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Yang Y, Harrison RC, Zhang D, Shen B, Yan Y, Kang D. Effect of genetic distances of different genotypes of maize on the authenticity of single seeds detected by NIR spectroscopy. FRONTIERS IN PLANT SCIENCE 2024; 15:1361328. [PMID: 38486851 PMCID: PMC10937569 DOI: 10.3389/fpls.2024.1361328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Accepted: 02/12/2024] [Indexed: 03/17/2024]
Abstract
Introduction NIR spectroscopy combined with chemometric algorithms has been widely used for seed authenticity detection. However, the study of seed genetic distance, an internal feature that affects the discriminative performance of classification models, has rarely been reported. Methods Therefore, maize seed samples of different genotypes were selected to investigate the effect of genetic distance on the authenticity of single seeds detected by NIR spectroscopy. Firstly, the Support vector machine (SVM) model was established using spectral information combined with a preprocessing algorithm, and then the DNA of the samples was extracted to study the correlation between genetic and relative spectral distances, the model identification performance, and finally to compare the similarities and differences between the results of genetic clustering and relative spectral clustering. Results The results were as follows: the average accuracy of the models was 93.6% (inbred lines) and 93.7% (hybrids), respectively; Genetic distance and correlation spectral distance exhibited positive correlation significantly (inbred lines: r=0.177, p<0.05; hybrids: r=0.238, p<0.05), likewise genetic distance and model accuracy also showed positive correlation (inbred lines: r=0.611, p<0.01; hybrids: r=0.6158, p<0.01); Genetic clustering and spectral clustering results were essentially uniform for 94.3% (inbred lines) and 93.9% (hybrids), respectively. Discussion This study reveals the relationship between the genetic and relative spectral distances of seeds and the accuracy of the model, which provides theoretical basis for the establishment of the standardized system for detecting the authenticity of seeds by NIR spectroscopic techniques.
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Affiliation(s)
- Yongqin Yang
- Ministry of Education of the People's Republic of China (MOE) Key Laboratory of Crop Heterosis and Utilization, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Rashaun Candace Harrison
- Ministry of Education of the People's Republic of China (MOE) Key Laboratory of Crop Heterosis and Utilization, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Dun Zhang
- Ministry of Education of the People's Republic of China (MOE) Key Laboratory of Crop Heterosis and Utilization, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Binghui Shen
- Department of Applied Physics, College of Science, China Agricultural University, Beijing, China
| | - Yanlu Yan
- Department of Electrical Engineering, College of Information and Electrical Engineering, China Agricultural University, Beijing, China
| | - Dingming Kang
- Ministry of Education of the People's Republic of China (MOE) Key Laboratory of Crop Heterosis and Utilization, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
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Mohamed WMA, Moustafa MAM, Thu MJ, Kakisaka K, Chatanga E, Ogata S, Hayashi N, Taya Y, Ohari Y, Naguib D, Qiu Y, Matsuno K, Bawm S, Htun LL, Barker SC, Katakura K, Ito K, Nonaka N, Nakao R. Comparative mitogenomics elucidates the population genetic structure of
Amblyomma testudinarium
in Japan and a closely related
Amblyomma
species in Myanmar. Evol Appl 2022; 15:1062-1078. [PMID: 35899249 PMCID: PMC9309438 DOI: 10.1111/eva.13426] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 04/27/2022] [Accepted: 05/29/2022] [Indexed: 12/05/2022] Open
Abstract
Ticks are the second most important vector capable of transmitting diseases affecting the health of both humans and animals. Amblyomma testudinarium Koch 1844 (Acari: Ixodidae), is a hard tick species having a wide geographic distribution in Asia. In this study, we analyzed the composition of A. testudinarium whole mitogenomes from various geographical regions in Japan and investigated the population structure, demographic patterns, and phylogeographic relationship with other ixodid species. In addition, we characterized a potentially novel tick species closely related to A. testudinarium from Myanmar. Phylogeographic inference and evolutionary dynamics based on the 15 mitochondrial coding genes supported that A. testudinarium population in Japan is resolved into a star‐like haplogroup and suggested a distinct population structure of A. testudinarium from Amami island in Kyushu region. Correlation analysis using Mantel test statistics showed that no significant correlation was observed between the genetic and geographic distances calculated between the A. testudinarium population from different localities in Japan. Finally, demographic analyses, including mismatch analysis and Tajima’s D test, suggested a possibility of recent population expansion occurred within Japanese haplogroup after a bottleneck event. Although A. testudinarium has been considered widespread and common in East and Southeast Asia, the current study suggested that potentially several cryptic Amblyomma spp. closely related to A. testudinarium are present in Asia.
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Affiliation(s)
- Wessam Mohamed Ahmed Mohamed
- Laboratory of Parasitology, Department of Disease Control, Faculty of Veterinary Medicine Hokkaido University Sapporo Hokkaido Japan
- Division of Bioinformatics, International Institute for Zoonosis Control Hokkaido University Sapporo Hokkaido Japan
| | - Mohamed Abdallah Mohamed Moustafa
- Laboratory of Parasitology, Department of Disease Control, Faculty of Veterinary Medicine Hokkaido University Sapporo Hokkaido Japan
- Department of Animal Medicine, Faculty of Veterinary Medicine South Valley University Qena Egypt
| | - May June Thu
- Laboratory of Parasitology, Department of Disease Control, Faculty of Veterinary Medicine Hokkaido University Sapporo Hokkaido Japan
- Department of Food and Drug Administration, Ministry of Health, Zabu Thiri, Nay Pyi Taw 15011 Myanmar
| | - Keita Kakisaka
- Laboratory of Parasitology, Department of Disease Control, Faculty of Veterinary Medicine Hokkaido University Sapporo Hokkaido Japan
| | - Elisha Chatanga
- Laboratory of Parasitology, Department of Disease Control, Faculty of Veterinary Medicine Hokkaido University Sapporo Hokkaido Japan
- Department of Veterinary Pathobiology, Faculty of Veterinary Medicine Lilongwe University of Agriculture and Natural Resources Lilongwe Malawi
| | - Shohei Ogata
- Laboratory of Parasitology, Department of Disease Control, Faculty of Veterinary Medicine Hokkaido University Sapporo Hokkaido Japan
| | - Naoki Hayashi
- Laboratory of Parasitology, Department of Disease Control, Faculty of Veterinary Medicine Hokkaido University Sapporo Hokkaido Japan
| | - Yurie Taya
- Laboratory of Parasitology, Department of Disease Control, Faculty of Veterinary Medicine Hokkaido University Sapporo Hokkaido Japan
| | - Yuma Ohari
- Laboratory of Parasitology, Department of Disease Control, Faculty of Veterinary Medicine Hokkaido University Sapporo Hokkaido Japan
| | - Doaa Naguib
- Laboratory of Parasitology, Department of Disease Control, Faculty of Veterinary Medicine Hokkaido University Sapporo Hokkaido Japan
- Department of Hygiene and Zoonoses, Faculty of Veterinary Medicine Mansoura University Mansoura Egypt
| | - Yongjin Qiu
- Division of International Research Promotion, International Institute for Zoonosis Control Hokkaido University Sapporo Hokkaido Japan
| | - Keita Matsuno
- Division of Risk Analysis and Management, International Institute for Zoonosis Control Hokkaido University Sapporo Hokkaido Japan
- International Collaboration Unit, International Institute for Zoonosis Control Hokkaido University Sapporo Hokkaido Japan
- One Health Research Center Hokkaido University Sapporo Hokkaido Japan
| | - Saw Bawm
- Department of International Relations and Information Technology University of Veterinary Science Yezin, Nay Pyi Taw Myanmar
- Department of Pharmacology and Parasitology University of Veterinary Science Yezin, Nay Pyi Taw Myanmar
| | - Lat Lat Htun
- Department of Pharmacology and Parasitology University of Veterinary Science Yezin, Nay Pyi Taw Myanmar
| | - Stephen C. Barker
- Department of Parasitology, School of Chemistry and Molecular Biosciences The University of Queensland Brisbane QLD Australia
| | - Ken Katakura
- Laboratory of Parasitology, Department of Disease Control, Faculty of Veterinary Medicine Hokkaido University Sapporo Hokkaido Japan
| | - Kimihito Ito
- Division of Bioinformatics, International Institute for Zoonosis Control Hokkaido University Sapporo Hokkaido Japan
| | - Nariaki Nonaka
- Laboratory of Parasitology, Department of Disease Control, Faculty of Veterinary Medicine Hokkaido University Sapporo Hokkaido Japan
| | - Ryo Nakao
- Laboratory of Parasitology, Department of Disease Control, Faculty of Veterinary Medicine Hokkaido University Sapporo Hokkaido Japan
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Shi Q, Liu Y, Shi A, Cai Z, Nian H, Hartmann M, Lian T. Rhizosphere Soil Fungal Communities of Aluminum-Tolerant and -Sensitive Soybean Genotypes Respond Differently to Aluminum Stress in an Acid Soil. Front Microbiol 2020; 11:1177. [PMID: 32547532 PMCID: PMC7270577 DOI: 10.3389/fmicb.2020.01177] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Accepted: 05/08/2020] [Indexed: 01/22/2023] Open
Abstract
Different soybean genotypes can differ in their tolerance toward aluminum stress depending on their rhizosphere-inhabiting microorganisms. However, there is limited understanding of the response of fungal communities to different aluminum concentrations across different genotypes. Here, we used metabarcoding of fungal ribosomal markers to assess the effects of aluminum stress on the rhizosphere fungal community of aluminum-tolerant and aluminum-sensitive soybean genotypes. Shifts in fungal community structure were related to changes in plant biomass, fungal abundance and soil chemical properties. Aluminum stress increased the difference in fungal community structure between tolerant and sensitive genotypes. Penicillium, Cladosporium and Talaromyces increased with increasing aluminum concentration. These taxa associated with the aluminum-tolerant genotypes were enriched at the highest aluminum concentration. Moreover, complexity of the co-occurrence network associated with the tolerant genotypes increased at the highest aluminum concentration. Collectively, increasing aluminum concentrations magnified the differences in fungal community structure between the two studied tolerant and sensitive soybean genotypes. This study highlights the possibility to focus on rhizosphere fungal communities as potential breeding target to produce crops that are more tolerant toward heavy metal stress or toxicity in general.
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Affiliation(s)
- Qihan Shi
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China.,The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Yuantai Liu
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China.,The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Aoqing Shi
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China.,The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Zhandong Cai
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China.,The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Hai Nian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China.,The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Martin Hartmann
- Institute of Agricultural Sciences, ETH Zurich, Zurich, Switzerland
| | - Tengxiang Lian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, Guangdong, China.,The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China
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Xing X, Liu Q, Gao Y, Shao S, Guo L, Jacquemyn H, Zhao Z, Guo S. The Architecture of the Network of Orchid–Fungus Interactions in Nine Co-occurring Dendrobium Species. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00130] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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