Article
Agronomy
Qian You, Sushma Sood, Ziliang Luo, Hongbo Liu, Md Sariful Islam, Muqing Zhang, Jianping Wang
Summary: The study aimed to identify quantitative trait loci (QTL) associated with sugarcane ratoon stunting disease (RSD) resistance and develop molecular markers for marker-assisted breeding. A total of 23 QTL associated with RSD resistance were identified, along with 82 disease resistance genes. GACD V.1.2 was found to be more efficient in QTL analysis than IciMapping V.3.3 in clonal species.
Article
Biochemistry & Molecular Biology
Eniko Szep, Barbora Trubenova, Katalin Csillery
Summary: This study used spatially explicit coalescence simulations to explore the properties of genetic diversity distribution and genetic divergence between populations, finding that F-ST mainly depends on recent demography and genetic diversity is dependent on the distant past. Factors such as simulation time compared to effective deme size and spatio-temporal autocorrelation across the grid may cause deviations from theoretical expectations.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Agronomy
Francesca Taranto, Ermanno Di Serio, Monica Marilena Miazzi, Stefano Pavan, Sergio Saia, Pasquale De Vita, Nunzio D'Agostino
Summary: This study aims to analyze the genetic variation patterns of two large germplasm collections of Timilia and Russello durum wheat landraces using SNP genotyping. The results showed that there are two genetic groups of Russello associated with different geographical areas in Sicily, which differ in important traits related to gluten quality and adaptation. Meanwhile, Timilia landraces have undergone conservative selection despite their wide genetic variation, likely associated with their distinctive traits. This study provides a foundation for further exploration of the genetic diversity in Sicilian landraces and emphasizes the importance of considering intra-population genetic diversity when registering conservation varieties in national crop registers.
Article
Multidisciplinary Sciences
Buddhika A. Dahanayaka, Anke Martin
Summary: In recent years, multi-parental mapping populations (MPPs) have been widely used to detect genomic regions associated with host-pathogenic interactions in many crops. This study reports the first use of multi-parental nested association mapping (MP-NAM) population to detect QTLs in haploid fungal pathogens. The results show that MP-NAM populations have greater power of QTL detection compared to bi-parental mapping populations.
SCIENTIFIC REPORTS
(2023)
Article
Genetics & Heredity
Logan S. Whitehouse, Daniel R. Schrider
Summary: Timesweeper is a convolutional neural network-based tool that can identify selective sweeps using continuous genomic time-series data. It demonstrates that more accurate inferences about natural selection can be made using genomic time-series data.
Article
Plant Sciences
Waltram Ravelombola, Ainong Shi, Bao-Lam Huynh
Summary: Large phenotypic variation in drought tolerance indices was observed among cowpea genotypes in the MAGIC population. A total of 14, 18, 5, 5, and 35 SNPs were associated with different traits related to drought tolerance. The network-guided approach revealed clear interactions between loci associated with drought tolerance traits, and genomic selection yielded varying levels of accuracy.
HORTICULTURE RESEARCH
(2021)
Review
Biotechnology & Applied Microbiology
Jeremy R. Shearman
Summary: A chromosome segment substitution line population was developed, and QTL related to drought stress were mapped. The introduced chromosome segments showed yield traits under drought stress.
Article
Ecology
Priscila M. Salloum, Anna W. Santure, Shane D. Lavery, Pierre de Villemereuil
Summary: Genome scans are powerful tools to understand genetic adaptation to future environmental conditions. However, low gene flow and population structure can lead to errors in these scans. This study compared different methods and identified candidate loci associated with environmental factors in a marine mollusc. The results highlight the importance of careful statistical controls in genome scans and suggest that further research is needed to determine the potential of non-model species to adapt to future environments.
JOURNAL OF ANIMAL ECOLOGY
(2022)
Article
Plant Sciences
Buddhika A. Dahanayaka, Lisle Snyman, Niloofar Vaghefi, Anke Martin
Summary: This study identified quantitative trait loci (QTL) associated with virulence and leaf symptoms in the net blotches caused by Pyrenophora teres. The accumulation of QTL in hybrid isolates may result in enhanced virulence.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Genetics & Heredity
Sneha Chakraborty, Bruce Rannala
Summary: The identification of individuals with recent hybrid ancestry has been a long-standing goal for researchers. Existing methods for hybrid inference do not take into account the linkage disequilibrium, resulting in inaccurate identification of hybrid ancestry. In this study, the authors develop a new method, Mongrail, that explicitly models linkage and recombination for more accurate identification of hybrid genealogical classes. The method is validated using simulated data and genome sequence data for hybridizing species of owls.
Article
Genetics & Heredity
Kevin M. Bowling, Michelle L. Thompson, David E. Gray, James M. J. Lawlor, Kelly Williams, Kelly M. East, Whitley V. Kelley, Irene P. Moss, Devin M. Absher, E. Christopher Partridge, Anna C. E. Hurst, Jeffrey C. Edberg, Gregory S. Barsh, Bruce R. Korf, Gregory M. Cooper
Summary: In AGHI, an array-based process has been implemented to screen for highly penetrant genetic variants in actionable disease genes. The study demonstrates the necessity for clinical validation of array-identified variants in direct-to-consumer or population testing, especially for diverse populations.
GENETICS IN MEDICINE
(2021)
Article
Fisheries
Rajesh Joshi, Diones Bender Almeida, Arthur Roberto da Costa, Anders Skaarud, Ulisses de Padua Pereira, Tim M. Knutsen, Thomas Moen, Alejandro Tola Alvarez
Summary: The Nile tilapia is the most important species in freshwater aquaculture globally, with the global market expected to reach $25 billion by the end of 2028. Genetic parameters for resistance to Francisellosis in Nile tilapia were estimated in this study, with moderate to high heritabilities found. The study showed that genomic models, especially Bayesian models, significantly increased predictive ability for resistance to Francisellosis in commercial breeding programs.
Article
Biodiversity Conservation
Veronica Mendoza-Portillo, Francisco J. Garcia-De Leon, Sophie von Der Heyden
Summary: In this study, the researchers examined the genetic diversity and population structure of the Almaco jack and found that climate change and fishing pressure can negatively impact the species' geographic distribution and genomic diversity. The loss of genomic diversity in the eastern-central Pacific Ocean can have significant effects on fisheries that rely on this resource.
GLOBAL CHANGE BIOLOGY
(2023)
Article
Nutrition & Dietetics
Qi Shao, Jing Li, Yiling Wu, Xing Liu, Na Wang, Yonggen Jiang, Qi Zhao, Genming Zhao
Summary: The purpose of this research was to evaluate the accuracy and predictive value of lipid accumulation product (LAP) in identifying metabolic syndrome (MS) in the general Chinese population compared with other obesity indicators. The study found that LAP is a more accurate predictor of MS in China.
Article
Pharmacology & Pharmacy
Junjun Mao, Qing Li, Pei Li, Weiwei Qin, Bobin Chen, Mingkang Zhong
Summary: This study assessed the predictability of published methotrexate (MTX) population pharmacokinetic (popPK) models and analyzed the potential risk factors for delayed MTX elimination. The results showed that the current published models are not reliable for cross-center use and that elderly patients and those with renal dysfunction and hypoalbuminemia are at higher risk of delayed elimination.
FRONTIERS IN PHARMACOLOGY
(2022)
Review
Genetics & Heredity
James M. Alfieri, Guosong Wang, Michelle M. Jonika, Clare A. Gill, Heath Blackmon, Giridhar N. Athrey
Summary: Single-cell sequencing has revolutionized our understanding of cell diversity, organizational connections, and genotype-phenotype relationships. While most research has been focused on model organisms, applying this technology to non-model organisms can uncover new insights that are inaccessible using traditional model organisms.
Article
Multidisciplinary Sciences
Johnathan Lo, Heath Blackmon
Summary: This study examines the correlation between retrogene survival and changes in genetic linkage. The results suggest that selection on linkage may not be a significant factor in retrogene survival overall, but it might still play a role in the survival of specific retrogenes.
Article
Biology
Nazila Koochekian, Alfredo Ascanio, Keaka Farleigh, Daren C. Card, Drew R. Schield, Todd A. Castoe, Tereza Jezkova
Summary: This study investigates the chromosomal structure and composition of the desert horned lizard genome and compares it to genomes of other reptiles. The results indicate dynamic karyotypic evolution across reptiles, with frequent splits, fusions, and rearrangements of chromosomal blocks between macrochromosomes and microchromosomes. The study also provides evidence for distinct gene content and chromosomal structure between microchromosomes and macrochromosomes within reptiles.
Editorial Material
Ecology
Michelle M. Jonika, James M. Alfieri, Terrence Sylvester, Andrew Riley Buhrow, Heath Blackmon
Article
Ecology
Magnolia W. Morelli, Heath Blackmon, Carl E. Hjelmen
Summary: Karyotypes and chromosome data have been widely used in biology, but are often scattered and difficult to access. Researchers have built two datasets for true flies, providing a public database resource for exploring karyotypes.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2022)
Review
Ecology
Katie E. Lotterhos, Matthew C. Fitzpatrick, Heath Blackmon
Summary: The fields of ecology, evolution, and systematics lack standardized principles for evaluating methods, leading to inconsistencies in method testing, ambiguity in limitations, and the risk of misapplication. This review highlights common pitfalls, the benefits of testing methods with simulated data, and best practices for method evaluations. It emphasizes the difference between evaluation and validation and discusses the strengths and limitations of different evaluation metrics.
ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS
(2022)
Article
Evolutionary Biology
Drew R. Schield, Blair W. Perry, Daren C. Card, Giulia I. M. Pasquesi, Aundrea K. Westfall, Stephen P. Mackessy, Todd A. Castoe
Summary: After recombination suppression, sex chromosomes diverge and develop differential sex-linkage, resulting in the presence of degenerated Y and W chromosomes in one sex. This study characterizes the structure and gene content of the female-specific W chromosome in the prairie rattlesnake, revealing a high degree of repetition and enrichment of retroviral sequences. The W chromosome is specialized for reproductive and developmental functions since recombination suppression.
GENOME BIOLOGY AND EVOLUTION
(2022)
Article
Cell Biology
Jacqueline Smith, James M. Alfieri, Nick Anthony, Peter Arensburger, Giridhar N. Athrey, Jennifer Balacco, Adam Balic, Philippe Bardou, Paul Barela, Yves Bigot, Heath Blackmon, Pavel M. Borodin, Rachel Carroll, Meya C. Casono, Mathieu Charles, Hans Cheng, Maddie Chiodi, Lacey Cigan, Lyndon M. Coghill, Richard Crooijmans, Neelabja Das, Sean Davey, Asya Davidian, Fabien Degalez, Jack M. Dekkers, Martijn Derks, Abigail B. Diack, Appolinaire Djikeng, Yvonne Drechsler, Alexander Dyomin, Olivier Fedrigo, Steven R. Fiddaman, Giulio Formenti, Laurent A. F. Frantz, Janet E. Fulton, Elena Gaginskaya, Svetlana Galkina, Rodrigo A. Gallardo, Johannes Geibel, Almas Gheyas, Cyrill John P. Godinez, Ashton Goodell, Jennifer A. M. Graves, Daren K. Griffin, Bettina Haase, Jian-Lin Han, Olivier Hanotte, Lindsay J. Henderson, Zhuo-Cheng Hou, Kerstin Howe, Lan Huynh, Evans Ilatsia, Erich Jarvis, Sarah M. Johnson, Jim Kaufman, Terra Kelly, Steve Kemp, Colin Kern, Jacob H. Keroack, Christophe Klopp, Sandrine Lagarrigue, Susan J. Lamont, Margaret Lange, Anika Lanke, Denis M. Larkin, Greger Larson, John King N. Layos, Ophelie Lebrasseur, Lyubov P. Malinovskaya, Rebecca J. Martin, Maria Luisa Martin Cerezo, Andrew S. Mason, Fiona M. McCarthy, Michael J. McGrew, Jacquelyn Mountcastle, Christine Kamidi Muhonja, William Muir, Kevin Muret, Terence Murphy, Ismael Ng'ang'a, Masahide Nishibori, Rebecca E. O'Connor, Moses Ogugo, Ron Okimoto, Ochieng Ouko, Hardip R. Patel, Francesco Perini, Maria Ines Pigozzi, Krista C. Potter, Peter D. Price, Christian Reimer, Edward S. Rice, Nicolas Rocos, Thea F. Rogers, Perot Saelao, Jens Schauer, Robert Schnabel, Valerie Schneider, Henner Simianer, Adrian Smith, Mark P. Stevens, Kyle Stiers, Christian Keambou Tiambo, Michele Tixier-Boichard, Anna A. Torgasheva, Alan Tracey, Clive A. Tregaskes, Lonneke Vervelde, Ying Wang, Wesley C. Warren, Paul D. Waters, David Webb, Steffen Weigend, Anna Wolc, Alison E. Wright, Dominic Wright, Zhou Wu, Masahito Yamagata, Chentao Yang, Zhong-Tao Yin, Michelle C. Young, Guojie Zhang, Bingru Zhao, Huaijun Zhou
CYTOGENETIC AND GENOME RESEARCH
(2023)
Article
Ecology
James M. Alfieri, Taryn Johnson, Anna Linderholm, Heath Blackmon, Giridhar N. Athrey
Summary: This study sequenced the DNA of a suspected bird hybrid and confirmed its parentage through analysis. Although the hybrid is not between Numida meleagris and Penelope superciliaris, it still represents the most diverged avian hybrid confirmed with genetic data.
ECOLOGY AND EVOLUTION
(2023)
Article
Genetics & Heredity
James M. Alfieri, Michelle M. Jonika, Jennifer N. Dulin, Heath Blackmon
Summary: In this article, the authors synthesized data from thousands of insect species and used biologically realistic models to infer the tempo and mode of chromosome evolution among insect orders. The results showed significant variation in the rate and pattern of chromosome number evolution among different orders. These findings have important implications for understanding speciation and guiding future genome sequencing studies.
Article
Genetics & Heredity
Daren C. Card, Andrew G. Van Camp, Trenten Santonastaso, Michael I. Jensen-Seaman, Nicola M. Anthony, Scott V. Edwards
Summary: The study identified the core MHC genomic region in two squamate species and revealed similarities and differences in the genomic structure and composition of MHC regions between squamates and mammals. The investigation also highlighted unique features of the anole MHC, such as higher proportions of DNA transposons and larger MHC region size. Evolutionary analyses of MHC homologs in squamates and other amniotes demonstrated species-specific relationships and functional relevance of certain codons under diversifying selection.
FRONTIERS IN GENETICS
(2022)
Review
Agriculture, Dairy & Animal Science
Daren C. Card, W. Bryan Jennings, Scott V. Edwards
Summary: Non-avian reptiles, especially squamate reptiles (lizards and snakes), have become the most species-rich group among tetrapods, surpassing birds. However, genomic resources in non-avian reptiles have been accumulating at a slower pace compared to mammals and birds. This review highlights the importance of studying the natural history, physical traits, genomic characteristics, and sequence compositional patterns of non-avian reptiles, as well as the need for high-quality genomic resources and methods to extract different markers from genome assemblies. The development of a comprehensive phylogenomic tree of life for non-avian reptiles and amniotes will contribute to a better understanding of biodiversity.
Article
Evolutionary Biology
James M. Alfieri, Reina Hingoranee, Giridhar N. Athrey, Heath Blackmon
Summary: This study investigates the impact of divergence time, domestication, and mismatches in morphology, habitat, and clutch size on reproductive isolation in hybridizing bird species. The findings suggest that divergence time and clutch size are significant predictors of reproductive isolation. Interestingly, domestication is also found to be related to reproductive compatibility after considering phylogeny and addressing potential biases.
JOURNAL OF HEREDITY
(2023)
Article
Biochemistry & Molecular Biology
Keaka Farleigh, Alfredo Ascanio, Mackenzie E. Farleigh, Drew R. Schield, Daren C. Card, Manuel Leal, Todd A. Castoe, Tereza Jezkova, Javier A. Rodriguez-Robles
Summary: The study found different patterns of differential introgression in hybrids of Caribbean anoles, with pulchellus-derived alleles dominating in the hybrids. A. krugi loci in hybrids exhibited a signal of non-random differential introgression, which was linked to genes involved in development and immune function.
Correction
Evolutionary Biology
Drew R. Schield, Blair W. Perry, Daren C. Card, Giulia I. M. Pasquesi, Aundrea K. Westfall, Stephen P. Mackessy, Todd A. Castoe
GENOME BIOLOGY AND EVOLUTION
(2022)
