hunter Holmoy, Elisabeth Kommisrud, Caroline Sorknes Haadem, Adam Dunstan Martin
Summary: Under commercial conditions, Norwegian Red cows exhibit a high level of estrus behavior.
FRONTIERS IN VETERINARY SCIENCE
(2023)
Article
Agriculture, Dairy & Animal Science
Tesfaye K. Belay, Leiv S. Eikje, Arne B. Gjuvsland, Oyvind Nordbo, Thierry Tribout, Theo Meuwissen
Summary: This study focused on reducing biases and improving stability of genomic predictions of breeding values by combining genotyped and non-genotyped animals. Incompatibilities between the pedigree- and the genomics-based relationship matrices were addressed by fitting a covariate (J) that corrects for base-population differences. Alternative ways of combining the J covariate and genetic group effects were evaluated to account for missing parental information. Fitting J as fixed or random reduced biases and increased stability of genomic predictions. Combining group and J effects performed better than existing models. A model that fits group regression coefficients minus the part explained by pedigree was recommended for its least bias and highest stability.
JOURNAL OF ANIMAL SCIENCE
(2022)
Review
Food Science & Technology
Nani Gopal Das, Mohammed R. Islam, Nathu Ram Sarker, Md Abdul Jalil, Cameron E. F. Clark
Summary: Red Chittagong cattle, a native breed of Bangladesh, has potential for addressing current and future challenges in animal production systems. This breed is characterized by small size, high levels of milk protein and fat, resistance to diseases and parasites, and adaptation to agro-ecological conditions. Through long-term breeding programs and improved management conditions, this breed could become a global resource for modern animal production systems.
FRONTIERS IN SUSTAINABLE FOOD SYSTEMS
(2021)
Article
Biology
Taehyung Kwon, Kwondo Kim, Kelsey Caetano-Anolles, Samsun Sung, Seoae Cho, Choongwon Jeong, Olivier Hanotte, Heebal Kim
Summary: Our study confirms the genotype discrepancy between mitochondrial and nuclear genome in African admixed cattle. We propose a novel hypothesis of selection induced by mitonuclear incompatibility to explain this discrepancy, and our results support the role of male-biased B. indicus introgression and selection induced by mitonuclear incompatibility in shaping the current genomic status of African admixed cattle. We also identified selection signatures at autosomal loci interacting with mitochondria, providing insights into the hybridization of mammalian species.
Article
Microbiology
Duanyong Zhou, Jianping Xu, Jianyong Dong, Haixia Li, Da Wang, Juan Gu, Ke-Qin Zhang, Ying Zhang
Summary: The study found historical divergence within the A. oligospora population in China, with genetically differentiated populations showing phenotypic differences related to ecological adaptations, and evidence for recent dispersion and hybridization among historically subdivided geographic populations.
Article
Agriculture, Dairy & Animal Science
Irene Novo, Pilar Ordas, Natalia Moraga, Enrique Santiago, Humberto Quesada, Armando Caballero
Summary: The estimation of historical Ne provided by the software GONE can be substantially biased by recent mixture of populations, low rates of continued migration, and high frequencies of chromosomal inversions. Population structure analyses and restriction of estimation to differentiated groups can help mitigate biases. Removing genomic regions involved in inversions can also improve the accuracy of Ne estimates.
GENETICS SELECTION EVOLUTION
(2023)
Article
Materials Science, Multidisciplinary
V. Jary, L. Havlak, M. Buryi, E. Mihokova, V. Babin, J. Barta, V. Vanecek, Z. Remes, M. Nikl
Summary: In this study, Eu2+-doped (Gd;Y)3Al5O12 (GYAG) powder samples with different Gd/Y ratio were synthesized through solid-state inorganic reaction. The structural, scintillation, and optical properties of the samples were investigated using various techniques to assess the impact of Gd admixture on the YAG host. The study also discussed the potential applications of these phosphors in scintillators or solid-state white LED phosphors.
Article
Immunology
Fernando Flores Cardoso, Oswald Matika, Appolinaire Djikeng, Ntanganedzeni Mapholi, Heather M. Burrow, Marcos Jun Iti Yokoo, Gabriel Soares Campos, Claudia Cristina Gulias-Gomes, Valentina Riggio, Ricardo Pong-Wong, Bailey Engle, Laercio Porto-Neto, Azwihangwisi Maiwashe, Ben J. Hayes
Summary: This study evaluated tick resistance in multiple beef cattle breeds, revealing differences in genetic correlations and heritability among populations, as well as the potential benefits of multi-trait genomic selection. The multi-trait approach improved predictive ability and corrected over-dispersion of GEBV, showing promise for enhancing tick resistance in beef cattle through genomic selection.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Agriculture, Dairy & Animal Science
Thi Thuy Ngo, Nguyen N. Bang, Peter Dart, Matthew Callaghan, Athol Klieve, Ben Hayes, David McNeill
Summary: This study confirmed that adding a new probiotic H57 can improve cattle's preference for feed pellets by reducing microbial spoilage, thus changing the pellets' odour. H57 was found to be effective only when stored at room temperature, decreasing the concentration of microbial volatile organic compounds and extending the shelf life of feed pellets.
Article
Biochemistry & Molecular Biology
Aurelie Allais-Bonnet, Aurelie Hintermann, Marie-Christine Deloche, Raphael Cornette, Philippe Bardou, Marina Naval-Sanchez, Alain Pinton, Ashleigh Haruda, Cecile Grohs, Jozsef Zakany, Daniele Bigi, Ivica Medugorac, Olivier Putelat, Ockert Greyvenstein, Tracy Hadfield, Slim Ben Jemaa, Gjoko Bunevski, Fiona Menzi, Nathalie Hirter, Julia M. Paris, John Hedges, Isabelle Palhiere, Rachel Rupp, Johannes A. Lenstra, Louisa Gidney, Josephine Lesur, Renate Schafberg, Michael Stache, Marie-Dominique Wandhammer, Rose-Marie Arbogast, Claude Guintard, Amandine Blin, Abdelhak Boukadiri, Julie Riviere, Diane Esquerre, Cecile Donnadieu, Coralie Danchin-Burge, Coralie M. Reich, David G. Riley, Este Van Marle-Koster, Noelle Cockett, Benjamin J. Hayes, Cord Drogemuller, James Kijas, Eric Pailhoux, Gwenola Tosser-Klopp, Denis Duboule, Aurelien Capitan
Summary: In rare populations of sheep and goats with polyceraty, occurring when more than two horns are present, distinct POLYCERATE alleles associated with defective HOXD1 function were identified. Haploinsufficiency at this locus leads to the splitting of horn bud primordia, suggesting an abnormal extension of an initial morphogenetic field. These findings emphasize the crucial role of the HOXD1 gene in headgear patterning and its evolutionarily used to fix the position and number of horns in Bovidae.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Immunology
Fernando Flores Cardoso, Oswald Matika, Appolinaire Djikeng, Ntanganedzeni Mapholi, Heather M. Burrow, Marcos Jun Iti Yokoo, Gabriel Soares Campos, Claudia Cristina Gulias-Gomes, Valentina Riggio, Ricardo Pong-Wong, Bailey Engle, Laercio Porto-Neto, Azwihangwisi Maiwashe, Ben J. Hayes
Summary: This study evaluated tick resistance in multiple beef cattle breeds, revealing differences in genetic correlations and heritability among populations, as well as the potential benefits of multi-trait genomic selection. The multi-trait approach improved predictive ability and corrected over-dispersion of GEBV, showing promise for enhancing tick resistance in beef cattle through genomic selection.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Biology
Mehrnush Forutan, Elizabeth Ross, Amanda J. Chamberlain, Loan Nguyen, Brett Mason, Stephen Moore, Josie B. Garner, Ruidong Xiang, Ben J. Hayes
Summary: By profiling genome-wide transcriptional start sites (TSSs) in two subspecies of cattle, researchers identified evolutionary and developmental differences in TSSs, with some SNPs located in differentially used TSS clusters showing significant shifts in allele frequency. Additionally, higher relative TSS expression of heat shock protein genes was observed in Bos indicus compared to Bos taurus, which may contribute to the tropical adaptation of Bos indicus. This study provides insights into cattle adaptation and highlights the rapid evolution of TSS between recently diverged subspecies.
COMMUNICATIONS BIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Seema Yadav, Elizabeth M. Ross, Karen S. Aitken, Lee T. Hickey, Owen Powell, Xianming Wei, Kai P. Voss-Fels, Ben J. Hayes
Summary: A LD-based algorithm is proposed to allocate unassigned SNPs to chromosome regions from sparse genetic maps, with an average proportion of over 94% SNP accuracy in placing them to chromosomes in sugarcane, wheat, and barley. This approach can improve genome-wide association studies and genomic prediction in crop species with fragmented and incomplete genome assemblies, benefiting genomic-assisted breeding for orphan crops.
Article
Agriculture, Dairy & Animal Science
Nguyen N Bang, Ben J. Hayes, Russell E. Lyons, Imtiaz A. S. Randhawa, John B. Gaughan, David M. McNeill
Summary: The study found that Vietnamese smallholder dairy cows (VDC) are primarily composed of Holstein genetics, but also contain small percentages of Jersey, Brown Swiss, and zebu genes. The genetic makeup of VDC consists of various dairy breeds, making them a good genetic base for selecting high milk-producing cows with some degree of adaptation to tropical conditions.
JOURNAL OF ANIMAL BREEDING AND GENETICS
(2022)
Article
Agriculture, Dairy & Animal Science
Chian Teng Ong, Elizabeth M. Ross, Gry B. Boe-Hansen, Conny Turni, Ben J. Hayes, Ala E. Tabor
Summary: This study compares the effectiveness of different sequencing methods for profiling bovine vaginal metagenomic samples. It finds that ONT adaptive sequencing yields a higher amount of metagenomic data per 1 Gb of sequence data and has increased sequencing efficiency and long read continuity. This method improves the amount and accuracy of metagenomic data for samples with high host-to-microbe DNA ratio.
JOURNAL OF ANIMAL SCIENCE
(2022)
Article
Multidisciplinary Sciences
Marte Sodeland, Sissel Jentoft, Per Erik Jorde, Morten Mattingsdal, Jon Albretsen, Alf Ring Kleiven, Ann-Elin Waroy Synnes, Sigurd Heiberg Espeland, Esben Moland Olsen, Carl Andre, Nils Chr Stenseth, Halvor Knutsen
Summary: Life on Earth has experienced cycles of ecological stasis and disruption, linking biological and geological transitions. Human influences have caused increasing ecological disruption, leading some to argue that we are now in the Anthropocene era. Understanding the drivers of ecological stasis is crucial for intervention and mitigation. The Atlantic cod, a keystone species in the northern Atlantic Ocean, has experienced collapses and ecosystem reshuffling. Whole-genome resequencing revealed that stabilizing selection maintains three supergenes in Atlantic cod, which are linked to species persistence and ecological stasis. Historic population size inference indicates continued declines due to industrialization and commercialization of fisheries.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Evolutionary Biology
Jose M. Yanez, Peng Xu, Roberto Carvalheiro, Ben Hayes
Summary: The increasing global demand for food and the challenges facing animal farming require improvements in efficiency and sustainable practices. Genomic technologies can accelerate genetic progress in animal breeding and help meet the protein needs of future human consumption.
EVOLUTIONARY APPLICATIONS
(2022)
Article
Agriculture, Dairy & Animal Science
Bailey N. Engle, Ben J. Hayes
Summary: The allele of PLAG1 genotype is significantly and positively related to Brahman heifer fertility, but the effect diminishes with age and does not affect mature cow weight.
JOURNAL OF ANIMAL SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Halvor Knutsen, Diana Catarino, Lauren Rogers, Marte Sodeland, Morten Mattingsdal, Marlene Jahnke, Jeffrey A. Hutchings, Ida Mellerud, Sigurd H. Espeland, Kerstin Johanneson, Olivia Roth, Michael M. Hansen, Sissel Jentoft, Carl Andre, Per Erik Jorde
Summary: Gene flow has a significant impact on spatial genetic structure and local adaptation. The presence or absence of a pelagic larval stage and the spatial distribution of suitable habitats play important roles in shaping gene flow and the genetic structure of populations. This study used whole genome sequencing and reduced representation sequencing data to analyze the genetic structure of the broadnosed pipefish. The findings revealed changes in population connectivity and were compared to two other fish species with a pelagic larval stage.
Correction
Multidisciplinary Sciences
Rajeev K. Varshney, Manish Roorkiwal, Shuai Sun, Prasad Bajaj, Annapurna Chitikineni, Mahendar Thudi, Narendra P. Singh, Xiao Du, Hari D. Upadhyaya, Aamir W. Khan, Yue Wang, Vanika Garg, Guangyi Fan, Wallace A. Cowling, Jose Crossa, Laurent Gentzbittel, Kai Peter Voss-Fels, Vinod Kumar Valluri, Pallavi Sinha, Vikas K. Singh, Cecile Ben, Abhishek Rathore, Ramu Punna, Muneendra K. Singh, Bunyamin Tar'an, Chellapilla Bharadwaj, Mohammad Yasin, Motisagar S. Pithia, Servejeet Singh, Khela Ram Soren, Himabindu Kudapa, Diego Jarquin, Philippe Cubry, Lee T. Hickey, Girish Prasad Dixit, Anne-Celine Thuillet, Aladdin Hamwieh, Shiv Kumar, Amit A. Deokar, Sushil K. Chaturvedi, Aleena Francis, Reka Howard, Debasis Chattopadhyay, David Edwards, Eric Lyons, Yves Vigouroux, Ben J. Hayes, Eric von Wettberg, Swapan K. Datta, Huanming Yang, Henry T. Nguyen, Jian Wang, Kadambot H. M. Siddique, Trilochan Mohapatra, Jeffrey L. Bennetzen, Xun Xu, Xin Liu
Article
Genetics & Heredity
Elizabeth M. Ross, Hari Sanjana, Loan T. Nguyen, YuanYuan Cheng, Stephen S. Moore, Ben J. Hayes
Summary: This study investigates the expression variation of fertility-related genes in cattle using different sequencing technologies. The findings reveal a large amount of transcriptional variation within fertility genes and highlight the limitations of using a single technology to fully characterize the transcriptional landscape.
FRONTIERS IN GENETICS
(2022)
Article
Biotechnology & Applied Microbiology
Emily F. Mantilla Valdivieso, Elizabeth M. Ross, Ali Raza, Muhammad Noman Naseem, Muhammad Kamran, Ben J. Hayes, Nicholas N. Jonsson, Peter James, Ala E. Tabor
Summary: This study investigated the gene expression profiles of leukocytes in Brangus cattle with different resistance phenotypes to tick infestation. The findings revealed that tick infestation leads to changes in leukocyte gene expression related to chemotaxis, cytokine secretion, and inflammatory response. The altered expression of genes from the bovine MHC complex in highly resistant animals also supports the relevance of this genomic region for disease resilience.
Article
Agriculture, Dairy & Animal Science
James P. Copley, Bailey N. Engle, Elizabeth M. Ross, Shannon Speight, Geoffry Fordyce, Benjamin J. Wood, Kai P. Voss-Fels, Benjamin J. Hayes
Summary: This study aimed to understand the impact of environmental conditions on the reproductive performance of beef cattle in Northern Australia. The results showed that early puberty is important for reproductive success. The temperature humidity index had a negative effect on first lactation pregnancy and puberty, while deviation from long-term average rainfall did not significantly affect reproductive traits. Average daily weight gain was positively correlated with first lactation pregnancy and heifer pregnancy.
TRANSLATIONAL ANIMAL SCIENCE
(2022)