Article
Genetics & Heredity
Cris L. Wijnen, Frank F. M. Becker, Andries A. Okkersen, C. Bastiaan de Snoo, Martin P. Boer, Fred A. van Eeuwijk, Erik Wijnker, Joost J. B. Keurentjes
Summary: Plants can exhibit different phenotypic responses after polyploidization, and the genetic factors responsible for ploidy-dependent phenotypic variation have not yet been identified. In this study, a population of segregating haploid and diploid offspring derived from Arabidopsis thaliana with different ploidy levels was compared to map the genotype x ploidy (G x P) interactions. Ploidy-specific quantitative trait loci (QTLs) were detected at both ploidy levels, indicating that including phenotypic measurements of haploids in QTL analyses can increase mapping power. The study also revealed pleiotropic effects and opposite effects at different ploidy levels for some QTLs. Overall, the research provides evidence that genetic variation between different Arabidopsis accessions is responsible for differences in phenotypic responses to altered ploidy levels, demonstrating a G x P effect.
Article
Engineering, Biomedical
Jacob Seifert, Charlotte Kirchhelle, Ian Moore, Sonia Contera
Summary: The shapes of living organisms are formed and maintained by precise control in time and space of growth, achieved by dynamically fine-tuning the mechanical properties of their structures. The study demonstrates the continuity of simple, linear, viscoelastic behavior of cell walls across scales, with characteristic nanometer scale patterns of relaxation times, elasticity and viscosity correlating with the speed of macroscopic growth. The approach provides a method to quantitatively map energy stored, dissipated and time response of cell walls in living organisms with nanometer resolution.
ACTA BIOMATERIALIA
(2021)
Article
Multidisciplinary Sciences
Devesh Shukla, Prabodh Kumar Trivedi, Shivendra Sahi
Summary: Comprehensive understanding of plant root system architecture (RSA) development is crucial for enhancing nutrient use efficiency and increasing crop cultivar tolerance to environmental challenges. This study presents an experimental protocol for establishing a hydroponic system, promoting plantlet growth, spreading and imaging the RSA. The method utilizes a magenta box-based hydroponic system supported by polypropylene mesh and polycarbonate wedges. The approach was initially designed for assessing the RSA of Arabidopsis, but can be easily adapted for studying other plants such as Medicago sativa (Alfalfa). The measurement of RSA traits is achieved through capturing high-resolution images of the carefully spread root systems using freely available ImageJ software.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2023)
Article
Biochemistry & Molecular Biology
Chetana Tamadaddi, Vinay Sagar, Amit K. Verma, Fathima Afsal, Chandan Sahi
Summary: Our study reveals that selective interactions between JDPs in plant mitochondria may determine their functional specificity and provide resilience to protein import processes in mitochondria.
PLANT MOLECULAR BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Mireille Cambert, Adeline Berger, Christine Salle, Stephanie Esling, Delphine Charif, Tudel Cadoret, Marie-Christine Ralet, Helen M. North, Corinne Rondeau-Mouro
Summary: The seeds of Arabidopsis thaliana produce a mucilage layer when imbibed, comprising an outer and inner layer. By studying 19 natural accessions, researchers have generated datasets for further exploration of mucilage polysaccharides and their adaptive traits. This data will serve as a valuable resource for genetic, biochemical, structural, and functional analyses.
Article
Biochemistry & Molecular Biology
Yue Hao, Makenzie E. Mabry, Patrick P. Edger, Michael Freeling, Chunfang Zheng, Lingling Jin, Robert VanBuren, Marivi Colle, Hong An, R. Shawn Abrahams, Jacob D. Washburn, Xinshuai Qi, Kerrie Barry, Christopher Daum, Shengqiang Shu, Jeremy Schmutz, David Sankoff, Michael S. Barker, Eric Lyons, J. Chris Pires, Gavin C. Conant
Summary: The study investigates the gene loss history after whole-genome triplication (WGT) in Brassiceae tribe members, confirming a two-step formation model with significant temporal gaps. It highlights distinguishable homoeolog loss rates among subgenomes and proposes a mix and match model of allopolyploidy where genes from different subgenomes function together without difficulty.
Article
Biochemistry & Molecular Biology
Joseph A. Edwards, Usha Bishnoi Saran, Jason Bonnette, Alice MacQueen, Jun Yin, Tu Uyen Nguyen, Jeremy Schmutz, Jane Grimwood, Len A. Pennacchio, Chris Daum, Tijana Glavina del Rio, Felix B. Fritschi, David B. Lowry, Thomas E. Juenger
Summary: A fundamental goal in plant microbiome research is to determine the relative impacts of host and environmental effects on root microbiota composition. This study characterized the root microbiota of switchgrass in its native range and found that field location is the primary determinant of microbiome composition. They also identified loci impacting the abundance of microbial strains and found a genetic relationship between a basal plant immunity pathway and relative abundances of root microbiota.
Article
Environmental Sciences
Zhihong Liu, Cheng Guo, Peidong Tai, Lizong Sun, Zhenbo Chen
Summary: This study investigated the effects of gadolinium (Gd) addition on Arabidopsis thaliana (L.) at both physiological and molecular levels. Results showed that low concentration of Gd could increase plant biomass and root length, while high concentrations of Gd appeared to cause DNA damage. Molecular analysis revealed changes in genetic variation and DNA methylation under Gd stress, suggesting that genes related to cell cycle, oxidative stress, and apoptosis were regulated by methylation. These findings provide new insights into the ecotoxicity mechanisms of rare earth elements on plants.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2021)
Article
Multidisciplinary Sciences
Guanrong Huang, Xuegui Yin, Jiannong Lu, Liuqin Zhang, Dantong Lin, Yu Xie, Haiyan Liu, Chaoyu Liu, Jinying Zuo, Xiaoxiao Zhang
Summary: This study used dynamic QTL mapping to reveal the genetic structure of photosynthetic traits in castor plants. Multiple QTLs and genetic effects related to photosynthetic traits were identified, providing important references for breeding for high photosynthetic efficiency.
SCIENTIFIC REPORTS
(2023)
Article
Plant Sciences
Yesica C. Menendez, Diego H. Sanchez, Rod J. Snowdon, Deborah P. Rondanini, Javier F. Botto
Summary: This study investigated the growth and yield traits of canola under different plant densities, revealing both density-independent and density-dependent associations. Through transcriptomic analysis and gene mutation experiments, the research identified specific genes that regulate plant growth and flowering time in response to different densities.
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Article
Biochemistry & Molecular Biology
Lucie Kriegshauser, Samuel Knosp, Etienne Grienenberger, Kanade Tatsumi, Desiree D. Guetle, Iben Sorensen, Laurence Herrgott, Julie Zumsteg, Jocelyn K. C. Rose, Ralf Reski, Daniele Werck-Reichhart, Hugues Renault
Summary: The HCT gene plays a critical role in the phenylpropanoid pathway in the moss species Physcomitrium patens, similar to its function in seed plants. Phylogenetic analysis suggests deep conservation of HCT function across embryophytes. Enzyme assays and metabolic profiling indicate that P. patens HCT is involved in the production of caffeate derivatives and cuticle formation in bryophytes.
Review
Plant Sciences
Claude Becker, Richard Berthome, Philippe Delavault, Timothee Flutre, Helene Freville, Stephanie Gibot-Leclerc, Valerie Le Corre, Jean-Benoit Morel, Nathalie Moutier, Stephane Munos, Celine Richard-Molard, James Westwood, Pierre-Emmanuel Courty, Alexandre de Saint Germain, Gaetan Louarn, Fabrice Roux
Summary: Interactions among plants are important for plant community dynamics and crop yield, but our understanding of the genetics associated with these interactions is limited. By studying phenotypic traits and their underlying genetic and molecular pathways, and considering environmental fluctuations, we can improve our predictions and modeling of plant interactions in wild habitats and crop fields.
TRENDS IN PLANT SCIENCE
(2023)
Article
Ecology
Kristofer T. Sasser, Jesse N. Weber
Summary: The costs and benefits of immune responses have long been a focus in ecoimmunology. This article highlights two underrepresented methodological approaches in the field and emphasizes the need for using modern techniques to collect diverse and ecologically relevant data. It also stresses the importance of considering the specific immune responses induced by pathogens and employing a comparative approach to understand the evolution of immune defenses.
EVOLUTIONARY ECOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Leah DeLorenzo, Destiny Mathews, A. Allyson Brandon, Mansi Joglekar, Aldo Carmona Baez, Emily C. Moore, Patrick J. Ciccotto, Natalie B. Roberts, Reade B. Roberts, Kara E. Powder
Summary: Divergence in body shape is a common pattern in fish and is associated with habitat specification and swimming mechanics. The genetic basis of this body shape variation was studied in cichlids using two hybrid crosses and 34 quantitative trait loci (QTL) were identified that underlie various aspects of body shape variation. These QTL are distinct between different crosses and compared to other fish species, indicating that convergent body shape phenotypes are likely due to distinct genetic and molecular mechanisms.
Article
Chemistry, Multidisciplinary
Luca Pagano, Marta Marmiroli, Marco Villani, Jacopo Magnani, Riccardo Rossi, Andrea Zappettini, Jason C. White, Nelson Marmiroli
Summary: This study found that nanoparticles can affect the functionality and genome of chloroplasts and mitochondria in A. thaliana, and different nanoparticles have different effects, which are related to the toxicity and dissolution rate of the metal salts. These findings suggest that changes in stoichiometry are an adaptive response to nanoparticle exposure.
Article
Behavioral Sciences
David Curtis, Leda Coelewij, Shou-Hwa Liu, Jack Humphrey, Richard Mott
Article
Biochemical Research Methods
Thorhildur Juliusdottir, Karina Banasik, Neil R. Robertson, Richard Mott, Mark I. McCarthy
Article
Biochemistry & Molecular Biology
Filip Ruzicka, Mark S. Hill, Tanya M. Pennell, Ilona Flis, Fiona C. Ingleby, Richard Mott, Kevin Fowler, Edward H. Morrow, Max Reuter
Article
Biochemical Research Methods
Leilei Cui, Bin Yang, Nikolas Pontikos, Richard Mott, Lusheng Huang
Article
Multidisciplinary Sciences
Roei Levy, Clemence Levet, Keren Cohen, Matthew Freeman, Richard Mott, Fuad Iraqi, Yankel Gabet
SCIENTIFIC REPORTS
(2020)
Article
Genetics & Heredity
Richard Mott, Christian Fischer, Pjotr Prins, Robert William Davies
Article
Genetics & Heredity
Jennifer Zou, Shyam Gopalakrishnan, Clarissa C. Parker, Jerome Nicod, Richard Mott, Na Cai, Arimantas Lionikas, Robert W. Davies, Abraham A. Palmer, Jonathan Flint
Summary: Combining samples in genetic association studies for complex traits can identify more loci, but replication between studies may be challenging. The Winner's Curse effect, study heterogeneity, and trait differences are factors that affect replication, and integrating various information can assign variants to different confidence levels.
G3-GENES GENOMES GENETICS
(2022)
Editorial Material
Medicine, General & Internal
Richard Mott
Article
Cell Biology
Wesley L. Crouse, Swapan K. Das, Thu Le, Gregory Keele, Katie Holl, Osborne Seshie, Ann L. Craddock, Neeraj K. Sharma, Mary E. Comeau, Carl D. Langefeld, Gregory A. Hawkins, Richard Mott, William Valdar, Leah C. Solberg Woods
Summary: This study conducted transcriptomic analysis in metabolically active tissues of outbred heterogeneous stock (HS) rats and humans, identifying consensus genes and networks associated with body weight/body mass index (BW/BMI). The identified genes and networks are involved in various metabolic processes, expanding our understanding of the genetics underlying obesity.
PHYSIOLOGICAL GENOMICS
(2022)
Article
Agronomy
Chin Jian Yang, Olufunmilayo Ladejobi, Richard Mott, Wayne Powell, Ian Mackay
Summary: By modeling the distribution of allele frequency over the year of variety release, we have successfully identified major loci involved in historical breeding of winter wheat. Our study reveals that historical selection in winter wheat has mainly targeted yield improvement, but may have negative effects on traits such as flowering time, lodging, plant height and grain protein content. These findings provide important insights for guiding future breeding of winter wheat.
THEORETICAL AND APPLIED GENETICS
(2022)
Article
Agronomy
Nick Fradgley, Keith A. Gardner, Alison R. Bentley, Phil Howell, Ian J. Mackay, Michael F. Scott, Richard Mott, James Cockram
Summary: Through analyzing a genetically diverse wheat population, it was found that multi-trait genetic models and non-parametric models can improve prediction accuracy for complex traits and optimize relationships between multiple traits. These findings provide important insights for crop improvement.
Article
Biotechnology & Applied Microbiology
Leilei Cui, Bin Yang, Shijun Xiao, Jun Gao, Amelie Baud, Delyth Graham, Martin Mcbride, Anna Dominiczak, Sebastian Schafer, Regina Lopez Aumatell, Carme Mont, Albert Fernandez Teruel, Norbert Huebner, Jonathan Flint, Richard Mott, Lusheng Huang
Summary: Dominance effects play a significant role in genetic variation in mammals, especially in hematological and immunological traits. While most genetic effects in gene expression and quantitative traits are additive, a portion of these effects exhibit dominance. Causal genes for dominance physiological traits are often not physically linked to the trait loci, but instead act through other genetic effects.
Article
Biotechnology & Applied Microbiology
Michael F. Scott, Nick Fradgley, Alison R. Bentley, Thomas Brabbs, Fiona Corke, Keith A. Gardner, Richard Horsnell, Phil Howell, Olufunmilayo Ladejobi, Ian J. Mackay, Richard Mott, James Cockram
Summary: The study found that genetic diversity in bread wheat is low, with most genes clustering in a few haplotypes. By analyzing the genome data of the diverse MAGIC multi-parent population, extensive pleiotropy and polygenic traits were revealed. Limited haplotypes and the interactions among multiple genes could lead to adverse effects on other traits when selecting for one trait.
Article
Biotechnology & Applied Microbiology
Ilona Binenbaum, Hanifa Abu-Toamih Atamni, Georgios Fotakis, Georgia Kontogianni, Theodoros Koutsandreas, Eleftherios Pilalis, Richard Mott, Heinz Himmelbauer, Fuad A. Iraqi, Aristotelis A. Chatziioannou
Article
Plant Sciences
Michael F. Scott, Laura R. Botigue, Selina Brace, Chris J. Stevens, Victoria E. Mullin, Alice Stevenson, Mark G. Thomas, Dorian Q. Fuller, Richard Mott
