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Gerard D, Thakkar M, Ferrão LFV. Tests for segregation distortion in tetraploid F1 populations. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2025; 138:30. [PMID: 39814998 PMCID: PMC11735573 DOI: 10.1007/s00122-025-04816-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 01/01/2025] [Indexed: 01/18/2025]
Abstract
KEY MESSAGE In tetraploid F1 populations, traditional segregation distortion tests often inaccurately flag SNPs due to ignoring polyploid meiosis processes and genotype uncertainty. We develop tests that account for these factors. Genotype data from tetraploid F1 populations are often collected in breeding programs for mapping and genomic selection purposes. A common quality control procedure in these groups is to compare empirical genotype frequencies against those predicted by Mendelian segregation, where SNPs detected to have segregation distortion are discarded. However, current tests for segregation distortion are insufficient in that they do not account for double reduction and preferential pairing, two meiotic processes in polyploids that naturally change gamete frequencies, leading these tests to detect segregation distortion too often. Current tests also do not account for genotype uncertainty, again leading these tests to detect segregation distortion too often. Here, we incorporate double reduction, preferential pairing, and genotype uncertainty in likelihood ratio and Bayesian tests for segregation distortion. Our methods are implemented in a user-friendly R package, menbayes. We demonstrate the superiority of our methods to those currently used in the literature on both simulations and real data.
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Affiliation(s)
- David Gerard
- Department of Mathematics and Statistics, American University, Washington, DC, 20016, USA.
| | - Mira Thakkar
- Department of Mathematics and Statistics, American University, Washington, DC, 20016, USA
| | - Luis Felipe V Ferrão
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
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Chebaro Z, Mesmar JE, Badran A, Al-Sawalmih A, Maresca M, Baydoun E. Halophila stipulacea: A Comprehensive Review of Its Phytochemical Composition and Pharmacological Activities. Biomolecules 2024; 14:991. [PMID: 39199379 PMCID: PMC11353240 DOI: 10.3390/biom14080991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2024] [Revised: 08/09/2024] [Accepted: 08/10/2024] [Indexed: 09/01/2024] Open
Abstract
Halophila stipulacea (Forsskål and Niebuhr) Ascherson is a small marine seagrass that belongs to the Hydrocharitaceae family. It is native to the Red Sea, Persian Gulf, and Indian Ocean and has successfully invaded the Mediterranean and Caribbean Seas. This article summarizes the pharmacological activities and phytochemical content of H. stipulacea, along with its botanical and ecological characteristics. Studies have shown that H. stipulacea is rich in polyphenols and terpenoids. Additionally, it is rich in proteins, lipids, and carbohydrates, contributing to its nutritional value. Several biological activities are reported by this plant, including antimicrobial, antioxidant, anticancer, anti-inflammatory, anti-metabolic disorders, and anti-osteoclastogenic activities. Further research is needed to validate the efficacy and safety of this plant and to investigate the mechanisms of action underlying the observed effects.
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Affiliation(s)
- Ziad Chebaro
- Department of Biology, American University of Beirut, Riad El Solh, Beirut 1107 2020, Lebanon; (Z.C.); (J.E.M.)
| | - Joelle Edward Mesmar
- Department of Biology, American University of Beirut, Riad El Solh, Beirut 1107 2020, Lebanon; (Z.C.); (J.E.M.)
| | - Adnan Badran
- Department of Nutrition, University of Petra, Amman 11196, Jordan;
| | - Ali Al-Sawalmih
- Marine Science Station, University of Jordan, Aqaba 11942, Jordan;
| | - Marc Maresca
- Aix Marseille Univ, CNRS, Centrale Med, ISM2, 13013 Marseille, France
| | - Elias Baydoun
- Department of Biology, American University of Beirut, Riad El Solh, Beirut 1107 2020, Lebanon; (Z.C.); (J.E.M.)
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Niu X, Ren W, Xu C, Wang R, Zhang J, Wang H. Taxonomic and functional β-diversity patterns reveal stochastic assembly rules in microbial communities of seagrass beds. FRONTIERS IN PLANT SCIENCE 2024; 15:1367773. [PMID: 38481397 PMCID: PMC10932972 DOI: 10.3389/fpls.2024.1367773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 02/14/2024] [Indexed: 08/22/2024]
Abstract
Microorganisms are important members of seagrass bed ecosystems and play a crucial role in maintaining the health of seagrasses and the ecological functions of the ecosystem. In this study, we systematically quantified the assembly processes of microbial communities in fragmented seagrass beds and examined their correlation with environmental factors. Concurrently, we explored the relative contributions of species replacement and richness differences to the taxonomic and functional β-diversity of microbial communities, investigated the potential interrelation between these components, and assessed the explanatory power of environmental factors. The results suggest that stochastic processes dominate community assembly. Taxonomic β-diversity differences are governed by species replacement, while for functional β-diversity, the contribution of richness differences slightly outweighs that of replacement processes. A weak but significant correlation (p < 0.05) exists between the two components of β-diversity in taxonomy and functionality, with almost no observed significant correlation with environmental factors. This implies significant differences in taxonomy, but functional convergence and redundancy within microbial communities. Environmental factors are insufficient to explain the β-diversity differences. In conclusion, the assembly of microbial communities in fragmented seagrass beds is governed by stochastic processes. The patterns of taxonomic and functional β-diversity provide new insights and evidence for a better understanding of these stochastic assembly rules. This has important implications for the conservation and management of fragmented seagrass beds.
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Affiliation(s)
- Xiaofeng Niu
- School of Marine Biology and Fisheries, State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, China
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Wenjing Ren
- School of Marine Biology and Fisheries, State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, China
| | - Congjun Xu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Ruilong Wang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Jingwei Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Huan Wang
- School of Marine Biology and Fisheries, State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, China
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, China
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Yan W, Wang Z, Pei Y, Zhou B. Adaptive responses of eelgrass (Zostera marina L.) to ocean warming and acidification. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 206:108257. [PMID: 38064900 DOI: 10.1016/j.plaphy.2023.108257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 11/12/2023] [Accepted: 11/30/2023] [Indexed: 02/15/2024]
Abstract
Ocean warming (OW) and ocean acidification (OA), driven by rapid global warming accelerating at unprecedented rates, are profoundly impacting the stability of seagrass ecosystems. Yet, our current understanding of the effects of OW and OA on seagrass remains constrained. Herein, we investigated the response of eelgrass (Zostera marina L.), a representative seagrass species, to OW and OA through comprehensive transcriptomic and metabolomic analyses. The results showed notable variations in plant performance under varying conditions: OW, OA, and OWA (a combination of both conditions). Specifically, under average oceanic temperature conditions for eelgrass growth over the past 20 years -from May to November-OA promoted the production of differentially expressed genes and metabolites associated with alanine, aspartate, and glutamate metabolism, as well as starch and sucrose metabolism. Under warming condition, eelgrass was resistant to OA by accelerating galactose metabolism, along with glycine, serine, and threonine metabolism, as well as the tricarboxylic acid (TCA) cycle. Under the combined OW and OA condition, eelgrass stimulated fructose and mannose metabolism, glycolysis, and carbon fixation, in addition to galactose metabolism and the TCA cycle to face the interplay. Our findings suggest that eelgrass exhibits adaptive capacity by inducing different metabolites and associated genes, primarily connected with carbon and nitrogen metabolism, in response to varying degrees of OW and OA. The data generated here support the exploration of mechanisms underlying seagrass responses to environmental fluctuations, which hold critical significance for the future conservation and management of these ecosystems.
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Affiliation(s)
- Wenjie Yan
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao, 266003, China.
| | - Zhaohua Wang
- First Institute of Oceanography, MNR, Qingdao, 266061, China
| | - Yanzhao Pei
- College of Marine Life Science, Ocean University of China, Qingdao, 266003, China
| | - Bin Zhou
- College of Marine Life Science, Ocean University of China, Qingdao, 266003, China.
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Thinh PD, Hang CTT, Trung DT, Nguyen TD. Pectin from Three Vietnamese Seagrasses: Isolation, Characterization, and Antioxidant Activity. Processes (Basel) 2023. [DOI: 10.3390/pr11041054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023] Open
Abstract
This study focused on the isolation and structural characterization of pectin from three distinct species of Vietnamese seagrass including Enhalus acoroides, Thalassia hemprichii, and Halophila ovalis. The pectin yield obtained from Enhalus acoroides was the highest, corresponding to 24.15%, followed by those from Thalassia hemprichii (20.04%) and Halophila ovalis (19.14%). The physicochemical properties of pectin including total carbohydrate content, anhydrouronic acid (AUA) content, equivalent weight (EW), methoxyl content (MeO), and degree of esterification (DE) were determined using various analysis techniques. The pectin obtained from all three species were found to be low-methyl-esterified pectin, with the MeO content and DE for E. acoroides, T. hemprichii, and H. ovalis being 6.15% and 27.18%, 3.26% and 43.31%, and 4.65% and 33.25%, respectively. The average molecular weight (MW) of pectin was analyzed by size-exclusion chromatography. Pectin from T. hemprichii had the highest MW of 173.01 kDa, followed by pectin from E. acoroides, with a MW of 127.32 kDa, and that from H. ovalis, with a MW of 56.06 kDa. Furthermore, the pectins from all three seagrass species exhibited high antioxidant activity and might be promising as antioxidants.
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