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Giolai M, Verweij W, Martin S, Pearson N, Nicholson P, Leggett RM, Clark MD. Measuring air metagenomic diversity in an agricultural ecosystem. Curr Biol 2024:S0960-9822(24)00933-3. [PMID: 39096906 DOI: 10.1016/j.cub.2024.07.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 04/26/2024] [Accepted: 07/04/2024] [Indexed: 08/05/2024]
Abstract
All species shed DNA during life or in death, providing an opportunity to monitor biodiversity via environmental DNA (eDNA). In recent years, combining eDNA, high-throughput sequencing technologies, bioinformatics, and increasingly complete sequence databases has promised a non-invasive and non-destructive environmental monitoring tool. Modern agricultural systems are often large monocultures and so are highly vulnerable to disease outbreaks. Pest and pathogen monitoring in agricultural ecosystems is key for efficient and early disease prevention, lower pesticide use, and better food security. Although the air is rich in biodiversity, it has the lowest DNA concentration of all environmental media and yet is the route for windborne spread of many damaging crop pathogens. Our work suggests that ecosystems can be monitored efficiently using airborne nucleic acid information. Here, we show that the airborne DNA of microbes can be recovered, shotgun sequenced, and taxonomically classified, including down to the species level. We show that by monitoring a field growing key crops we can identify the presence of agriculturally significant pathogens and quantify their changing abundance over a period of 1.5 months, often correlating with weather variables. We add to the evidence that aerial eDNA can be used as a source for biomonitoring in terrestrial ecosystems, specifically highlighting agriculturally relevant species and how pathogen levels correlate with weather conditions. Our ability to detect dynamically changing levels of species and strains highlights the value of airborne eDNA in agriculture, monitoring biodiversity changes, and tracking taxa of interest.
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Affiliation(s)
- Michael Giolai
- Natural History Museum, London SW7 5BD, UK; Research Centre for Ecological Change, Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki 00014, Finland
| | - Walter Verweij
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK; Enza Zaden, Enkhuizen 1602 DB, the Netherlands
| | - Samuel Martin
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Neil Pearson
- Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Paul Nicholson
- Crop Genetics Department, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
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Zhang Z, Fu Y, Huang J, Peng Y, Zhou X, Gao H, Wang B, Li Q. Genetic Analysis Reveals Relationships Among Populations of Puccinia striiformis f. sp. tritici from Shaanxi-Gansu-Ningxia-Xinjiang of Northwestern and Sichuan-Yunnan of Southwestern China. PLANT DISEASE 2024; 108:1659-1669. [PMID: 38128078 DOI: 10.1094/pdis-09-23-1852-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most destructive diseases worldwide. In China, wheat stripe rust generally occurs in the northwestern and southwestern regions; however, the genetic relationships of Pst populations between these regions are largely unclear. To determine the population structure and potential migration route in these regions, 235 isolates collected from Xinjiang (XJ), Gansu (GS), Ningxia (NX), Shaanxi (SX), Sichuan (SC), and Yunnan (YN) provinces in 2021 and 2022 were phenotyped using two sets of Pst differentials and genotyped using 20 competitive allele-specific PCR-single nucleotide polymorphism (KASP-SNP) markers. The phenotype tests indicated that CYR34, CYR32, and CYR33 were the predominant races with different occurrence frequencies in different regions and years. Genotypic analysis revealed that a total of 183 multilocus genotypes were identified, and the genetic diversity in the YN subpopulation was the highest. The genetic background in the SX subpopulation was similar to that in the GS and NX subpopulations, and the genetic background in the YN subpopulation was similar to that in the SC and SX subpopulations. A high level of gene flow (Nm) was found between the SX and GS, SX and NX, GS and NX, and SC and YN subpopulations, suggesting the migration of Pst among these regions, while a small amount of Nm existed between the SX and SC subpopulations. SC may serve as a bridge connecting Pst subpopulations between the northwestern provinces (SX, GS, and NX) and the southwestern provinces (SC and YN). With a relatively high genetic distance and low Nm values compared with other Pst subpopulations, XJ is considered a relatively independent epidemiological region in China. These results improved our current understanding of the wheat stripe rust epidemic in northwestern and southwestern regions of China.
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Affiliation(s)
- Zhuoyue Zhang
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yanzi Fu
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jie Huang
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yunliang Peng
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan 610066, China
| | - Xinli Zhou
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan 621010, China
| | - Haifeng Gao
- Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
| | - Baotong Wang
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Qiang Li
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
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Zhou A, Wang J, Chen X, Xia M, Feng Y, Ji F, Huang L, Kang Z, Zhan G. Virulence Characterization of Puccinia striiformis f. sp. tritici in China Using the Chinese and Yr Single-Gene Differentials. PLANT DISEASE 2024; 108:671-683. [PMID: 37721522 DOI: 10.1094/pdis-08-23-1524-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most important diseases of wheat. Identifying Pst races is essential for developing resistant cultivars and managing the disease. In this study, 608 isolates collected from China in 2021 were tested with the Chinese set of 19 wheat variety differentials and the set of 18 Yr single-gene differentials. Of the 119 races detected with the Chinese set of differentials, 94 were new. A higher number (149) of races were identified using the Yr single-gene differentials. The frequencies of virulence factors to 17 of the 19 Chinese differential varieties and to 10 of the 18 Yr single-gene differentials were high (>60%). None of the isolates were virulent to the differentials Zhong 4 (Yr genes unknown) and Triticum spelta Album (Yr5) in the Chinese set and the Yr5 and Yr15 lines in the single-gene set of differentials, indicating that these genes or varieties are effective against the Pst population detected in 2021. Using Nei's genetic distance, the 16 provincial Pst populations were clustered into six groups based on the Chinese set and eight groups based on the Yr single-gene set of differentials. In addition, we found that the same races identified using the Chinese differentials could be further differentiated into different races using the Yr single-gene differentials, suggesting a higher differential capability than the Chinese set of differentials. The results provide a scientific basis for monitoring Pst populations and guiding resistance breeding in China.
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Affiliation(s)
- Aihong Zhou
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Jie Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Xianming Chen
- USDA-ARS, Wheat Health, Genetics, and Quality Research Unit and Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, U.S.A
| | - Minghao Xia
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Yaoxuan Feng
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Fan Ji
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Lili Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Gangming Zhan
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
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Liu B, Ma M, Liu X, Wang J, Zhong M, Feng Y, Huang L, Kang Z, Zhan G. Inoculum Sources of Puccinia striiformis f. sp. tritici for Stripe Rust Epidemics on the Eastern Coast of China. PHYTOPATHOLOGY 2024; 114:211-219. [PMID: 37486148 DOI: 10.1094/phyto-06-23-0205-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Stripe rust, a fungal disease caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most destructive diseases affecting wheat production areas worldwide. In recent years in China, wheat stripe rust has caused huge yield losses throughout the vast Huang-Huai-Hai region, including the eastern coast regions, especially Shandong province. The aim of the present study was to explore the population structure and potential inoculum sources of the pathogen in this region. A total of 234 Pst isolates in 2021 were collected and isolated from seven provinces and identified for virulence phenotypes using 19 Chinese differentials and for genotypes using 17 single-nucleotide polymorphism-based Kompetitive allele-specific PCR markers. The virulence phenotype tests identified predominant races CYR34 (18.0%) and CYR32 (16.0%) in Shandong, which were similar to the results in Henan province, also with the predominant races CYR34 (21.9%) and CYR32 (18.8%). Based on the virulence data of phenotyping, the Pst populations in Shandong, Hubei, and Henan were similar. The genotypic analysis revealed remarkable gene flows among the Shandong, Hubei, Henan, Yunnan, and Guizhou populations, showing a migration of Pst from the southwestern oversummering regions to Shandong through the winter spore production regions. Genetic structure analysis also indicated an additional migration route from the northwestern oversummering regions through winter spore production regions to Shandong. The results are useful for understanding stripe rust epidemiology in the eastern coast region and improving control of the disease throughout the country.
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Affiliation(s)
- Bofan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Mengjie Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Xinyun Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Jianfeng Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Mingjuan Zhong
- Zhucheng Agricultural and Rural Bureau, Zhucheng, Shandong 262200, P.R. China
| | - Yaoxuan Feng
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Lili Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
| | - Gangming Zhan
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, P.R. China
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Li Y, Dai J, Zhang T, Wang B, Zhang S, Wang C, Zhang J, Yao Q, Li M, Li C, Peng Y, Cao S, Zhan G, Tao F, Gao H, Huang W, Feng X, Bai Y, Qucuo Z, Shang H, Huang C, Liu W, Zhan J, Xu X, Chen X, Kang Z, Hu X. Genomic analysis, trajectory tracking, and field surveys reveal sources and long-distance dispersal routes of wheat stripe rust pathogen in China. PLANT COMMUNICATIONS 2023:100563. [PMID: 36809881 PMCID: PMC10363508 DOI: 10.1016/j.xplc.2023.100563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 01/08/2023] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
Identifying sources of phytopathogen inoculum and determining their contributions to disease outbreaks are essential for predicting disease development and establishing control strategies. Puccinia striiformis f. sp. tritici (Pst), the causal agent of wheat stripe rust, is an airborne fungal pathogen with rapid virulence variation that threatens wheat production through its long-distance migration. Because of wide variation in geographic features, climatic conditions, and wheat production systems, Pst sources and related dispersal routes in China are largely unclear. In the present study, we performed genomic analyses of 154 Pst isolates from all major wheat-growing regions in China to determine Pst population structure and diversity. Through trajectory tracking, historical migration studies, genetic introgression analyses, and field surveys, we investigated Pst sources and their contributions to wheat stripe rust epidemics. We identified Longnan, the Himalayan region, and the Guizhou Plateau, which contain the highest population genetic diversities, as the Pst sources in China. Pst from Longnan disseminates mainly to eastern Liupan Mountain, the Sichuan Basin, and eastern Qinghai; that from the Himalayan region spreads mainly to the Sichuan Basin and eastern Qinghai; and that from the Guizhou Plateau migrates mainly to the Sichuan Basin and the Central Plain. These findings improve our current understanding of wheat stripe rust epidemics in China and emphasize the need for managing stripe rust on a national scale.
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Affiliation(s)
- Yuxiang Li
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Taicheng Road 3, Yangling, Shaanxi, China
| | - Jichen Dai
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Taicheng Road 3, Yangling, Shaanxi, China
| | - Taixue Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Taicheng Road 3, Yangling, Shaanxi, China
| | - Baotong Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Taicheng Road 3, Yangling, Shaanxi, China
| | - Siyue Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Taicheng Road 3, Yangling, Shaanxi, China
| | - Conghao Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Taicheng Road 3, Yangling, Shaanxi, China
| | - Jiguang Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Taicheng Road 3, Yangling, Shaanxi, China
| | - Qiang Yao
- Key Laboratory of Agricultural Integrated Pest Management, Qinghai Province, Academy of Agriculture and Forestry Science, Qinghai University, Xining, Qinghai, China
| | - Mingju Li
- Yunnan Key Laboratory of Green Prevention and Control of Agricultural Transboundary Pests, Agricultural Environment and Resource Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, China
| | - Chengyun Li
- State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Yuelin Peng
- Department of Plant Pathology, Tibet Agricultural and Animal Husbandry College, Linzhi, Tibet, China
| | - Shiqin Cao
- Wheat Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Gangming Zhan
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Taicheng Road 3, Yangling, Shaanxi, China
| | - Fei Tao
- Biocontrol Engineering Laboratory of Crop Diseases and Pests of Gansu Province, College of Plant Protection, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Haifeng Gao
- Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, China
| | - Weili Huang
- Xi'an Huang's Bio-technology Company Ltd, Xi'an, Shaanxi, China
| | - Xiaojun Feng
- Shaanxi Plant Protection Extension Station, Xi'an, Shaanxi, China
| | - Yingwen Bai
- Baoji Plant Protection Extension Station, Baoji, Shaanxi, China
| | - Zhuoma Qucuo
- Department of Plant Pathology, Tibet Agricultural and Animal Husbandry College, Linzhi, Tibet, China
| | - Hongsheng Shang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Taicheng Road 3, Yangling, Shaanxi, China
| | - Chong Huang
- National Agricultural Technology Extension and Service Center, Ministry of Agriculture, Beijing, China
| | - Wancai Liu
- National Agricultural Technology Extension and Service Center, Ministry of Agriculture, Beijing, China
| | - Jiasui Zhan
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Xiangming Xu
- Pest & Pathogen Ecology, NIAB EMR, East Malling, West Malling, Kent, UK
| | - Xianming Chen
- Agricultural Research Service, United States Department of Agriculture and Department of Plant Pathology, Washington State University, Pullman, WA, USA
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Taicheng Road 3, Yangling, Shaanxi, China.
| | - Xiaoping Hu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Taicheng Road 3, Yangling, Shaanxi, China.
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