Article
Agricultural Engineering
V. M. V. Cruz, D. A. Dierig, A. Lynch, K. Hunnicutt, T. R. Sullivan, G. Wang, J. Zhu
Summary: The study focused on the phenotypic characterization of historical breeding lines and wild genetic resources of guayule plant, with analysis conducted on seed weight, germination, leaf traits, trichomes, and ploidy levels. The results indicated a predominant tetraploid type in the germplasm collection, with significant positive correlation between seed weight, germination, and seed size. The findings are useful for germplasm optimization and crop improvement activities.
INDUSTRIAL CROPS AND PRODUCTS
(2022)
Article
Genetics & Heredity
Md. Abdullah Al Bari, Ping Zheng, Indalecio Viera, Hannah Worral, Stephen Szwiec, Yu Ma, Dorrie Main, Clarice J. Coyne, Rebecca J. McGee, Nonoy Bandillo
Summary: This study applied genomic prediction to optimize the selection of pea germplasm accessions in the USDA Pea Germplasm Collection. Different genomic prediction models showed varying predictive abilities across traits, with an increase in training population size improving the predictive ability of most traits, including seed yield. By utilizing the best genomic prediction model, it was found that genotyped but non-phenotyped accessions were expected to perform within the range of phenotyped accessions, indicating the potential for using reliable breeding values to identify favorable germplasm accessions.
FRONTIERS IN GENETICS
(2021)
Article
Genetics & Heredity
Lais B. Martins, Peter Balint-Kurti, S. Chris Reberg-Horton
Summary: Peas are the second most cultivated pulse crop and can be used for human food, fodder, and cover crop. Ascochyta blight caused by Peyronella pinodes is the most serious foliar disease of pea cultivars worldwide. We identified genomic loci associated with variation in pea traits through genetic analysis and genome-wide association study.
G3-GENES GENOMES GENETICS
(2022)
Article
Plant Sciences
Philipp E. Bayer, Babu Valliyodan, Haifei Hu, Jacob I. Marsh, Yuxuan Yuan, Tri D. Vuong, Gunvant Patil, Qijian Song, Jacqueline Batley, Rajeev K. Varshney, Hon-Ming Lam, David Edwards, Henry T. Nguyen
Summary: Plant gene content varies between individuals of the same species due to gene presence/absence variation, and selection can alter the frequency of specific genes in a population. Selection during domestication and breeding leads to changes in gene and allele frequency, with a reduction in genetic diversity and a decrease in the average number of protein-coding genes per individual. However, some genes and allelic variants increase in frequency due to selection for agronomic traits. This analysis provides a genomic perspective of domestication and breeding in soybean.
Article
Agricultural Engineering
Hussein Abdel-Haleem, Zinan Luo, Aaron Szczepanek
Summary: This study investigated the genetic diversity and relatedness in the USDA collection of Brassica juncea. By genotyping 340 samples, a total of 99030 high-quality SNP markers were identified. Population structure and PCA analysis revealed five distinct subpopulations, with the largest subpopulation traced back to Pakistan and India. The results demonstrated a high genetic diversity and genetic differentiation among subpopulations in the USDA collection of B. juncea.
INDUSTRIAL CROPS AND PRODUCTS
(2022)
Article
Agriculture, Multidisciplinary
Stephanie Lavergne, Anne Vanasse, Marie-Noelle Thivierge, Caroline Halde
Summary: In this study, the aboveground and belowground biomass as well as yield stability of pea-based cover crop mixtures were evaluated. Pure stand of field pea had the highest aboveground biomass but lowest belowground biomass and stability, while mixtures showed higher stability and potential soil-related ecosystem services. The study highlights the importance of cover crop mixtures over pure stands in maximizing ecosystem services.
AGRICULTURE ECOSYSTEMS & ENVIRONMENT
(2021)
Article
Biochemistry & Molecular Biology
Jian-Min Song, Muhammad Arif, Yan Zi, Sing-Hoi Sze, Meiping Zhang, Hong -Bin Zhang
Summary: This study developed a large number of high-quality SNPs for a rice mini-core collection and classified it into different subpopulations. The research revealed significant genetic diversity differences among the subpopulations and confirmed extensive variation in genes controlling agronomic traits among them. Additionally, the study found reproductive barriers or gene flow between the Indica and Japonica groups.
Article
Agronomy
Kulbir Sandhu, Arti Singh
Summary: The study explores the potential of mung bean in the northern latitudes of the U.S. using USDA germplasm resources, identifying genetic markers for important traits and uncovering potential epistatic interactions. The research highlights the adaptability of mung bean in the midwestern U.S. and the possibility of crop diversification through utilizing diverse germplasm resources.
Article
Environmental Studies
Visalakshy Sasikala, Venkataraman Sankaranarayanan
Summary: Gender diversity has become an important criterion for investors, but the mining sector has struggled with this due to its traditional emphasis on masculine identity. A qualitative study of 24 major mining companies in eight regions reveals that stronger gender diversity performance is linked to a higher degree of coherence between diversity aspirations and initiatives. Lack of coherence reflects a superficial approach to diversity management that hinders progress.
Article
Environmental Sciences
Xinxin Guo, Xiaoan Zuo, Eduardo Medina-Roldan, Aixia Guo, Ping Yue, Xueyong Zhao, Jingjuan Qiao, Xiangyun Li, Min Chen, Cunzheng Wei, Tian Yang, Yuguang Ke, Qiang Yu
Summary: The change of plant biodiversity caused by resource-enhancing global changes has greatly affected grassland productivity. The effects of multi-resource enrichment on grassland biodiversity and productivity depend on site resource constraints.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Plant Sciences
Takehiro Sasaki, Naohiro I. Ishii, Daichi Makishima, Rui Sutou, Akihito Goto, Yutaka Kawai, Hayami Taniguchi, Kunihiro Okano, Ayumi Matsuo, Alfred Lochner, Simone Cesarz, Yoshihisa Suyama, Kouki Hikosaka, Nico Eisenhauer
Summary: This study provides observational evidence that plant and microbial community composition, rather than diversity, are crucial for sustaining multifunctionality in subalpine moorlands. Furthermore, plant and bacterial beta diversity enhance the dissimilarity of moorland multifunctionality.
JOURNAL OF ECOLOGY
(2022)
Article
Multidisciplinary Sciences
Mingzhen Lu, William J. Bond, Efrat Sheffer, Michael D. Cramer, Adam G. West, Nicky Allsopp, Edmund C. February, Samson Chimphango, Zeqing Ma, Jasper A. Slingsby, Lars O. Hedin
Summary: Recent research suggests that plant root traits play a crucial role in shaping biome boundaries and maintaining plant communities. The study conducted in South Africa revealed that thin-rooted plant strategies are favored in biomes with low soil resources, and these strategies, along with intense belowground competition, help maintain the sharp boundary between different biomes. The findings challenge the traditional belief that external abiotic factors primarily determine biome boundaries and highlight the importance of internal biotic mechanisms in maintaining these boundaries.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Microbiology
Sheridan Lois Woo, Francesca De Filippis, Maurizio Zotti, Albert Vandenberg, Pierre Hucl, Giuliano Bonanomi
Summary: Intensive cultivation based on monocultures has a significant impact on ecosystem function, and sustainable agriculture must rely on alternative methods, including crop rotation. This study investigated the effect of pea-wheat rotation on soil microbial communities in Canadian prairies and found that rotations can alter the diversity and composition of soil communities.
Article
Agriculture, Dairy & Animal Science
Z. Du, L. Sun, C. Chen, J. Lin, F. Yang, Y. Cai
Summary: In this study, PacBio single-molecule, real-time sequencing was used to explore the microbial community structure and metabolic pathways during paper mulberry silage fermentation, revealing a shift from pathogenic Proteobacteria to beneficial Firmicutes, with lactic acid bacteria playing a key role in fermentation quality.
ANIMAL FEED SCIENCE AND TECHNOLOGY
(2021)
Article
Agronomy
Xin Lv, Qiankun Wang, Xiaoyan Zhang, Junjie Hao, Li Li, Wang Chen, Haokun Li, Yuhui Wang, Cuiping Ma, Jialin Wang, Quanlan Liu
Summary: This study focused on the endophytic bacterial community of pea roots throughout its life cycle, revealing that the structure and complexity of root endophytes were significantly influenced by the developmental stage. The dominant bacteria species were Rhizobium, Pseudomonas, and Bacteroides, with Rhizobium being the most abundant throughout the developmental stages. Pea cultivars did not have a significant impact on the root endophytic bacterial community patterns.
Article
Biochemistry & Molecular Biology
Honglin Feng, Lucia Acosta-Gamboa, Lars H. Kruse, Jake D. Tracy, Seung Ho Chung, Alba Ruth Nava Fereira, Sara Shakir, Hongxing Xu, Garry Sunter, Michael A. Gore, Clare L. Casteel, Gaurav D. Moghe, Georg Jander
Summary: The Nicotiana benthamiana acylsugar acyltransferase (ASAT) plays a crucial role in plant defense against desiccation and insect herbivory. Knockout mutations of ASAT genes in N. benthamiana significantly reduce insect resistance and lead to increased susceptibility to herbivores.
PLANT MOLECULAR BIOLOGY
(2022)
Article
Genetics & Heredity
Lauren J. Brzozowski, Haixiao Hu, Malachy T. Campbell, Corey D. Broeckling, Melanie Caffe, Lucia Gutierrez, Kevin P. Smith, Mark E. Sorrells, Michael A. Gore, Jean-Luc Jannink
Summary: This study investigates the variation and genetic influence on the metabolite profiles of oats, specifically the seed metabolites with antioxidant properties. The research finds reduced genetic variation in modern oat germplasm compared to diverse germplasm, mainly due to increased seed size from intensive breeding. The abundance of avenanthramides, one of the specialized metabolites, increases with seed size, while avenacoside abundance decreases. The study highlights the importance of understanding how plant breeding influences plant traits and the genetic basis behind these changes.
G3-GENES GENOMES GENETICS
(2022)
Article
Multidisciplinary Sciences
Nathan Fumia, Daniel Rubinoff, Rosana Zenil-Ferguson, Colin K. Khoury, Samuel Pironon, Michael A. Gore, Michael B. Kantar
Summary: Understanding the ecological and evolutionary interactions of economically important plant species is crucial for sustainable agriculture. In this study, the geography and phylogenetic histories of wild potatoes were analyzed in combination with genomic composition and reproductive systems to identify potential species for breeding abiotic stress tolerance. The results showed that certain breeding system and ploidy combinations increase the niche breadth of wild potato species, making them promising candidates for crop adaptation to a changing climate.
ROYAL SOCIETY OPEN SCIENCE
(2022)
Article
Agronomy
Nathan Fumia, Samuel Pironon, Daniel Rubinoff, Colin K. Khoury, Michael A. Gore, Michael B. Kantar
Summary: Food production strategies and patterns are being altered in response to climate change. Enhancing the adaptation of important food crops to novel climate regimes will be critical to maintaining world food supplies. Climate change is altering the suitability of production areas for crops such as potato (Solanum tuberosum L.) making future productivity, resilience, and sustainability of this crop dependent on breeding for climate adaptation, including through the introgression of novel traits from its wild relatives. In doing so, researchers have developed a prioritization value system to locate potentially beneficial species possessing local adaptability, climatic plasticity, and interspecific crossability. The study found significant shifts in potato production areas by 2070 and varying degrees of climate overlap between potato and its wild relatives. This research highlights the importance of utilizing unique species with local adaptability to adapt potato to changing local climates.
FOOD AND ENERGY SECURITY
(2022)
Article
Genetics & Heredity
Nicolas Morales, Alex C. Ogbonna, Bryan J. Ellerbrock, Guillaume J. Bauchet, Titima Tantikanjana, Isaak Y. Tecle, Adrian F. Powell, David Lyon, Naama Menda, Christiano C. Simoes, Surya Saha, Prashant Hosmani, Mirella Flores, Naftali Panitz, Ryan S. Preble, Afolabi Agbona, Ismail Rabbi, Peter Kulakow, Prasad Peteti, Robert Kawuki, Williams Esuma, Micheal Kanaabi, Doreen M. Chelangat, Ezenwanyi Uba, Adeyemi Olojede, Joseph Onyeka, Trushar Shah, Margaret Karanja, Chiedozie Egesi, Hale Tufan, Agre Paterne, Asrat Asfaw, Jean-Luc Jannink, Marnin Wolfe, Clay L. Birkett, David J. Waring, Jenna M. Hershberger, Michael A. Gore, Kelly R. Robbins, Trevor Rife, Chaney Courtney, Jesse Poland, Elizabeth Arnaud, Marie-Angelique Laporte, Heneriko Kulembeka, Kasele Salum, Emmanuel Mrema, Allan Brown, Stanley Bayo, Brigitte Uwimana, Violet Akech, Craig Yencho, Bert de Boeck, Hugo Campos, Rony Swennen, Jeremy D. Edwards, Lukas A. Mueller
Summary: Modern breeding methods rely on robust data management systems and analytics tools to integrate next-generation sequencing and phenomics, allowing the selection of plants with the best characteristics and genetic advantage as parents to create improved cultivars for high adoption rates. Breedbase is a web-based breeding database system that enables better management and utilization of breeding data for decision making in various crops and projects.
G3-GENES GENOMES GENETICS
(2022)
Article
Plant Sciences
Lauren J. Brzozowski, Malachy T. Campbell, Haixiao Hu, Melanie Caffe, Lucia Gutierrez, Kevin P. Smith, Mark E. Sorrells, Michael A. Gore, Jean-Luc Jannink
Summary: In this study, we tested the applicability of genomic prediction methods based on biochemical pathways for oat seed metabolites. The results showed that metabolite kernels developed from the discovery panel significantly improved the prediction accuracy of the same metabolites in the validation panel. However, this method did not improve the prediction accuracy for GC-MS metabolites.
Article
Plant Sciences
Jenna Hershberger, Ryokei Tanaka, Joshua C. Wood, Nicholas Kaczmar, Di Wu, John P. Hamilton, Dean DellaPenna, C. Robin Buell, Michael A. Gore
Summary: This study conducted transcriptome-wide association studies (TWAS) and prediction studies for carotenoid and tocochromanol traits in fresh sweet corn kernels. The results identified significant associations for key genes involved in these traits and highlighted the importance of regulatory variation in the accumulation of vitamins in sweet corn kernels.
Article
Biochemistry & Molecular Biology
Gregory Vogel, Garrett Giles, Kelly R. Robbins, Michael A. Gore, Christine D. Smart
Summary: The investigation of the genetic basis of P. capsici virulence on individual pepper genotypes identified significant genotype-by-genotype interactions and pathogen loci associated with virulence. Additionally, it was found that mapping host genotype-specific virulence variants in P. capsici through GWAS may be challenging.
MOLECULAR PLANT-MICROBE INTERACTIONS
(2022)
Article
Multidisciplinary Sciences
Elise Albert, Sungsoo Kim, Maria Magallanes-Lundback, Yan Bao, Nicholas Deason, Benoit Danilo, Di Wu, Xiaowei Li, Joshua C. Wood, Nolan Bornowski, Michael A. Gore, C. Robin Buell, Dean DellaPenna
Summary: The tocopherol biosynthetic pathway in plants is encoded by VTE genes, but many quantitative trait loci for seed total tocopherols do not have VTE genes, suggesting other activities are involved. A study on Arabidopsis seed tocopherols found a significant interval without VTE genes, which mapped to an uncharacterized, seed-specific, envelope-localized, alpha/beta hydrolase. Mutations in AtVTE7 and its maize ortholog ZmVTE7 significantly decreased seed and leaf total tocopherols, while overexpression of these genes increased leaf totaltocopherols. These findings suggest a model where VTE7 releases prenyl alcohols from chlorophyll biosynthetic intermediates for tocopherol biosynthesis.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Genetics & Heredity
Di Wu, Xiaowei Li, Ryokei Tanaka, Joshua C. Wood, Laura E. Tibbs-Cortes, Maria Magallanes-Lundback, Nolan Bornowski, John P. Hamilton, Brieanne Vaillancourt, Christine H. Diepenbrock, Xianran Li, Nicholas T. Deason, Gregory R. Schoenbaum, Jianming Yu, C. Robin Buell, Dean DellaPenna, Michael A. Gore
Summary: Tocochromanols, which are important antioxidants for both plants and humans, are found in seed oils. However, the genetic and regulatory mechanisms underlying tocochromanol levels in cereal crops are not well understood. In this study, we used a high-resolution mapping approach to identify candidate genes and regulatory loci associated with tocochromanol accumulation in maize grain. Our findings provide valuable insights for breeding and engineering vitamin E and antioxidant levels in maize and other cereals.
Article
Plant Sciences
Ryokei Tanaka, Di Wu, Xiaowei Li, Laura E. Tibbs-Cortes, Joshua C. Wood, Maria Magallanes-Lundback, Nolan Bornowski, John P. Hamilton, Brieanne Vaillancourt, Xianran Li, Nicholas T. Deason, Gregory R. Schoenbaum, C. Robin Buell, Dean DellaPenna, Jianming Yu, Michael A. Gore
Summary: With low vitamin E content in maize grain, the use of the multikernel genomic best linear unbiased prediction (MK-GBLUP) approach can improve the accuracy of predicting vitamin E content. By leveraging existing genomic and transcriptomic information, combined with biological knowledge of known QTL and candidate causal genes, the prediction models can be further enhanced.
Article
Plant Sciences
Laura E. Tibbs-Cortes, Tingting Guo, Xianran Li, Ryokei Tanaka, Adam E. Vanous, David Peters, Candice Gardner, Maria Magallanes-Lundback, Nicholas T. Deason, Dean DellaPenna, Michael A. Gore, Jianming Yu
Summary: This study investigated the feasibility of genomic prediction for tocochromanol traits in maize population and found that the use of optimal training population design methods can improve prediction accuracies. It also highlighted the importance of leveraging genotype data to incorporate new exotic germplasm into a plant breeding program.
Review
Biochemical Research Methods
Lufs Felipe Ferrao, Rakshya Dhakal, Raquel Dias, Denise Tieman, Vance Whitaker, Michael A. Gore, Carlos Messina, Marcio F. R. Resende Jr
Summary: Significant progress has been made in understanding the biochemical factors influencing the nutritional content and flavor profile of fruits and vegetables. The increased demand for flavorful varieties and the need to reduce micronutrient malnutrition are expected to prioritize breeding for these traits. This Perspective outlines the opportunities and challenges for developing more flavorful and nutritious crops and discusses the potential of artificial intelligence (AI) in supporting breeding initiatives.
CURRENT OPINION IN BIOTECHNOLOGY
(2023)
Article
Plant Sciences
Lauren J. J. Brzozowski, Malachy T. T. Campbell, Haixiao Hu, Linxing Yao, Melanie Caffe, Lucia Gutierrez, Kevin P. P. Smith, Mark E. E. Sorrells, Michael A. A. Gore, Jean-Luc Jannink
Summary: This study examines genomic prediction methods for predicting seed fatty acid content traits in oat, and finds that using related germplasm panels as training populations can improve prediction accuracy.
Editorial Material
Biology
Dayane Cristina Lima, Jacob D. Washburn, Jose Ignacio Varela, Qiuyue Chen, Joseph L. Gage, Maria Cinta Romay, James Holland, David Ertl, Marco Lopez-Cruz, Fernando M. Aguate, Gustavo de los Campos, Shawn Kaeppler, Timothy Beissinger, Martin Bohn, Edward Buckler, Jode Edwards, Sherry Flint-Garcia, Michael A. Gore, Candice N. Hirsch, Joseph E. Knoll, John McKay, Richard Minyo, Seth C. Murray, Osler A. Ortez, James C. Schnable, Rajandeep S. Sekhon, Maninder P. Singh, Erin E. Sparks, Addie Thompson, Mitchell Tuinstra, Jason Wallace, Teclemariam Weldekidan, Wenwei Xu, Natalia de Leon
Summary: The Genomes to Fields (G2F) 2022 Maize Genotype by Environment (GxE) Prediction Competition aimed to develop models for predicting grain yield for the 2022 Maize GxE project field trials, leveraging the datasets previously generated by this project and other publicly available data. The dataset included phenotypic and genotypic data of the hybrids evaluated in 45 locations from 2014 to 2022, as well as soil, weather, environmental covariates data, and metadata information for all environments.
BMC RESEARCH NOTES
(2023)