Article
Plant Sciences
Joao M. Kafer, Mayla D. C. Molinari, Fernando A. Henning, Alessandra Koltun, Viviani V. Marques, Silvana R. R. Marin, Alexandre L. Nepomuceno, Liliane M. Mertz-Henning
Summary: This study aimed to identify genes associated with soybean seed quality by comparing the transcriptomes of soybean seeds with different seed coat colors. Through RNA-seq analysis and validation with real-time PCR, 318 differentially expressed genes were found in all cultivars. These genes are involved in pathways related to ethylene, lipid, brassinosteroid, lignin, and sulfur amino acid biosynthesis.
Article
Plant Sciences
Junmei Hu, Yongbin Zhuang, Xianchong Li, Xiaoming Li, Chanchan Sun, Zhaojun Ding, Ran Xu, Dajian Zhang
Summary: By comparing the transcriptome of two soybean cultivars under salt stress, we found significant differences in gene expression between the salt-tolerant and salt-sensitive cultivars. Phytohormone signaling, oxidoreduction, phenylpropanoid biosynthesis, the mitogen-activated protein kinase pathway, and ribosome metabolism may play crucial roles in the response to salt stress.
Article
Horticulture
Ariana Silva Santos, Edson Mario de Andrade, Andressa Rodrigues de Oliveira Sousa, Marcos Mota do Carmo Costa, Roberto Togawa, Priscila Grynberg, Carlos Priminho Pirovani, Saulo Alves Santos Oliveira, Walter dos Santos Soares Filho, Mauricio Antonio Coelho Filho, Abelmon da Silva Gesteira, Claudia Fortes Ferreira
Summary: This study analyzed the transcriptomes of citrus rootstocks 'Sunki Maravilha' and 'Sunki Tropical' under water deficit conditions, revealing significant gene expression variations and providing candidate genes for engineering or breeding citrus plants with drought tolerance. The differentially expressed genes identified are involved in various biological processes and molecular functions, with a focus on oxidoreductase, protein phosphorylation, transcriptional regulation, ligation processes, and response to oxidative stress.
SCIENTIA HORTICULTURAE
(2021)
Article
Biochemistry & Molecular Biology
Jiahui Liang, Jing Zheng, Ze Wu, Hongqing Wang
Summary: This study investigated the gene activity and regulatory mechanisms during the key period of floral induction in strawberries through transcriptome analysis. Several important genes involved in floral induction were identified, and a preliminary regulatory network was constructed. This provides potential candidate genes for future studies of flowering in strawberries.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Plant Sciences
Julia C. Hooker, Myron Smith, Gerardo Zapata, Martin Charette, Doris Luckert, Ramona M. Mohr, Ketema A. Daba, Thomas D. Warkentin, Mehri Hadinezhad, Brent Barlow, Anfu Hou, Francois Lefebvre, Ashkan Golshani, Elroy R. Cober, Bahram Samanfar
Summary: A study found that soybeans grown in western Canada have lower seed protein content compared to those grown in eastern Canada. Molecular biology and gene expression analysis revealed that this difference may be related to variations in key pathways such as amino acid metabolism and starch metabolism. Specifically, it was observed that western-grown soybeans had persistent upregulation of asparaginase and persistent downregulation of asparagine synthetase, and these enzymes were positively correlated with seed protein content and free asparagine in developing seeds.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Ivan Friero, Eduardo Larriba, Purificacion A. Martinez-Melgarejo, Maria Salud Justamante, M. Victoria Alarcon, Alfonso Albacete, Julio Salguero, Jose Manuel Perez-Perez
Summary: Prolonged cold stress affects plant growth and development, particularly in subtropical crops like maize. Soil temperature hinders primary root elongation, especially during early seedling establishment. However, the impact of moderate temperature fluctuations on root growth at the molecular and physiological levels is still poorly understood. We investigated the root tips of young maize seedlings grown hydroponically at 30 degrees C and subjected to short-term cooling (up to 24 h) at 20 degrees C. Our findings demonstrate that temperature affects both cell division and elongation in the root apical meristem. Time-course analyses of hormone and transcriptomic profiles revealed a complex regulation of endogenous pathways that contribute to adaptive root responses under moderate cooling conditions.
Article
Horticulture
Dongmei Li, Yujie Pang, Hui Li, Dinghan Guo, Ruiqi Wang, Chao Ma, Wenping Xu, Lei Wang, Shiping Wang
Summary: Root restriction is a crucial cultivation technique that enhances fruit quality by increasing ABA production in grapes. Transcriptomic analysis identified key genes involved in plant hormone synthesis and signaling, shedding light on the mechanism underlying fruit quality improvement through root restriction. This study lays a foundation for further enhancing cultivation practices based on ABA-mediated mechanisms.
SCIENTIA HORTICULTURAE
(2021)
Article
Agronomy
Bixian Zhang, Kezhen Zhao, Honglei Ren, Sobhi F. Lamlom, Xiulin Liu, Xueyang Wang, Fengyi Zhang, Rongqiang Yuan, Jiajun Wang
Summary: In this study, potential differentially expressed genes (DEGs) were identified in two wild soybean cultivars with different isoflavone compositions at different seed developmental stages. The results revealed that the difference in isoflavone levels between the two cultivars may be attributable to the differential expression of six identified genes at later stages of seed development. These findings provide insights into the underlying mechanisms for the complexity of isoflavone compositions in soybean seeds.
Article
Plant Sciences
Sani Ibrahim, Nazir Ahmad, Lieqiong Kuang, Keqi Li, Ze Tian, Salisu Bello Sadau, Sani Muhammad Tajo, Xinfa Wang, Hanzhong Wang, Xiaoling Dun
Summary: Root transcriptome analysis was conducted on 20 Brassica napus accessions with high and low potassium utilization efficiency (KUE) using RNA-seq. Differences in expression profiles of 71,437 genes were found between the two contrasting genotype groups. Functional classification analysis revealed that these differentially expressed genes were involved in hormone and signaling pathways, as well as glucose, lipid, and amino acid metabolism. Moreover, 33 transcription factors related to root development were identified. By combining differential expression analysis, gene co-expression network analysis, and genome-wide association study results, four candidate hub genes regulating root system formation were identified.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Lin Lin, Jie Wang, Qun Wang, Mengcheng Ji, Sidan Hong, Linxue Shang, Guozhe Zhang, Yu Zhao, Qingqing Ma, Cuihua Gu
Summary: In this study, the molecular mechanism of drought resistance in Heimia myrtifolia was investigated through transcriptome analysis. The significantly enriched pathways included photosynthesis, plant hormone signal transduction, and others. Transcription factors and related genes on these pathways played important roles in the drought process.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Oncology
Bian Wu, Jinwei Yang, Zhiwei Qin, Hongping Yang, Jingyi Shao, Yun Shang
Summary: This study investigated prognostic factors for stage IV colorectal cancer patients who underwent primary cancer resection without metastasis resection. The location was found to be an independent risk factor for patient prognosis, and a panel of eight genes with significant mRNA level alterations was established to predict the prognosis of this patient group.
Article
Biotechnology & Applied Microbiology
Malarvizhi Sathasivam, Basavalingayya K. K. Swamy, Kushagra Krishnan, Rita Sharma, Spurthi N. N. Nayak, D. S. Uppar, Ravikumar Hosamani
Summary: This study investigates the molecular basis of enhanced root growth under hypergravity conditions by analyzing root transcriptome. The results reveal significant changes in transcript expression, including increased cell division, demand for cell wall constituents, and enhanced hormonal responses.
Article
Biochemistry & Molecular Biology
Yunfeng Shi, Baiyang Yu, Shan Cheng, Weiming Hu, Fen Liu
Summary: Through whole-genome bisulfite sequencing and RNA-seq, the potential impact of autophagy in regulating DNA methylation in Arabidopsis and its role in coping with nitrogen deficiency were determined. Differential expression of genes associated with DNA demethylation was observed, suggesting a correlation between DNA demethylation and the ability of Arabidopsis to cope with nitrogen deficiency. Additionally, DNA methylation was found to impact the biosynthesis of salicylic acid, providing insights into how autophagy defects may lead to SA-activated senescence.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemical Research Methods
Mayla Daiane Correa Molinari, Renata Fuganti-Pagliarini, Daniel de Amorim Barbosa, Elton Gargioni Grisoste Barbosa, Joao Matheus Kafer, Daniel Rockenbach Marin, Silvana Regina Rockenbach Marin, Liliane Marcia Mertz-Henning, Alexandre Lima Nepomuceno
Summary: This study identified ABA-responsive genes and enriched pathways related to ABA in soybeans, and these findings are significant for the development of drought-tolerant soybean varieties.
PLANT MOLECULAR BIOLOGY REPORTER
(2023)
Article
Biochemistry & Molecular Biology
Qingnan Hao, Hongli Yang, Shuilian Chen, Yanhui Qu, Chanjuan Zhang, Limiao Chen, Dong Cao, Songli Yuan, Wei Guo, Zhonglu Yang, Yi Huang, Zhihui Shan, Haifeng Chen, Xinan Zhou
Summary: Asian soybean rust (ASR) is a destructive foliar disease affecting soybeans, and developing resistant cultivars is the most effective strategy for control. However, the understanding of soybean resistance to Phakopsora pachyrhizi is limited, posing a challenge. This study used transcriptomic profiling to investigate the regulation between soybean and P. pachyrhizi, identifying differentially expressed genes (DEGs) and gene co-expression modules associated with pathogen defense.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biotechnology & Applied Microbiology
Davoud Torkamaneh, Jerome Laroche, Babu Valliyodan, Louise O'Donoughue, Elroy Cober, Istvan Rajcan, Ricardo Vilela Abdelnoor, Avinash Sreedasyam, Jeremy Schmutz, Henry T. Nguyen, Francois Belzile
Summary: The GmHapMap is a worldwide haplotype map for soybean that covers extensive diversity and can be applied in soybean genomics and breeding. Genetic data analysis can help identify candidate causal SNPs and alleles that contribute to phenotypic differences. Additionally, predicting loss-of-function mutations allows for exploration of gene function.
PLANT BIOTECHNOLOGY JOURNAL
(2021)
Article
Plant Sciences
Silvas J. Prince, Tri D. Vuong, Xiaolei Wu, Yonghe Bai, Fang Lu, Siva P. Kumpatla, Babu Valliyodan, J. Grover Shannon, Henry T. Nguyen
FRONTIERS IN PLANT SCIENCE
(2020)
Article
Multidisciplinary Sciences
Babu Valliyodan, Anne V. Brown, Juexin Wang, Gunvant Patil, Yang Liu, Paul I. Otyama, Rex T. Nelson, Tri Vuong, Qijian Song, Theresa A. Musket, Ruth Wagner, Pradeep Marri, Sam Reddy, Allen Sessions, Xiaolei Wu, David Grant, Philipp E. Bayer, Manish Roorkiwal, Rajeev K. Varshney, Xin Liu, David Edwards, Dong Xu, Trupti Joshi, Steven B. Cannon, Henry T. Nguyen
Summary: This study reported the genetic diversity and structure of 481 soybean accessions, identifying millions of SNPs and specific linages selected at distinct geographic locations. Conserved regions in cultivated varieties indicated selection during domestication, with most re-sequenced accessions showing high similarity to their genotyped counterparts. The study also identified errors in seed source or genotype tracking in approximately 5% of accessions.
Article
Biochemistry & Molecular Biology
Shuai Zeng, Ziting Mao, Yijie Ren, Duolin Wang, Dong Xu, Trupti Joshi
Summary: G2PDeep is an open-access web server that provides a deep-learning framework for quantitative phenotype prediction and genomic marker discovery. It allows researchers to create and train models through an interactive web interface, monitor training process, and compare model performance. Additionally, G2PDeep integrates multiple datasets, including the soybean nested association mapping data, for predictions of quantitative phenotypes and genomic markers.
NUCLEIC ACIDS RESEARCH
(2021)
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
Plant Sciences
Radha Beena, Silvas Kirubakaran, Narayanan Nithya, Alagu Manickavelu, Rameshwar Prasad Sah, Puthenpeedikal Salim Abida, Janardanan Sreekumar, Poolakkal Muhammed Jaslam, Rajendrakumar Rejeth, Vijayalayam Gengamma Jayalekshmy, Stephen Roy, Ramakrishnan Vimala Manju, Mariasoosai Mary Viji, Kadambot H. M. Siddique
Summary: The study found that Asian cultivars were mainly used to discover new alleles for drought tolerance, while genetic resources adapted to the Indian subcontinent, despite being diverse, were not adequately represented. Through analyzing the genotype and traits of rice under different water conditions, key genes related to yield can be identified.
Article
Agronomy
Jacob Marsh, Haifei Hu, Jakob Petereit, Philipp E. Bayer, Babu Valliyodan, Jacqueline Batley, Henry T. Nguyen, David Edwards
Summary: This study characterized the major high-protein/low-oil associated locus cqProt-003 in soybeans by analyzing the haplotype diversity and global distribution. The results revealed that a 304 bp deletion and variable tandem repeats in the protein coding regions are likely causal candidates. It was found that the high-protein haplotype is common in wild accessions, rare in landraces, and near absent in cultivated breeding pools, suggesting a correlation with domestication and improvement.
THEORETICAL AND APPLIED GENETICS
(2022)
Article
Plant Sciences
Ranjita Sinha, Sara I. Zandalinas, Yosef Fichman, Sidharth Sen, Shuai Zeng, Aurelio Gomez-Cadenas, Trupti Joshi, Felix B. Fritschi, Ron Mittler
Summary: Drought and heat stress can significantly reduce crop yield, especially when they occur together. A study on soybean plants found that during a combination of drought and heat stress, the plants prioritize transpiration through flowers over leaves by opening the flower stomata, protecting the reproductive processes.
Review
Plant Sciences
Juexin Wang, Sen Sidharth, Shuai Zeng, Yuexu Jiang, Yen On Chan, Zhen Lyu, Tyler McCubbin, Rachel Mertz, Robert E. Sharp, Trupti Joshi
Summary: This article reviews bioinformatic and computational methods, models, and platforms for multiomics data analysis, integration, and management. It presents a case study on maize nodal root growth under water deficit stress to demonstrate the power of multiomics datasets. The study also introduces currently available bioinformatic tools for plant and crop science research and explores emerging trends for the future.
PHYSIOLOGIA PLANTARUM
(2022)
Article
Plant Sciences
Silvas Prince, Md Rokebul Anower, Christy M. Motes, Timothy D. Hernandez, Fuqi Liao, Laura Putman, Rob Mattson, Anand Seethepalli, Kushendra Shah, Michael Komp, Perdeep Mehta, Larry M. York, Carolyn Young, Maria J. Monteros
Summary: Drought stress has negative impacts on crop growth and profitability. This study compared two different alfalfa subspecies and identified key morphological and physiological traits for enhancing biomass yield under drought stress. Field surveys and root architecture analysis further validated the importance of these traits. Different drought-adaptive strategies were identified across subspecies populations, which will contribute to the development of alfalfa cultivars suitable for various growing conditions. Combining genes from both subspecies can lead to the development of drought-tolerant alfalfa with higher productivity under limited water availability.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Genetics & Heredity
Jana Biova, Nicholas Dietz, Yen On Chan, Trupti Joshi, Kristin Bilyeu, Maria Skrabisova
Summary: Genome-wide association studies (GWAS) are used to identify genomic regions associated with phenotypes and discover causative mutations (CM) in genes. However, current methods have limitations in comparing candidate genes and actual CMs. In our recent work, we developed a novel approach called Synthetic phenotype to causative mutation (SP2CM), along with a web-based tool called AccuTool. We extended this tool to other species and named it AccuCalc, enhancing its analysis capabilities for datasets with rare phenotypes by automating synthetic phenotype formatting and adding an accuracy-based GWAS evaluation criterion.
Article
Biotechnology & Applied Microbiology
Yen On Chan, Nicholas Dietz, Shuai Zeng, Juexin Wang, Sherry Flint-Garcia, M. Nancy Salazar-Vidal, Maria Skrabisova, Kristin Bilyeu, Trupti Joshi
Summary: The research developed an interactive Allele Catalog Tool for exploring allelic variation in the coding region from re-sequenced data of soybean, Arabidopsis, and maize. The tool allows data query, result visualization, categorical filtering, and download functions, helping researchers connect variant alleles with species meta-information.
Article
Plant Sciences
Ranjita Sinha, Benjamin Shostak, Sai Preethi Induri, Sidharth Sen, Sara Zandalinas, Trupti Joshi, Felix B. Fritschi, Ron Mittler
Summary: Climate change causes more frequent and intense droughts, heat waves, and their combinations, which reduces agricultural productivity and destabilizes societies worldwide. A study on soybean plants found that under water deficit and heat stress, the stomata on leaves close while those on flowers and developing pods remain open, resulting in differential transpiration. This differential transpiration strategy helps to cool the flowers and developing pods and protect seed production from heat-induced damage.
Article
Plant Sciences
Maria Angeles Pelaez-Vico, Adama Tukuli, Pallav Singh, David G. Mendoza-Cozatl, Trupti Joshi, Ron Mittler
Summary: Waterlogging stress induces systemic physiological and transcriptomic responses in plants, involving reactive oxygen species, calcium, and hydraulic waves, as well as the induction of hypoxia acclimation mechanisms.
Article
Oncology
Jing Zhou, Nan Lyu, Qiongling Wang, Ming Yang, Eric T. Kimchi, Kun Cheng, Trupti Joshi, Adama R. Tukuli, Kevin F. Staveley-O'Carroll, Guangfu Li
Summary: Tumor-associated macrophages (TAMs) play a critical role in pancreatic cancer tumorigenesis and their function is regulated by TGFBI. Disruption of TGFBI not only inhibits TAM polarization and their stimulating effect on pancreatic cancer growth, but also improves anti-tumor immunity and sensitizes pancreatic cancer to chemotherapy.