Article
Biochemical Research Methods
Dat Thanh Nguyen, Quan Hoang Nguyen, Nguyen Thuy Duong, Nam S. Vo
Summary: Despite the advancement of sequencing technology, SNP arrays remain the most cost-effective genotyping solution for large-scale genomic research. This study introduces a novel method called LmTag for tag SNP selection, which improves imputation performance and prioritizes highly functional SNP markers. It is particularly suitable for under-represented populations and non-model species in developing countries.
BRIEFINGS IN BIOINFORMATICS
(2022)
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
Biochemistry & Molecular Biology
Colin Jackson, Nanette Christie, Sharon Melissa Reynolds, Gerhard C. Marais, Yokateme Tii-kuzu, Madison Caballero, Tamanique Kampman, Erik A. Visser, Sanushka Naidoo, Dominic Kain, Ross W. Whetten, Fikret Isik, Jill Wegrzyn, Gary R. Hodge, Juan J. Acosta, Alexander A. Myburg
Summary: This study focused on gene and genome targeted SNP discovery to develop a genome-wide, multispecies genotyping array for tropical pines. The developed Pitro50K SNP chip will be valuable for population genomics and molecular breeding in a group of pine species, which represent the majority of fast-growing tropical and subtropical pine plantations globally.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Agronomy
Guangning Yu, Yanru Cui, Yuxin Jiao, Kai Zhou, Xin Wang, Wenyan Yang, Yiyi Xu, Kun Yang, Xuecai Zhang, Pengcheng Li, Zefeng Yang, Yang Xu, Chenwu Xu
Summary: Genomic selection (GS) is a powerful tool for improving genetic gain in maize breeding, but its widespread use is limited by the high cost of genotyping platforms. This study compared the predictabilities of four agronomic traits in maize hybrids using three different genotyping platforms: genotyping by sequencing (GBS), a 40K SNP array, and target sequence capture (TSC). The GBS marker dataset yielded the highest predictabilities, followed by TSC and SNP array datasets. Additionally, the study found that 1K SNPs were sufficient to achieve comparable predictabilities to 10K and all SNPs, and certain statistical models performed well while others performed poorly.
Article
Ecology
Macarena Blanco-Pimentel, Carly D. Kenkel, Sheila A. Kitchen, Johanna Calle-Trivino, Iliana B. Baums, Camilo Cortes-Useche, Megan K. Morikawa
Summary: Reef restoration efforts aim to enhance resilience by safeguarding the genetic diversity of coral populations. This study explores the use of a grafting method based on self-recognition phenomena to estimate genotypic diversity in Caribbean coral. The results show that this method is highly accurate and can be a powerful tool for assessing genetic diversity and tracking key traits in coral nurseries.
RESTORATION ECOLOGY
(2023)
Article
Plant Sciences
Thomas Nothnagel, Janine Koenig, Jens Keilwagen, Eva-Maria Graner, Joerg Plieske, Holger Budahn
Summary: An introgression breeding programme successfully transferred the virus resistance gene AV-1(pro) from the wild species Asparagus prostratus to the garden asparagus Asparagus officinalis. By overcoming crossing barriers and analyzing segregation, the location of the AV-1 resistance gene on Chromosome 2 in asparagus was identified. Further development of a diagnostic marker was initiated based on the genotyping data.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Fisheries
Pierre Boudry, Francois Allal, Muhammad L. Aslam, Luca Bargelloni, Tim P. Bean, Sophie Brard-Fudulea, Marine S. O. Brieuc, Federico C. F. Calboli, John Gilbey, Pierrick Haffray, Jean-Baptiste Lamy, Romain Morvezen, Catherine Purcell, Paulo A. Prodohl, Marc Vandeputte, Geoffrey C. Waldbieser, Anna K. Sonesson, Ross D. Houston
Summary: Selective breeding has been successfully utilized in improving profitability and sustainability of aquatic species, and the implementation of genomic selection aims to further predict breeding value. While the potential of genomic selection is evident, customized species-specific applications are necessary to maximize its benefits for the aquaculture sector.
AQUACULTURE REPORTS
(2021)
Review
Biochemistry & Molecular Biology
Pasquale Tripodi
Summary: This review examines the application of genomic technologies in studying the diversity of tomatoes, with a focus on next-generation sequencing strategies and methods. It also discusses how genomics has provided insights into the domestication process of tomatoes and presents perspectives on utilizing natural variation for breeding purposes through pan-genome construction and graphical pan-genome development.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Biotechnology & Applied Microbiology
Ran Wang, Siyuan Xing, Peter M. M. Bourke, Xiuquan Qi, Miaomiao Lin, Danny Esselink, Paul Arens, Roeland E. E. Voorrips, Richard G. F. Visser, Leiming Sun, Yunpeng Zhong, Hong Gu, Yukuo Li, Sikai Li, Chris Maliepaard, Jinbao Fang
Summary: Kiwifruit is a woody, perennial and deciduous vine with multiple ploidy levels. Despite the availability of genomic resources, SNP genotyping is still challenging due to different levels of polyploidy. In this study, a high-density SNP genotyping array was developed and evaluated for genetic studies and breeding applications in kiwifruit.
PLANT BIOTECHNOLOGY JOURNAL
(2023)
Article
Fisheries
Baltasar F. Garcia, Alvaro Bonaguro, Carolina Araya, Roberto Carvalheiro, Jose M. Yanez
Summary: The inclusion of genomic information has accelerated genetic gain in shrimp breeding. Evaluating LD decay is crucial for assessing the feasibility of genomic selection. A study using a 50K SNP array tool characterized genomic diversity and LD in a farmed shrimp population.
AQUACULTURE REPORTS
(2021)
Article
Agriculture, Dairy & Animal Science
Nora Laseca, Antonio Molina, Mercedes Valera, Alicia Antonini, Sebastian Demyda-Peyras
Summary: This study provides a detailed characterization of CNV regions in the Pura Raza Espanola horse breed, revealing a unique pattern of genomic regions enriched in CNVs and the incidence of CNVs across the entire genome. The study also identifies genes related to olfactory pathways and immune response. The findings contribute to our understanding of CNVs in equines and their impact on genetic and phenotypic variations.
Article
Forestry
Yu-Ming Lin, Mohammad Nasir Shalizi, Trevor D. D. Walker, Edwin Lauer, Claudio D. D. Carrasco, Krishna Reddy Gujjula, Haktan Suren, Fikret Isik
Summary: This study compared the efficiency of an Affymetrix genotyping array and a targeted genotyping-by-sequencing panel in estimating genomic relationships and detecting pedigree errors in a Pinus taeda population. The AgriSeq SNP markers were validated and showed a correlation of 0.90 with the Pita50K genotyping array. Inbreeding coefficients and genetic clustering analysis supported the reliability and cost-effectiveness of the AgriSeq platform for genotyping large numbers of P. taeda samples.
TREE GENETICS & GENOMES
(2023)
Article
Biochemistry & Molecular Biology
Julia Zaborowska, Bartosz Labiszak, Annika Perry, Stephen Cavers, Witold Wachowiak
Summary: This study identified highly adapted genomic regions in two closely related European pine species, contrasting them with a lowland relative. It also found candidate genes for altitude-dependent selection between mountain pines and lowland species, as well as outlier SNPs related to gene expression and metabolism between the two mountain pine species.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Carolina Bernhardsson, Yanjun Zan, Zhiqiang Chen, Par K. Ingvarsson, Harry X. Wu
Summary: This study introduces the design and performance of a 50K SNP genotyping array for Norway spruce, developed based on whole genome resequencing. The array shows high probe specificity, genetic accuracy, and an even coverage across the 12 linkage groups in Norway spruce. This high-quality genotyping array will serve as a valuable resource for genetic and genomic studies in Norway spruce as well as in other conifer species of the same genus.
MOLECULAR ECOLOGY RESOURCES
(2021)
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
Marine & Freshwater Biology
Sheila A. Kitchen, C. Cornelia Osborne, Nicole D. Fogarty, Iliana B. Baums
Summary: The study found that the morphology of Caribbean Acropora corals is not necessarily linked to their maternal species and cannot be predicted by mitochondrial haplogroups. Expert classification showed lower accuracy in identifying hybrids and A. palmata.
Article
Ecology
Lydia J. Baker, Hannah G. Reich, Sheila A. Kitchen, J. Grace Klinges, Hanna R. Koch, Iliana B. Baums, Erinn M. Muller, Rebecca Vega Thurber
Summary: This study investigated the infection and ecology of the symbiont Candidatus Aquarickettsia rohweri in threatened Acropora corals, finding that the infection magnitude is influenced by coral host and geographic location. Phylogenomic analysis showed clustering by geographic region, with positive selection observed in Florida populations due to greater nutrient stress. Aquarickettsia was not found to codiversify significantly with coral animal or algal symbiont, suggesting horizontal transmission as the likely route of infection.
Article
Biochemistry & Molecular Biology
Kathryn H. Stankiewicz, Kate L. Vasquez Kuntz, Iliana B. Baums
Summary: The traditional method Delta K for determining population structure may underestimate the true number of clusters and be sensitive to uneven sampling. Using a combination of different estimators is recommended for more accurate results, as relying on a single estimator may not be sufficient in determining the optimal number of clusters.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Plant Sciences
Emma F. Camp, Matthew R. Nitschke, David Clases, Raquel Gonzalez de Vega, Hannah G. Reich, Samantha Goyen, David J. Suggett
Summary: This study investigates the elementomes of diverse dinoflagellates within the Symbiodiniaceae family and explores how they are influenced by nutrient availability and elevated temperature. The results reveal unique elementomes among Symbiodiniaceae isolates, driven by differential micronutrients content, and a more homogenised elementome under elevated temperature conditions. The findings suggest that Symbiodiniaceae possess evolutionary conserved preferential elemental acquisition and may have a common elemental signature to warming.
Article
Entomology
Adrian Bruckner, Austen A. Barnett, Prashant Bhat, Igor A. Antoshechkin, Sheila A. Kitchen
Summary: The study presents a chromosome-level genome assembly of the oribatid mite species Archegozetes longisetosus, revealing patterns of reduced body segmentation and unexpected expression of eye development genes. The research also identifies species-specific expansion of gustatory receptors and the presence of horizontally transferred genes related to plant and fungal matter degradation. The study further elucidates the biosynthesis of monoterpenes in oribatid mites. The high-quality resources provided in this study will contribute to molecular research and a better understanding of chelicerate evolution.
Article
Biodiversity Conservation
Eslam O. Osman, Samuel A. Vohsen, Fanny Girard, Rafaelina Cruz, Orli Glickman, Lena M. Bullock, Kaitlin E. Anderson, Alexis M. Weinnig, Erik E. Cordes, Charles R. Fisher, Iliana B. Baums
Summary: This study investigates the reliance of coral species living near deep-sea cold seeps on chemosynthetically-derived food and the impact of proximity to cold seeps. The researchers find that some coral species utilize chemosynthetically derived food and that the restructuring of the microbiome community may aid corals in utilizing seepage-derived carbon.
GLOBAL CHANGE BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Sheila A. Kitchen, Duo Jiang, Saki Harii, Noriyuki Satoh, Virginia M. Weis, Chuya Shinzato
Summary: The study examines the effects of thermal stress and symbiosis onset on colonization dynamics, survival, metamorphosis, and gene expression in coral larvae. It finds that thermal stress decreases symbiont colonization and density, and influences larval survival and metamorphosis. The transcriptomic responses to colonization and thermal stress are mostly independent. Furthermore, host immune suppression turns to immune activation under heat stress. The study suggests that colonization may hinder larval survival and recruitment under projected climate scenarios.
Article
Multidisciplinary Sciences
Kate L. Vasquez Kuntz, Sheila A. Kitchen, Trinity L. Conn, Samuel A. Vohsen, Andrea N. Chan, Mark J. A. Vermeij, Christopher Page, Kristen L. Marhaver, Iliana B. Baums
Summary: The study reveals that somatic mutations in animals can be passed on to offspring, increasing genetic diversity and facilitating adaptation across generations.
Article
Biology
Hannah G. G. Reich, Emma F. F. Camp, Liza M. M. Roger, Hollie M. M. Putnam
Summary: This review explores the role of trace metals in the physiological performance and functional ecology of coral holobiont in oligotrophic environments. It emphasizes the importance of metal exchanges among holobiont partners and their contribution to partner compatibility, stress coping ability, and overall organismal fitness and distribution. The review also highlights the influence of abiotic factors and climate change on trace metal availability and the potential consequences for coral survival. Future research directions are suggested to further understand the impacts of trace metals on coral holobiont symbioses and nutrient cycling in coral ecosystems.
BIOLOGICAL REVIEWS
(2023)
Article
Multidisciplinary Sciences
Elise F. Keister, Shelby E. Gantt, Hannah G. Reich, Kira E. Turnham, Timothy G. Bateman, Todd C. LaJeunesse, Mark E. Warner, Dustin W. Kemp
Summary: Coral reefs worldwide are declining, but some populations in Palau, Micronesia are better adapted to survive in warmer and more acidic oceans. These coral populations can resist and recover from thermal stress better than their offshore counterparts. The difference in tissue biomass and energy reserves between the nearshore and offshore colonies may be explained by the increased metabolic demand of the warmer and more acidic nearshore environment. Despite the differences in symbiont species and prey availability, the lipid compositions of colonies from both habitats were similar. The regulation of colony biomass and energy reserves may be influenced by various factors, but they converge to a similar homeostatic set point under different environmental conditions.
SCIENTIFIC REPORTS
(2023)
Article
Microbiology
Immy A. Ashley, Sheila A. Kitchen, Lucy M. Gorman, Arthur R. Grossman, Clinton A. Oakley, David J. Suggett, Virginia M. Weis, Sabrina L. Rosset, Simon K. Davy
Summary: This study analyzed the phosphatidylinositol (PI) signaling pathway in the cnidarian-dinoflagellate symbiosis and found that it is conserved in symbiotic cnidarians and expanded in symbiotic dinoflagellates. The study also identified unique proteins in the symbiotic dinoflagellates that are not found in non-symbiotic unicellular organisms.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Ecology
Macarena Blanco-Pimentel, Carly D. Kenkel, Sheila A. Kitchen, Johanna Calle-Trivino, Iliana B. Baums, Camilo Cortes-Useche, Megan K. Morikawa
Summary: Reef restoration efforts aim to enhance resilience by safeguarding the genetic diversity of coral populations. This study explores the use of a grafting method based on self-recognition phenomena to estimate genotypic diversity in Caribbean coral. The results show that this method is highly accurate and can be a powerful tool for assessing genetic diversity and tracking key traits in coral nurseries.
RESTORATION ECOLOGY
(2023)
