Article
Biology
Zhanying Feng, Zhana Duren, Jingxue Xin, Qiuyue Yuan, Yaoxi He, Bing Su, Wing Hung Wong, Yong Wang
Summary: Systems genetics uses comprehensive multi-omics data to decode complex traits by constructing context-specific regulatory networks and integrating them with genome-wide association studies (GWAS). SpecVar method improves heritability enrichment by associating SNPs with regulatory elements and prioritizes gene regulations underlying relevant tissues. Experimental validation shows that SpecVar enhances heritability enrichment, accurately detects relevant tissues, and reveals causal regulations. It also outperforms existing methods in revealing shared SNP-associated regulations of phenotypes.
Article
Fisheries
Hanyuan Zhang, Youxiu Zhu, Peng Xu, Zixia Zhao, Jianxin Feng, Biyin Wu, Yanliang Jiang, Chuanju Dong, Jian Xu
Summary: This study identified candidate genes and pathways related to amino acid metabolism in common carp through genomic, transcriptomic, and epigenomic analyses. The study revealed divergent patterns in individuals with different amino acid contents. These findings are of significant importance for a better understanding of the mechanisms underlying amino acid metabolism in common carp.
Article
Biochemical Research Methods
Yaniv Shlosberg, Yair Farber, Salah Hasson, Valery Bulatov, Israel Schechter
Summary: Rapid identification of pathogenic bacteria is crucial for patient diagnosis in hospitals and environmental monitoring. A new method using synchronous fluorescence has been developed to quantify the concentrations of three amino acids and differentiate six pathogenic bacterial species, showing potential for broad applicability in rapid cell identification.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Vijay Joshi, Padma Nimmakayala, Qiushuo Song, Venkata Abburi, Purushothaman Natarajan, Amnon Levi, Kevin Crosby, Umesh K. Reddy
Summary: The study reveals significant natural variation in seed-bound free amino acids and total protein content across different watermelon accessions and geographic regions. Accessions with high protein content and essential amino acids proportion can be utilized for added value in food and feed industries through biofortification. Genome-wide association study identifies candidate genes associated with watermelon seed-bound amino acids and total protein.
Article
Plant Sciences
Xukai Li, Yajun Li, Ruyang Xi, Mengmeng Hu, Yuanhuai Han, Jianhua Gao, Xingchun Wang
Summary: This study identified candidate genes associated with water absorption capacity in foxtail millet through Genome-wide Association Study (GWAS) and hypothesized that these genes may be involved in starch synthesis. Additionally, analyzing the starch content and granule characteristics provided insights into water uptake, suggesting a potential association between the compactness of starch granules and seed imbibition.
PLANT GROWTH REGULATION
(2023)
Article
Biochemistry & Molecular Biology
Watchara Phetluan, Samart Wanchana, Wanchana Aesomnuk, Julian Adams, Mutiara K. Pitaloka, Vinitchan Ruanjaichon, Apichart Vanavichit, Theerayut Toojinda, Julie E. Gray, Siwaret Arikit
Summary: Stomatal density in rice varies significantly and is regulated by multiple QTLs and candidate genes, some of which have been previously associated with stomatal traits in Arabidopsis. These findings provide valuable genetic information for future breeding programs aimed at improving photosynthetic capacity, water use efficiency, and drought tolerance in rice.
Article
Medicine, General & Internal
Jian Zhao, Isobel D. Stewart, Denis Baird, Dan Mason, John Wright, Jie Zheng, Tom R. Gaunt, David M. Evans, Rachel M. Freathy, Claudia Langenberg, Nicole M. Warrington, Deborah A. Lawlor, Maria Carolina Borges
Summary: This study used two-sample Mendelian randomisation to explore the effect of maternal circulating amino acids on fetal growth. The results indicate that increased levels of maternal glutamine and serine are associated with higher birthweight, while increased levels of leucine and phenylalanine are associated with lower birthweight.
Article
Food Science & Technology
Xin Yan, Shu Li, Tingyao Tu, Yiqin Li, Mansi Niu, Yuqin Tong, Yang Yang, Tao Xu, Jian Zhao, Caihong Shen, Songtao Wang
Summary: This study investigated the impact of different parameters on the contents and dynamics of free amino acids (FAAs) in greengage wine. The results showed that higher glucose proportion, lower yeast inoculation, higher temperature, and higher initial pH led to increased total and essential amino acid (EAA) content. The optimum conditions for a 14.9-fold increase of EAAs in fermented greengage wine were found to be 22.4°C, pH 4.5, and 3% inoculation.
JOURNAL OF FOOD SCIENCE
(2023)
Article
Immunology
Xueying Liu, Yahu Miao, Chao Liu, Wan Lu, Qing Feng, Qiu Zhang
Summary: This study utilized TWAS method to analyze GWAS summary statistics from 755,406 AITD individuals, and levels of gene expression from two tissue datasets, to identify differentially expressed genes associated with AITD. Further analysis revealed 94 genes potentially playing important roles in AITD, and new susceptibility genes were detected using FUMA and SMR methods. Additionally, pheWAS study identified the risk of other related phenotypes for AITD-related genes.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Yan Liu, Huan Long, Simin Feng, Tingting Ma, Mufeng Wang, Lizhu Niu, Xinyi Zhang, Lianni Wang, Yu Lei, Yilong Chen, Qiankun Wang, Xuewen Xu
Summary: This study identified a correlation between intramuscular fat content and gene expression levels in pigs, highlighting the significant role of the AMPK/PPAR signaling pathway in regulating IMF content. Through a combination of QTL mapping and candidate gene identification, novel genes related to IMF content were proposed.
Article
Biochemistry & Molecular Biology
Do Soon Kim, Andrew Watkins, Erik Bidstrup, Joongoo Lee, Ved Topkar, Camila Kofman, Kevin J. Schwarz, Yan Liu, Grigore Pintilie, Emily Roney, Rhiju Das, Michael C. Jewett
Summary: The study introduces a method called Evolink, which enables high-throughput evolution of sequence-distant regions in large macromolecular machines and guides library design through computational RNA modeling. This approach may enhance the engineering of macromolecular machines for new functions in synthetic biology.
NATURE CHEMICAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Pei Song, Wubei Dong
Summary: This study identified an antifungal gene, Mt1, from Bacillus subtilis 330-2, which significantly reduced the pathogenicity of Fusarium graminearum by inhibiting amino acid metabolism. Transcriptome analysis indicated that the most affected metabolic pathway was branched-chain amino acids (BCAAs). These findings provide new targets for developing strategies to control Fusarium head blight in wheat.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Agriculture, Dairy & Animal Science
Xiaoke Zhang, Qing Lin, Weili Liao, Wenjing Zhang, Tingting Li, Jiaqi Li, Zhe Zhang, Xiang Huang, Hao Zhang
Summary: By using weighted single-step GWAS, we identified genetic regions and candidate genes associated with semen traits in Duroc boars, providing a deeper understanding of the genetic structure of semen traits and the biological information provided by gene networks. This study can accelerate the genetic process of semen traits in boars.
Article
Agronomy
Xiaoqian Wang, Lihong Xie, Jiachuang Fang, Yunlong Pang, Jianlong Xu, Zhikang Li
Summary: The genome-wide haplotype association study identified 174 genes associated with the amino acid content of rice, including 34 genes associated with at least two components. In addition, the associated SNPs in specific genes were also identified through a traditional genome-wide association study. This study provides valuable resources for further characterization and improvement of rice nutritional quality.
Article
Biotechnology & Applied Microbiology
Keqi Li, Jie Wang, Lieqiong Kuang, Ze Tian, Xinfa Wang, Xiaoling Dun, Jinxing Tu, Hanzhong Wang
Summary: This study identified 16 QTL clusters and four candidate genes controlling persistently root development, as well as 32 QTL clusters and eight candidate genes stage-specifically regulating root growth in rapeseed. The results provide new insights into the genetic mechanisms of root growth by identifying key candidate QTL/genes in rapeseed.
BIOTECHNOLOGY FOR BIOFUELS
(2021)
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
Genetics & Heredity
Nataliya E. Yelina, Daniel Holland, Sabrina Gonzalez-Jorge, Dominique Hirsz, Ziyi Yang, Ian R. Henderson
Summary: Meiotic crossovers play an important role in crop improvement, with uneven distribution along chromosomes posing challenges. Targeting specific genome locations for crossovers requires further research to fully understand its implications for plant genome targeting.
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
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
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.
Article
Plant Sciences
Maria Dolores Camalle, Shimon Pivonia, Udi Zurgil, Aaron Fait, Noemi Tel Zur
Summary: Grafting can improve melon fruit yield and quality, but lack of compatibility between rootstock and scion hampers its effect. We studied melon-pumpkin graft combinations with different compatibility levels to assess the impact of rootstock identity on melon fruit yield and quality. Our results showed that rootstock identity (and compatibility level with scion) was associated with increased fruit nutritional values, including high concentrations of organic acids and soluble carbohydrates.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Noga Sikron-Persi, Gila Granot, Albert Batushansky, David Toubiana, Gideon Grafi, Aaron Fait
Summary: A study on the petioles of perennial desert shrub Zygophyllum dumosum Boiss revealed a consistent seasonal pattern in petiole metabolism, involving organic acids, polyols, phenylpropanoids, sulfate conjugates, and piperazines. The metabolic changes were primarily related to the plant's development stage and its interaction with the environment, rather than specific environmental conditions.
Article
Plant Sciences
Corrado Perin, Pankaj Kumar Verma, Gil Harari, Yedidya Suued, Matanya Harel, Danielle Ferman-Mintz, Elyashiv Drori, Yishai Netzer, Aaron Fait
Summary: Continuously increasing global temperature could have a significant impact on grape berry metabolite accumulation, wine polyphenol concentration, and color intensity. Field trials were conducted to explore the effect of late shoot pruning on grape berry and wine metabolite composition. The results showed that late pruning treatments had a significant effect on must and wine metabolites, with higher metabolite content observed in the late shoot pruning treatments for Syrah grapes, but not consistently for Malbec grapes. This suggests that late shoot pruning can impact must and wine quality-related metabolites, which may be related to enhanced photosynthetic efficiency, especially in warm climates.
FRONTIERS IN PLANT SCIENCE
(2023)
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)
