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Liu S, Chen L, Qiao X, Ren J, Zhou C, Yang Y. Functional Evolution of Pseudofabraea citricarpa as an Adaptation to Temperature Change. J Fungi (Basel) 2024; 10:109. [PMID: 38392781 PMCID: PMC10890082 DOI: 10.3390/jof10020109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/15/2024] [Accepted: 01/25/2024] [Indexed: 02/24/2024] Open
Abstract
Citrus target spot, caused by Pseudofabraea citricarpa, was formerly considered a cold-tolerant fungal disease. However, it has now spread from high-latitude regions to warmer low-latitude regions. Here, we conducted physiological observations on two different strains of the fungus collected from distinct regions, and evaluated their pathogenicity. Interestingly, the CQWZ collected from a low-latitude orchard, exhibited higher temperature tolerance and pathogenicity when compared to the SXCG collected from a high-latitude orchard. To further understand the evolution of temperature tolerance and virulence in these pathogens during the spread process, as well as the mechanisms underlying these differences, we performed genomic comparative analysis. The genome size of CQWZ was determined to be 44,004,669 bp, while the genome size of SXCG was determined to be 45,377,339 bp. Through genomic collinearity analysis, we identified two breakpoints and rearrangements during the evolutionary process of these two strains. Moreover, gene annotation results revealed that the CQWZ possessed 376 annotated genes in the "Xenobiotics biodegradation and metabolism" pathway, which is 79 genes more than the SXCG. The main factor contributing to this difference was the presence of salicylate hydroxylase. We also observed variations in the oxidative stress pathways and core pathogenic genes. The CQWZ exhibited the presence of a heat shock protein (HSP SSB), a catalase (CAT2), and 13 core pathogenic genes, including a LysM effector, in comparison to the SXCG. Furthermore, there were significant disparities in the gene clusters responsible for the production of seven metabolites, such as Fumonisin and Brefeldin. Finally, we identified the regulatory relationship, with the HOG pathway at its core, that potentially contributes to the differences in thermotolerance and virulence. As the global climate continues to warm, crop pathogens are increasingly expanding to new territories. Our findings will enhance understanding of the evolution mechanisms of pathogens under climate change.
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Affiliation(s)
- Saifei Liu
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Plant Protection, Southwest University, Beibei, Chongqing 400716, China
| | - Li Chen
- Plant Protection and Fruit Tree Technology Extension Station of Wanzhou District in Chongqing, Chongqing 404199, China
| | - Xinghua Qiao
- Plant Protection and Fruit Tree Technology Extension Station of Wanzhou District in Chongqing, Chongqing 404199, China
| | - Jiequn Ren
- The Chongqing Three Gorges Academy of Agricultural Sciences, Chongqing 404150, China
| | - Changyong Zhou
- Citrus Research Institute, Southwest University, Beibei, Chongqing 400712, China
| | - Yuheng Yang
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Plant Protection, Southwest University, Beibei, Chongqing 400716, China
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2
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Nawaz I, Zeb T, Ali GM, Zeb BS, Jalal A, Rehman MU, Bakht T, Ali S. High Genetic Diversity in the Himalayan Common Bean ( Phaseolus vulgaris) Germplasm with Divergence from Its Center of Origin in the Mesoamerica and Andes. ACS OMEGA 2023; 8:48787-48797. [PMID: 38162784 PMCID: PMC10753573 DOI: 10.1021/acsomega.3c05150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 11/24/2023] [Accepted: 11/27/2023] [Indexed: 01/03/2024]
Abstract
The common bean is found in the Himalayan region of Pakistan with substantial morphological variability. Genetic diversity within any crop species is a precursor for genetic improvement; however, little is known about common bean genetic diversity in this region. We explored the genetic diversity in the common bean from the Himalayan region (Khyber Pakhtunkhwa, Gilgit-Baltistan, Kashmir) of Pakistan. Microsatellite genotyping was carried out for 147 samples with 40 simple sequence repeat (SSR) markers. The results revealed a clear divergence of the Pakistani population from the primary gene pool (with FST values of 0.2 with Andes and 0.27 with Mesoamerica). However, within the Himalayan germplasm, no clear evidence of spatial structure was observed (with the maximum FST values of only 0.025), probably due to the dispersal of seeds by human activity within the region. This was further elucidated by the discriminant analyses of principal components. Considering the diversity parameters, high genotypic diversity was observed for the indigenous lines (0.990), comparable to the primary gene pool (0.976 for Mesoamerica and 0.976 for Andes populations). A high genotypic diversity was observed within the Himalayan population (ranging from 0.500 for Upper Dir to 0.952 for Mansehra). Gene diversity across loci varied between 0.28 for Chitral to 0.38 for Kurram. Our results suggested a divergent and independent evolution of the Himalayan population, which might have led to the diversification of the common bean germplasm in the region postintroduction into the region. The diversity observed could also be exploited in future breeding programs for the development and introduction of climate-resilient varieties.
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Affiliation(s)
- Iffat Nawaz
- The
University of Agriculture Peshawar, Peshawar 25130, Khyber Pakhtunkhwa, Pakistan
| | - Tehseen Zeb
- The
University of Agriculture Peshawar, Peshawar 25130, Khyber Pakhtunkhwa, Pakistan
| | | | - Bibi Saima Zeb
- The
University of Agriculture Peshawar, Peshawar 25130, Khyber Pakhtunkhwa, Pakistan
| | - Abdullah Jalal
- The
University of Agriculture Peshawar, Peshawar 25130, Khyber Pakhtunkhwa, Pakistan
| | - Monsif Ur Rehman
- Department
of Agriculture, Hazara University, Mansehra, Mansehra 21120, Pakistan
| | - Tamana Bakht
- Shaheed
Benazir Bhutto university Sheringal Dir upper, Dir Upper 18200, Pakistan
| | - Sajid Ali
- Department
of Agriculture, Hazara University, Mansehra, Mansehra 21120, Pakistan
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3
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Ma J, Awais M, Chen L, Yang H, Lai H, Shen Y, Wang H, Li G, Gao H. Identification of Puccinia striiformis races from the spring wheat crop in Xinjiang, China. FRONTIERS IN PLANT SCIENCE 2023; 14:1273306. [PMID: 37868304 PMCID: PMC10586046 DOI: 10.3389/fpls.2023.1273306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 09/11/2023] [Indexed: 10/24/2023]
Abstract
Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a foliar disease that affects both winter and spring wheat crops in Xinjiang, China, which is linked to Central Asia. Race identification of Pst from spring wheat in Xinjiang was not done before. In this study, a total of 216 isolates were recovered from stripe rust samples of spring wheat in the region in 2021 and multiplied using the susceptible cultivar Mingxian 169. These isolates were tested on the Chinese set of 19 wheat differential lines for identifying Pst races. A total of 46 races were identified. Races Suwon-11-1, Suwon11-12, and CYR32 had high frequencies in the spring wheat region. The frequencies of virulence factors on differentials "Fulhard" and "Early Premium" were high (>95%), whereas the virulence factor to differential "Triticum spelta var. Album" (Yr5) was not detected, while virulence to other differentials showed variable frequency within different counties. The predominant races in winter wheat in the same season were also detected from spring wheat cultivars, indicating Pst spreading from winter wheat to spring wheat crops. Deploying resistance genes in spring and winter wheat cultivars is critical for control stripe rust.
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Affiliation(s)
- Jinbiao Ma
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Muhammad Awais
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Shaanxi, Xianyang, China
| | - Li Chen
- Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences/Key Laboratory of Integrated Pest Management on Crop in Northwestern Oasis, Ministry of Agriculture and Rural Affairs, Urumqi, China
| | - Hong Yang
- College of Agriculture, Xinjiang Agricultural University/Key Laboratory of the Pest Monitoring and Safety Control of Crops and Forests, Urumqi, China
| | - Hanlin Lai
- College of Life Science, Xinjiang Agricultural University, Urumqi, China
| | - Yuyang Shen
- Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences/Key Laboratory of Integrated Pest Management on Crop in Northwestern Oasis, Ministry of Agriculture and Rural Affairs, Urumqi, China
| | - Huiqing Wang
- Xinjiang Plant Protection Station, Department of Xinjiang Agriculture, Urumqi, China
| | - Guangkuo Li
- Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences/Key Laboratory of Integrated Pest Management on Crop in Northwestern Oasis, Ministry of Agriculture and Rural Affairs, Urumqi, China
| | - Haifeng Gao
- Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences/Key Laboratory of Integrated Pest Management on Crop in Northwestern Oasis, Ministry of Agriculture and Rural Affairs, Urumqi, China
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4
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Din I, Khan S, Khan FU, Khan M, Khan MN, Hafeez A, Wahab S, Wahid N, Ali B, Qasim UB, Manan F, Alwahibi MS, Elshikh MS, Ercisli S, Khalifa EMA. Genetic Characterization of Advance Bread Wheat Lines for Yield and Stripe Rust Resistance. ACS OMEGA 2023; 8:25988-25998. [PMID: 37521679 PMCID: PMC10372943 DOI: 10.1021/acsomega.3c01981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 06/27/2023] [Indexed: 08/01/2023]
Abstract
Wheat (Triticum aestivum L.) is a prominent grain crop. The goal of the current experiment was to examine the genetic potential of advanced bread wheat genotypes for yield and stripe rust resistance. Ninety-three bread wheat genotypes including three varieties (Kohat-2017, Pakistan-2013, and Morocco) were field tested in augmented design as observational nurseries at three locations (i.e., Kohat, Nowshera, and Peshawar) during the 2018-19 crop season. Various parameters related to yield and stripe rust resistance showed significant differences among genotypes for most of the characters with few exceptions. The analysis of variance revealed significant variations for all the genotypes for all the traits at all three sites with few exceptions where nonsignificant differences were noticed among genotypes. Averaged over three locations, genotypes exhibiting maximum desirable values for yield and yield components were KT-86 (325 tillers) for tillers m-2, KT-50 (2.86 g) for grain weight spike-1, KT-49 (41.6 g) for 1000-grain weight, KT-50 (74 grains) for grains spikes-1, KT-55 (4.76 g) for spike weight, and KT-36 and KT-072 (4586 kg ha-1) for grain yield. Correlation analysis revealed that grain yield had a significant positive correlation with grain spike-1 and grain weight spike-1 at Kohat, with grains spike-1, tillers m-2, and grain weight spike-1 at Nowshera, and with plant height, spike weight, 1000-grain weight, and tillers m-2 at Peshawar. Molecular marker data and host response in the field at the adult stage revealed that Yr15 and Yr10 are both still effective in providing adequate resistance to wheat against prevalent races of stripe rust. Four lines showing desirable lower average coefficient of infection (ACI) values without carrying Yr15 and Yr10 genes show the presence of unique/new resistance gene(s) in the genetic composition of these four lines. Genotype KT-072 (4586 kg ha-1 and 1.3 ACI), KT-07 (4416 kg ha-1 and 4.3 ACI), KT-10 (4346 kg ha-1 and 1.0 ACI), and KT-62 (4338 kg ha-1 and 2.7 ACI) showed maximum values for grain yield and low desirable ACI values, and these lines could be recommended for general cultivation after procedural requirements of variety release.
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Affiliation(s)
- Israr
Ud Din
- The
University of Agriculture Peshawar, Institute
of Biotechnology and Genetic Engineering, Peshawar 25130, Pakistan
| | - Salman Khan
- Department
of Biotechnology, Abdul Wali Khan University
Mardan, Mardan 23200, Pakistan
| | - Fahim Ullah Khan
- Department
of Agriculture, Hazara University, Mansehra 21120, Pakistan
| | - Majid Khan
- The
University of Agriculture Peshawar, Institute
of Biotechnology and Genetic Engineering, Peshawar 25130, Pakistan
| | - Muhammad Nauman Khan
- Department
of Botany, Islamia College Peshawar, Peshawar 25120, Pakistan
- University
Public School, University of Peshawar, Peshawar 25120, Pakistan
| | - Aqsa Hafeez
- Department
of Plant Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Sana Wahab
- Department
of Plant Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Nazima Wahid
- Department
of Plant Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Baber Ali
- Department
of Plant Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Umair Bin Qasim
- Department
of Plant Breeding & Genetics, The University
of Agriculture Peshawar, Peshawar 25130, Pakistan
| | - Fazal Manan
- Department
of Plant Pathology, North Dakota State University, Fargo, North Dakota 58108-6050, United
States
| | - Mona S Alwahibi
- Department
of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Mohamed S Elshikh
- Department
of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Sezai Ercisli
- Department
of Horticulture Faculty of Agriculture, Ataturk University, Erzurum 25240, Türkiye
- HGF
Agro, Ata Teknokent, Erzurum 25240, Türkiye
| | - Ebaa Mohamed Ali Khalifa
- Agriculture
Research Center, Wheat Research Department, Field Crop Research Institute, Giza 3725005, Egypt
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5
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Chen L, Awais M, Yang H, Shen Y, Li G, Gao H, Ma J. Races CYR34 and Suwon11-1 of Puccinia striiformis f. sp. tritici Played an Important Role in Causing the Stripe Rust Epidemic in Winter Wheat in Yili, Xinjiang, China. J Fungi (Basel) 2023; 9:jof9040436. [PMID: 37108891 PMCID: PMC10145038 DOI: 10.3390/jof9040436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 03/28/2023] [Accepted: 03/29/2023] [Indexed: 04/07/2023] Open
Abstract
Wheat stripe rust caused by Puccinia striiformis f. sp. tritici is a destructive disease. Its pathogen frequently adapts to newly invaded regions and overcomes resistance in wheat cultivars. This disease is especially important in China due to its favorable conditions for the stripe rust epidemic and the recombination population structure of pathogens. Xinjiang is a vast epidemic region in China, but very limited research on this disease has been performed in this region. In this study, we identified 25 races from 129 isolates collected from winter wheat fields from five different regions (Nileke, Xinyuan, Gongliu, Huocheng, and Qapqal) of Yili, Xinjiang, using the Chinese set of 19 differential wheat lines. All isolates were virulent on the differentials Fulhad and Early Premium, but no isolates were virulent on Yr5. Among the 25 races, Suwon11-1 was the most prevalent, followed by CYR34. Both races were found in four out of the five locations. It is important to continue monitoring stripe rust and its pathogen races in this region, as it forms a pathway between China and Central Asia. Collaborative research is essential for controlling stripe rust in this region, other regions in China, and neighboring countries.
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Affiliation(s)
- Li Chen
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830000, China
- Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences/Key Laboratory of Integrated Pest Management on Crop in Northwestern Oasis, Ministry of Agriculture and Rural Affairs, Urumqi 830000, China
| | - Muhammad Awais
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Xianyang 712100, China
| | - Hong Yang
- College of Agriculture, Xinjiang Agricultural University/Key Laboratory of the Pest Monitoring and Safety Control of Crops and Forests, Urumqi 830000, China
| | - Yuyang Shen
- Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences/Key Laboratory of Integrated Pest Management on Crop in Northwestern Oasis, Ministry of Agriculture and Rural Affairs, Urumqi 830000, China
| | - Guangkuo Li
- Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences/Key Laboratory of Integrated Pest Management on Crop in Northwestern Oasis, Ministry of Agriculture and Rural Affairs, Urumqi 830000, China
| | - Haifeng Gao
- Institute of Plant Protection, Xinjiang Academy of Agricultural Sciences/Key Laboratory of Integrated Pest Management on Crop in Northwestern Oasis, Ministry of Agriculture and Rural Affairs, Urumqi 830000, China
| | - Jinbiao Ma
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830000, China
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6
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Awais M, Zhao J, Cheng X, Ghaffar Khoso A, Ju M, Ur Rehman Z, Iqbal A, Rameez Khan M, Chen W, Liu M, Ma X, Wang L, Liu W, Du Z, Sun M, Zhang G, Kang Z, Ali S. Himalayan mountains imposing a barrier on gene flow of wheat yellow rust pathogen in the bordering regions of Pakistan and China. Fungal Genet Biol 2023; 164:103753. [PMID: 36574524 DOI: 10.1016/j.fgb.2022.103753] [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: 02/28/2022] [Revised: 09/18/2022] [Accepted: 11/22/2022] [Indexed: 11/27/2022]
Abstract
The wheat yellow rust pathogen has been shown to be diverse and potentially originated in the Himalayan region. Although Himalayan populations of Pakistan, Nepal and Bhutan have been previously compared, little is known about the relative divergence and diversity in Puccinia striiformis populations in the bordering regions of Pakistan and China. To assess the relative diversity and divergence in these regions of Pakistan (Gilgit-Baltistan, Hazara and Azad Jammu Kashmir) and China (Xinjiang, Qinghai, Tibet, Sichuan, Guizhou and Yunnan), a total of 1245 samples were genotyped using 17 microsatellite SSR markers. A clear divergence was observed between the bordering regions of Pakistan and China (FST = 0.28) without any resampling of genetic groups and multilocus genotypes across two sides of the Himalayan mountains. The closest subpopulations across the two countries were Xinjiang and Gilgit-Baltistan (Nei's distance = 0.147), which were close geographically. A very high diversity and recombinant population structure was observed in both populations, though slightly higher in China (Genotypic diversity = 0.970; r¯d = 0.000) than in Pakistan (Genotypic diversity = 0.902; r¯d = 0.065). The distribution of genetic groups and resampling of MLGs revealed more gene flow across Yunnan, Guizhou and Sichuan regions in China, while between Hazara and Azad-Jammu Kashmir in Pakistan. The lack of gene flow between Pakistan and China populations is due to geographical barriers and a large patch of land without wheat. The information on the relative diversity and divergence in different geographical zones of the pathogen center of diversity and neighboring region should be considered in resistant wheat deployment while considering the invasion potential of the pathogen at regional and global contexts.
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Affiliation(s)
- Muhammad Awais
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Jie Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, PR China.
| | - Xiangrui Cheng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Abdul Ghaffar Khoso
- College of Plant Protection, Dept. Agriculture Entomology & pest control. Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Meng Ju
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Zia Ur Rehman
- Dept. of Agriculture, Hazara University Mansehra, Pakistan
| | - Aamir Iqbal
- Dept. of Agriculture, Hazara University Mansehra, Pakistan
| | | | - Wen Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, PR China; Guizhou Academy of Agricultural Sciences, Institute of Plant Protection, Guiyang, PR China
| | - Maxinzhi Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Xinyao Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Lin Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Wei Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Zhimin Du
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Mudi Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Gensheng Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, PR China.
| | - Sajid Ali
- Dept. of Agriculture, Hazara University Mansehra, Pakistan.
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Liu D, Yuan C, Singh RP, Randhawa MS, Bhavani S, Kumar U, Huerta-Espino J, Lagudah E, Lan C. Stripe rust and leaf rust resistance in CIMMYT wheat line "Mucuy" is conferred by combinations of race-specific and adult-plant resistance loci. FRONTIERS IN PLANT SCIENCE 2022; 13:880138. [PMID: 36061764 PMCID: PMC9437451 DOI: 10.3389/fpls.2022.880138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 07/28/2022] [Indexed: 06/15/2023]
Abstract
Developing wheat varieties with durable resistance is a core objective of the International Maize and Wheat Improvement Center (CIMMYT) and many other breeding programs worldwide. The CIMMYT advanced wheat line "Mucuy" displayed high levels of resistance to stripe rust (YR) and leaf rust (LR) in field evaluations in Mexico and several other countries. To determine the genetic basis of YR and LR resistance, 138 F5 recombinant inbred lines (RILs) derived from the cross of Apav#1× Mucuy were phenotyped for YR responses from 2015 to 2020 at field sites in India, Kenya, and Mexico, and LR in Mexico. Seedling phenotyping for YR and LR responses was conducted in the greenhouse in Mexico using the same predominant races as in field trials. Using 12,681 polymorphic molecular markers from the DArT, SNP, and SSR genotyping platforms, we constructed genetic linkage maps and QTL analyses that detected seven YR and four LR resistance loci. Among these, a co-located YR/LR resistance loci was identified as Yr29/Lr46, and a seedling stripe rust resistance gene YrMu was mapped on the 2AS/2NS translocation. This fragment also conferred moderate adult plant resistance (APR) under all Mexican field environments and in one season in Kenya. Field trial phenotyping with Lr37-virulent Puccinia triticina races indicated the presence of an APR QTL accounting for 18.3-25.5% of the LR severity variation, in addition to a novel YR resistance QTL, QYr.cim-3DS, derived from Mucuy. We developed breeder-friendly KASP and indel molecular markers respectively for Yr29/Lr46 and YrMu. The current study validated the presence of known genes and identified new resistance loci, a QTL combination effect, and flanking markers to facilitate accelerated breeding for genetically complex, durable rust resistance.
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Affiliation(s)
- Demei Liu
- Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Laboratory for Research and Utilization of Qinghai Tibet Plateau Germplasm Resources, Northwest Institute of Plateau Biology, Innovation Academy for Seed Design Chinese Academy of Sciences (CAS), Xining, China
| | - Chan Yuan
- Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ravi P. Singh
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | | | - Sridhar Bhavani
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Uttam Kumar
- Borlaug Institute for South Asia (BISA), New Delhi, India
| | - Julio Huerta-Espino
- Campo Experimental Valle de México, Instituto Nacional de Investigacion Forestales Agricolas y Pecuarias (INIFAP), Texcoco, Mexico
| | - Evans Lagudah
- Commonwealth Scientific and Industrial Research Organization (CSIRO) Plant Industry, Canberra, ACT, Australia
| | - Caixia Lan
- Hongshan Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
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8
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Awais M, Ali S, Ju M, Liu W, Zhang G, Zhang Z, Li Z, Ma X, Wang L, Du Z, Tian X, Zeng Q, Kang Z, Zhao J. Countrywide inter-epidemic region migration pattern suggests the role of southwestern population in wheat stripe rust epidemics in China. Environ Microbiol 2022; 24:4684-4701. [PMID: 35859329 DOI: 10.1111/1462-2920.16096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 06/01/2022] [Accepted: 06/04/2022] [Indexed: 11/26/2022]
Abstract
Understanding countrywide pathogen population structure and inter-epidemic region spread is crucial for deciphering crop potential losses. Wheat stripe rust caused by Puccinia striiformis f. sp. tritici is a destructive disease that affects worldwide wheat production, widespread in China, representing largest epidemic region globally. This study aimed to understand the population structure and migration route of P. striiformis f. sp. tritici across China based on sampling from 15 provinces representing six epidemic zones, viz., over-summering, over-wintering, eastern, Yun-Gui, Xinjiang and Tibet epidemic regions. High genotypic diversity was recorded in over-summering, Tibet and over-wintering epidemic regions. Epidemic regions partly explain population subdivision with variable divergence (FST = 0.005-0.344). Xinjiang and Tibet epidemic regions were independent epidemic zones with least sharing of genotypes. Among other epidemic zones, i.e. over-summering, over-wintering, eastern and Yun-Gui epidemic zones, re-sampling MLGs, clustering-based structure, DAPC analyses, relative migration and low divergence (FST from 0.006 to 0.073) revealed frequent geneflow. Yun-Gui epidemic regions, with a potential for both over-summering and over-wintering, could play an important role in causing epidemics in main wheat-cultivating areas of China. High diversity, recombination signatures and inter-epidemic region migration patterns need to be considered in host-resistant cultivar development in China and neighbouring countries, considering risk of long-distance migration capacity of pathogen.
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Affiliation(s)
- Muhammad Awais
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, the People's Republic of China
| | - Sajid Ali
- Department of Agriculture, Hazara University Mansehra, Mansehra, Pakistan
| | - Meng Ju
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, the People's Republic of China
| | - Wei Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, the People's Republic of China
| | - Gensheng Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, the People's Republic of China
| | - Zedong Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, the People's Republic of China
| | - Zejian Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, the People's Republic of China
| | - Xinyao Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, the People's Republic of China
| | - Lin Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, the People's Republic of China
| | - Zhimin Du
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, the People's Republic of China
| | - Xiaxia Tian
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, the People's Republic of China
| | - Qingdong Zeng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, the People's Republic of China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, the People's Republic of China
| | - Jie Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, the People's Republic of China
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9
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Gangwar OP, Kumar S, Bhardwaj SC, Prasad P, Lata C, Adhikari S, Singh GP. Elucidating the Population Structure and Genetic Diversity of Indian Puccinia striiformis f. sp. tritici Pathotypes Based on Microsatellite Markers. PHYTOPATHOLOGY 2022; 112:1444-1453. [PMID: 35050682 DOI: 10.1094/phyto-10-21-0422-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: 06/14/2023]
Abstract
In India, systematic wheat yellow rust survey and pathotype (race) analysis work began in 1930. However, information on population structure and genetic diversity of yellow rust pathogen has not been available. To address this, we conducted studies on population structure and genetic diversity of Puccinia striiformis f. sp. tritici (Pst) pathotypes using 38 simple sequence repeat primer-pairs. Bayesian assignment and discriminant analysis of principal components indicated the presence of two distinct Pst subpopulations (Pop1 and Pop2) along with 37.9% admixed pathotypes. The unweighted pair-group method with arithmetic mean also categorized these pathotypes into two major clusters. Principal coordinates analysis explained 20.06 and 12.50% variance in horizontal and vertical coordinates, respectively. Index of association (IA) and the standardized index of association ([Formula: see text]) values showed that Pst subpopulations reproduced asexually (clonally). In total, 102 alleles were detected, with the expected heterozygosity (Hexp) per locus ranging from 0.13 to 0.73, with a mean of 0.47. The average polymorphic information content value of 0.40 indicated high genetic diversity among pathotypes. Analysis of molecular variance revealed 12% of the total variance between subpopulations, 11% among the pathotypes of each subpopulation, and 77% within pathotypes. A significant moderate level of genetic differentiation (FST = 0.122, P < 0.001) and gene flow (Nm = 1.80) were observed between subpopulations. The Pst virulence phenotypes showed a weak positive correlation (R2 = 0.027, P < 0.02) with molecular genotypes.
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Affiliation(s)
- Om Prakash Gangwar
- Indian Council of Agricultural Research-Indian Institute of Wheat and Barley Research, Shimla, Himachal Pradesh, India
| | - Subodh Kumar
- Indian Council of Agricultural Research-Indian Institute of Wheat and Barley Research, Shimla, Himachal Pradesh, India
| | - Subhash Chander Bhardwaj
- Indian Council of Agricultural Research-Indian Institute of Wheat and Barley Research, Shimla, Himachal Pradesh, India
| | - Pramod Prasad
- Indian Council of Agricultural Research-Indian Institute of Wheat and Barley Research, Shimla, Himachal Pradesh, India
| | - Charu Lata
- Indian Council of Agricultural Research-Indian Institute of Wheat and Barley Research, Shimla, Himachal Pradesh, India
| | - Sneha Adhikari
- Indian Council of Agricultural Research-Indian Institute of Wheat and Barley Research, Shimla, Himachal Pradesh, India
| | - Gyanendra Pratap Singh
- Indian Council of Agricultural Research-Indian Institute of Wheat and Barley Research, Karnal, Haryana, India
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10
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Jambuthenne DT, Riaz A, Athiyannan N, Alahmad S, Ng WL, Ziems L, Afanasenko O, Periyannan SK, Aitken E, Platz G, Godwin I, Voss-Fels KP, Dinglasan E, Hickey LT. Mining the Vavilov wheat diversity panel for new sources of adult plant resistance to stripe rust. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1355-1373. [PMID: 35113190 PMCID: PMC9033734 DOI: 10.1007/s00122-022-04037-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 01/12/2022] [Indexed: 06/14/2023]
Abstract
Multi-year evaluation of the Vavilov wheat diversity panel identified new sources of adult plant resistance to stripe rust. Genome-wide association studies revealed the key genomic regions influencing resistance, including seven novel loci. Wheat stripe rust (YR) caused by Puccinia striiformis f. sp. tritici (Pst) poses a significant threat to global food security. Resistance genes commonly found in many wheat varieties have been rendered ineffective due to the rapid evolution of the pathogen. To identify novel sources of adult plant resistance (APR), 292 accessions from the N.I. Vavilov Institute of Plant Genetic Resources, Saint Petersburg, Russia, were screened for known APR genes (i.e. Yr18, Yr29, Yr46, Yr33, Yr39 and Yr59) using linked polymerase chain reaction (PCR) molecular markers. Accessions were evaluated against Pst (pathotype 134 E16 A + Yr17 + Yr27) at seedling and adult plant stages across multiple years (2014, 2015 and 2016) in Australia. Phenotypic analyses identified 132 lines that potentially carry novel sources of APR to YR. Genome-wide association studies (GWAS) identified 68 significant marker-trait associations (P < 0.001) for YR resistance, representing 47 independent quantitative trait loci (QTL) regions. Fourteen genomic regions overlapped with previously reported Yr genes, including Yr29, Yr56, Yr5, Yr43, Yr57, Yr30, Yr46, Yr47, Yr35, Yr36, Yrxy1, Yr59, Yr52 and YrYL. In total, seven QTL (positioned on chromosomes 1D, 2A, 3A, 3D, 5D, 7B and 7D) did not collocate with previously reported genes or QTL, indicating the presence of promising novel resistance factors. Overall, the Vavilov diversity panel provides a rich source of new alleles which could be used to broaden the genetic bases of YR resistance in modern wheat varieties.
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Affiliation(s)
- Dilani T Jambuthenne
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Adnan Riaz
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Naveenkumar Athiyannan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture and Food,, Canberra, ACT, Australia
| | - Samir Alahmad
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Wei Ling Ng
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Laura Ziems
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Olga Afanasenko
- Department of Plant Resistance To Diseases, All Russian Research Institute for Plant Protection, St Petersburg, Russia, 196608
| | - Sambasivam K Periyannan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture and Food,, Canberra, ACT, Australia
| | - Elizabeth Aitken
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia, QLD, Australia
| | - Greg Platz
- Department of Agriculture and Fisheries, Hermitage Research Facility, Warwick, QLD, Australia
| | - Ian Godwin
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Kai P Voss-Fels
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia
| | - Eric Dinglasan
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia.
| | - Lee T Hickey
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia.
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11
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Wang C, Li Y, Wang B, Hu X. Genetic Analysis Reveals Relationships Among Populations of Puccinia striiformis f. sp. tritici from the Longnan, Longdong, and Central Shaanxi Regions of China. PHYTOPATHOLOGY 2022; 112:278-289. [PMID: 34129356 DOI: 10.1094/phyto-07-20-0312-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici, is one of the most important diseases of wheat worldwide. In China, Longnan (LN) and Longdong (LD) in the south and east of Gansu province, respectively, are important P. striiformis f. sp. tritici oversummering areas and are a source of P. striiformis f. sp. tritici inoculum for the major wheat-growing regions in eastern China. Central Shaanxi (CS) is a wheat-growing region that acts as an important bridge zone for stripe rust epidemic development between LN and LD in the west and the Huanghuai wheat-growing region in the east, and thus, it plays an essential role in P. striiformis f. sp. tritici epidemics in China. To study the relationships among P. striiformis f. sp. tritici populations in the three regions (LN, LD, and CS), we sampled 284 isolates from different geographic locations. Based on 10 simple sequence repeat markers, the results demonstrated high genetic diversity in all three regions, although diversity did vary among regions, with LN > LD > CS. Genetic differentiation was lower, with more extensive gene flow between LD and CS. P. striiformis f. sp. tritici populations in the CS region were genetically closer to those from LD than those from LN, which may be a result of geographical proximity and topography. A positive and significant correlation existed between linearized fixation index (FST) and the log of geographical distances among all subpopulations. Linkage disequilibrium analysis showed that subpopulations of P. striiformis f. sp. tritici from Qinzhou, Qincheng, Beidao, and Maiji from LN and Qianyang and Longxian from CS were in equilibrium (P > 0.05), suggesting that somatic hybridization and/or sexual reproduction may exist in these subpopulations.
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Affiliation(s)
- Conghao Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling 712100, China
| | - Yuxiang Li
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling 712100, China
| | - Baotong Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling 712100, China
| | - Xiaoping Hu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling 712100, China
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12
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Huang M, Liu T, Cao S, Yuen J, Zhan J, Jia Q, Gao L, Liu B, Chen W, Berlin A. Analyses of Wheat Yellow Rust Populations Reveal Sexual Recombination and Seasonal Migration Pattern of Puccinia striiformis f. sp. tritici in Gangu, Northwestern China. PHYTOPATHOLOGY 2021; 111:2268-2277. [PMID: 34878826 DOI: 10.1094/phyto-12-20-0558-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Puccinia striiformis f. sp. tritici is the causal agent of wheat yellow rust with records of regular and severe epidemics in China. This study explored the population dynamics of the yellow rust pathogen in Gangu, northwestern China. In Gangu, the Weihe River runs from west to east and divides Gangu into three regions: North and South mountain, with the valley in between. To study the genetic structure of the pathogen in local populations, samples were collected over 3 years from the three regions at different altitudes both within and between the wheat cropping seasons. A total of 811 P. striiformis f. sp. tritici isolates were successfully genotyped using 16 simple sequence repeat markers. The results suggest that P. striiformis f. sp. tritici can survive year-round in Gangu. The P. striiformis f. sp. tritici populations migrated among the regions, and the migration pattern was not related to altitude. The oversummering populations in the North and South mountain regions were genetically different from each other; and the P. striiformis f. sp. tritici populations collected from the lower altitude in the valley had no relationship with any of the populations collected in the spring or fall, indicating that they too have a different origin. Signatures of random mating were found in the populations collected in both North and South mountain regions, but not in the valley populations.
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Affiliation(s)
- Miaomiao Huang
- State Key Laboratory for the Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Science, Beijing 100193, China
- National Agricultural Experimental Station for Plant Protection, Gangu, Ministry of Agriculture and Rural Affairs, Gansu 741200, China
- College of Plant Protection, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Taiguo Liu
- State Key Laboratory for the Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Science, Beijing 100193, China
- National Agricultural Experimental Station for Plant Protection, Gangu, Ministry of Agriculture and Rural Affairs, Gansu 741200, China
| | - Shiqin Cao
- National Agricultural Experimental Station for Plant Protection, Gangu, Ministry of Agriculture and Rural Affairs, Gansu 741200, China
- Institute of Plant Protection, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu 730070, China
| | - Jonathan Yuen
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala SE-750 07, Sweden
| | - Jiasui Zhan
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala SE-750 07, Sweden
| | - Qiuzhen Jia
- National Agricultural Experimental Station for Plant Protection, Gangu, Ministry of Agriculture and Rural Affairs, Gansu 741200, China
- Institute of Plant Protection, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu 730070, China
| | - Li Gao
- State Key Laboratory for the Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Science, Beijing 100193, China
- National Agricultural Experimental Station for Plant Protection, Gangu, Ministry of Agriculture and Rural Affairs, Gansu 741200, China
| | - Bo Liu
- State Key Laboratory for the Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Science, Beijing 100193, China
| | - Wanquan Chen
- State Key Laboratory for the Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Science, Beijing 100193, China
- National Agricultural Experimental Station for Plant Protection, Gangu, Ministry of Agriculture and Rural Affairs, Gansu 741200, China
- College of Plant Protection, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Anna Berlin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala SE-750 07, Sweden
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13
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Cook NM, Chng S, Woodman TL, Warren R, Oliver RP, Saunders DG. High frequency of fungicide resistance-associated mutations in the wheat yellow rust pathogen Puccinia striiformis f. sp. tritici. PEST MANAGEMENT SCIENCE 2021; 77:3358-3371. [PMID: 33786966 DOI: 10.1002/ps.6380] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 03/23/2021] [Accepted: 03/31/2021] [Indexed: 05/14/2023]
Abstract
BACKGROUND Reliance on fungicides to manage disease creates selection pressure for the evolution of resistance in fungal and oomycete pathogens. Rust fungi (Pucciniales) are major pathogens of cereals and other crops and have been classified as low-risk for developing resistance to fungicides; no case of field failure of fungicides in a cereal rust disease has yet been recorded. Recently, the Asian soybean rust pathogen, Phakopsora pachyrhizi evolved resistance to several fungicide classes, prompting us to screen a large sample of the globally widespread wheat yellow rust pathogen, Puccinia striiformis f. sp. tritici (Pst), for mutations associated with fungicide resistance. RESULTS We evaluated 363 Pst isolates from Europe, the USA, Ethiopia, Chile, China and New Zealand for mutations in the target genes of demethylase inhibitor (DMI; Cyp51) and succinate dehydrogenase inhibitor (SDHI; SdhB, SdhC and SdhD) fungicides. A high proportion of Pst isolates carrying a Y134F DMI resistance-associated substitution in the Cyp51 gene was found among those from China and New Zealand. A set of geographically diverse Pst isolates was also found to display a substitution in SdhC (I85V) that is homologous to that reported recently in P. pachyrhizi and linked to SDHI resistance. CONCLUSION The identification of resistance-associated alleles confirms that cereal rusts are not immune to fungicide resistance and that selection for resistance evolution is operating at high levels in certain locations. It highlights the need to adopt fungicide resistance management practices and to monitor cereal rust species for development of resistance. © 2021 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Nicola M Cook
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Soonie Chng
- The New Zealand Institute for Plant & Food Research Limited, Lincoln, New Zealand
| | | | - Rachael Warren
- The New Zealand Institute for Plant & Food Research Limited, Lincoln, New Zealand
| | - Richard P Oliver
- Molecular and Life Sciences, Curtin University, Bentley, Australia
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14
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Scortichini M, Loreti S, Pucci N, Scala V, Tatulli G, Verweire D, Oehl M, Widmer U, Codina JM, Hertl P, Cesari G, De Caroli M, Angilè F, Migoni D, Del Coco L, Girelli CR, Dalessandro G, Fanizzi FP. Progress towards Sustainable Control of Xylella fastidiosa subsp. pauca in Olive Groves of Salento (Apulia, Italy). Pathogens 2021; 10:668. [PMID: 34072394 PMCID: PMC8228964 DOI: 10.3390/pathogens10060668] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/19/2021] [Accepted: 05/26/2021] [Indexed: 11/16/2022] Open
Abstract
Xylella fastidiosa subsp. pauca is the causal agent of "olive quick decline syndrome" in Salento (Apulia, Italy). On April 2015, we started interdisciplinary studies to provide a sustainable control strategy for this pathogen that threatens the multi-millennial olive agroecosystem of Salento. Confocal laser scanning microscopy and fluorescence quantification showed that a zinc-copper-citric acid biocomplex-Dentamet®-reached the olive xylem tissue either after the spraying of the canopy or injection into the trunk, demonstrating its effective systemicity. The biocomplex showed in vitro bactericidal activity towards all X. fastidiosa subspecies. A mid-term evaluation of the control strategy performed in some olive groves of Salento indicated that this biocomplex significantly reduced both the symptoms and X. f. subsp. pauca cell concentration within the leaves of the local cultivars Ogliarola salentina and Cellina di Nardò. The treated trees started again to yield. A 1H-NMR metabolomic approach revealed, upon the treatments, a consistent increase in malic acid and γ-aminobutyrate for Ogliarola salentina and Cellina di Nardò trees, respectively. A novel endotherapy technique allowed injection of Dentamet® at low pressure directly into the vascular system of the tree and is currently under study for the promotion of resprouting in severely attacked trees. There are currently more than 700 ha of olive groves in Salento where this strategy is being applied to control X. f. subsp. pauca. These results collectively demonstrate an efficient, simple, low-cost, and environmentally sustainable strategy to control this pathogen in Salento.
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Affiliation(s)
- Marco Scortichini
- Research Centre for Olive, Fruit Trees and Citrus Crops, Council for Agricultural Research and Economics (CREA), 00134 Roma, Italy
| | - Stefania Loreti
- Research Centre for Plant Protection and Certification, Council for Agricultural Research and Economics (CREA), 00156 Roma, Italy; (S.L.); (N.P.); (V.S.); (G.T.)
| | - Nicoletta Pucci
- Research Centre for Plant Protection and Certification, Council for Agricultural Research and Economics (CREA), 00156 Roma, Italy; (S.L.); (N.P.); (V.S.); (G.T.)
| | - Valeria Scala
- Research Centre for Plant Protection and Certification, Council for Agricultural Research and Economics (CREA), 00156 Roma, Italy; (S.L.); (N.P.); (V.S.); (G.T.)
| | - Giuseppe Tatulli
- Research Centre for Plant Protection and Certification, Council for Agricultural Research and Economics (CREA), 00156 Roma, Italy; (S.L.); (N.P.); (V.S.); (G.T.)
| | - Dimitri Verweire
- Invaio Sciences, Cambridge, MA 02138, USA; (D.V.); (M.O.); (U.W.); (J.M.C.); (P.H.)
| | - Michael Oehl
- Invaio Sciences, Cambridge, MA 02138, USA; (D.V.); (M.O.); (U.W.); (J.M.C.); (P.H.)
| | - Urs Widmer
- Invaio Sciences, Cambridge, MA 02138, USA; (D.V.); (M.O.); (U.W.); (J.M.C.); (P.H.)
| | - Josep Massana Codina
- Invaio Sciences, Cambridge, MA 02138, USA; (D.V.); (M.O.); (U.W.); (J.M.C.); (P.H.)
| | - Peter Hertl
- Invaio Sciences, Cambridge, MA 02138, USA; (D.V.); (M.O.); (U.W.); (J.M.C.); (P.H.)
| | | | - Monica De Caroli
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Monteroni-Lecce, Italy; (M.D.C.); (F.A.); (D.M.); (L.D.C.); (C.R.G.); (G.D.); (F.P.F.)
| | - Federica Angilè
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Monteroni-Lecce, Italy; (M.D.C.); (F.A.); (D.M.); (L.D.C.); (C.R.G.); (G.D.); (F.P.F.)
| | - Danilo Migoni
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Monteroni-Lecce, Italy; (M.D.C.); (F.A.); (D.M.); (L.D.C.); (C.R.G.); (G.D.); (F.P.F.)
| | - Laura Del Coco
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Monteroni-Lecce, Italy; (M.D.C.); (F.A.); (D.M.); (L.D.C.); (C.R.G.); (G.D.); (F.P.F.)
| | - Chiara Roberta Girelli
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Monteroni-Lecce, Italy; (M.D.C.); (F.A.); (D.M.); (L.D.C.); (C.R.G.); (G.D.); (F.P.F.)
| | - Giuseppe Dalessandro
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Monteroni-Lecce, Italy; (M.D.C.); (F.A.); (D.M.); (L.D.C.); (C.R.G.); (G.D.); (F.P.F.)
| | - Francesco Paolo Fanizzi
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Monteroni-Lecce, Italy; (M.D.C.); (F.A.); (D.M.); (L.D.C.); (C.R.G.); (G.D.); (F.P.F.)
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15
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Sinha P, Chen X. Potential Infection Risks of the Wheat Stripe Rust and Stem Rust Pathogens on Barberry in Asia and Southeastern Europe. PLANTS 2021; 10:plants10050957. [PMID: 34064962 PMCID: PMC8151100 DOI: 10.3390/plants10050957] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/07/2021] [Accepted: 05/07/2021] [Indexed: 11/16/2022]
Abstract
Barberry (Berberis spp.) is an alternate host for both the stripe rust pathogen, Puccinia striiformis f. sp. tritici (Pst), and the stem rust pathogen, P. graminis f. sp. tritici (Pgt), infecting wheat. Infection risk was assessed to determine whether barberry could be infected by either of the pathogens in Asia and Southeastern Europe, known for recurring epidemics on wheat and the presence of barberry habitats. For assessing infection risk, mechanistic infection models were used to calculate infection indices for both pathogens on barberry following a modeling framework. In East Asia, Bhutan, China, and Nepal were found to have low risks of barberry infection by Pst but high risks by Pgt. In Central Asia, Azerbaijan, Iran, Kazakhstan, southern Russia, and Uzbekistan were identified to have low to high risks of barberry infection for both Pst and Pgt. In Northwest Asia, risk levels of both pathogens in Turkey and the Republic of Georgia were determined to be high to very high. In Southwest Asia, no or low risk was found. In Southeastern Europe, similar high or very high risks for both pathogens were noted for all countries. The potential risks of barberry infection by Pst and/or Pgt should provide guidelines for monitoring barberry infections and could be valuable for developing rust management programs in these regions. The framework used in this study may be useful to predict rust infection risk in other regions.
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Affiliation(s)
- Parimal Sinha
- ICAR-Indian Agricultural Research Institute, New Delhi 110012, India;
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, USA
| | - Xianming Chen
- Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, USA
- US Department of Agriculture—Agricultural Research Service, Wheat Health, Genetics, and Quality Research Unit, Pullman, WA 99164-6430, USA
- Correspondence: ; Tel.: +1-509-335-8086
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16
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Stoeckel S, Porro B, Arnaud-Haond S. The discernible and hidden effects of clonality on the genotypic and genetic states of populations: Improving our estimation of clonal rates. Mol Ecol Resour 2021; 21:1068-1084. [PMID: 33386695 DOI: 10.1111/1755-0998.13316] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 11/05/2020] [Accepted: 12/21/2020] [Indexed: 11/29/2022]
Abstract
Partial clonality is widespread across the tree of life, but most population genetic models are designed for exclusively clonal or sexual organisms. This gap hampers our understanding of the influence of clonality on evolutionary trajectories and the interpretation of population genetic data. We performed forward simulations of diploid populations at increasing rates of clonality (c), analysed their relationships with genotypic (clonal richness, R, and distribution of clonal sizes, Pareto β) and genetic (FIS and linkage disequilibrium) indices, and tested predictions of c from population genetic data through supervised machine learning. Two complementary behaviours emerged from the probability distributions of genotypic and genetic indices with increasing c. While the impact of c on R and Pareto β was easily described by simple mathematical equations, its effects on genetic indices were noticeable only at the highest levels (c > 0.95). Consequently, genotypic indices allowed reliable estimates of c, while genetic descriptors led to poorer performances when c < 0.95. These results provide clear baseline expectations for genotypic and genetic diversity and dynamics under partial clonality. Worryingly, however, the use of realistic sample sizes to acquire empirical data systematically led to gross underestimates (often of one to two orders of magnitude) of c, suggesting that many interpretations hitherto proposed in the literature, mostly based on genotypic richness, should be reappraised. We propose future avenues to derive realistic confidence intervals for c and show that, although still approximate, a supervised learning method would greatly improve the estimation of c from population genetic data.
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Affiliation(s)
- Solenn Stoeckel
- Institute for Genetics, Environment and Plant Protection, INRAE, Le Rheu, France
| | - Barbara Porro
- Institute for Research on Cancer and Aging (IRCAN), Université Côte d'Azur, Nice, France.,MARBEC - Marine Biodiversity Exploitation and Conservation, University of Montpellier, CNRS, Ifremer, IRD, MARBEC, Sète, France
| | - Sophie Arnaud-Haond
- MARBEC - Marine Biodiversity Exploitation and Conservation, University of Montpellier, CNRS, Ifremer, IRD, MARBEC, Sète, France
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Khan MR, Imtiaz M, Ahmad B, Munir A, Rattu AUR, Facho ZH, Ali S. Diversity in Puccinia striiformis populations causing the 2013 yellow rust epidemics on major wheat cultivars of Pakistan. Mycologia 2020; 112:871-879. [PMID: 32813615 DOI: 10.1080/00275514.2020.1792263] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Wheat yellow/stripe rust pathogen Puccinia striiformis is highly diverse and recombinant in the north of Pakistan in the Himalayan region. However, little is known about the role of this diversity in disease epidemics in areas where wheat yellow rust is an important disease in both irrigated and rain-fed wheat (i.e., in the plains of Pakistan). We explored the population diversity in P. striiformis during the rust epidemics of 2013 in the major wheat-growing regions of Pakistan (the Himalayan region, central Khyber Pakhtunkhwa [KP], southern KP, central and northern Punjab). Disease severities among commonly grown cultivars ranged from 5% to 100%. Microsatellite genotyping with 16 simple sequence repeat (SSR) markers revealed a high diversity among 266 isolates collected during the season, with the Simpson diversity index (Simpson 1949) ranging from 0.870 (Himalayan) to 0.955 (southern KP). The recombination signature was stronger in the Himalayan population and central KP compared with wheat-growing regions of Punjab and southern KP. The overall diversity was higher in Pakistan relative to the clonal populations present in Europe, Australia, and the Americas. Analyses of population subdivision revealed no clear evidence of spatial structure for samples from Pakistan, with a maximum fixation index (FST) value of only 0.10. The lack of clear population subdivision could be attributed to migration of pathogen. In turn, the high diversity of P. striiformis in Pakistan represents a potential threat to wheat production in the region and worldwide, as a possible source to found clonal populations in diverse wheat-growing areas.
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Affiliation(s)
- Muhammad Rameez Khan
- Institute of Biotechnology & Genetic Engineering, The University of Agriculture , Peshawar, Pakistan
| | - Muhammad Imtiaz
- International Maize and Wheat Improvement Centre (CIMMYT) , Islamabad, Pakistan
| | - Bashir Ahmad
- Directorate of Agriculture Research, Khyber Pakhtunkhwa, Peshawar, Pakistan
| | - Anjum Munir
- Crop Disease Research Institute, National Agricultural Research Centre , Islamabad, Pakistan
| | | | - Zakir Hussain Facho
- Department of Plant Breeding & Genetics, The University of Agriculture , Peshawar, Pakistan
| | - Sajid Ali
- Institute of Biotechnology & Genetic Engineering, The University of Agriculture , Peshawar, Pakistan
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Susi H, Burdon JJ, Thrall PH, Nemri A, Barrett LG. Genetic analysis reveals long-standing population differentiation and high diversity in the rust pathogen Melampsora lini. PLoS Pathog 2020; 16:e1008731. [PMID: 32810177 PMCID: PMC7454959 DOI: 10.1371/journal.ppat.1008731] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 08/28/2020] [Accepted: 06/22/2020] [Indexed: 11/18/2022] Open
Abstract
A priority for research on infectious disease is to understand how epidemiological and evolutionary processes interact to influence pathogen population dynamics and disease outcomes. However, little is understood about how population adaptation changes across time, how sexual vs. asexual reproduction contribute to the spread of pathogens in wild populations and how diversity measured with neutral and selectively important markers correlates across years. Here, we report results from a long-term study of epidemiological and genetic dynamics within several natural populations of the Linum marginale-Melampsora lini plant-pathogen interaction. Using pathogen isolates collected from three populations of wild flax (L. marginale) spanning 16 annual epidemics, we probe links between pathogen population dynamics, phenotypic variation for infectivity and genomic polymorphism. Pathogen genotyping was performed using 1567 genome-wide SNP loci and sequence data from two infectivity loci (AvrP123, AvrP4). Pathogen isolates were phenotyped for infectivity using a differential set. Patterns of epidemic development were assessed by conducting surveys of infection prevalence in one population (Kiandra) annually. Bayesian clustering analyses revealed host population and ecotype as key predictors of pathogen genetic structure. Despite strong fluctuations in pathogen population size and severe annual bottlenecks, analysis of molecular variance revealed that pathogen population differentiation was relatively stable over time. Annually, varying levels of clonal spread (0–44.8%) contributed to epidemics. However, within populations, temporal genetic composition was dynamic with rapid turnover of pathogen genotypes, despite the dominance of only four infectivity phenotypes across the entire study period. Furthermore, in the presence of strong fluctuations in population size and migration, spatial selection may maintain pathogen populations that, despite being phenotypically stable, are genetically highly dynamic. Melampsora lini is a rust fungus that infects native flax, Linum marginale in south-eastern Australia where its epidemiology and evolution have been intensively studied since 1987. Over that time, substantial diversity in the pathotypic structure of M. lini has been demonstrated but an understanding of how genetic diversity in pathogen populations is maintained through space and time is lacking. Here we integrated phenotypic, genotypic and epidemiological datasets spanning 16 annual epidemics across three host populations to examine long-term pathogen genetic dynamics. The results show that host ecotype is the dominant selective force in the face of strong bottlenecks and annual patterns of genetic turnover. Results from previous studies indicate that in this geographic region, M. lini lacks the capacity to reproduce sexually–we thus expected to find limited genetic diversity and evidence for strong clonality influencing genetic dynamics within growing seasons. However, the breadth of genomic coverage provided by the SNP markers revealed high levels of genotypic variation within M. lini populations. This discovery contrasts with observed phenotypic dynamics as the epidemics of this pathogen were largely dominated by four pathotypes across the study period. Based on a detailed assessment and comparison of pathotypic and genotypic patterns, our study increases the understanding of how genetic diversity is generated and maintained through space and time within wild pathogen populations. The implications for the management of resistance to pathogens in agricultural or conservation contexts are significant: the appearance of clonality may be hiding high levels of pathogen diversity and recombination. Understanding how this diversity is generated could provide new and unique ways to mitigate or suppress the emergence of infectious strains, allowing to efficiently combat harmful diseases.
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Affiliation(s)
- Hanna Susi
- CSIRO Agriculture & Food, Canberra, Australia
- * E-mail:
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Carmona M, Sautua F, Pérez-Hérnandez O, Reis EM. Role of Fungicide Applications on the Integrated Management of Wheat Stripe Rust. FRONTIERS IN PLANT SCIENCE 2020; 11:733. [PMID: 32582257 PMCID: PMC7296138 DOI: 10.3389/fpls.2020.00733] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 05/07/2020] [Indexed: 05/14/2023]
Abstract
First described in Europe in 1777, stripe rust (SR) caused by Puccinia striiformis Westend. f. sp. tritici Erikss (Pst) is one of the most important and destructive diseases of wheat worldwide. Until 2000, SR was mainly endemic to cooler regions, but since then, new aggressive strains have emerged, spread intercontinentally, and caused severe epidemics in warmer regions across the world. This has put SR as a disease that poses a threat to the world food security. At present, the preferred strategy for control of SR is the access to wheat cultivars with adequate levels of SR resistance. However, wheat breeding programs are not sufficiently advanced to cope with the recently emerged Pst strains. Under this scenario, foliar fungicide applications have become an important component of SR management, but information on the effects of fungicide applications on SR control and wheat cultivar yield response is scarce. This review seeks to provide an overview of the impact and role of fungicides on SR management. With focus on wheat management in the major wheat-growing regions of the world, the review addresses: (a) the efficacy of different fungicide active ingredients, optimal fungicide timing and number of applications in controlling SR, and (b) the impact of fungicide on wheat grain yield response. Inclusion of fungicides in an integrated crop management approach is discussed.
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Affiliation(s)
- Marcelo Carmona
- Cátedra de Fitopatología, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Francisco Sautua
- Cátedra de Fitopatología, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Oscar Pérez-Hérnandez
- School of Agricultural Sciences, Northwest Missouri State University, Maryville, MO, United States
| | - Erlei M. Reis
- Escuela Para Graduados “Alberto Soriano”, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina
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Alternate Hosts of Puccinia striiformis f. sp. tritici and Their Role. Pathogens 2020; 9:pathogens9060434. [PMID: 32498285 PMCID: PMC7350320 DOI: 10.3390/pathogens9060434] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 05/24/2020] [Accepted: 05/27/2020] [Indexed: 01/06/2023] Open
Abstract
Understanding the interactions between the host and the pathogen is important in developing resistant cultivars and strategies for controlling the disease. Since the discovery of Berberis and Mahonia spp. as alternate hosts of the wheat stripe rust pathogen, Puccinia striiformis Westend. f. sp. tritici Erikss. (Pst), their possible role in generating new races of Pst through sexual reproduction has become a hot topic. To date, all the investigations about the role of alternate hosts in the occurrence of the wheat stripe rust epidemics revealed that it depends on alternate host species and environmental conditions. In this review, we summarized the current status of alternate hosts of Pst, their interactions with the pathogen, their importance in genetic diversity and disease epidemics. Most importantly, the recent research progress in understanding the role of alternate hosts of Pst is provided.
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Genetic diversity in exotic oat germplasm & resistance against barley yellow dwarf virus. Saudi J Biol Sci 2020; 27:2622-2631. [PMID: 32994720 PMCID: PMC7499088 DOI: 10.1016/j.sjbs.2020.05.042] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 05/23/2020] [Accepted: 05/24/2020] [Indexed: 11/24/2022] Open
Abstract
Oat (Avena sativa L.) is an important fodder crop of Pakistan, though with low productivity. The present study was conducted to evaluate the performance and genetic diversity of exotic oat germplasm, with emphasis on cereal yellow dwarf virus resistance. A total of 16 exotic line (introduced from Aarhus University Denmark) and 1 local line (provided by The University of Agriculture Peshawar), were grown during the season 2017–18 in Completely Randomized Block Design with three replications across two locations of Khyber Pakhtunkhwa i.e., Peshawar and Kohat. Field testing enabled to collect the data on BYDV incidence, BYDV severity, aphid infestation, plant height, leaf area, panicle length, panicle weight, spikelets per panicle, 1000 grain weight (g), grain yield (g), biological yield (g) and harvest index (%). Prevalence of BYDV was variable across location and over time. Six weeks data showed high disease pressure at Peshawar (85%), with SA-O-01 genotype having AUDPC value of 95%. Almost all the varieties showed less tolerance towards the Aphids attack. Line SA-O-15 showed the maximum 1000 grain weight (42.6 g) at Kohat, while SA-O-4 showed the maximum 1000 grain weight (60.7 g) at Peshawar. Line SA-O-05 (3634 g per (0.9 m2) plot) gave the maximum biological yield at Kohat station, while Line SA-O-01 gave the maximum biological yield (2517 g) at Peshawar. Mean grain yield for Kohat was recorded 0.155 g per (0.9 m2) plot while for Peshawar it was 0.231 g per (0.9 m2) plot. At Kohat line SA-O-10 produced the maximum grain yield (0.229 g), while line SA-O-12 produced the maximum grain yield at Peshawar (0.288 g). Molecular genotyping with a set of 4 RAPD primers revealed substantial diversity among17 oat lines. A total of 23 loci were amplified showing a high level of variations and polymorphism among the proposed lines. The maximum number of loci was recorded for GLA-04 (8), while the minimum number of loci was recorded for GLD-18 (4). Among the tested RAPD primers the maximum gene diversity (0.529) was recorded for loci GLA-03B230, GLA-04B130, GLA-04B300, GLB-05B150 and GLA-18B100 while the minimum (0.118) genetic diversity was recorded for loci GLA-03B600, GLB-05B330 and GLA-18B500. A clear divergence was found between most of the exotic oat lines. The observed genetic diversity in exotic oat germplasm and its resistance towards Barley Yellow Dwarf virus could be useful for oat genetic improvement and broadening the genetic background of cultivated oat germplasm.
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Atta BM, Saleem M, Ali H, Bilal M, Fayyaz M. Application of Fluorescence Spectroscopy in Wheat Crop: Early Disease Detection and Associated Molecular Changes. J Fluoresc 2020; 30:801-810. [PMID: 32430862 DOI: 10.1007/s10895-020-02561-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 05/14/2020] [Indexed: 11/24/2022]
Abstract
The application of fluorescence spectroscopy combined with chemometrics was explored in the current study for the detection of stripe rust in wheat. The healthy and stripe rust leaves were collected from the disease screening nursery. The variations in the blue-green region and chlorophyll fluorescence intensity in leaves provides the basis for the detection of stripe rust infection. With the progress of disease, the variations in the synchronous fluorescence spectroscopy (SFS) spectrum was witnessed. SFS is an excellent tool for the simultaneous measurement of multiple compound samples, in case of plants it generates evidence regarding the occurrence of leaf fluorophore bands thus revealing the biochemical variations going on at different infection stages. Based on the results of the current study, it is inferred that p-coumaric acid has the highest intensity in healthy samples followed by the asymptomatic leaf samples, whereas the band intensity of α-tocopherol, sinapic acid, chlorogenic acid, ferulic acid, tannins, flavonoid, carotenoids and anthocyanins increases in the diseased and the asymptomatic samples accordingly to the rust infection. Principal component analysis (PCA) beautifully differentiated the healthy and the infected leaf samples. It is evident that the asymptomatic samples are grouped with the diseased samples or independently; indicating the start of disease infection, the decision that is hard to make with the visual assessments. The results of the current study suggest that the fluorescence emission and the SFS spectral signatures acquired for stripe rust could be utilized as fingerprints for early disease detection.
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Affiliation(s)
- Babar Manzoor Atta
- Agri. & Biophotonics Division, National Institute of Lasers and Optronics College, Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, 45650, Pakistan.
| | - Muhammad Saleem
- Agri. & Biophotonics Division, National Institute of Lasers and Optronics College, Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, 45650, Pakistan
| | - Hina Ali
- Agri. & Biophotonics Division, National Institute of Lasers and Optronics College, Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, 45650, Pakistan
| | - Muhammad Bilal
- Agri. & Biophotonics Division, National Institute of Lasers and Optronics College, Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, 45650, Pakistan
| | - Muhammad Fayyaz
- Crop Diseases Research Institute (CDRI), National Agricultural Research Centre (NARC), Park Road, Islamabad, 44000, Pakistan
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Schwessinger B, Chen YJ, Tien R, Vogt JK, Sperschneider J, Nagar R, McMullan M, Sicheritz-Ponten T, Sørensen CK, Hovmøller MS, Rathjen JP, Justesen AF. Distinct Life Histories Impact Dikaryotic Genome Evolution in the Rust Fungus Puccinia striiformis Causing Stripe Rust in Wheat. Genome Biol Evol 2020; 12:597-617. [PMID: 32271913 DOI: 10.1101/859728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/03/2020] [Indexed: 05/27/2023] Open
Abstract
Stripe rust of wheat, caused by the obligate biotrophic fungus Puccinia striiformis f.sp. tritici, is a major threat to wheat production worldwide with an estimated yearly loss of US $1 billion. The recent advances in long-read sequencing technologies and tailored-assembly algorithms enabled us to disentangle the two haploid genomes of Pst. This provides us with haplotype-specific information at a whole-genome level. Exploiting this novel information, we perform whole-genome comparative genomics of two P. striiformis f.sp. tritici isolates with contrasting life histories. We compare one isolate of the old European lineage (PstS0), which has been asexual for over 50 years, and a Warrior isolate (PstS7 lineage) from a novel incursion into Europe in 2011 from a sexual population in the Himalayan region. This comparison provides evidence that long-term asexual evolution leads to genome expansion, accumulation of transposable elements, and increased heterozygosity at the single nucleotide, structural, and allele levels. At the whole-genome level, candidate effectors are not compartmentalized and do not exhibit reduced levels of synteny. Yet we were able to identify two subsets of candidate effector populations. About 70% of candidate effectors are invariant between the two isolates, whereas 30% are hypervariable. The latter might be involved in host adaptation on wheat and explain the different phenotypes of the two isolates. Overall, this detailed comparative analysis of two haplotype-aware assemblies of P. striiformis f.sp. tritici is the first step in understanding the evolution of dikaryotic rust fungi at a whole-genome level.
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Affiliation(s)
- Benjamin Schwessinger
- Research School of Biology, The Australian National University, Acton, Canberra, Australian Capital Territory, Australia
| | - Yan-Jun Chen
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Richard Tien
- School of Dentistry, The University of Western Australia, Nedlands, Western Australia, Australia
| | - Josef Korbinian Vogt
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Denmark
| | - Jana Sperschneider
- Biological Data Science Institute, The Australian National University, Acton, Canberra, Australian Capital Territory, Australia
| | - Ramawatar Nagar
- Research School of Biology, The Australian National University, Acton, Canberra, Australian Capital Territory, Australia
| | - Mark McMullan
- Earlham Institute, Norwich Research Park, United Kingdom
| | - Thomas Sicheritz-Ponten
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Chris K Sørensen
- Department of Agroecology, Faculty of Science and Technology, Aarhus University, Slagelse, Denmark
| | | | - John P Rathjen
- Research School of Biology, The Australian National University, Acton, Canberra, Australian Capital Territory, Australia
| | - Annemarie Fejer Justesen
- Department of Agroecology, Faculty of Science and Technology, Aarhus University, Slagelse, Denmark
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24
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Scald on gramineous hosts in Iran and their potential threat to cultivated barley. Mycol Prog 2020. [DOI: 10.1007/s11557-019-01553-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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25
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Khan MR, Rehman ZU, Nazir SN, Tshewang S, Baidya S, Hodson D, Imtiaz M, Ali S. Genetic Divergence and Diversity in Himalayan Puccinia striiformis Populations from Bhutan, Nepal, and Pakistan. PHYTOPATHOLOGY 2019; 109:1793-1800. [PMID: 31179857 DOI: 10.1094/phyto-01-19-0031-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The western Himalayan region in Pakistan has been shown to be the center of diversity of Puccinia striiformis; however, little is known about its genetic relations with the eastern part of the Himalayas. We studied the genetic structure of P. striiformis from Nepal (35 isolates) and Bhutan (31 isolates) in comparison with 81 Pakistani samples collected during 2015 and 2016, through microsatellite genotyping. Genetic analyses revealed a recombinant and highly diverse population structure in Pakistan, Bhutan, and Nepal. A high level of genotypic diversity (>0.90) was observed for the three countries of Pakistan (0.96), Bhutan (0.96), and Nepal (0.91) with the detection of 108 distinct multilocus genotypes (MLGs) in the overall population; 59 for Pakistan, 27 for Bhutan, and 26 for Nepal. Mean number of alleles per locus and gene diversity were higher in Nepal (3.19 and 0.458, respectively) than Bhutan (3.12 and 0.458, respectively). A nonsignificant difference between the observed and the expected heterozygosity in all populations further confirmed the recombinant structure. A clear population subdivision between the Himalayan region of Nepal, Bhutan, and Pakistan was evident, as revealed by FST values (ranging between 0.111 to 0.198), discriminant analysis of principal components, and resampling of MLGs. Limited gene flow could be present between Nepal and Bhutan, while the population from Pakistan was clearly distinct, and no divergence was present between two populations from Pakistan (Bajaur and Malakand). The overall high diversity and recombination signature suggested the potential role of recombination in the eastern Himalayan region (Nepal and Bhutan), which needs to be considered during host resistance deployment and in the context of aerial dispersal of the pathogen. Further surveillance should be made in the Himalayan region for disease management in the region and in the context of worldwide invasions.
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Affiliation(s)
- Muhammad Rameez Khan
- Institute of Biotechnology & Genetic Engineering, The University of Agriculture, Peshawar, Pakistan
| | - Zia-Ur Rehman
- Institute of Biotechnology & Genetic Engineering, The University of Agriculture, Peshawar, Pakistan
| | - Sidra Noreen Nazir
- Institute of Biotechnology & Genetic Engineering, The University of Agriculture, Peshawar, Pakistan
| | - Sangay Tshewang
- Department of Agriculture, Ministry of Agriculture and Forests, Tsirang, Bhutan
| | - Suraj Baidya
- Plant Pathology Division, Nepal Agriculture Research Council, Nepal
| | - David Hodson
- International Maize and Wheat Improvement Center, CIMMYT, Mexico
| | - Muhammad Imtiaz
- International Maize and Wheat Improvement Center, CIMMYT, Islamabad, Pakistan
| | - Sajid Ali
- Institute of Biotechnology & Genetic Engineering, The University of Agriculture, Peshawar, Pakistan
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Ennos RA, Hu XS. Estimating the number of sexual events per generation in a facultatively sexual haploid population. Heredity (Edinb) 2019; 122:729-741. [PMID: 30531814 PMCID: PMC6781114 DOI: 10.1038/s41437-018-0171-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 11/22/2018] [Accepted: 11/24/2018] [Indexed: 12/18/2022] Open
Abstract
In populations of facultatively sexual organisms, the proportion of sexually produced offspring contributed to each generation is a critical determinant of their evolutionary potential. However, estimating this parameter in natural populations has proved difficult. Here we develop a population genetic model for estimating the number of sexual events occurring per generation for facultatively sexual haploids possessing a biallelic mating-type locus (e.g., Chlamydomonas, ascomycete fungi). Our model treats the population as two subpopulations possessing opposite mating-type alleles, which exchange genes only when a sexual event takes place. Where mating types are equally abundant, we show that, for a neutral genetic marker, genetic differentiation between mating-type subpopulations is a simple function of the effective population size, the frequency of sexual reproduction, and the recombination fraction between the genetic marker and the mating-type locus. We employ simulations to examine the effects of linkage of markers to the mating-type locus, inequality of mating-type frequencies, mutation rate, and selection on this relationship. Finally, we apply our model to estimate the number of sexual reproduction events per generation in populations of four species of facultatively sexual ascomycete fungi, which have been jointly scored for mating type and a range of polymorphic molecular markers. Relative estimates are in line with expectations based on the known reproductive biology of these species.
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Affiliation(s)
- Richard A Ennos
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Building, Charlotte Auerbach Road, Edinburgh, EH9 3FL, UK.
| | - Xin-Sheng Hu
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, 510642, Guangdong, China.
- College of Forestry and Landscape Architecture, South China Agricultural University, 510642, Guangdong, China.
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Mehmood S, Sajid M, Zhao J, Khan T, Zhan G, Huang L, Kang Z. Identification of Berberis Species Collected from the Himalayan Region of Pakistan Susceptible to Puccinia striiformis f. sp. tritici. PLANT DISEASE 2019; 103:461-467. [PMID: 30657429 DOI: 10.1094/pdis-01-18-0154-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Puccinia striiformis f. sp. tritici (Pst), the stripe rust pathogen infecting cereal crops and grasses, was believed to have a hemicyclic life cycle consisting of uredinial and telial stages before the recent discovery of barberry (Berberis spp.) as an alternate (aecial) host for the fungus. This discovery has improved the understanding of the biology of the stripe rust pathogen. The Himalayan and near-Himalayan regions of Pakistan, China, and Nepal are considered as the center of diversity for Pst pathogen. High genetic diversity has been reported in these areas, probably resulting from the sexual reproduction of the stripe rust fungus. To determine if Berberis species growing in Pakistan are susceptible to Pst, we collected seeds of five species and two subspecies from the Himalayan region in 2016 and inoculated the seedlings with germinated teliospores of a Pakistani Pst isolate under controlled conditions. Pycnia and aecia were produced on all inoculated plants of these species and subspecies, and were demonstrated as Pst by successful infection of wheat plants with aeciospores. This study showed that the tested Pakistani Berberis species and subspecies are susceptible to Pst under controlled conditions.
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Affiliation(s)
- Sajid Mehmood
- 1 State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Marina Sajid
- 2 College of Food Science and Engineering, Northwest A&F University, Yangling 712100, Shaanxi, China; and
| | - Jie Zhao
- 1 State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Tika Khan
- 3 Integrated Mountain Area Research Center, Department of Biological Sciences, Karakoram International University, Gilgit 15100, Gilgit-Baltistan, Pakistan
| | - Gangming Zhan
- 1 State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Lili Huang
- 1 State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Zhensheng Kang
- 1 State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
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Knight NL, Vaghefi N, Hansen ZR, Kikkert JR, Pethybridge SJ. Temporal Genetic Differentiation of Cercospora beticola Populations in New York Table Beet Fields. PLANT DISEASE 2018; 102:2074-2082. [PMID: 30156961 DOI: 10.1094/pdis-01-18-0175-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Annual epidemics of Cercospora leaf spot (CLS), caused by the fungus Cercospora beticola, can result in substantial defoliation in table beet fields in New York. High allelic and genotypic diversity have been described within C. beticola populations; however, information on the temporal stability of populations is lacking. C. beticola isolates were obtained from symptomatic leaves in three table beet fields in successive years. Two of the fields were organic mixed-cropping farms and the third was managed conventionally in a broad-acre cropping system. C. beticola isolates (n = 304) were genotyped using 12 microsatellite markers. Genotypic diversity (Simpson's complement index = 0.178 to 0.990), allele frequencies, and indices of differentiation between years varied. Pairwise index of differentiation values ranged from 0.02 to 0.25 for clone-corrected data, and indicated significant genetic differentiation at Farm 2. No multilocus genotype was shared between years. The shift in multilocus genotypes between years questions the role of clonally reproducing primary inoculum. Collectively, these results suggest that a dominant inoculum source for initiating annual CLS epidemics is external to the field of interest. These findings have implications for CLS disease management in conventional and organic table beet production.
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Affiliation(s)
- Noel L Knight
- Plant Pathology & Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell AgriTech at the New York State Agricultural Experiment Station, Cornell University, Geneva, NY 14456
| | - Niloofar Vaghefi
- Plant Pathology & Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell AgriTech at the New York State Agricultural Experiment Station, Cornell University, Geneva, NY 14456
| | - Zachariah R Hansen
- Plant Pathology & Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell AgriTech at the New York State Agricultural Experiment Station, Cornell University, Geneva, NY 14456
| | | | - Sarah J Pethybridge
- Plant Pathology & Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell AgriTech at the New York State Agricultural Experiment Station, Cornell University, Geneva, NY 14456
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Abstract
The rice blast fungus Magnaporthe oryzae (syn., Pyricularia oryzae) is both a threat to global food security and a model for plant pathology. Molecular pathologists need an accurate understanding of the origins and line of descent of M. oryzae populations in order to identify the genetic and functional bases of pathogen adaptation and to guide the development of more effective control strategies. We used a whole-genome sequence analysis of samples from different times and places to infer details about the genetic makeup of M. oryzae from a global collection of isolates. Analyses of population structure identified six lineages within M. oryzae, including two pandemic on japonica and indica rice, respectively, and four lineages with more restricted distributions. Tip-dating calibration indicated that M. oryzae lineages separated about a millennium ago, long after the initial domestication of rice. The major lineage endemic to continental Southeast Asia displayed signatures of sexual recombination and evidence of DNA acquisition from multiple lineages. Tests for weak natural selection revealed that the pandemic spread of clonal lineages entailed an evolutionary “cost,” in terms of the accumulation of deleterious mutations. Our findings reveal the coexistence of multiple endemic and pandemic lineages with contrasting population and genetic characteristics within a widely distributed pathogen. The rice blast fungus Magnaporthe oryzae (syn., Pyricularia oryzae) is a textbook example of a rapidly adapting pathogen, and it is responsible for one of the most damaging diseases of rice. Improvements in our understanding of Magnaporthe oryzae’s diversity and evolution are required to guide the development of more effective control strategies. We used genome sequencing data for samples from around the world to infer the evolutionary history of M. oryzae. We found that M. oryzae diversified about 1,000 years ago, separating into six main lineages: two pandemic on japonica and indica rice, respectively, and four with more restricted distributions. We also found that a lineage endemic to continental Southeast Asia displayed signatures of sexual recombination and the acquisition of genetic material from multiple lineages. This work provides a population-level genomic framework for defining molecular markers for the control of rice blast and investigations of the molecular basis of differences in pathogenicity between M. oryzae lineages.
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Brar GS, Ali S, Qutob D, Ambrose S, Lou K, Maclachlan R, Pozniak CJ, Fu YB, Sharpe AG, Kutcher HR. Genome re-sequencing and simple sequence repeat markers reveal the existence of divergent lineages in the Canadian Puccinia striiformis
f. sp. tritici
population with extensive DNA methylation. Environ Microbiol 2018; 20:1498-1515. [DOI: 10.1111/1462-2920.14067] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 01/30/2018] [Accepted: 02/02/2018] [Indexed: 12/25/2022]
Affiliation(s)
- Gurcharn S. Brar
- Crop Development Centre/Department of Plant Sciences, College of Agriculture and Bioresources; University of Saskatchewan, 51 Campus Dr; Saskatoon SK S7N 5A8 Canada
| | - Sajid Ali
- Institute of Biotechnology and Genetic Engineering; University of Agriculture; Peshawar Pakistan
| | - Dinah Qutob
- Aquatic and Crop Resource Development; National Research Council of Canada, 110 Gymnasium Place; Saskatoon SK S7N 0W9 Canada
| | - Stephen Ambrose
- Aquatic and Crop Resource Development; National Research Council of Canada, 110 Gymnasium Place; Saskatoon SK S7N 0W9 Canada
| | - Kun Lou
- Crop Development Centre/Department of Plant Sciences, College of Agriculture and Bioresources; University of Saskatchewan, 51 Campus Dr; Saskatoon SK S7N 5A8 Canada
| | - Ron Maclachlan
- Crop Development Centre/Department of Plant Sciences, College of Agriculture and Bioresources; University of Saskatchewan, 51 Campus Dr; Saskatoon SK S7N 5A8 Canada
| | - Curtis J. Pozniak
- Crop Development Centre/Department of Plant Sciences, College of Agriculture and Bioresources; University of Saskatchewan, 51 Campus Dr; Saskatoon SK S7N 5A8 Canada
| | - Yong-Bi Fu
- Plant Gene Resources of Canada, Agriculture & Agri-Food Canada- Saskatoon Research and Development Centre, 107 Science Place; Saskatoon SK S7N 0X2 Canada
| | - Andrew G. Sharpe
- Global Institute for Food Security, University of Saskatchewan, 110 Gymnasium Place; Saskatoon SK S7N 0W9 Canada
| | - Hadley R. Kutcher
- Crop Development Centre/Department of Plant Sciences, College of Agriculture and Bioresources; University of Saskatchewan, 51 Campus Dr; Saskatoon SK S7N 5A8 Canada
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Schwessinger B, Sperschneider J, Cuddy WS, Garnica DP, Miller ME, Taylor JM, Dodds PN, Figueroa M, Park RF, Rathjen JP. A Near-Complete Haplotype-Phased Genome of the Dikaryotic Wheat Stripe Rust Fungus Puccinia striiformis f. sp. tritici Reveals High Interhaplotype Diversity. mBio 2018; 9:e02275-17. [PMID: 29463659 PMCID: PMC5821087 DOI: 10.1128/mbio.02275-17] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 01/09/2018] [Indexed: 01/01/2023] Open
Abstract
A long-standing biological question is how evolution has shaped the genomic architecture of dikaryotic fungi. To answer this, high-quality genomic resources that enable haplotype comparisons are essential. Short-read genome assemblies for dikaryotic fungi are highly fragmented and lack haplotype-specific information due to the high heterozygosity and repeat content of these genomes. Here, we present a diploid-aware assembly of the wheat stripe rust fungus Puccinia striiformis f. sp. tritici based on long reads using the FALCON-Unzip assembler. Transcriptome sequencing data sets were used to infer high-quality gene models and identify virulence genes involved in plant infection referred to as effectors. This represents the most complete Puccinia striiformis f. sp. tritici genome assembly to date (83 Mb, 156 contigs, N50 of 1.5 Mb) and provides phased haplotype information for over 92% of the genome. Comparisons of the phase blocks revealed high interhaplotype diversity of over 6%. More than 25% of all genes lack a clear allelic counterpart. When we investigated genome features that potentially promote the rapid evolution of virulence, we found that candidate effector genes are spatially associated with conserved genes commonly found in basidiomycetes. Yet, candidate effectors that lack an allelic counterpart are more distant from conserved genes than allelic candidate effectors and are less likely to be evolutionarily conserved within the P. striiformis species complex and Pucciniales In summary, this haplotype-phased assembly enabled us to discover novel genome features of a dikaryotic plant-pathogenic fungus previously hidden in collapsed and fragmented genome assemblies.IMPORTANCE Current representations of eukaryotic microbial genomes are haploid, hiding the genomic diversity intrinsic to diploid and polyploid life forms. This hidden diversity contributes to the organism's evolutionary potential and ability to adapt to stress conditions. Yet, it is challenging to provide haplotype-specific information at a whole-genome level. Here, we take advantage of long-read DNA sequencing technology and a tailored-assembly algorithm to disentangle the two haploid genomes of a dikaryotic pathogenic wheat rust fungus. The two genomes display high levels of nucleotide and structural variations, which lead to allelic variation and the presence of genes lacking allelic counterparts. Nonallelic candidate effector genes, which likely encode important pathogenicity factors, display distinct genome localization patterns and are less likely to be evolutionary conserved than those which are present as allelic pairs. This genomic diversity may promote rapid host adaptation and/or be related to the age of the sequenced isolate since last meiosis.
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Affiliation(s)
- Benjamin Schwessinger
- Research School of Biology, the Australian National University, Acton, ACT, Australia
| | - Jana Sperschneider
- Centre for Environment and Life Sciences, CSIRO Agriculture and Food, Perth, WA, Australia
| | - William S Cuddy
- Plant Breeding Institute, Faculty of Agriculture and Environment, the University of Sydney, Narellan, NSW, Australia
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, NSW, Australia
| | - Diana P Garnica
- Research School of Biology, the Australian National University, Acton, ACT, Australia
| | - Marisa E Miller
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
| | - Jennifer M Taylor
- Black Mountain Laboratories, CSIRO Agriculture and Food, Canberra, ACT, Australia
| | - Peter N Dodds
- Black Mountain Laboratories, CSIRO Agriculture and Food, Canberra, ACT, Australia
| | - Melania Figueroa
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota, USA
- Stakman-Borlaug Center for Sustainable Plant Health, University of Minnesota, St. Paul, Minnesota, USA
| | - Robert F Park
- Plant Breeding Institute, Faculty of Agriculture and Environment, the University of Sydney, Narellan, NSW, Australia
| | - John P Rathjen
- Research School of Biology, the Australian National University, Acton, ACT, Australia
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32
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Liu T, Wan A, Liu D, Chen X. Changes of Races and Virulence Genes in Puccinia striiformis f. sp. tritici, the Wheat Stripe Rust Pathogen, in the United States from 1968 to 2009. PLANT DISEASE 2017; 101:1522-1532. [PMID: 30678601 DOI: 10.1094/pdis-12-16-1786-re] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Stripe (yellow) rust, caused by Puccinia striiformis f. sp. tritici, is a serious disease of wheat in the world. The obligate biotrophic fungal pathogen changes its virulence rapidly, which can circumvent resistance in wheat cultivars and cause severe epidemics. Because P. striiformis f. sp. tritici races have been identified in the United States using different wheat genotypes in different time periods, it is difficult to make direct comparisons of the current population with historical populations. The objective of this study was to characterize historical populations with 18 Yr single-gene lines that are currently used to differentiate P. striiformis f. sp. tritici races in order to understand virulence and race changes of the pathogen over 40 years in the United States. From 908 P. striiformis f. sp. tritici isolates collected from 1968 to 2009 in the United States, 171 races were identified and their frequencies were determined. More races, more new races, and races with more virulence genes were detected since the year 2000 than prior to 2000. None of the races were virulent to Yr5 and Yr15, indicating that these genes have been effective since the late 1960s. Virulence genes to the remaining 16 Yr genes were detected in different periods, and most of them increased in frequency over time. Some virulence genes such as those to Yr17, Yr27, Yr32, Yr43, Yr44, YrTr1, and YrExp2 appeared 14 to 37 years earlier than previously reported, indicating the greater value of using Yr single-gene lines as differentials. Positive and negative associations were detected between virulence genes. The continual information on virulence and races in the P. striiformis f. sp. tritici populations is useful for understanding the evolution of the pathogen and for breeding wheat cultivars with effective resistance to stripe rust.
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Affiliation(s)
- Tinglan Liu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China; and Department of Plant Pathology, Washington State University, Pullman 99164-6430
| | - Anmin Wan
- Department of Plant Pathology, Washington State University
| | - Dengcai Liu
- Triticeae Research Institute, Sichuan Agricultural University
| | - Xianming Chen
- United States Department of Agriculture-Agricultural Research Service, Wheat Health, Genetics, and Quality Research Unit and Department of Plant Pathology, Washington State University, Pullman 99164-6430
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Ali S, Rodriguez-Algaba J, Thach T, Sørensen CK, Hansen JG, Lassen P, Nazari K, Hodson DP, Justesen AF, Hovmøller MS. Yellow Rust Epidemics Worldwide Were Caused by Pathogen Races from Divergent Genetic Lineages. FRONTIERS IN PLANT SCIENCE 2017; 8:1057. [PMID: 28676811 PMCID: PMC5477562 DOI: 10.3389/fpls.2017.01057] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Accepted: 05/31/2017] [Indexed: 05/21/2023]
Abstract
We investigated whether the recent worldwide epidemics of wheat yellow rust were driven by races of few clonal lineage(s) or populations of divergent races. Race phenotyping of 887 genetically diverse Puccinia striiformis isolates sampled in 35 countries during 2009-2015 revealed that these epidemics were often driven by races from few but highly divergent genetic lineages. PstS1 was predominant in North America; PstS2 in West Asia and North Africa; and both PstS1 and PstS2 in East Africa. PstS4 was prevalent in Northern Europe on triticale; PstS5 and PstS9 were prevalent in Central Asia; whereas PstS6 was prevalent in epidemics in East Africa. PstS7, PstS8 and PstS10 represented three genetic lineages prevalent in Europe. Races from other lineages were in low frequencies. Virulence to Yr9 and Yr27 was common in epidemics in Africa and Asia, while virulence to Yr17 and Yr32 were prevalent in Europe, corresponding to widely deployed resistance genes. The highest diversity was observed in South Asian populations, where frequent recombination has been reported, and no particular race was predominant in this area. The results are discussed in light of the role of invasions in shaping pathogen population across geographical regions. The results emphasized the lack of predictability of emergence of new races with high epidemic potential, which stresses the need for additional investments in population biology and surveillance activities of pathogens on global food crops, and assessments of disease vulnerability of host varieties prior to their deployment at larger scales.
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Affiliation(s)
- Sajid Ali
- Department of Agroecology, Global Rust Reference Centre, Aarhus UniversitySlagelse, Denmark
| | | | - Tine Thach
- Department of Agroecology, Global Rust Reference Centre, Aarhus UniversitySlagelse, Denmark
| | - Chris K. Sørensen
- Department of Agroecology, Global Rust Reference Centre, Aarhus UniversitySlagelse, Denmark
| | - Jens G. Hansen
- Department of Agroecology, Global Rust Reference Centre, Aarhus UniversitySlagelse, Denmark
| | - Poul Lassen
- Department of Agroecology, Global Rust Reference Centre, Aarhus UniversitySlagelse, Denmark
| | - Kumarse Nazari
- International Center for Agricultural Research in the Dry Areas, Regional Cereal Rust Research Centre, Aegean Agricultural Research Instituteİzmir, Turkey
| | - David P. Hodson
- International Maize and Wheat Improvement Center, CIMMYTAddis Ababa, Ethiopia
| | - Annemarie F. Justesen
- Department of Agroecology, Global Rust Reference Centre, Aarhus UniversitySlagelse, Denmark
| | - Mogens S. Hovmøller
- Department of Agroecology, Global Rust Reference Centre, Aarhus UniversitySlagelse, Denmark
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Berlin A, Samils B, Andersson B. Multiple genotypes within aecial clusters in Puccinia graminis and Puccinia coronata: improved understanding of the biology of cereal rust fungi. Fungal Biol Biotechnol 2017; 4:3. [PMID: 28955472 PMCID: PMC5611640 DOI: 10.1186/s40694-017-0032-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Accepted: 04/21/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cereal rust fungi (Puccinia spp.) are among the most economically important plant pathogens. These fungi have a complex life cycle, including five spore stages and two hosts. They infect one grass host on which they reproduce clonally and cause the cereal rust diseases, while the alternate host is required for sexual reproduction. Although previous studies clearly demonstrate the importance of the alternate host in creating genetic diversity in cereal rust fungi, little is known about the amount of novel genotypes created in each successful completion of a sexual reproduction event. RESULTS In this study, single sequence repeat markers were used to study the genotypic diversity within aecial clusters by genotyping individual aecial cups. Two common cereal rusts, Puccinia graminis causing stem rust and Puccinia coronata the causal agent of crown rust were investigated. We showed that under natural conditions, a single aecial cluster usually include several genotypes, either because a single pycnial cluster is fertilized by several different pycniospores, or because aecia within the cluster are derived from more than one fertilized adjoining pycnial cluster, or a combination of both. CONCLUSION Our results imply that although sexual events in cereal rust fungi in most regions of the world are relatively rare, the events that occur may still significantly contribute to the genetic variation within the pathogen populations.
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Affiliation(s)
- Anna Berlin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, 750 07 Uppsala, Sweden
| | - Berit Samils
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, 750 07 Uppsala, Sweden
| | - Björn Andersson
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, 750 07 Uppsala, Sweden
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Schwessinger B. Fundamental wheat stripe rust research in the 21 st century. THE NEW PHYTOLOGIST 2017; 213:1625-1631. [PMID: 27575735 DOI: 10.1111/nph.14159] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 07/05/2016] [Indexed: 05/27/2023]
Abstract
Contents 1625 I. 1625 II. 1626 III. 1626 IV. 1626 V. 1628 VI. 1629 VII. 1629 1630 References 1630 SUMMARY: In the 21st century, the wheat stripe rust fungus has evolved to be the largest biotic limitation to global wheat production. New pathogen genotypes are more aggressive and able to infect previously resistant wheat varieties, leading to rapid pathogen migration across and between continents. We now know the full life cycle, microevolutionary relationships and past migration routes on a global scale. Current sequencing technologies have provided the first fungal draft genomes and simplified plant resistance gene cloning. Yet, we know nothing about the molecular and microevolutionary mechanisms that facilitate the infection process and cause new devastating pathogen races. These are the questions that need to be addressed by exploiting the synergies between novel 21st century biology tools and decades of dedicated pathology work.
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Affiliation(s)
- Benjamin Schwessinger
- The Australian National University, Research School Biology, 134 Linnaeus Way, Acton, ACT, 2601, Australia
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36
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Hu X, Ma L, Liu T, Wang C, Peng Y, Pu Q, Xu X. Population Genetic Analysis of Puccinia striiformis f. sp. tritici Suggests Two Distinct Populations in Tibet and the Other Regions of China. PLANT DISEASE 2017; 101:288-296. [PMID: 30681929 DOI: 10.1094/pdis-02-16-0190-re] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is an important disease on wheat, seriously threatening wheat production worldwide. China is one of the largest stripe rust epidemic regions in the world. The pathogen sexual reproduction and migration routes between Tibet and the other regions in China are still unknown. In this study, we obtained 961 Pst isolates from 1,391 wheat leaf samples from Gansu (277), Shaanxi (253), Sichuan (172), and Tibet (259), comprising 13 natural populations, and genotyped them with simple sequence repeat (SSR) markers. The isolates can be divided into two distinct clusters based on DAPC and STRUCTURE analyses. The genetic diversity of Longnan (in Gansu) and Yibin (in Sichuan) populations was the highest and lowest among the 13 populations, respectively. The hypothesis of multilocus linkage disequilibrium was rejected for the populations from Linzhi in the Himalayan, Longnan, Hanzhong, Guangyuan, Mianyang, Liangshan, and Chendu in the south Qinling Mountains at the level of P = 0.01, which indicated significant linkage among markers in these populations. Populations in the other regions had extensive gene exchange (Nm > 4); little gene exchange was found between Tibet and the other regions (Nm < 1). The results suggest that the Tibet epidemic region of Pst is highly differentiated from the other epidemic regions in China.
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Affiliation(s)
- Xiaoping Hu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Lijie Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Taiguo Liu
- State Key Laboratory for the Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Science, Beijing 100193, China
| | - Conghao Wang
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yuelin Peng
- Tibet Agricultural and Animal Husbandry College, Linzhi 860000, China
| | - Qiong Pu
- Tibet Autonomous Region Agricultural Technology Extension and Service Center, Lhasa 850000, Tibet
| | - Xiangming Xu
- NIAB East Malling Research, New Road, East Malling, ME19 6BJ, Kent, U.K
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Ali S, Hodson D. Wheat Rust Surveillance: Field Disease Scoring and Sample Collection for Phenotyping and Molecular Genotyping. Methods Mol Biol 2017; 1659:3-11. [PMID: 28856636 DOI: 10.1007/978-1-4939-7249-4_1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Long-distance migration capacity, emergence of invasive lineages, and variability in adaptation to a wide range of climatic conditions make wheat rusts the most important threat to wheat production worldwide. Efficient and coordinated efforts are required for surveillance of the pathogen population at different geographical levels to enable tracking of rust pathogen populations at local, regional, continental, and ultimately worldwide scale. Here we describe a standard procedure for rust surveillance to enable comparison across various research groups for a final compilation. The procedure described would enable tracking of disease severity, field level expression of host resistance, and collection of samples for further virulence phenotyping and molecular genotyping.
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Affiliation(s)
- Sajid Ali
- Institute of Biotechnology & Genetic Engineering, University of Agriculture, Peshawar, 25130, Khyber Pakhtunkhwa, Pakistan.
| | - David Hodson
- ILRI/CIMMYT, P.O. Box 5689, Addis Ababa, Ethiopia.
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38
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Ali S, Khan MR, Gautier A, Swati ZA, Walter S. Microsatellite Genotyping of the Wheat Yellow Rust Pathogen Puccinia striiformis. Methods Mol Biol 2017; 1659:59-70. [PMID: 28856641 DOI: 10.1007/978-1-4939-7249-4_6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
To combat the ever-increasing threat of wheat yellow rust worldwide, understanding of the pathogen (Puccinia striiformis) population biology is indispensable. Molecular markers, particularly microsatellites, have been reported to be important tools for deciphering pathogen population structure, invasion sources, and migration history. The utility of these DNA-based markers and sequencing has been increased by the direct DNA extraction from infected leaves with subsequent multiplex-based SSR genotyping. In this chapter we describe the protocol for direct DNA extraction and its genotyping with microsatellite markers in multiplex reactions. We describe the procedure for allele scoring, and various troubles faced during microsatellite scoring and potential solutions for them.
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Affiliation(s)
- Sajid Ali
- Institute of Biotechnology & Genetic Engineering, The University of Agriculture, Peshawar, 25130, Khyber Pakhtunkhwa, Pakistan.
| | - Muhammad R Khan
- Institute of Biotechnology & Genetic Engineering, The University of Agriculture, Peshawar, 25130, Khyber Pakhtunkhwa, Pakistan
| | - Angelique Gautier
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
| | - Zahoor A Swati
- Institute of Biotechnology & Genetic Engineering, The University of Agriculture, Peshawar, 25130, Khyber Pakhtunkhwa, Pakistan
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Roman-Reyna V, Rathjen JP. Apoplastic Sugar Extraction and Quantification from Wheat Leaves Infected with Biotrophic Fungi. Methods Mol Biol 2017; 1659:125-134. [PMID: 28856646 DOI: 10.1007/978-1-4939-7249-4_11] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Biotrophic fungi such as rusts modify the nutrient status of their hosts by extracting sugars. Hemibiotrophic and biotrophic fungi obtain nutrients from the cytoplasm of host cells and/or the apoplastic spaces. Uptake of nutrients from the cytoplasm is via intracellular hyphae or more complex structures such as haustoria. Apoplastic nutrients are taken up by intercellular hyphae. Overall the infection creates a sink causing remobilization of nutrients from local and distal tissues. The main mobile sugar in plants is sucrose which is absorbed via plant or fungal transporters once unloaded into the cytoplasm or the apoplast. Infection by fungal pathogens alters the apoplastic sugar contents and stimulates the influx of nutrients towards the site of infection as the host tissue transitions to sink. Quantification of solutes in the apoplast can help to understand the allocation of nutrients during infection. However, separation of apoplastic fluids from whole tissue is not straightforward and leakage from damaged cells can alter the results of the extraction. Here, we describe how variation in cytoplasmic contamination and infiltrated leaf volumes must be controlled when extracting apoplastic fluids from healthy and rust-infected wheat leaves. We show the importance of correcting the data for these parameters to measure sugar concentrations accurately.
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Affiliation(s)
- Veronica Roman-Reyna
- Research School of Biology, Australian National University, Linnaeus Way, Canberra, Australia
| | - John P Rathjen
- Research School of Biology, Australian National University, Linnaeus Way, Canberra, Australia.
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40
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Croll D, McDonald BA. The genetic basis of local adaptation for pathogenic fungi in agricultural ecosystems. Mol Ecol 2016; 26:2027-2040. [DOI: 10.1111/mec.13870] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Revised: 09/13/2016] [Accepted: 09/26/2016] [Indexed: 12/20/2022]
Affiliation(s)
- Daniel Croll
- Plant Pathology; Institute of Integrative Biology; ETH Zurich; 8092 Zurich Switzerland
| | - Bruce A. McDonald
- Plant Pathology; Institute of Integrative Biology; ETH Zurich; 8092 Zurich Switzerland
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Zhao J, Wang M, Chen X, Kang Z. Role of Alternate Hosts in Epidemiology and Pathogen Variation of Cereal Rusts. ANNUAL REVIEW OF PHYTOPATHOLOGY 2016; 54:207-28. [PMID: 27296143 DOI: 10.1146/annurev-phyto-080615-095851] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Cereal rusts, caused by obligate and biotrophic fungi in the genus Puccinia, are important diseases that threaten world food security. With the recent discovery of alternate hosts for the stripe rust fungus (Puccinia striiformis), all cereal rust fungi are now known to be heteroecious, requiring two distinct plant species serving as primary or alternate hosts to complete their sexual life cycle. The roles of the alternate hosts in disease epidemiology and pathogen variation vary greatly from species to species and from region to region because of different climatic and cropping conditions. We focus this review on rust fungi of small grains, mainly stripe rust, stem rust, leaf rust, and crown rust of wheat, barley, oat, rye, and triticale, with emphases on the contributions of alternate hosts to the development and management of rust diseases.
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Affiliation(s)
- Jie Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China;
| | - Meinan Wang
- Department of Plant Pathology, Washington State University, Pullman, Washington 99164-6430
| | - Xianming Chen
- US Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics, and Quality Research Unit, and Department of Plant Pathology, Washington State University, Pullman, Washington 99164-6430;
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China;
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Weeds, as ancillary hosts, pose disproportionate risk for virulent pathogen transfer to crops. BMC Evol Biol 2016; 16:101. [PMID: 27176034 PMCID: PMC4866072 DOI: 10.1186/s12862-016-0680-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 05/06/2016] [Indexed: 11/11/2022] Open
Abstract
Background The outcome of the arms race between hosts and pathogens depends heavily on the interactions between their genetic diversity, population size and transmission ability. Theory predicts that genetically diverse hosts will select for higher virulence and more diverse pathogens than hosts with low genetic diversity. Cultivated hosts typically have lower genetic diversity and thus small effective population sizes, but can potentially harbour large pathogen population sizes. On the other hand, hosts, such as weeds, which are genetically more diverse and thus have larger effective population sizes, usually harbour smaller pathogen population sizes. Large pathogen population sizes may lead to more opportunities for mutation and hence more diverse pathogens. Here we test the predictions that pathogen neutral genetic diversity will increase with large pathogen population sizes and host diversity, whereas diversity under selection will increase with host diversity. We assessed and compared the diversity of a fungal pathogen, Rhynchosporium commune, on weedy barley grass (which have a large effective population size) and cultivated barley (low genetic diversity) using microsatellites, effector locus nip1 diversity and pathogen aggressiveness in order to assess the importance of weeds in the evolution of the neutral and selected diversity of pathogens. Results The findings indicated that the large barley acreage and low host diversity maintains higher pathogen neutral genetic diversity and lower linkage disequilibrium, while the weed maintains more pathotypes and higher virulence diversity at nip1. Strong evidence for more pathogen migration from barley grass to barley suggests transmission of virulence from barley grass to barley is common. Conclusions Pathogen census population size is a better predictor for neutral genetic diversity than host diversity. Despite maintaining a smaller pathogen census population size, barley grass acts as an important ancillary host to R. commune, harbouring highly virulent pathogen types capable of transmission to barley. Management of disease on crops must therefore include management of weedy ancillary hosts, which may harbour disproportionate supplies of virulent pathogen strains. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0680-6) contains supplementary material, which is available to authorized users.
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Zhan GM, Wang FP, Luo HY, Jiang SC, Zheng WM, Huang LL, Kang ZS. Screening for simple sequence repeat markers in Puccinia striiformis tritici based on genomic sequence. J Zhejiang Univ Sci B 2016; 16:727-32. [PMID: 26238548 DOI: 10.1631/jzus.b1400364] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Puccinia striiformis f. sp. tritici (Pst) is the obligate biotrophic fungus responsible for stripe rust wheat. In this study, we developed and characterized 20 polymorphic microsatellite markers from the genomic sequence of an isolate of Chinese Pst race CY32. Polymorphism at each simple sequence repeat (SSR) locus was determined using 32 Pst isolates from 7 countries. The number of alleles varied from 2 to 7 across isolates, and the observed and expected heterozygosities ranged from 0.33 to 0.97 (mean 0.62) and 0.23 to 0.73 (mean 0.51), respectively. As expected the genomic SSR markers were more polymorphic than the expressed sequence tag (EST)-SSR markers developed previously. These markers will be more useful for population genetics and molecular genetics studies in Pst.
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Affiliation(s)
- Gang-ming Zhan
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling 712100, China
| | - Fu-ping Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling 712100, China
| | - Huai-yong Luo
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling 712100, China
| | - Shu-chang Jiang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling 712100, China
| | - Wen-ming Zheng
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Life Science, Henan Agricultural University, Zhengzhou 450002, China
| | - Li-li Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling 712100, China
| | - Zhen-sheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling 712100, China;
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Walter S, Ali S, Kemen E, Nazari K, Bahri BA, Enjalbert J, Hansen JG, Brown JK, Sicheritz‐Pontén T, Jones J, de Vallavieille‐Pope C, Hovmøller MS, Justesen AF. Molecular markers for tracking the origin and worldwide distribution of invasive strains of Puccinia striiformis. Ecol Evol 2016; 6:2790-804. [PMID: 27066253 PMCID: PMC4800029 DOI: 10.1002/ece3.2069] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 02/15/2016] [Accepted: 02/22/2016] [Indexed: 01/07/2023] Open
Abstract
Investigating the origin and dispersal pathways is instrumental to mitigate threats and economic and environmental consequences of invasive crop pathogens. In the case of Puccinia striiformis causing yellow rust on wheat, a number of economically important invasions have been reported, e.g., the spreading of two aggressive and high temperature adapted strains to three continents since 2000. The combination of sequence-characterized amplified region (SCAR) markers, which were developed from two specific AFLP fragments, differentiated the two invasive strains, PstS1 and PstS2 from all other P. striiformis strains investigated at a worldwide level. The application of the SCAR markers on 566 isolates showed that PstS1 was present in East Africa in the early 1980s and then detected in the Americas in 2000 and in Australia in 2002. PstS2 which evolved from PstS1 became widespread in the Middle East and Central Asia. In 2000, PstS2 was detected in Europe, where it never became prevalent. Additional SSR genotyping and virulence phenotyping revealed 10 and six variants, respectively, within PstS1 and PstS2, demonstrating the evolutionary potential of the pathogen. Overall, the results suggested East Africa as the most plausible origin of the two invasive strains. The SCAR markers developed in the present study provide a rapid, inexpensive, and efficient tool to track the distribution of P. striiformis invasive strains, PstS1 and PstS2.
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Affiliation(s)
- Stephanie Walter
- Department of AgroecologyAarhus UniversityFlakkebjergDK‐4200SlagelseDenmark
| | - Sajid Ali
- Department of AgroecologyAarhus UniversityFlakkebjergDK‐4200SlagelseDenmark
- Institute of Biotechnology & Genetic EngineeringThe University of Agriculture, Peshawar25000PeshawarPakistan
| | - Eric Kemen
- The Sainsbury LaboratoryNorwich Research ParkNorwichNR4 7UHUK
- Present address: Eric Kemen Max Planck Institute for Plant Breeding ResearchCarl‐von‐Linné‐Weg 1050829CologneGermany
| | - Kumarse Nazari
- ICARDARegional Cereal Rust Research CentreAegean Agricultural Research Institute P.K. 9Menemen/İZMİRTurkey
| | - Bochra A. Bahri
- National Institute of Agronomy of Tunisia (INAT)Avenue Charles Nicolle43 TN‐1082 El MahrajèneTunisia
| | - Jérôme Enjalbert
- INRA UMR 320 Génétique VégétaleFerme du MoulonF‐91190Gif sur YvetteFrance
| | - Jens G. Hansen
- Department of AgroecologyAarhus UniversityFlakkebjergDK‐4200SlagelseDenmark
| | | | - Thomas Sicheritz‐Pontén
- Center for Biological Sequence AnalysisDepartment of Systems BiologyTechnical University of DenmarkBuilding 208DK‐2800Kongens LyngbyDenmark
| | - Jonathan Jones
- The Sainsbury LaboratoryNorwich Research ParkNorwichNR4 7UHUK
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Kenaley SC, Hudler GW, Bergstrom GC. Detection and phylogenetic relationships of Puccinia emaculata and Uromyces graminicola (Pucciniales) on switchgrass in New York State using rDNA sequence information. Fungal Biol 2016; 120:791-806. [PMID: 27109375 DOI: 10.1016/j.funbio.2016.01.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 01/25/2016] [Accepted: 01/27/2016] [Indexed: 10/22/2022]
Abstract
The species of rust fungi (Pucciniales) inciting disease on switchgrass (Panicum virgatum) grown in bioenergy feedstock systems across the north-central and eastern United States remain unclear. In the present study, the species number and phylogenetic relationships of rust species affecting switchgrass were examined in 2011-2013 at two sites in New York State as well as selected sites in Alabama, Iowa, Nebraska, Pennsylvania, South Dakota, and West Virginia using ribosomal RNA gene data (partial internal transcribed spacer [ITS] 1, complete 5.8 subunit [S] and ITS2, and partial 28S). Uredinial group and teliospore morphology were also utilized to delimit taxa in collection years 2012 and 2013. Maximum likelihood, maximum parsimony, and Bayesian analyses demonstrated two monophyletic clades. Clade I consisted of Puccinia emaculata and included the majority of single-sorus samples across sites, whereas, Clade II included multiple samples from Iowa, Nebraska, and South Dakota. Single-telial samples for Clade I possessed only two-celled teliospores while Clade II samples possessed only one-celled teliospores, and hence, were readily diagnosed morphologically to P. emaculata and Uromyces graminicola, respectively. No U. graminicola sequences exist in GenBank to compare with our Clade II samples; however, based on teliospore morphology, the identity of Clade II taxa is U. graminicola.
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Affiliation(s)
- Shawn C Kenaley
- School of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, NY 14853-5904, USA.
| | - George W Hudler
- School of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, NY 14853-5904, USA
| | - Gary C Bergstrom
- School of Integrative Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, NY 14853-5904, USA
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Cheng P, Chen XM, See DR. Grass Hosts Harbor More Diverse Isolates of Puccinia striiformis Than Cereal Crops. PHYTOPATHOLOGY 2016; 106:362-371. [PMID: 26667189 DOI: 10.1094/phyto-07-15-0155-r] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Puccinia striiformis causes stripe rust on cereal crops and many grass species. However, it is not clear whether the stripe rust populations on grasses are able to infect cereal crops and how closely they are related to each other. In this study, 103 isolates collected from wheat, barley, triticale, rye, and grasses in the United States were characterized by virulence tests and simple sequence repeat (SSR) markers. Of 69 pathotypes identified, 41 were virulent on some differentials of wheat only, 10 were virulent on some differentials of barley only, and 18 were virulent on some differentials of both wheat and barley. These pathotypes were clustered into three groups: group one containing isolates from wheat, triticale, rye, and grasses; group two isolates were from barley and grasses; and group three isolates were from grasses and wheat. SSR markers identified 44 multilocus genotypes (MLGs) and clustered them into three major molecular groups (MG) with MLGs in MG3 further classified into three subgroups. Isolates from cereal crops were present in one or more of the major or subgroups, but not all, whereas grass isolates were present in all of the major and subgroups. The results indicate that grasses harbor more diverse isolates of P. striiformis than the cereals.
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Affiliation(s)
- P Cheng
- First, second, and third authors: Department of Plant Pathology, Washington State University, Pullman 99164-6430; and second and third authors: U.S. Department of Agriculture-Agriculture Research Service, Wheat Genetics, Quality, Physiology and Disease Research Unit, Pullman, WA 99164-6430
| | - X M Chen
- First, second, and third authors: Department of Plant Pathology, Washington State University, Pullman 99164-6430; and second and third authors: U.S. Department of Agriculture-Agriculture Research Service, Wheat Genetics, Quality, Physiology and Disease Research Unit, Pullman, WA 99164-6430
| | - D R See
- First, second, and third authors: Department of Plant Pathology, Washington State University, Pullman 99164-6430; and second and third authors: U.S. Department of Agriculture-Agriculture Research Service, Wheat Genetics, Quality, Physiology and Disease Research Unit, Pullman, WA 99164-6430
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Ali S, Soubeyrand S, Gladieux P, Giraud T, Leconte M, Gautier A, Mboup M, Chen W, de Vallavieille-Pope C, Enjalbert J. cloncase: Estimation of sex frequency and effective population size by clonemate resampling in partially clonal organisms. Mol Ecol Resour 2016; 16:845-61. [DOI: 10.1111/1755-0998.12511] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 01/29/2016] [Accepted: 02/02/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Sajid Ali
- UMR1290, BIOGER; INRA-AgroParisTech; BP01 78850 Thiverval-Grignon France
- Institute of Biotechnology and Genetic Engineering; the University of Agriculture, Peshawar; 25000 Peshawar Pakistan
| | - Samuel Soubeyrand
- UR546 Biostatistics and Spatial Processes; INRA; 84914 Avignon France
| | - Pierre Gladieux
- Ecologie Systématique Evolution; CNRS; Univ. Paris-Sud; AgroParisTech; Université Paris-Saclay; 91400 Orsay France
- UMR385 Biologie et Génétique des Interactions Plante-Parasite; CIRAD; INRA; F-34398 Montpellier France
| | - Tatiana Giraud
- Ecologie Systématique Evolution; CNRS; Univ. Paris-Sud; AgroParisTech; Université Paris-Saclay; 91400 Orsay France
| | - Marc Leconte
- UMR1290, BIOGER; INRA-AgroParisTech; BP01 78850 Thiverval-Grignon France
| | - Angélique Gautier
- UMR1290, BIOGER; INRA-AgroParisTech; BP01 78850 Thiverval-Grignon France
| | - Mamadou Mboup
- DuPont de Nemours (France) SAS Crop Protection - European Research & Development Center; 24, rue du Moulin 68740 Nambsheim France
| | - Wanquan Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests; Institute of Plant Protection; Chinese Academy of Agricultural Sciences; No. 2 Yuanmingyuan West Road Beijing 100193 China
| | | | - Jérôme Enjalbert
- Ecologie Systématique Evolution; CNRS; Univ. Paris-Sud; AgroParisTech; Université Paris-Saclay; 91400 Orsay France
- GQE - Le Moulon; INRA; Univ. Paris-Sud; CNRS; AgroParisTech; Université Paris-Saclay; F-91190 Gif-sur-Yvette France
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Secreted protein gene derived-single nucleotide polymorphisms (SP-SNPs) reveal population diversity and differentiation of Puccinia striiformis f. sp. tritici in the United States. Fungal Biol 2016; 120:729-44. [PMID: 27109369 DOI: 10.1016/j.funbio.2016.02.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Revised: 02/18/2016] [Accepted: 02/23/2016] [Indexed: 11/21/2022]
Abstract
Single nucleotide polymorphism (SNP) is a powerful molecular marker technique that has been widely used in population genetics and molecular mapping studies for various organisms. However, the technique has not been used for studying Puccinia striiformis f. sp. tritici (Pst), the wheat stripe rust pathogen. In this study, we developed over a hundred secreted protein gene-derived SNP (SP-SNP) markers and used 92 markers to study the population structure of Pst. From 352 isolates collected in the United States, we identified 242 multi-locus genotypes. The SP-SNP genotypes had a moderate, but significant correlation with the virulence phenotype data. Clustering of the multi-locus genotypes was consistent by various analyses, revealing distinct genetic groups. Analysis of molecular variance detected significant differences between the eastern and western US Pst populations. High heterozygosity was found in the US population with significant differences identified among epidemiological regions. Analysis of population differentiation revealed that populations between the eastern and western US were highly differentiated while moderate differentiation was found in populations within the western or eastern US. Isolates from the western US were more diverse than isolates from the eastern US. The information is useful for guiding the disease management in different epidemiological regions.
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Thach T, Ali S, de Vallavieille-Pope C, Justesen A, Hovmøller M. Worldwide population structure of the wheat rust fungus Puccinia striiformis in the past. Fungal Genet Biol 2016; 87:1-8. [DOI: 10.1016/j.fgb.2015.12.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2015] [Revised: 12/22/2015] [Accepted: 12/23/2015] [Indexed: 12/23/2022]
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50
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Wang Z, Zhao J, Chen X, Peng Y, Ji J, Zhao S, Lv Y, Huang L, Kang Z. Virulence Variations of Puccinia striiformis f. sp. tritici Isolates Collected from Berberis spp. in China. PLANT DISEASE 2016; 100:131-138. [PMID: 30688563 DOI: 10.1094/pdis-12-14-1296-re] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The stripe rust pathogen Puccinia striiformis f. sp. tritici frequently causes significant yield losses in China, due to rapid development of new races that overcome resistance in wheat cultivars. Indirect evidence suggests that sexual reproduction occurs in the P. striiformis f. sp. tritici population in China but direct evidence was still lacking. In this study, a large-scale survey of barberry (Berberis spp.) was conducted in Gansu, Shaanxi, Tibet, and Xinjiang provinces in western China. In total, 9,297 single-aecial (SA) samples were used to inoculate a susceptible wheat cultivar to identify samples of P. striiformis f. sp. tritici. Sixteen of the SA samples were identified as P. striiformis f. sp. tritici. When tested on the wheat differentials for identifying P. striiformis f. sp. tritici races, 15 of the 16 SA samples had different virulence patterns, indicating that they were sexually produced through barberry. From the 16 SA samples, 118 single-uredinium (SU) isolates were obtained, from which 88 virulence patterns were identified when tested on 17 Yr single-gene lines. The virulence patterns had relatively narrow virulence spectra, ranging from 0 to 9, with a mean of four virulences per SU isolates. Of the 17 Yr genes, no virulences were detected for Yr5, Yr10, and Yr15; virulences to YrTr1, Yr24, and Yr27 were extremely low (<3%); those to YrSP, Yr9, Yr28, and Yr2 were low (13.6 to 28.0%); those to Yr7, Yr17, Yr8, and YrExp2 were moderate (33.1 to 48.3%); and those to Yr6, Yr44, and Yr25 were high (52.5 to 72.9%). This study provides direct evidence that natural sexual reproduction occurs in the P. striiformis f. sp. tritici population in China, but the frequency appears to be very low. The sexual reproduction on alternate host plants can generate a great virulence diversity, which may have contributed to the high variation in the P. striiformis f. sp. tritici population in China.
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Affiliation(s)
- Zhiyan 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
| | - Jie Zhao
- 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
- United States Department of Agriculture-Agricultural Research Service, Wheat Genetics, Quality, Physiology, and Disease Research Unit and Department of Plant Pathology, Washington State University, Pullman 99164-6430
| | - Yuelin Peng
- Department of Plant Sciences, Agricultural and Animal Husbandry College of Tibet University, Linzhi, Tibet 86000, P. R. China
| | - Jingjing Ji
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University
| | - Shilei Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University
| | - Yanjie Lv
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University
| | - Lili Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University
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