Article
Plant Sciences
Kevin O. Chiteri, Talukder Zaki Jubery, Somak Dutta, Baskar Ganapathysubramanian, Steven Cannon, Arti Singh
Summary: This study investigates the root traits of 375 mung bean genotypes and identifies markers associated with important root-related traits. The findings have implications for the improvement and breeding of mung beans.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Agronomy
Joanna Dziurdziak, Grzegorz Gryziak, Jolanta Groszyk, Wieslaw Podyma, Maja Boczkowska
Summary: Spring barley landraces exhibit considerable genetic diversity, with distinct groups identified based on their country of origin and grain type. Heterogeneity in accessions may pose challenges for breeding, necessitating the establishment of special collections composed of pure lines accessible to breeders. Regions lacking genetic diversity have been pinpointed, while SNPs associated with traits related to grain weight and size in hulless forms could be valuable for breeding high-quality, health-promoting foods.
Article
Plant Sciences
Pavel Travnicek, Zuzana Chumova, Eliska Zaveska, Johana Hanzlickova, Lucie Kupkova (Jankolova), Jaromir Kucera, Eliska Gburova Stubnova, Ludmila Rejlova, Terezie Mandakova, Jan Ponert
Summary: Knowledge of population variation across species' ranges is crucial for understanding evolutionary history, taxonomy, and conservation strategies. In this study, the genus Neotinea was examined using various biosystematic methods, revealing four major lineages with distinct phenotypic variations. Relationships within the genus were identified, highlighting the importance of considering both morphological and phylogenetic data when delineating cryptic taxa among orchids.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biotechnology & Applied Microbiology
Lina Heistinger, Juliane C. Dohm, Barbara G. Paes, Daniel Koizar, Christina Troyer, Oezge Ata, Teresa Steininger-Mairinger, Diethard Mattanovich
Summary: By characterizing 25 natural isolates from all seven described Komagataella species, this study identified strains with differences in tolerance to high pH, high temperature, and growth on xylose. The genotypic and phenotypic diversity within this genus provides a basis for utilizing neglected Komagataella strains with interesting characteristics and understanding genetic determinants for improved growth and stress tolerance.
MICROBIAL CELL FACTORIES
(2022)
Review
Plant Sciences
Hao Tong, Zoran Nikoloski
Summary: Genomic selection utilizes machine learning and genotyping data to predict agronomically relevant phenotypic traits, thus reducing the reliance on phenotypic data and improving breeding efficiency. To further improve genomic selection, it is necessary to collect intermediate phenotype data and develop modeling techniques, while also considering the transferability of models between different environments.
JOURNAL OF PLANT PHYSIOLOGY
(2021)
Article
Microbiology
Alexandre Nicolas, Julie Migraine, Jacques Dutrieux, Maud Salmona, Alexandra Tauzin, Atsuko Hachiya, Jerome Estaquier, Jean-Michel Molina, Francois Clavel, Allan J. Hance, Fabrizio Mammano
Summary: In this study, the genotypic and phenotypic diversity of replication-competent near-full-length HIV genomes were explored in eight patients with different delays in viremia control and treatment durations. The results showed that delayed effective treatment was associated with increased genetic diversity of the reservoir. The duration of treatment did not impact the diversity, but was associated with a higher frequency of clonally expanded sequences. Therefore, early treatment initiation has the advantage of reducing both the size and diversity of the reservoir.
MICROBIOLOGY SPECTRUM
(2022)
Article
Multidisciplinary Sciences
Nguyen Thi Le Hang, Minako Hijikata, Shinji Maeda, Akiko Miyabayashi, Keiko Wakabayashi, Shintaro Seto, Nguyen Thi Kieu Diem, Nguyen Thi Thanh Yen, Le Van Duc, Pham Huu Thuong, Hoang Van Huan, Nguyen Phuong Hoang, Satoshi Mitarai, Naoto Keicho, Seiya Kato
Summary: The study found genetic differences among different subtypes of Mycobacterium tuberculosis in central Vietnam, with some subtypes having lower infection rates and genetic clustering frequencies in younger people. Patients infected with ZERO strains exhibited less lung infiltration. Specific deletions in the genome were identified in different subtypes, providing a basis for investigating modern versus ancestral Mtb lineages.
SCIENTIFIC REPORTS
(2021)
Article
Mathematical & Computational Biology
Lacey-Anne Sanderson, Carolyn T. Caron, Reynold L. Tan, Kirstin E. Bett
Summary: Researchers are looking for cost-effective solutions to manage and analyze large-scale genotypic and phenotypic data, where open-source software and Tripal can fulfill this need. Tripal utilizes the GMOD Chado database schema in PostgreSQL for flexible storage and follows FAIR principles for data provision.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2021)
Article
Agronomy
Nirman Nepal, Jorge Alberto Condori-Apfata, Rupesh Gaire, Mayela Elizabeth Mayta Anco, Steven Scofield, Cankui Zhang, Mohsen Mohammadi
Summary: Quinoa is a nutritious grain with balanced amino acid composition and adaptability to saline conditions. A study evaluated 148 quinoa accessions for various traits and found significant differences among them. Genetic analysis revealed four main groups with varying characteristics. These findings provide important resources for germplasm conservation and the development of improved quinoa varieties to ensure food security.
Article
Plant Sciences
Ankita Negi, Kalpana Singh, Sarika Jaiswal, Johnson George Kokkat, Ulavappa B. B. Angadi, Mir Asif Iquebal, P. Umadevi, Anil Rai, Dinesh Kumar
Summary: This study successfully identified polymorphic markers of black pepper genotypes using a low-cost and efficient technique, and developed a web resource for genomic and polymorphic SSRs. The database has significant implications for varietal identification and gene discovery in black pepper production.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Do Yoon Hyun, Raveendar Sebastin, Gi-An Lee, Kyung Jun Lee, Seong-Hoon Kim, Eunae Yoo, Sookyeong Lee, Man-Jung Kang, Seung Bum Lee, Ik Jang, Na-Young Ro, Gyu-Taek Cho
Summary: Melon is an economically important horticultural crop with rich morphological and genetic variability. Utilizing genotyping-by-sequencing (GBS)-derived SNP analysis, this study revealed the genetic structure and diversity among muskmelon, makuwa, and cantaloupes, showing rapid linkage disequilibrium decay in muskmelon varieties. Bayesian phylogenetic tree and haplotype analysis supported the intraspecific relationships among the three melon varieties.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Microbiology
Clara Duffner, Susanne Kublik, Barbel Fosel, Asa Frostegard, Michael Schloter, Lars Bakken, Stefanie Schulz
Summary: Stimulating litho-autotrophic denitrification with hydrogen is a promising strategy to remove excess NO3-, but it often leads to the accumulation of cytotoxic intermediate NO2- and greenhouse gas N2O. This study investigated if the genomic composition, gene transcription regulation, or kinetics of reductases contribute to the high concentrations of NO2- and N2O. The findings suggest that the kinetics of reductases and the expression of N2O reductase play a role in the accumulation of NO2- and N2O during denitrification.
ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Agronomy
Manoj Kumar Yadav, Mukesh Kumar Yadav, Sanjay Kumar Lal, Amitha Mithra Sevanthi, Sajad Un Nabi, Virendra Kumar Baranwal
Summary: This study aimed to identify soybean genotypes resistant to Cowpea mild mottle virus (CPMMV) using mechanical inoculation-based phenotyping and marker trait association. Among the 288 genotypes evaluated, 43 were resistant, 59 were moderately resistant, and the remaining 186 were susceptible. Three markers were found to be significantly associated with CPMMV resistance. This study is important for breeding new resistant varieties.
Review
Endocrinology & Metabolism
Julian Martinez-Mayer, Maria Ines Perez-Millan
Summary: PROKR2 encodes a receptor that binds PROK1 and PROK2. Mutations in PROKR2 can cause abnormal olfactory bulb formation and defects in GnRH neuron migration. Patients with PROKR2 mutations typically present with hypogonadotropic hypogonadism, anosmia/hyposmia, or Kallmann Syndrome. Recent studies have also linked PROKR2 variants to pituitary disorders.
FRONTIERS IN ENDOCRINOLOGY
(2023)
Article
Clinical Neurology
Yanjun Guo, Iyas Daghlas, Padhraig Gormley, Franco Giulianini, Paul M. Ridker, Samia Mora, Tobias Kurth, Pamela Rist, Daniel Chasman
Summary: The study found significant associations between certain lipoprotein subfractions, especially triglyceride-rich lipoproteins (TRLPs), and migraine in populations of European ancestry. Genetic correlations indicated that the relationships were likely due to shared genetic components rather than causality.
Article
Plant Sciences
Hamid Khazaei, Carolyn T. Caron, Michael Fedoruk, Marwan Diapari, Albert Vandenberg, Clarice J. Coyne, Rebecca McGee, Kirstin E. Bett
FRONTIERS IN PLANT SCIENCE
(2016)
Article
Plant Sciences
Hamid Khazaei, Rajib Podder, Carolyn T. Caron, Shudhangshu S. Kundu, Marwan Diapari, Albert Vandenberg, Kirstin E. Bett
Article
Plant Sciences
Hamid Khazaei, Michael Fedoruk, Carolyn T. Caron, Albert Vandenberg, Kirstin E. Bett
Article
Plant Sciences
Krishna K. Gali, Yong Liu, Anoop Sindhu, Marwan Diapari, Arun S. K. Shunmugam, Gene Arganosa, Ketema Daba, Carolyn Caron, Reddy V. B. Lachagari, Bunyamin Tar'an, Thomas D. Warkentin
Article
Microbiology
Sinisa Vidovic, Carolyn Caron, Ali Taheri, Sidharath D. Thakur, Timothy D. Read, Anthony Kusalik, Jo-Anne R. Dillon
JOURNAL OF CLINICAL MICROBIOLOGY
(2014)
Article
Multidisciplinary Sciences
Melissa M. L. Wong, Neha Gujaria-Verma, Larissa Ramsay, Hai Ying Yuan, Carolyn Caron, Marwan Diapari, Albert Vandenberg, Kirstin E. Bett
Article
Agronomy
Tadesse S. Gela, Chu Shin Koh, Carolyn T. Caron, Li-An Chen, Albert Vandenberg, Kirstin E. Bett
Summary: This study aimed to identify quantitative trait loci associated with anthracnose resistance in lentil, revealing major resistance loci on chromosomes 3 and 7 and showcasing the potential for introgression of resistance genes into elite lentil cultivars.
Article
Plant Sciences
Hai Ying Yuan, Carolyn T. Caron, Larissa Ramsay, Richard Fratini, Marcelino Perez de la Vega, Albert Vandenberg, James L. Weller, Kirstin E. Bett
Summary: This study investigated the genetic basis for differences in flowering response to light quality in lentil, discovering 13 QTLs associated with flowering time under different light quality environments. A candidate gene, LcFTa1, as well as other potentially important genes and transcription factors were identified through transcriptomic analysis, shedding light on the molecular mechanisms of flowering time regulation in response to light quality.
Article
Mathematical & Computational Biology
Lacey-Anne Sanderson, Carolyn T. Caron, Reynold L. Tan, Kirstin E. Bett
Summary: Researchers are looking for cost-effective solutions to manage and analyze large-scale genotypic and phenotypic data, where open-source software and Tripal can fulfill this need. Tripal utilizes the GMOD Chado database schema in PostgreSQL for flexible storage and follows FAIR principles for data provision.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2021)
