Article
Veterinary Sciences
Amanda Kravitz, Ron Tyler, B. Murali Manohar, B. Samuel Masilamoni Ronald, Michael T. Collins, Nammalwar Sriranganathan
Summary: This study evaluates the repair and genotyping of veterinary species FFPE DNA using Illumina technology, demonstrating improved assay metrics and genotype calls post-restoration. The results indicate the potential for successful utilization of this technology in other veterinary species.
VETERINARY RESEARCH COMMUNICATIONS
(2023)
Article
Plant Sciences
Mariangela Arca, Tristan Mary-Huard, Brigitte Gouesnard, Aurelie Berard, Cyril Bauland, Valerie Combes, Delphine Madur, Alain Charcosset, Stephane D. Nicolas
Summary: This study developed a high-throughput and cost-saving DNA bulk approach for genotyping landraces, which provides accurate allelic frequency estimations. By testing 23,412 SNPs, the genetic distances between American and European maize diversity estimated from the SNP data highly correlated with those obtained from simple sequence repeats.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Plant Sciences
Ruslan Kalendar, Akmaral Baidyussen, Dauren Serikbay, Lyudmila Zotova, Gulmira Khassanova, Marzhan Kuzbakova, Satyvaldy Jatayev, Yin-Gang Hu, Carly Schramm, Peter A. Anderson, Colin L. D. Jenkins, Kathleen L. Soole, Yuri Shavrukov
Summary: The proposed ASQ method is an improved version of the existing ASQ method for SNP genotyping, with higher specificity and allele discrimination. It is cost-effective and suitable for various applications.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biology
Taras K. Oleksyk, Walter W. Wolfsberger, Alexandra M. Weber, Khrystyna Shchubelka, Olga T. Oleksyk, Olga Levchuk, Alla Patrus, Nelya Lazar, Stephanie O. Castro-Marquez, Yaroslava Hasynets, Patricia Boldyzhar, Mikhailo Neymet, Alina Urbanovych, Viktoriya Stakhovska, Kateryna Malyar, Svitlana Chervyakova, Olena Podoroha, Natalia Kovalchuk, Juan L. Rodriguez-Flores, Weichen Zhou, Sarah Medley, Fabia Battistuzzi, Ryan Liu, Yong Hou, Siru Chen, Huanming Yang, Meredith Yeager, Michael Dean, Ryan E. Mills, Volodymyr Smolanka
Summary: The collaborative effort aimed to provide genome-wide data for underrepresented populations in Eastern Europe and cross-validate genome sequences and genotypes acquired by different technologies. Results indicate that the genetic diversity of the Ukrainian population is uniquely shaped by evolutionary and demographic forces.
Article
Agronomy
Yikun Zhao, Bin Jiang, Yongxue Huo, Hongmei Yi, Hongli Tian, Haotian Wu, Rui Wang, Jiuran Zhao, Fengge Wang
Summary: The PSNPdms is a simple yet efficient tool for plant molecular research, providing comprehensive technical support for various fields such as crop breeding and genetic analysis. It offers effective data quality control through multiple dimensions and features a simple laboratory management structure.
Article
Food Science & Technology
Yi Lin, Wentao Yu, Chunping Cai, Pengjie Wang, Shuilian Gao, Jianming Zhang, Xiaojing Fan, Wanping Fang, Naixing Ye
Summary: This study used microfluidic technology and SNP biomarkers to authenticate the varieties of oolong tea products, and found that the most frequent adulterant of Tieguanyin oolong tea on the market is Benshan. It also reported for the first time the commercial behavior of using Fuyun6 and Jinguanyin as adulterants or contamination in the production of Tieguanyin oolong tea. This research proposes rapid authentication technology for oolong tea to promote consumer trust and food quality supervision.
FOOD RESEARCH INTERNATIONAL
(2022)
Article
Biochemistry & Molecular Biology
Mari Gogniashvili, Yoshihiro Matsuoka, Tengiz Beridze
Summary: The aim of this study was to genetically characterize hexaploid wheat Triticum aestivum L. Two approaches were used - complete sequencing of chloroplast DNA and PCR-based haplotype analysis of specific gene regions. The results revealed genetic differences between samples collected in different regions, with samples grouped into two main categories: those collected in Armenia, and those collected in Europe. This study identified single nucleotide polymorphisms (SNPs) in various regions of the wheat genome, providing insights into the genetic diversity and evolutionary history of hexaploid wheats.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Psychiatry
Laura Pineda-Cirera, Judit Cabana-Dominguez, Lara Grau-Lopez, Constanza Daigre, Cristina Sanchez-Mora, Raul Felipe Palma-Alvarez, Josep Antoni Ramos-Quiroga, Marta Ribases, Bru Cormand, Noelia Fernandez-Castillo
Summary: This study identified several gene variants associated with drug dependence susceptibility, with CTNNBL1, SCP2, and ECHDC2 genes highlighted as potential contributors. The findings suggest a complex interplay between genetic and epigenetic factors in drug dependence susceptibility.
JOURNAL OF PSYCHIATRIC RESEARCH
(2021)
Article
Agriculture, Dairy & Animal Science
John W. Keele, Tara G. McDaneld, Larry A. Kuehn
Summary: The genetic evaluation of seedstock cattle could benefit from commercial data, but the hidden relationships between the commercial and seedstock sectors pose a challenge. Single nucleotide polymorphism genotypes can reveal these relationships, but the cost of genotyping can be prohibitive. Pooling DNA is a cost-effective strategy to capture commercial data, but inexact pool formation can complicate interpretation.
JOURNAL OF ANIMAL SCIENCE
(2023)
Article
Infectious Diseases
Rocio Montejano, Lourdes Dominguez-Dominguez, Rosa de Miguel, David Rial-Crestelo, Andres Esteban-Cantos, Paula Aranguren-Rivas, Monica Garcia-Alvarez, Belen Alejos, Otilia Bisbal, Mireia Santacreu-Guerrero, Asuncion Hernando, Laura Bermejo-Plaza, Julen Cadinanos, Mario Mayoral, Juan Miguel Castro, Victoria Moreno, Luz Martin-Carbonero, Berta Rodes, Rafael Delgado, Rafael Rubio, Federico Pulido, Jose Ramon Arribas
Summary: This study evaluated the ability of proviral DNA genotyping to detect lamivudine resistance-associated mutations (RAMs) in HIV-1 virologically suppressed participants. The results showed that next generation sequencing (NGS) significantly increased the detection rates of RAMs, especially in participants with historical lamivudine resistance.
JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY
(2021)
Article
Genetics & Heredity
Binyam Dagnachew, Muhammad Luqman Aslam, Borghild Hillestad, Theo Meuwissen, Anna Sonesson
Summary: Genomic selection has great potential in aquaculture breeding, but high genotyping costs have limited its implementation. This study explores the use of DNA pooling as a tool to optimize the balance between cost and accuracy of selection. By analyzing two datasets, the researchers found that increasing the number of pools can improve prediction accuracy, but alternative effective pooling strategies should be studied to reduce the number of pools without reducing prediction power.
FRONTIERS IN GENETICS
(2022)
Review
Plant Sciences
Hilde Nybom, Gunars Lacis
Summary: Recent national and international projects have focused on large-scale genotyping of vegetatively propagated crops, aiming to identify true-to-type plant material, detect synonyms, investigate genetic diversity, and create sustainable databases for research and breeding. Different DNA markers and next-generation sequencing methods have their advantages and disadvantages, with large-scale phenotyping methods lagging behind but crucial for understanding commercially important traits. Collaborative projects with broad-scale data collection are likely to produce more reliable results in the analysis of gene action and development of robust DNA markers.
Article
Oncology
Shota Nishitani, Takashi X. Fujisawa, Akiko Yao, Shinichiro Takiguchi, Akemi Tomoda
Summary: The pooled sample method is effective in replicating methylation levels and can be used for epigenomic studies. However, it fails to replicate statistical results for individual samples. Therefore, the method should be combined with candidate gene analyses and its advantages and disadvantages should be carefully considered.
CLINICAL EPIGENETICS
(2023)
Article
Agronomy
Muhammad Massub Tehseen, Yaojie Zheng, Nathan A. Wyatt, Melvin D. Bolton, Shengming Yang, Steven S. Xu, Xuehui Li, Chenggen Chu
Summary: A STARP marker system was developed to enable the allelic discrimination of SNPs in sugarbeet plants using both fluorescence signals and traditional gel electrophoresis. The system is particularly useful for crops with strong background signal noise during PCR reactions and has potential applications in other plant species.
Article
Genetics & Heredity
Michele Ragazzo, Giulio Puleri, Valeria Errichiello, Laura Manzo, Laura Luzzi, Saverio Potenza, Claudia Strafella, Cristina Peconi, Fabio Nicastro, Valerio Caputo, Emiliano Giardina
Summary: The study evaluated a custom plate of OpenArray (TM) technology for testing 60 SNPs validated for predicting eye color, hair color, skin pigmentation, and personal identification. The technology showed high concordance rates, good sensitivity to different DNA concentrations, and high accuracy in human identification.
Article
Biochemistry & Molecular Biology
Marion Sinclair-Waters, Nikolai Piavchenko, Annukka Ruokolainen, Tutku Aykanat, Jaakko Erkinaro, Craig R. Primmer
Summary: Efforts to understand the genetic basis of phenotypic variation in molecular ecology are increasing. In Atlantic salmon, a study utilizing natural recombination between two candidate genes, vgll3 and akap11, found strong association between vgll3 single nucleotide polymorphisms (SNPs) and early maturation, while little or no association was found with akap11 SNPs. This suggests vgll3 as the primary candidate gene influencing early maturation.
Article
Biochemistry & Molecular Biology
Alexandra M. Sparks, Susan E. Johnston, Ian Handel, Jill G. Pilkington, Jacqueline Berry, Josephine M. Pemberton, Daniel H. Nussey, Richard J. Mellanby
Summary: This study reveals that vitamin D levels in wild Soay sheep are genetically influenced and positively associated with female survival and fecundity. It provides evidence for the potential response of vitamin D levels to natural selection and offers new insights into the association between vitamin D metabolism and fitness in wild environments.
Article
Biology
Petri T. Niemela, Ines Klemme, Anssi Karvonen, Pekka Hyvarinen, Paul Debes, Jaakko Erkinaro, Marion Sinclair-Waters, Victoria L. Pritchard, Laura S. Harkonen, Craig R. Primmer
Summary: Research shows that there are differences in activity expression among Atlantic salmon life-history genotypes. The vgll3*E allele is associated with increased activity in females, while the vgll3*L allele is associated with increased activity in males. These sex-dependent effects may contribute to maintaining genetic life-history variation within populations.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Endocrinology & Metabolism
Ehsan Pashay Ahi, Marion Sinclair-Waters, Jacqueline Moustakas-Verho, Shadi Jansouz, Craig R. Primmer
Summary: Age at maturity is important for diversity in life history strategies among organisms, but the factors leading to variations in maturation timing are poorly understood. Previous research has found a strong association between different alleles of the vgll3 gene and maturation timing in Atlantic salmon. This study provides evidence for the strong vgll3 genotype-dependent transcriptional regulation of reproductive axis genes prior to sexual maturation.
GENERAL AND COMPARATIVE ENDOCRINOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Ehsan Pashay Ahi, Marion Sinclair-Waters, Iikki Donner, Craig R. Primmer
Summary: Age at maturity is an important life history trait influenced by genetic and environmental factors. The maturation process and timing in Atlantic salmon is regulated by gnrh3 and other factors, as it lacks the gnrh1 gene. Previous research has shown a strong association between vgll3 alleles and maturation timing. In this study, a gene regulatory network involving c-jun and sf1 in the pituitary was identified, suggesting a potential regulatory connection between vgll3 genotypes and these regulators.
COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY A-MOLECULAR & INTEGRATIVE PHYSIOLOGY
(2023)
Article
Ecology
Marion Sinclair-Waters, Torfinn Nome, Jing Wang, Sigbjorn Lien, Matthew P. Kent, Harald Saegrov, Bjorn Floro-Larsen, Geir H. Bolstad, Craig R. Primmer, Nicola J. Barson
Summary: This study investigates the mutational composition of sea age at maturation in Atlantic salmon and finds that the genetic architecture may involve multiple loci with simple alleles and a locus with potentially more complex alleles. It provides a useful multi-SNP framework for characterizing genetic variation underlying phenotypes in wild populations using sequencing data.
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
Biochemistry & Molecular Biology
Ashok Aspatwar, Alessandro Bonardi, Heidi Aisala, Ksenia Zueva, Craig R. Primmer, Jaakko Lumme, Seppo Parkkila, Claudiu T. Supuran
Summary: The inhibitory effects of a beta-class carbonic anhydrase (CA) from the fish parasite Gyrodactylus salaris were investigated. Several effective inhibitors were identified, including simple heterocyclic sulphonamides and clinically used agents. This preliminary investigation provides insights into the inhibition profile of the parasite enzyme and potential development of more effective and selective inhibitors.
JOURNAL OF ENZYME INHIBITION AND MEDICINAL CHEMISTRY
(2023)
Article
Fisheries
Katja S. Maamela, Eirik R. Asheim, Paul V. Debes, Andrew H. House, Jaakko Erkinaro, Petra Liljestrom, Craig R. Primmer, Kenyon B. Mobley
Summary: The environment, including temperature and diet, affects reproductive traits in female fish. In this study, the effect of temperature and diet on maturation and egg traits in Atlantic salmon was investigated. A temperature difference of 2 degrees Celsius delayed maturation in female salmon, while a reduction in dietary energy content had no effect. Diet did not impact body size, condition, fecundity, egg size, or protein content, but a higher energy diet increased egg lipid content. These findings suggest that the nutritional quality of the female's diet can impact the energy provisioning of eggs and potentially affect the fitness of offspring.
JOURNAL OF FISH BIOLOGY
(2023)
Editorial Material
Biology
Susan E. E. Johnston, Nancy Chen, Emily B. B. Josephs
Summary: This editorial provides an overview of the history of wild quantitative genetic and genomic studies, discusses the main themes in the papers published in this special issue, and highlights the future outlook of this dynamic field.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Genetics & Heredity
Julie Gauzere, Josephine M. Pemberton, Jon Slate, Alison Morris, Sean Morris, Craig A. Walling, Susan E. Johnston
Summary: This study re-evaluates the genetic architecture of birth weight in wild red deer using genomic approaches. The results show that most of the genetic variation in birth weight is controlled by genes with small effects, contradicting previous studies that reported loci with large effects. This suggests a highly polygenic architecture for this trait.
G3-GENES GENOMES GENETICS
(2023)
Article
Biodiversity Conservation
Eirik R. asheim, Paul Debes, Andrew House, Petra Liljestrom, Petri T. Niemela, Jukka P. Siren, Jaakko Erkinaro, Craig R. Primmer
Summary: Age at maturity in Atlantic salmon is greatly influenced by temperature and an age-at-maturity gene. The effect of temperature differs between populations, but the gene has a similar effect in both temperatures and populations. Age at maturity is important for population structures and involves a trade-off between survival risk and reproductive investment.
CONSERVATION PHYSIOLOGY
(2023)
Article
Ecology
Anna M. Hewett, Martin A. Stoffel, Lucy Peters, Susan E. Johnston, Josephine M. Pemberton
Summary: The distribution of runs of homozygosity (ROH) in a wild population of red deer is shaped by selection, recombination, and population history. Population history and local recombination rate have been found to have an effect on ROH distribution by comparing populations and using different map types. Genetic drift resulting from a historical population bottleneck is the most likely cause of the observed ROH distribution in this population, with selection possibly playing a minor role.
Article
Biology
Andrew H. House, Paul V. Debes, Johanna Kurko, Jaakko Erkinaro, Craig R. Primmer
Summary: Organisms utilize resource allocation strategies to adapt to seasonal changes and life stage transitions. A transcription cofactor, vgll3, has been found to have an impact on maturation timing and body condition in mice and juvenile salmon. This study investigates the influence of larval and juvenile temperatures, vgll3 genotype, and their interactions with body condition and maturation rate in Atlantic salmon. The results suggest that vgll3 influences resource allocation strategies, with early maturing individuals having a higher maturation rate and body condition in the spring.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Review
Genetics & Heredity
Kathrin Theissinger, Carlos Fernandes, Giulio Formenti, Iliana Bista, Paul R. Berg, Christoph Bleidorn, Aureliano Bombarely, Angelica Crottini, Guido R. Gallo, Jose A. Godoy, Sissel Jentoft, Joanna Malukiewicz, Alice Mouton, Rebekah A. Oomen, Sadye Paez, Per J. Palsboll, Christophe Pampoulie, Maria J. Ruiz-Lopez, Simona Secomandi, Hannes Svardal, Constantina Theofanopoulou, Jan de Vries, Ann-Marie Waldvogel, Guojie Zhang, Erich D. Jarvis, Miklos Balint, Claudio Ciofi, Robert M. Waterhouse, Camila J. Mazzoni, Jacob Hoglund
Summary: The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts. Reference genomes play a key role in facilitating biodiversity research and conservation. Integrating the use of reference genomes as a best practice in conservation genomics is essential.
TRENDS IN GENETICS
(2023)