Article
Biochemistry & Molecular Biology
Steven T. Gardner, Emily M. Bertucci, Randall Sutton, Andy Horcher, Doug Aubrey, Benjamin B. Parrott
Summary: Biological ageing is related to life history variation, and DNA methylation dynamics is a conserved feature that can be used to predict age in vertebrate species. This study demonstrates the association between DNA methylation and ageing in loblolly pine trees and creates an epigenetic clock for predicting age in plants, highlighting the importance of understanding biological ageing in plants for conservation and management practices.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Genetics & Heredity
Jingjia Li, Jason B. West, Alexander Hart, Jill L. Wegrzyn, Matthew A. Smith, Jean-Christophe Domec, Carol A. Loopstra, Claudio Casola
Summary: The response to water limitation in drought-tolerant and -sensitive loblolly pine genotypes differs significantly at the gene level, although involving similar genetic networks. Upregulated transcripts under drought conditions represent the most diverging component between genotypes, which might depend on the activation and repression of substantially different groups of transcription factors.
FRONTIERS IN GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Zachary Bragg, Lynne K. Rieske
Summary: In this study, it was confirmed through hydroponic experiments that exogenously applied dsRNA can persist in different tissues of pine seedlings, providing a viable delivery route for combating tree feeding pests through root soak application of dsRNA.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Forestry
Steven E. McKeand, Kitt G. Payn, Austin J. Heine, Robert C. Abt
Summary: Continuing or increasing tree improvement efforts for loblolly pine in the southern United States will result in significant economic benefits for landowners and the wood-product supply chain. With ongoing improvements in breeding strategies and deployment options, planted plantations will continue to provide sustained value for decades to come.
JOURNAL OF FORESTRY
(2021)
Article
Plant Sciences
Jipeng Mao, Linwang Huang, Manyu Chen, Weishan Zeng, Zhiheng Feng, Shaowei Huang, Tianyi Liu
Summary: Through transcriptome and metabolome analysis, this study identified genes and metabolites related to biosynthesis in loblolly pine, providing valuable genomic and metabolome information for understanding the species at the molecular level and laying a foundation for further development of the loblolly pine-related pharmaceutical industry.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Entomology
E. McCarty, V. C. Cassidy, D. Clabo, D. Dickens, C. Asaro, K. J. K. Gandhi
Summary: The efficacy of four systemic insecticide treatments (chlorantraniliprole, dinotefuran, fipronil, and imidacloprid) for suppressing NPTM populations in loblolly pines was assessed. The results showed that chlorantraniliprole consistently reduced NPTM infestation rates for two growing seasons, while fipronil and dinotefuran improved several growth metrics. Imidacloprid was effective in controlling NPTM infestation in one trial only.
JOURNAL OF ECONOMIC ENTOMOLOGY
(2023)
Article
Fisheries
Antoine Jourdan, Romain Morvezen, Florian Enez, Pierrick Haffray, Adeline Lange, Emilie Vetois, Francois Allal, Florence Phocas, Jerome Bugeon, Lionel Degremont, Pierre Boudry
Summary: Selective breeding programs have been initiated for the Pacific oyster Crassostrea gigas, using genomic tools to improve growth and disease resistance. The study evaluated the potential of genomic selection (GS) for growth-related and shell color traits in commercially selected populations. The results showed a high correlation between growth-related traits and low correlation with color traits. The accuracy of prediction was higher with the genomic model compared to the classical model, indicating the potential of GS in mixed-family breeding programs for C. gigas.
Review
Plant Sciences
Lilian P. Matallana-Ramirez, Ross W. Whetten, Georgina M. Sanchez, Kitt G. Payn
Summary: The warming of Earth's atmosphere is leading to changes in temperature and precipitation, impacting forest ecosystems. New technologies offer opportunities to address these changes, but also come with challenges. Management and breeding strategies can enhance forest resilience to climate change.
FRONTIERS IN PLANT SCIENCE
(2021)
Review
Agronomy
Theo Meuwissen, Ben Hayes, Iona MacLeod, Michael Goddard
Summary: This review discusses the possibility of identifying causal variants for complex traits, stressing the importance of large and diverse samples, accurate genotypes, multiple phenotypes, annotation of genomic sites, and other types of evidence required for this task.
Article
Forestry
Harold E. Burkhart, Sheng- Yang
Summary: Research conducted in two generations of loblolly pine plantations in the southeastern US with varying management intensity and environmental factors showed significant increases in site index and maximum stand density in the second generation plantings. Productivity gains varied by physiographic regions, with the Piedmont region showing the highest estimated increase.
FOREST ECOLOGY AND MANAGEMENT
(2022)
Article
Plant Sciences
Wenchong Chen, Weiwu Yu, Ang Dong, Yanru Zeng, Huwei Yuan, Bingsong Zheng, Rongling Wu
Summary: This study utilizes advanced genotyping technologies to investigate the genetic structure of Torreya grandis, a species with high economic and ornamental values. A high-density linkage map is constructed, and the results suggest that the identified QTLs are relatively young and can be better utilized through clonal propagation.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Forestry
Gabriel W. D. Ferreira, Benjamin M. Rau, Doug P. Aubrey
Summary: Forest production heavily relies on nutrient uptake, and understanding the relationship between nutrient availability and silvicultural practices is crucial for sustainable management of intensively managed plantations. The study on early loblolly pine stand development showed that management practices such as controlling competing vegetation and early fertilization can significantly increase nitrogen content, but long-term nitrogen dynamics and growth are dependent on early fertilization.
FOREST ECOLOGY AND MANAGEMENT
(2021)
Article
Evolutionary Biology
Hongwei Li, Zezhao Wang, Lei Xu, Qian Li, Han Gao, Haoran Ma, Wentao Cai, Yan Chen, Xue Gao, Lupei Zhang, Huijiang Gao, Bo Zhu, Lingyang Xu, Junya Li
Summary: In this study, haplotype blocks were constructed using LD-based and fixed-SNP methods in beef cattle. The predictive performance of different haplotype block partitioning methods was evaluated, and it was found that LD-based and fixed-SNP haplotype Bayesian methods outperform the Bayesian models. Filtering minor haplotype allele frequency can also improve the performance of genomic prediction.
EVOLUTIONARY APPLICATIONS
(2022)
Article
Forestry
Krishna P. Poudel, Samantha C. Avery, Joshua J. Granger
Summary: The growth and production potential of a tree is closely related to its crown dimensions, with nonlinear models such as exponential, Weibull, and Richards functions often used for prediction. A new study found that using a generalized linear model for predicting crown ratio can result in slightly smaller errors compared to other models.
Article
Forestry
Noah T. Shephard, Omkar Joshi, Cassandra R. Meek, Rodney E. Will
Summary: The study found that drought, fertilization, and thinning all have significant impacts on the productivity of loblolly pine plantations. While drought tends to decrease diameter and height growth, fertilization can counteract these effects by increasing foliar nutrient concentrations. Thinning also has positive effects on growth, especially in combination with fertilization treatments.
FOREST ECOLOGY AND MANAGEMENT
(2021)
Article
Plant Sciences
Susan L. McEvoy, U. Uzay Sezen, Alexander Trouern-Trend, Sean M. McMahon, Paul G. Schaberg, Jie Yang, Jill L. Wegrzyn, Nathan G. Swenson
Summary: The first chromosome-scale assemblies for sugar maple and boxelder, as well as transcriptomic evaluation of the abiotic stress response in sugar maple, were reported in this study. The integrated research provides insights into the contribution of different factors to tolerance in each species and utilizes knowledge from various areas of plant genome biology and Acer physiology to understand the genomic complexities underlying tolerance in broadleaf tree species.
Article
Multidisciplinary Sciences
W. John Kress, Douglas E. Soltis, Paul J. Kersey, Jill L. Wegrzyn, James H. Leebens-Mack, Morgan R. Gostel, Xin Liu, Pamela S. Soltis
Summary: Green plants are essential to ecosystems, human health, and agriculture, but generating and storing their genomes is a major challenge. Currently, there are fewer than 300 complete chromosome-scale genome assemblies for green plants, representing less than 900 species. Many species, especially those from extreme environments, still lack suitable tissue samples for genomic sequencing. The annotation of plant genomes also needs improvement.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Forestry
Oleksandra Kuchma, Jessica Rebola-Lichtenberg, Dennis Janz, Konstantin V. Krutovsky, Christian Ammer, Andrea Polle, Oliver Gailing
Summary: Mixed cropping in short rotation coppice can replace monocultures. RNA sequencing was used to monitor the gene expression of poplar under mixed and pure cultivations. Black locust and the abiotic environment exerted strong competition pressure on poplar. Shading effects and water competition influenced the growth and gene expression in mixed stands.
Article
Plant Sciences
Galina Shevchenko, Konstantin Krutovsky
Summary: A new approach combining pharmacological analysis and mechanical stimulation was used to study the regulation of plant cytoskeleton. The results suggest feedback between the organization of microtubules and actin filaments and the expression of specific genes. The regulation of this feedback may be altered during slow rotation due to changes in mechanical impact.
PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS
(2022)
Article
Biotechnology & Applied Microbiology
Birgit Kersten, Christian Rellstab, Hilke Schroeder, Sabine Brodbeck, Matthias Fladung, Konstantin V. Krutovsky, Felix Gugerli
Summary: In this study, the first mitogenome sequence of Abies alba was assembled and studied. The results revealed that the A. alba mitogenome has a complex and dynamic structure with high combinatorial variation. Comparative analysis also showed a moderate but significant positive correlation between mitogenome size and proportion of repetitive elements in gymnosperms. This research provides a basis for further understanding the structure, phylogeny, and evolution of A. alba.
Review
Genetics & Heredity
K. Krutovsky
Summary: Dendrogenomics is an interdisciplinary field that integrates dendrology and genomics to study temporal dynamics of forest treelines, population structure, and adaptive genetic potential, with particular relevance to predicting the impact of climate change on boreal forest species distribution.
RUSSIAN JOURNAL OF GENETICS
(2022)
Article
Forestry
Dina F. Zhirnova, Liliana V. Belokopytova, Konstantin V. Krutovsky, Yulia A. Kholdaenko, Elena A. Babushkina, Eugene A. Vaganov
Summary: The radial growth of Siberian stone pine was studied in subalpine stands near the upper timberline along the Western Sayan Mountains in Southern Siberia. The study revealed weak but spatially coherent responses of tree growth to temperature and precipitation. Temperature stimulated growth, while precipitation suppressed growth, and snowfall had a neutral or positive impact. Extreme weather events influenced the width of tree rings. The climatic sensitivity of mature trees increased, except for temperature in the previous October-January. The current winter warming trend is advantageous for young pine trees.
Review
Forestry
Tatyana S. Tikhomirova, Konstantin V. Krutovsky, Konstantin A. Shestibratov
Summary: Betula spp., Quercus spp., and Populus spp. are promising deciduous woody plants in forestry, but they are sensitive to climate change which can negatively impact their plantations. Understanding the genetic mechanisms of adaptation to adverse environmental conditions is crucial in preventing the decline of deciduous forest area. This mini review discusses the stress responses of these species to drought and salt stresses.
Article
Genetics & Heredity
Vera Marjorie Elauria Velasco, Alyssa Ferreira, Sumaira Zaman, Devin Noordermeer, Ingo Ensminger, Jill L. Wegrzyn
Summary: In this study, a highly accurate and complete reference transcriptome and genome annotation of Douglas-fir were generated. Deep sequencing of the transcriptome using long-read and short-read platforms was performed on Douglas-fir needles grown under nonstress control conditions or a combination of heat and drought stress conditions. Two computational approaches were used for transcriptome assembly, and the results showed that the de novo assembly approach identified more high-quality transcripts, complete genes, and functionally annotated genes compared to the genome-guided assembly approach. Additionally, a refined genome annotation was generated using an improved informatics approach.
G3-GENES GENOMES GENETICS
(2023)
Review
Agronomy
Helmuth E. E. Nieves-Orduna, Konstantin V. V. Krutovsky, Oliver Gailing
Summary: The cacao tree is cultivated in the tropics to produce seeds, which are valuable raw materials for the chocolate industry. It is crucial to conserve and use cacao genetic resources for breeding programs to enhance yield, improve quality, and disease resistance. This review focuses on three important aspects of cacao genetics necessary for sustainable production and crop improvement: geographic distribution and genetic variation of wild cacao populations, conservation and utilization of cacao genetic resources, and genetic basis of agronomic traits and its application for cacao improvement. We also emphasize the critical research areas required for sustainable cacao cultivation.
Review
Biochemistry & Molecular Biology
Anastasia Y. Batalova, Konstantin V. Krutovsky
Summary: Trees are unique in their development, sustainability, and longevity, with some species living for several millennia. This review focuses on the genetic and epigenetic mechanisms of longevity in forest trees, highlighting the genetic aspects of well-studied species like oak, ginkgo, fig, poplar, Welwitschia, and Dracaena. Enhanced immune defense, increased gene families associated with disease resistance, and steady expression of specific genes were found to be key traits in long-lived trees. The study also identified the involvement of epigenetic regulators and changes in gene expression through grafting, cutting, and pruning.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Serafima V. Novikova, Vadim V. Sharov, Natalia V. Oreshkova, Evgeniy P. Simonov, Konstantin V. Krutovsky
Summary: This paper presents the results of studying the genetic differentiation of Siberian larch populations and identifies genetic markers associated with adaptation to high altitude conditions. The study reveals significant genetic differentiation among populations and identifies genes associated with cell metabolism, organic synthesis, and stress response.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Horticulture
Alla I. Perfileva, Anastasia R. Kharasova, Olga A. Nozhkina, Alexander V. Sidorov, Irina A. Graskova, Konstantin V. Krutovsky
Summary: The use of nanocomposites (NCs) in crop production has been actively studied in recent decades. Previous research has shown that chemically synthesized selenium nanocomposites (Se NCs) based on natural polymeric matrices stimulated the growth and development of potatoes and had an antibacterial effect against the phytopathogen Clavibacter sepedonicus. This study aimed to confirm the reproducibility of these results in field conditions and explore the broader biological activity of NCs on other cultivated plants and phytopathogens. The results demonstrated the stimulating effect of Se NCs on the productivity of potatoes and soybeans, as well as their antibacterial effect against Gram-positive and Gram-negative phytopathogenic bacteria.
Article
Ecology
S. V. Novikova, N. V. Oreshkova, V. V. Sharov, V. L. Semerikov, K. V. Krutovsky
Summary: The genetic differentiation of Siberian larch populations along the latitudinal gradient of climatic conditions was studied using ddRADseq data. The correlation between environmental factors and SNP variation was examined, and several SNPs with signatures of selection were identified. It was also found that some SNPs were located in mitochondrial and nuclear genes.
CONTEMPORARY PROBLEMS OF ECOLOGY
(2023)
Article
Evolutionary Biology
Heng Zhao, Yu-Cheng Dai, Fang Wu, Xiao-Yong Liu, Sundy Maurice, Konstantin Krutovsky, Igor N. Pavlov, Daniel L. Lindner, Francis M. Martin, Yuan Yuan
Summary: In this study, the genomic traits of ecological diversification in the Hymenochaetales were elucidated through sequencing of new genomes. The ectomycorrhizal (EcM) Coltricia species were of particular interest. Comparative analysis of 32 genomes, including 31 Hymenochaetales and one outgroup, revealed that EcM species have unique genomic characteristics compared to parasitic and saprophytic members of the group. These characteristics include a reduced number of plant cell wall degrading enzyme genes and an expansion of transposable elements, genome size, small secreted proteins, and secreted proteases. However, EcM species still retain some secreted carbohydrate-active enzymes (CAZymes) for degrading microbial cell walls. The study also provided insights into the phylogenetic relationships and divergence times within the Hymenochaetales, particularly for the EcM genus Coltricia.
GENOME BIOLOGY AND EVOLUTION
(2023)
