Sorghum, the fifth most important food crop globally, serves not only as a source of silage forage, fiber, syrup, and biofuel, but also is widely recognized as an ideal model crop for studying stress biology due to its exceptional ability to tolerate multiple abiotic stresses, including high salt-alkali conditions, drought, and heat. However, conducting functional genomics studies on sorghum has been challenging, primarily due to the limited availability of genetic resources and effective genetic transformation techniques. In this study, we developed a comprehensive and systematic resource platform (https://sorghum.genetics.ac.cn/SGMD) aiming to advance the genetic understanding of sorghum. Our effort encompassed a telomere-to-telomere (T2T) genome assembly of an inbred sorghum line, E048, yielding 729.46 Mb of sequence data representing the complete genome. Alongside the high-quality sequence data, a gene-expression atlas covering 13 distinct tissues was developed. Furthermore, we constructed a saturated ethyl methane sulfonate (EMS) mutant library, comprising 13,226 independent mutants. Causal genes in chlorosis and leafy mutants from the library were easily identified by leveraging the MutMap and MutMap+ methodologies, demonstrating the powerful application of this library for identifying functional genes. To further facilitate the sorghum research community, we performed whole-genome sequencing (WGS) of 179 M mutant lines, resulting a total of 2,291,074 mutations that covered 97.54% of all genes. In addition, an Agrobacterium-mediated sorghum transformation platform was established for gene function studies. In summary, this work established a comprehensive platform, providing valuable resources for functional genomics investigations and genetic improvement of sorghum.
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http://dx.doi.org/10.1016/j.molp.2025.03.005 | DOI Listing |
EBioMedicine
February 2025
Institute of Medical Sciences, School of Medicine, Medical Sciences & Nutrition, University of Aberdeen, Aberdeen, UK; Institute for Clinical Research and Systems Medicine, Health and Medical University, Potsdam, Germany.
Background: Maternal smoking and foetal exposure to nicotine and other harmful chemicals in utero remains a serious public health issue with little knowledge about the underlying genetics and consequences of maternal smoking in ageing individuals. Here, we investigated the epidemiology and genomic architecture of maternal smoking in a middle-aged population and compare the results to effects observed in the developing foetus.
Methods: In the current project, we included 351,562 participants from the UK Biobank (UKB) and estimated exposure to maternal smoking status during pregnancy through self-reporting from the UKB participants about the mother's smoking status around their birth.
Trends Microbiol
March 2025
Department of Microbiology, University of Washington, Seattle, WA, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA; Microbial Interactions and Microbiome Center, University of Washington, Seattle, WA, USA. Electronic address:
The type VI secretion system mediates interbacterial antagonism between Gram-negative bacteria through delivery of toxic effector proteins. A recent comprehensive genomic analysis by Habich et al. reveals interesting features of the evolution of T6SSs and their corresponding effectors in Pseudomonas aeruginosa, raising questions about functional specialization of the system.
View Article and Find Full Text PDFTrends Plant Sci
March 2025
School of Basic Medical Sciences, Soochow University, Suzhou, Jiangsu 215123, China. Electronic address:
Anal Chim Acta
May 2025
State Key Laboratory of Natural Medicines, China Pharmaceutical University, No. 639 Longmian Dadao, Nanjing, 211198, China. Electronic address:
Background: Traditional studies of protein responses to external stimuli primarily focus on changes in protein abundance, often overlooking the critical role of protein conformational alterations. To address this gap, we developed Protein Abundance and Conformation Analysis (PACA), an integrative method that quantifies both protein abundance and conformational changes. PACA combines conventional quantitative proteomics for abundance measurements with Target Response Accessibility Profiling (TRAP), a technique that captures conformational changes in situ by applying reductive dimethylation to label accessible lysine residues in living cells before lysis.
View Article and Find Full Text PDFJ Genet Eng Biotechnol
March 2025
ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012 India. Electronic address:
Pigeonpea is an important legume valued for its high nutritional, agricultural, and economic significance in the Asian subcontinent. Despite its potential for high yield, productivity remains stagnant due to several abiotic and biotic stresses. To mitigate these challenges, biotechnological interventions like genome editing offer promising solutions.
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