Article
Biotechnology & Applied Microbiology
O. Gervais, A. Barria, A. Papadopoulou, R. L. Gratacap, B. Hillestad, A. E. Tinch, S. A. M. Martin, D. Robledo, R. D. Houston
Summary: The study found that the heritability of ISAV resistance is moderate with a polygenic architecture, but a significant quantitative trait locus was detected on chromosome 13. A mild up-regulation of the interferon pathway characterizes the response to the virus in heart samples from this population of Atlantic salmon, and candidate genes showing differential expression between samples with high and low breeding values for resistance were identified.
Article
Biotechnology & Applied Microbiology
Ophelie Gervais, Carolina Penaloza, Remi Gratacap, Athina Papadopoulou, Mariana Beltran, Neil C. Henderson, Ross D. Houston, Musa A. Hassan, Diego Robledo
Summary: In this study, single-cell RNA sequencing was used to provide a high-dimensional insight into the transcriptional landscape of Atlantic salmon cells during early Infectious Salmon Anaemia Virus (ISAV) infection. The results showed a clear anti-viral response in infected cells, characterized by the upregulation of IFNA2 or IRF2. Additionally, uninfected bystander cells exhibited transcriptional differences, suggesting paracrine signaling from infected cells. This study identified potential key genes involved in the host-virus interaction, which can be targeted in future functional studies to enhance the resistance of Atlantic salmon to ISAV.
Article
Biotechnology & Applied Microbiology
Ophelie Gervais, Athina Papadopoulou, Remi Gratacap, Borghild Hillestad, Alan E. Tinch, Samuel A. M. Martin, Ross D. Houston, Diego Robledo
Summary: This study investigates the transcriptomic responses of ISAV-infected salmon with contrasting levels of resistance, revealing that the responses to ISAV are organ-specific with a strong immune response observed in the head kidney. Other biological processes such as ubiquitination and ribosomal processing also play a role during early infection.
Article
Fisheries
Camilla A. Santos, Sonia C. S. Andrade, Ana K. Teixeira, Flavio Farias, Ana C. Guerrelhas, Joao L. Rocha, Patricia D. Freitas
Summary: This study used RNA-seq data to analyze gene expression patterns related to growth performance and weight gain in Litopenaeus vannamei shrimp. The results show that certain genes are up-regulated in higher growth families, potentially involved in weight gain and immune response.
Article
Genetics & Heredity
Hui Zhang, Ming Li Wang, Phat Dang, Tao Jiang, Shuzhen Zhao, Marshall Lamb, Charles Chen
Summary: A genome-wide association study identified 178 significant QTLs associated with seed composition traits in cultivated peanuts, providing a genetic basis for understanding oil quality and protein synthesis. RNA-Seq analysis revealed 282 differentially expressed genes, with 16 candidate genes potentially involved in seed fatty acid metabolism and protein synthesis.
Article
Biotechnology & Applied Microbiology
Thomas J. Hall, Michael P. Mullen, Gillian P. McHugo, Kate E. Killick, Siobhan C. Ring, Donagh P. Berry, Carolina N. Correia, John A. Browne, Stephen Gordon, David E. MacHugh
Summary: This study analyzed host gene expression data from bovine alveolar macrophages infected with M. bovis, identifying core infection response pathways and gene modules at the transcriptome level. Integrating this data with GWAS datasets enhanced the detection of genomic variants associated with susceptibility/resistance to M. bovis infection. The results showed that network-based integration of transcriptomics data can provide additional information from GWAS datasets, with significant differences among breeds in SNP discovery for bTB resilience traits.
Article
Agriculture, Dairy & Animal Science
Olyad Erba Urgessa, Adugna Abdi Woldesemayat
Summary: In poultry production, the cost of feed ingredients has been continuously increasing, resulting in higher production costs. By improving feed efficiency traits, feed costs can be reduced and the environmental impact of poultry production can be decreased. Feed efficiency is considered one of the most important economic traits in chicken breeding programs. Recent OMICs experimental studies have focused on characterizing biological differences between chickens with high and low feed efficiency. Due to the complexity of biology, researchers have combined multiple assays to create multi-OMICs datasets. OMICs findings are crucial for improving poultry breeding approaches. This review highlights the components of feed efficiency and discusses the application of OMICs in chicken breeding programs.
ANIMAL BIOTECHNOLOGY
(2023)
Review
Agronomy
Longlan Xu, Yuhua He, Lingli Tang, Yongyang Xu, Guangwei Zhao
Summary: This review discusses the advancements in genetics, genomics, and breeding of melon, emphasizing the importance of identifying new genetic resources with resistance and special fruit quality traits for the development of effective and useful breeding technologies in melon.
Article
Immunology
Natasha A. Botwright, Amin R. Mohamed, Joel Slinger, Paula C. Lima, James W. Wynne
Summary: Through studying the pathogenesis of amoebic gill disease in Atlantic salmon, the localized and systemic immune responses of the host and parasite were identified, along with transcription factors and gene networks significantly altered in disease states. This dual transcriptomic study provides novel molecular insights into the pathology of AGD, offering alternative theories for future research and improved management strategies.
FRONTIERS IN IMMUNOLOGY
(2021)
Review
Plant Sciences
Muez Berhe, Komivi Dossa, Jun You, Pape Adama Mboup, Idrissa Navel Diallo, Diaga Diouf, Xiurong Zhang, Linhai Wang
Summary: The study reviewed the progress in discovering important traits in sesame through the GWAS method, developed a new online database SiGeDiD, and tested various new GWAS multi-locus models for the first time in sesame.
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
Biotechnology & Applied Microbiology
Carlo C. Lazado, Marianne Iversen, Arvind Y. M. Sundaram
Summary: This study provides the first insight into the basal transcriptome of the olfactory rosette in Atlantic salmon. Comparative transcriptomic analysis with gills, another organ possessing MALT, reveals shared cytokine-cytokine interaction and neuroactive ligand-receptor interaction pathways. The immunological characteristics of both organs are further characterized by the overrepresentation of immune-related pathways, particularly important for pathogen recognition. The differential regulation of markers for interleukins, extracellular matrix, antimicrobial peptides, and complement highlights the immunological differences between the two organs. The basal transcriptome of the Atlantic salmon olfactory rosette is a valuable molecular toolbox for understanding nasal immunity in teleost fish.
Review
Fisheries
G. H. Yue, K. Y. Ma, J. H. Xia
Summary: Aquaculture is crucial for global food security. Developing species and varieties of omnivorous fish that can tolerate high salinity will enhance fish production. Certain tilapia species, such as Oreochromis mossambicus and Oreochromis aureus, are highly tolerant to salinity and have been used in aquaculture production in brackish and seawater. Different breeding methods, both conventional and molecular, have been implemented to improve the growth rate and salinity tolerance of tilapia. Advances in genomic resources and disruptive technologies provide optimism for novel breeding approaches to further enhance the production of salinity-tolerant tilapia.
REVIEWS IN AQUACULTURE
(2023)
Review
Behavioral Sciences
Milka Martinez, C. Nibaldo Inestrosa
Summary: Alzheimer's disease is a neurological disorder that primarily affects the elderly, characterized by progressive cognitive decline and loss of autonomy. Transcriptional changes in susceptible signaling pathways, particularly the Wnt signaling pathway, have been linked to synaptic dysfunction and neuronal degeneration, highlighting synapse failure as a key pathological event in early stages of the disease.
NEUROSCIENCE AND BIOBEHAVIORAL REVIEWS
(2021)
Article
Agronomy
Qing Li, Xueli Lu, Changjian Wang, Lan Shen, Liping Dai, Jinli He, Long Yang, Peiyuan Li, Yifeng Hong, Qiang Zhang, Guojun Dong, Jiang Hu, Guangheng Zhang, Deyong Ren, Zhenyu Gao, Longbiao Guo, Qian Qian, Li Zhu, Dali Zeng
Summary: This study investigates the regulatory mechanisms of rice in response to low nitrogen and identifies genes and quantitative trait loci associated with this response through genome-wide association study and transcriptomic investigation.
Article
Multidisciplinary Sciences
Androniki Psifidi, Andreas Kranis, Lisa M. Rothwell, Abi Bremner, Kay Russell, Diego Robledo, Stephen J. Bush, Mark Fife, Paul M. Hocking, Georgios Banos, David A. Hume, Jim Kaufman, Richard A. Bailey, Santiago Avendano, Kellie A. Watson, Pete Kaiser, Mark. P. Stevens
Summary: This study identified quantitative trait loci associated with Campylobacter load in commercial broilers, including on chromosomes 14, 16, 19, and 26. RNA-Seq analysis revealed differentially transcribed genes near the key QTL on chromosome 16. Strong cis-QTLs within the MHC gene region were identified, implicating pathways related to antigen presentation, immune responses, and signaling. Despite the potential for breeding selection, high frequency of resistance alleles and non-genetic factors significantly influenced Campylobacter colonization.
SCIENTIFIC REPORTS
(2021)
Article
Cell Biology
Ismael Hernandez-Nunez, Diego Robledo, Helene Mayeur, Sylvie Mazan, Laura Sanchez, Fatima Adrio, Anton Barreiro-Iglesias, Eva Candal
Summary: Neurogenesis is the process of generating new neurons by progenitor cells, which is restricted to specific neurogenic niches. The retina of cartilaginous fish such as catsharks shows active proliferation and neurogenesis in juveniles but a reduction in cell proliferation after sexual maturation. RNA-Seq analysis revealed a decrease in gene expression related to cell proliferation and neurogenesis in adult catsharks, providing valuable insight into signaling pathways controlling neurogenesis in vertebrate retinas.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
O. Gervais, A. Barria, A. Papadopoulou, R. L. Gratacap, B. Hillestad, A. E. Tinch, S. A. M. Martin, D. Robledo, R. D. Houston
Summary: The study found that the heritability of ISAV resistance is moderate with a polygenic architecture, but a significant quantitative trait locus was detected on chromosome 13. A mild up-regulation of the interferon pathway characterizes the response to the virus in heart samples from this population of Atlantic salmon, and candidate genes showing differential expression between samples with high and low breeding values for resistance were identified.
Review
Biology
Robert W. A. Potts, Alejandro P. Gutierrez, Carolina S. Penaloza, Tim Regan, Tim P. Bean, Ross D. Houston
Summary: Molluscan aquaculture is important for global seafood production, but faces challenges from infectious disease outbreaks. Selective breeding, genomic technologies, and genome editing show promise in improving genetic resistance to disease in molluscs, with tailored approaches needed due to their unique characteristics.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Biology
Carolina Penaloza, Alejandro P. Gutierrez, Lel Eory, Shan Wang, Ximing Guo, Alan L. Archibald, Tim P. Bean, Ross D. Houston
Summary: A chromosome-level assembly for the Pacific oyster (C. gigas) was created and annotated, providing a valuable resource for genetics and genomics studies, as well as selective breeding in aquaculture.
Article
Microbiology
Sophie Fridman, Smaragda Tsairidou, Nilantha Jayasuriya, Halina Sobolewska, Alastair Hamilton, Carlos Lobos, Ross D. Houston, Hamish Rodger, James Bron, Tharangani Herath
Summary: This study aimed to develop a novel gross pathological scoring system for assessing complex or multifactorial gill disease in farmed Atlantic salmon. The scoring system combines presumptive or healed amoebic gill disease (AGD) with other types of gill lesions, providing a standardized approach to characterize severe proliferative pathologies in affected gills.
Article
Biotechnology & Applied Microbiology
Robert Mukiibi, Carolina Penaloza, Alejandro Gutierrez, Jose M. Yanez, Ross D. Houston, Diego Robledo
Summary: This study investigated DNA methylation changes in response to P. salmonis infection in the head kidney and liver tissue of Atlantic salmon, and the interaction between gene expression and DNA methylation in the same tissues. The results suggest that methylation plays an important role in gene expression regulation and response to infectious diseases, providing valuable insights for utilizing epigenetic markers to improve disease resistance and manage fish health in salmon aquaculture.
Review
Fisheries
Nicholas A. Robinson, Diego Robledo, Lene Sveen, Rose Ruiz Daniels, Aleksei Krasnov, Andrew Coates, Ye Hwa Jin, Luke T. Barrett, Marie Lillehammer, Anne H. Kettunen, Ben L. Phillips, Tim Dempster, Andrea Doeschl-Wilson, Francisca Samsing, Gareth Difford, Sarah Salisbury, Bjarne Gjerde, John-Erik Haugen, Erik Burgerhout, Binyam S. Dagnachew, Dominic Kurian, Mark D. Fast, Morten Rye, Marcela Salazar, James E. Bron, Sean J. Monaghan, Celeste Jacq, Mike Birkett, Howard I. Browman, Anne Berit Skiftesvik, David M. Fields, Erik Selander, Samantha Bui, Anna Sonesson, Stanko Skugor, Tone-Kari Knutsdatter Ostbye, Ross D. Houston
Summary: Disease and parasitism pose significant challenges to global aquaculture, and genetic technologies offer potential solutions. Understanding genetic mechanisms, developing tools for boosting host resistance, and applying genetic technologies can improve disease resistance and transform aquaculture.
REVIEWS IN AQUACULTURE
(2023)
Editorial Material
Genetics & Heredity
Wei Huang, Qiang Gao, Kai Fu, Rodrigo Pulgar Tejo, Lucile Maria Floeter-Winter, Alejandro P. Gutierrez
FRONTIERS IN GENETICS
(2022)
Article
Multidisciplinary Sciences
Nidia de Sousa, Diego Robledo, Laura Gonzalez-Llera, Andreia G. Pinho, Diogo J. Santos, Susana Monteiro, Jonas Campos, Jorge R. Cibrao, Nuno A. Silva, Laura Sanchez, Antonio J. Salgado, Anton Barreiro-Iglesias
Summary: Spinal cord injury (SCI) has no available pharmacological treatments for promoting neurological recovery. Baclofen treatment has been shown to promote functional recovery in mice with compression SCI. This study provides transcriptomic data from adult mouse spinal cords collected 7 days after compression SCI and baclofen administration. The data includes raw RNA-seq data and bioinformatic analyses.
Review
Fisheries
Rose Ruiz Daniels, Richard S. S. Taylor, Diego Robledo, Daniel J. J. Macqueen
Summary: Single cell genomics is a rapidly advancing technology that measures the molecular characteristics of individual cells in target samples. It provides more biological information compared to traditional 'bulk' methods and has revolutionized our understanding of cellular biology in humans and model organisms. This review highlights the potential applications of single cell genomics in aquaculture research, discussing the challenges and solutions in its broad adoption. The review focuses on single cell transcriptomics, discussing considerations in experimental design and data analysis tailored to under-characterized aquaculture species.
REVIEWS IN AQUACULTURE
(2023)