Article
Agriculture, Dairy & Animal Science
Simon F. Lashmar, Donagh P. Berry, Rian Pierneef, Farai C. Muchadeyi, Carina Visser
Summary: Genomic selection in less-developed countries can be hindered by high genotyping costs, but imputation from lower to higher densities can reduce these costs. This study found that SNP selection strategies and density can significantly impact imputation accuracy in locally adapted cattle breeds. Ultimately, a genotyping panel of around 10,000 SNP chosen based on a combination of MAF and LD criteria can achieve a low error rate in genomic imputation for admixed breeds like the SA Drakensberger.
JOURNAL OF ANIMAL SCIENCE
(2021)
Article
Multidisciplinary Sciences
Jae Young Choi, Xiaoguang Dai, Ornob Alam, Julie Z. Peng, Priyesh Rughani, Scott Hickey, Eoghan Harrington, Sissel Juul, Julien F. Ayroles, Michael D. Purugganan, Elizabeth A. Stacy
Summary: The study conducted an evolutionary genomics analysis of genus Metrosideros, a landscape-dominant adaptive radiation of woody plants in Hawaii. It was found that Hawaiian Metrosideros originated from a single colonization event and showed evidence of extensive reticulation and admixture between taxa. Divergent selection was identified as driving the formation of differentiation outliers in early stages of speciation/divergence.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Marco Antonio Perpetuo de Sousa, Flavia Regina Florencio de Athayde, Mariangela Bueno Cordeiro Maldonado, Andressa Oliveira de Lima, Marina Rufino S. Fortes, Flavia Lombardi Lopes
Summary: The study found that approximately 71.6% of the predicted miRNA targets were altered as a result of SNPs located within the seed region of the mature miRNAs, potentially affecting miRNA maturation. Analysis revealed that 48.6% of the sequences had values sufficient enough to alter miRNA maturation.
Article
Genetics & Heredity
Byung Woo Yoon, Hyun-Tae Shin, Je Hyun Seo
Summary: This study provides insights into the genetic differences in prostate cancer incidence among different ethnicities, using data on single-nucleotide polymorphisms associated with prostate cancer. The study reveals that the polygenic risk score, as well as certain genes such as AR, CDKN1B, and MAD1L1, are associated with ethnic differences in prostate cancer.
Review
Biochemistry & Molecular Biology
Federico Scossa, Alisdair R. Fernie
Summary: Ancestral proteins were more promiscuous than modern ones, with specificity often evolving after gene duplication; some modern proteins are found to have evolved de novo from ancestors lacking those functions; new interactions evolved from just a few mutations, suggesting acquisition of new functions is not difficult but often lost to subsequent mutations.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Biochemical Research Methods
Stefan Ebmeyer, Roelof Dirk Coertze, Fanny Berglund, Erik Kristiansson, D. G. Joakim Larsson
Summary: GEnView is a Python-based pipeline for comparative analysis of gene loci in a large number of bacterial genomes, providing users with automated, taxon-selective access to over 800,000 genomes and plasmids available in the NCBI Assembly and RefSeq databases.
Article
Biochemistry & Molecular Biology
Joseph W. Saelens, Mollie I. Sweeney, Gopinath Viswanathan, Ana Maria Xet-Mull, Kristen L. Jurcic Smith, Dana M. Sisk, Daniel D. Hu, Rachel M. Cronin, Erika J. Hughes, W. Jared Brewer, Jorn Coers, Matthew M. Champion, Patricia A. Champion, Craig B. Lowe, Clare M. Smith, Sunhee Lee, Jason E. Stout, David M. Tobin
Summary: The human pathogen Mycobacterium tuberculosis can cause lung disease and disseminate to other tissues. This study identified an outbreak of M. tuberculosis with high rates of extrapulmonary dissemination and bone disease. The causal strain carried a full-length ancestral version of the effector protein EsxM, which exacerbated dissemination through enhancement of macrophage motility and egress from granulomas, as well as alterations in macrophage actin dynamics. Reconstitution of ancestral EsxM in a modern attenuated strain altered the migratory mode of infected macrophages and promoted bone disease in a zebrafish model. The presence of a derived nonsense variant in EsxM in major M. tuberculosis lineages suggests a role for EsxM in regulating dissemination.
Article
Biochemistry & Molecular Biology
Jennifer Jessica Bruscadin, Taina Figueiredo Cardoso, Wellison Jarles da Silva Diniz, Juliana Afonso, Marcela Maria de Souza, Juliana Petrini, Bruno Gabriel Nascimento Andrade, Vinicius Henrique da Silva, Jose Bento Sterman Ferraz, Adhemar Zerlotini, Gerson Barreto Moura, Luiz Lehmann Coutinho, Luciana Correia de Almeida Regitano
Summary: This study utilized a large dataset of imputed SNP genotypes and RNA-Seq data from Nelore steers to identify ASE SNPs and aseQTLs in muscle, demonstrating the cis-regulatory effect of these variants and discovering numerous novel ASE regions. These findings highlight the potential of using ASE to uncover cis-regulatory SNPs affecting muscle-related traits.
BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS
(2022)
Article
Microbiology
Pranab Kumar Mahata, Regina Sharmila Dass, Archana Pan, Babylakshmi Muthusamy
Summary: This study extensively analyzed the morphological features of Aspergillus fungi isolated from fennel seeds, along with their classification, genetic characteristics, and SNP analysis. A total of 14 Aspergillus species were identified from 70 fennel samples, with A. niger and A. flavus being the most common species.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Genetics & Heredity
Byung-Woo Yoon, Hyun-Tae Shin, Jehyun Seo
Summary: This study provides insights into the genetic causes of differences in vitamin D concentrations among individuals of diverse ancestries. The analysis reveals distinct genetic patterns among different populations, with the genetic risk score for vitamin D concentration highest in Europeans followed by East Asians and Africans. The study suggests that genetic factors play a more significant role in vitamin D concentration differences than latitude effects.
Article
Biochemical Research Methods
Samuel Martin, Richard M. Leggett
Summary: Alvis is a simple command line tool that generates visualizations for various alignment analysis tasks, improving understanding of assembly quality and identifying potential errors. Splitting chimeric reads using Alvis output can enhance assembly contiguity while maintaining correctness.
BMC BIOINFORMATICS
(2021)
Article
Multidisciplinary Sciences
Xiao-fei Liu, Ying-bo Sun, Gen-fa Zhu, Li-li Huang, Bo Yu
Summary: In this study, the chloroplast genomes of Hippeastrum 'Milady', H. alberti, and H. reticulatum were analyzed using the Illumina NovaSeq sequencing platform. The results showed that all three genomes had the typical tetrad structure, and certain regions of H. reticulatum were longer compared to the other two varieties. Comparative analysis revealed their closer relationship with Lycoris and Narcissus.
Article
Veterinary Sciences
Ahmed I. Ateya, Samer S. Ibrahim, Mona M. Al-Sharif
Summary: This study investigated the single nucleotide polymorphisms, gene expression, and economic evaluation of mastitis susceptibility in Holstein and Brown Swiss dairy cows. The results showed that certain genes may play a significant role in mastitis tolerance/susceptibility, and mastitis has detrimental impacts on the economic efficiency of dairy farms.
VETERINARY SCIENCES
(2022)
Article
Biochemical Research Methods
Austin Chiao, Jianye Ge
Summary: Genetic genealogy is increasingly used in forensic investigations to identify criminals. However, current applications often overlook lineage markers, leading to inaccurate determinations of genetic lineages. This study presents a method that utilizes mismatch frequencies of single-nucleotide polymorphisms (SNPs) in Y-chromosomal and mitochondrial DNA to accurately determine paternal or maternal lineages.
Article
Genetics & Heredity
Kevin R. Bredemeyer, Ladeana Hillier, Andrew J. Harris, Graham M. Hughes, Nicole M. Foley, Colleen Lawless, Rachel A. Carroll, Jessica M. Storer, Mark A. Batzer, Edward S. Rice, Brian W. Davis, Terje Raudsepp, Stephen J. O'Brien, Leslie A. Lyons, Wesley C. Warren, William J. Murphy
Summary: This study reconstructed the evolutionary dynamics of structural variation in five cat species using near-gapless single-haplotype assemblies. The study found that cat genomes have fewer segmental duplications compared to great apes and identified X chromosomes as hotspots for structural variation. The study also highlighted the role of the DXZ4 macrosatellite in felid hybrid incompatibility.
Article
Agriculture, Dairy & Animal Science
Md Mesbah-Uddin, Bernt Guldbrandtsen, Aurelien Capitan, Mogens Sando Lund, Didier Boichard, Goutam Sahana
Summary: This study identifies fertility-associated quantitative trait loci in dairy cattle and proposes candidate genes using association analyses. The inclusion of these markers in future genomic evaluations can improve the accuracy of genomic predictions.
JOURNAL OF DAIRY SCIENCE
(2022)
Article
Agriculture, Dairy & Animal Science
M. P. Sanchez, T. Tribout, S. Fritz, V Wolf, C. Laithier, M. Brochard, D. Boichard
Summary: As part of the From'MIR project, this study assessed the reliability of ssEBVs for CMP, estimated genetic trends, and simulated different breeding objectives for the Montbeliarde breed. Reliability of ssEBVs ranged from 61% to 64%, with the TD3 model being the most accurate. The inclusion of additional candidate SNPs improved the reliabilities of ssEBVs and led to positive genetic trends for all CMP traits. The TMI-Cheese scenario yielded the best responses for CMP traits.
JOURNAL OF DAIRY SCIENCE
(2022)
Article
Oncology
Valentin Costes, Aurelie Chaulot-Talmon, Eli Sellem, Jean-Philippe Perrier, Anne Aubert-Frambourg, Luc Jouneau, Charline Pontlevoy, Chris Hoze, Sebastien Fritz, Mekki Boussaha, Chrystelle Le Danvic, Marie-Pierre Sanchez, Didier Boichard, Laurent Schibler, Helene Jammes, Florence Jaffrezic, Helene Kiefer
Summary: This study demonstrates the potential of sperm DNA methylation in predicting bull fertility and identifies differentially methylated cytosines related to fertility. The results are important for improving fertility prediction models and understanding the interplay between DNA methylation and other molecular features in fertility regulation. The findings may have potential applications in human medicine as well.
CLINICAL EPIGENETICS
(2022)
Article
Immunology
Jeremy Lesueur, Sarah Walachowski, Sarah Barbey, Nathan Cebron, Rachel Lefebvre, Frederic Launay, Didier Boichard, Pierre Germon, Fabien Corbiere, Gilles Foucras
Summary: Recent developments in multiplex technologies have allowed for the detection of soluble proteins in various biological samples. Cytokine profiling using these technologies can provide a more accurate description of conditions related to infectious diseases or vaccination.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Agriculture, Dairy & Animal Science
R. Lefebvre, P. Faverdin, S. Barbey, J. Jurquet, T. Tribout, D. Boichard, P. Martin
Summary: Body condition score (BCS) is a good estimate of stored fat on the body and can be used to proxy energy balance. Genomic evaluation of BCS has been implemented in several countries, including France, where estimated breeding values are based on individual BCS determination during the first lactation. This study investigates the use of genomic estimated breeding values based on a single phenotype record to predict and potentially limit body reserve mobilization during early lactation, as well as the effects of selection on BCS on other traits.
JOURNAL OF DAIRY SCIENCE
(2023)
Article
Biotechnology & Applied Microbiology
Marie-Pierre Sanchez, Clementine Escouflaire, Aurelia Baur, Fiona Bottin, Chris Hoze, Mekki Boussaha, Sebastien Fritz, Aurelien Capitan, Didier Boichard
Summary: This study aimed to assess the importance of the X chromosome in the genetic determinism of complex traits in dairy cattle. The results showed that the X chromosome explained about 3.5% of the genetic variance in these traits and revealed many new functional candidate genes. This study highlights the importance of the X chromosome in the genetic determinism of complex traits in dairy cattle and identifies new functional candidate genes for these traits.
Review
Agriculture, Dairy & Animal Science
G. Sahana, Z. Cai, M. P. Sanchez, A. C. Bouwman, D. Boichard
Summary: Genotype data from dairy cattle selection programs greatly facilitate GWAS to identify variants related to economic traits. Results can enhance the accuracy of genomic prediction, analyze more complex models, elucidate the genetic architecture of a trait, and decipher the underlying biology of traits.
JOURNAL OF DAIRY SCIENCE
(2023)
Article
Agriculture, Dairy & Animal Science
S. Fresco, D. Boichard, S. Fritz, R. Lefebvre, S. Barbey, M. Gaborit, P. Martin
Summary: Genetic selection for reducing methane emissions from dairy cows is an effective approach to mitigate climate change. This study investigated the feasibility of this approach by analyzing the interaction between methane and several traits of interest in dairy cows. The results suggest that methane emissions should be selected based on MeY, which has the highest correlation with the first and second parity of cows.
JOURNAL OF DAIRY SCIENCE
(2023)
Article
Multidisciplinary Sciences
Nicolas Gaiani, Lorraine Bourgeois-Brunel, Dominique Rocha, Arnaud Boulling
Summary: DGAT1 plays a crucial role in fat metabolism and triacylglyceride synthesis. Two DGAT1 loss-of-function variants, namely p.M435L and p.K232A, have been associated with milk production traits in cattle. The p.M435L variant leads to the skipping of exon 16, resulting in a non-functional truncated protein. The p.K232A variant affects the splicing rate of multiple DGAT1 introns, particularly intron 7.
SCIENTIFIC REPORTS
(2023)
Article
Multidisciplinary Sciences
Camille Eche, Carole Iampietro, Clement Birbes, Andreea Dreau, Claire Kuchly, Arnaud Di Franco, Christophe Klopp, Thomas Faraut, Sarah Djebali, Adrien Castinel, Matthias Zytnicki, Erwan Denis, Mekki Boussaha, Cecile Grohs, Didier Boichard, Christine Gaspin, Denis Milan, Cecile Donnadieu
Summary: Inspired by the Genome in a Bottle project, we sequenced a Charolais heifer using various technologies and generated high quality reference genomes. The PacBio HiFi assembly reached a larger size than the ARS-UCD1.2 reference, and the consensus assembly had a high BUSCO score and identified numerous structural variants. This assembly contributes to the bovine pangenome and provides valuable resources for SNP calling, variant analysis, and de novo assembly.
Article
Agriculture, Dairy & Animal Science
T. Tribout, S. Minery, R. Vallee, S. Saille, D. Saunier, P. Martin, V. Ducrocq, P. Faverdin, D. Boichard
Summary: This study aimed to estimate the genetic correlation between body weight loss and daily milk production in first- and second-lactation Holstein cows. The results showed a moderate to low correlation between body weight loss and milk production, indicating that it may be possible to select for high milk production without compromising cow health.
JOURNAL OF DAIRY SCIENCE
(2023)
Article
Agriculture, Dairy & Animal Science
Mekki Boussaha, Arnaud Boulling, Valerie Wolgust, Lorraine Bourgeois-Brunel, Pauline Michot, Cecile Grohs, Nicolas Gaiani, Pierre-Yves Grivaud, Helene Leclerc, Coralie Danchin-Burge, Marthe Vilotte, Julie Riviere, Didier Boichard, Jean-Marie Gourreau, Aurelien Capitan
Summary: A study found that Charolais calves have a congenital skin fragility disorder resembling inherited epidermolysis bullosa. Genetic analysis identified a mutation in the ITGA6 gene as the cause of this condition. This is the first evidence of an ITGA6 mutation causing EB in livestock species.
GENETICS SELECTION EVOLUTION
(2023)
Article
Agriculture, Dairy & Animal Science
Aurelie Vinet, Sophie Mattalia, Roxane Vallee, Christine Bertrand, Beatriz C. D. Cuyabano, Didier Boichard
Summary: Heat stress has negative effects on cattle welfare, health, and productivity. This study focuses on identifying heat-tolerant high-producing cattle using on-farm performance and weather data. The results show that the optimal temperature-humidity index (THI) for French Montbeliarde cows is below 55. Genetic interactions between genotype and THI are weak for production and udder health traits. However, individual animals may react differently to high temperatures. Selecting for heat tolerance in cattle breeding would be relevant to cope with expected temperature increases.
GENETICS SELECTION EVOLUTION
(2023)
Article
Agriculture, Dairy & Animal Science
Anne Vaiman, Sebastien Fritz, Christian Beauvallet, Mekki Boussaha, Cecile Grohs, Nathalie Daniel-Carlier, Anne Relun, Didier Boichard, Jean-Luc Vilotte, Amandine Duchesne
Summary: We describe a new form of hereditary cleft palate in Limousine cattle. We identified two fully linked and deleterious mutations, ultimately leading to the loss-of-function of the MYH3 protein. The mutations were included on the Illumina EuroG10k v8 and EuroGMD v1 SNP chips and are used to set up a reliable eradication strategy in the French Limousine breed.
GENETICS SELECTION EVOLUTION
(2022)
Article
Agriculture, Dairy & Animal Science
Marie-Pierre Sanchez, Thierry Tribout, Sebastien Fritz, Raphael Guatteo, Christine Fourichon, Laurent Schibler, Arnaud Delafosse, Didier Boichard
Summary: This study investigates the genetic determinism of resistance to bovine paratuberculosis and shows that this trait can be predicted from SNP genotypes. The study finds that resistance to JD is moderately heritable and identifies 16 genomic regions associated with this resistance. The study also highlights the importance of genomic predictions in controlling paratuberculosis.
GENETICS SELECTION EVOLUTION
(2022)
