Article
Multidisciplinary Sciences
Sarah L. Chang, Hillary G. M. Ward, Michael A. Russello
Summary: Differentiating life history variants is crucial for fisheries management, especially in mixed-stock fisheries where traditional survey methods may not be accurate. A study developed a GT-seq panel with 288 targeted SNPs to accurately identify kokanee stock in British Columbia, Canada, achieving high self-assignment accuracy and perfect assignment to geographic basin, migratory form, and reproductive ecotype. The GT-seq panel was successfully applied to Wood Lake, demonstrating high concordance with previous assignments and scalability for future applications.
Article
Agriculture, Dairy & Animal Science
Valentino Palombo, Elena De Zio, Giovanna Salvatore, Stefano Esposito, Nicolaia Iaffaldano, Mariasilvia D'Andrea
Summary: The study assessed the fine-scale genetic structure of Mediterranean trout in two main rivers in Molise region, Italy, using the Affymetrix 57K rainbow-trout-derived SNP array. Results showed that the SNP array can successfully be used for Mediterranean trout genotyping, revealing a fine-scale genetic structure in the populations to support conservation and management actions, including selection of candidate sites for collecting adults and eradication of alien trout.
Article
Ecology
Glaucia Del-Rio, Marco A. Rego, Bret M. Whitney, Fabio Schunck, Luis F. Silveira, Brant C. Faircloth, Robb T. Brumfield
Summary: The study investigates the formation of hybrid zones between two obligate army-ant-followers, the White-breasted Antbird and the Harlequin Antbird, in the Amazon Basin. Major geographic displacement between mitochondrial and nuclear clines was observed, with potential causes including sampling error, genetic drift, and asymmetric cytonuclear incompatibilities. Data indicates expansion and unidirectional introgression of one species into the distribution of the other.
Article
Biochemistry & Molecular Biology
Peter T. Euclide, Wesley A. Larson, Yue Shi, Kristen Gruenthal, Kris A. Christensen, Jim Seeb, Lisa Seeb
Summary: This study used whole genome resequencing to identify 64 islands of divergence in sockeye salmon, with 16 clustered in four genomic regions shared by two isolated populations. These islands were created by a variety of mechanisms, including structural and non-structural variation. The differentiation at these islands did not consistently correlate with established population attributes.
Article
Biotechnology & Applied Microbiology
Adela Noskova, Meenu Bhati, Naveen Kumar Kadri, Danang Crysnanto, Stefan Neuenschwander, Andreas Hofer, Hubert Pausch
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.
Article
Multidisciplinary Sciences
Christopher Setzke, Carmen Wong, Michael A. Russello
Summary: Historical DNA analysis of archival samples has been used to reconstruct population history and inform conservation management. GT-seq was demonstrated as an effective tool for collecting genome-wide data from archival samples, revealing genetic distinctiveness and biodiversity loss in a study of kokanee salmon in Canada.
SCIENTIFIC REPORTS
(2021)
Article
Plant Sciences
Juan Ma, Yanyong Cao, Yanzhao Wang, Yong Ding
Summary: A low-density genotyping platform containing 5.5K SNP markers was successfully developed in maize using genotyping by target sequencing (GBTS) technology. The platform was validated in two maize populations, showing average polymorphic information content and genetic diversity values ranging from 0.27 to 0.38. The platform demonstrated potential for genetic and molecular breeding studies.
FRONTIERS IN PLANT SCIENCE
(2022)
Review
Genetics & Heredity
Jonathan Downing, Lloyd D'Orsogna
Summary: Killer immunoglobulin-like receptors (KIR) regulate natural killer cell function through interactions with ligands on cell surfaces. High-resolution determination of KIR allele variation has the potential to optimize clinical outcomes and provide deeper insights into receptor-ligand interactions. This review discusses recently published high-resolution KIR genotyping methods and their application in transplantation and infectious disease control.
Article
Biochemistry & Molecular Biology
David Criado Ruiz, Irene Villa Machio, Alberto Herrero Nieto, Gonzalo Nieto Feliner
Summary: The understanding of the role of reticulation in phylogenetic inquiry has improved with the use of high throughput sequencing data. Despite this, unraveling old hybridization events remains a challenge due to the dynamism of genomes over evolutionary time. Through SNP data and Sanger sequences, a cryptic species was unexpectedly discovered within Phalacrocarpum oppositifolium subsp. anomalum, and a recent undocumented hybrid zone was identified in conflictive populations. The study suggests that old hybridization events may be compromised by subsequent evolutionary processes, especially in areas with a history of climatic instability.
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Joshua P. Jahner, Thomas L. Parchman, Marjorie D. Matocq
Summary: Analysis of genetic data from two ecologically distinct mammals in a hybrid zone in southern California shows that hybrids are rare and consist mostly of F-1 individuals and multigenerational backcrosses. More than half of loci show elevated introgression from one genetic background to the other, although introgression is not associated with measures of divergence and loci with extreme divergence values are not near detoxification enzymes related to woodrat dietary specialization.
Article
Evolutionary Biology
Carly F. Graham, Rebecca L. Eberts, Una Goncin, Christopher M. Somers
Summary: Anthropogenic activities may facilitate undesirable hybridization and genomic introgression between fish species. The study found potentially high levels of genomic introgression between walleye and sauger in Saskatchewan reservoirs, highlighting the importance of caution in using these populations in stocking programs. GBS offers a powerful tool for examining hybridization without preidentification of informative loci, addressing key challenges associated with other marker types.
EVOLUTIONARY APPLICATIONS
(2021)
Article
Pathology
J. Lippert, S. Bonlokke, A. Utke, B. R. Knudsen, B. S. Sorensen, T. Steiniche, M. Stougaard
Summary: The study demonstrates that targeted NGS is effective in detecting and genotyping HPV in both FFPE biopsies and plasma samples. This method provides early diagnosis and prognosis for cervical cancer progression, enhancing recovery and survival potential for patients.
EXPERIMENTAL AND MOLECULAR PATHOLOGY
(2021)
Article
Plant Sciences
Su-Kui Jin, Li-Na Xu, Qing-Qing Yang, Ming-Qiu Zhang, Shui-Lian Wang, Ruo-An Wang, Tao Tao, Lian-Min Hong, Qian-Qian Guo, Shu-Wen Jia, Tao Song, Yu-Jia Leng, Xiu-Ling Cai, Ji-Ping Gao
Summary: In this study, high-resolution QTL mapping was conducted to identify the genetic regions responsible for rice grain quality traits. A total of 15 QTLs were identified, including one overlapping with previously reported QTLs and the others being novel. These findings will facilitate the fine mapping and pyramiding of these QTLs, leading to genetic improvement of rice grain quality.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Genetics & Heredity
Andreas Tillmar, Kimberly Sturk-Andreaggi, Jennifer Daniels-Higginbotham, Jacqueline Tyler Thomas, Charla Marshall
Summary: The FORCE panel is an all-in-one SNP panel designed for forensic applications, containing common, relevant SNPs as well as a novel set of autosomal SNPs for extended kinship analysis. Evaluation using five WWII cases showed that the panel can predict relationships with strong statistical support.
Article
Genetics & Heredity
Deepali Vasoya, Thomas Tzelos, Lindert Benedictus, Anna Eleonora Karagianni, Scott Pirie, Celia Marr, Charlotta Oddsdottir, Constanze Fintl, Timothy Connelley
Summary: In this study, a MiSeq-based approach was developed and applied to analyze the expressed MHCI and MHCII repertoires in Thoroughbred, Icelandic, and Norwegian Fjord Horses. The results showed limited overlap in MHCI and MHCII haplotypes between different breeds, indicating diverse MHC repertoire among genetically divergent breeds. This study provided novel insights into the structure of the expressed equine MHC repertoire and highlighted unique features of the MHC in horses.
Article
Multidisciplinary Sciences
Sarah L. Chang, Hillary G. M. Ward, Michael A. Russello
Summary: Differentiating life history variants is crucial for fisheries management, especially in mixed-stock fisheries where traditional survey methods may not be accurate. A study developed a GT-seq panel with 288 targeted SNPs to accurately identify kokanee stock in British Columbia, Canada, achieving high self-assignment accuracy and perfect assignment to geographic basin, migratory form, and reproductive ecotype. The GT-seq panel was successfully applied to Wood Lake, demonstrating high concordance with previous assignments and scalability for future applications.
Article
Environmental Sciences
Sarah L. Chang, Who-Seung Lee, Stephan B. Munch
Summary: Climate change is rapidly altering the thermal environment in terrestrial and aquatic systems, and transgenerational thermal plasticity may help mitigate its effects. Research on sheepshead minnow offspring growth rates found that they were influenced by direct temperature exposure, parental temperatures, and were highest when all temperatures matched. The study suggests that thermal TGP has an epigenetic basis contributed by both parents.
FRONTIERS IN MARINE SCIENCE
(2021)
Article
Ecology
Thais A. Bernos, Sarah L. L. Chang, Rachael M. M. Giglio, Kaeli Davenport, Jeff Fisher, Erin Lowery, Andrew Bearlin, Ryan Simmons, Marie-Josee Fortin, Casey C. C. Day, Erin L. L. Landguth
Summary: This study investigated the influence of female mating preference, sneaker-specific mortality, and variation in age-at-maturity on the persistence of distinct alternative mating strategies in bull trout. The results showed that without other selective mechanisms, strong female preference for mating with territorial males and differences in reproductive lifespan allow the stable coexistence of distinct alternative mating strategies.
ECOLOGY AND EVOLUTION
(2023)