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Gultyaeva EI, Shaydayuk EL. Diversity of Northwestern and North Caucasian Populations of Puccinia striiformis f. sp. tritici by Virulence and Microsatellite Loci in 2022. DOKLADY BIOLOGICAL SCIENCES : PROCEEDINGS OF THE ACADEMY OF SCIENCES OF THE USSR, BIOLOGICAL SCIENCES SECTIONS 2024:10.1134/S0012496624701291. [PMID: 39400892 DOI: 10.1134/s0012496624701291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2024] [Revised: 08/15/2024] [Accepted: 08/17/2024] [Indexed: 10/15/2024]
Abstract
Yellow rust (Puccinia striiformis f. sp. tritici (Pst)) is a potentially dangerous disease of wheat. Genetic protection of wheat is an environmentally safe method to control the disease, but its successful application requires information on the structure of regional populations of the pathogen. Virulence and molecular polymorphism were characterized in two Russian Pst populations in 2022. Wheat leaves with Pst urediniopustules were collected from the North Caucasus (Krasnodar Krai, Dagestan, and Kalmykia) and Northwestern Russia (Leningrad Oblast). Virulence was tested on 14 isogenic lines (AvocetNIL) and 15 differentiator cultivars. Polymorphism at 20 microsatellite loci was evaluated in molecular analyses. The SSR markers were as recommended by the Global Rust Reference Center. Virulence was assessed in 74 monopustular isolates, including 29 Dagestan, 10 Krasnodar, 5 Kalmyk, and 30 Northwestern ones. Resistance to all isolates was observed in lines with the genes Yr5, Yr10, Yr15, Yr24, and Yr26 and the cultivars Moro (Yr10, YrMor) and Nord Desprez (Yr3, YrND, Yr+). Isolates virulent to the AvYr17 line were detected for the first time in the Dagestan and Krasnodar populations. Their occurrence was moderate (13%) in the Northwestern population. A significant variation was observed in lines and cultivars with the Yr1 and Yr3 genes. Virulence to Yr7 and YrSp was found to be lower than in 2019 to 2021. In total, 28 phenotypes (races) were determined in the virulence analysis (15 in Dagestan, 11 in the Northwestern region, 3 in Krasnodar, and 2 in Kalmykia). A common phenotype was detected in three North Caucasian Pst samples. Genetic distances between the phenotypes were estimated. Most phenotypes grouped together in a multidimensional diagram, with the exception of three Dagestan phenotypes with the fewest virulence alleles. Based on the Fst index, the Dagestan and Kalmyk Pst collections were high similar to each other and differed moderately from the other collections. Long-term trends in virulence (from 2019 to 2022) were assessed in the Pst populations. A high similarity was observed between all regional population samples in 2019 and 2020. The Northwestern and Dagestan populations slightly differed from the other populations in 2021 and 2022. In 2022, the Krasnodar and Kalmyk populations formed separate groups, which differed from each other and from the main group. The long-term virulence analysis indicated that the structure of Pst populations is highly dynamic in Russia. All North Caucasian isolates and 23 Northwestern isolates were used in the SSR analysis. Six loci (RYN3, RYN9, RYN12, WU6, RJO21, and RJO24) were monomorphic. Three polymorphic alleles were identified in each of the RYN13 and RJO27 loci; two alleles, in each of the remaining loci examined. Significant deviations from Hardy-Weinberg equilibrium were observed for most loci. The observed heterozygosity exceeded the expected one, suggesting a clonal origin of the Pst population. Twenty multilocus genotypes (MGs) were found in the total isolate collection (11 in Dagestan, 11 in the Northwestern region, 3 in Krasnodar, and 1 in Kalmykia). Common MGs were detected in the Dagestan, Krasnodar, and Northwestern populations (MG_1); Dagestan, Kalmyk, and Northwestern populations (MG_2); and Dagestan and Krasnodar populations (MG_3 and MG_4). Genetic distances between MGs were estimated. MGs formed four groups in a multidimensional diagram. A major group included 80% of MGs. One Dagestan MG, two Northwestern MGs, and MG_3 common for the Dagestan and Krasnodar collections were significantly differentiated from the major group and differed from each other. Based on Fst, most regional Pst collections were moderately differentiated from each other, with the exception of the Dagestan and Kalmyk collections. The finding was consistent with the virulence analysis results. The Mantel test detected a moderate correlation between the virulence and SSR data (r = 0.6). This indicates that both analyses can be used to assess genetic polymorphism in Pst. The high variability of the virulence and microsatellite loci warrants annual monitoring of regional Pst populations in Russia.
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Affiliation(s)
- E I Gultyaeva
- All-Russian Institute of Plant Protection, St. Petersburg, Russia.
| | - E L Shaydayuk
- All-Russian Institute of Plant Protection, St. Petersburg, Russia.
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Nemati Z, Dadkhodaie A, Mostowfizadeh-Ghalamfarsa R, Mehrabi R, Cacciola SO. Genetic Variation of Puccinia triticina Populations in Iran from 2010 to 2017 as Revealed by SSR and ISSR Markers. J Fungi (Basel) 2023; 9:jof9030388. [PMID: 36983556 PMCID: PMC10056552 DOI: 10.3390/jof9030388] [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: 01/22/2023] [Revised: 03/19/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
Puccinia triticina is a major wheat pathogen worldwide. Although Iran is within the Fertile Crescent, which is supposed to be the center of origin of both wheat and P. triticina, the knowledge of the genetic variability of local populations of this basidiomycete is limited. We analyzed 12 inter simple sequence repeats (ISSRs) and 18 simple sequence repeats (SSRs) of 175 P. triticina isolates sampled between 2010 and 2017 from wheat and other Poaceae in 14 provinces of Iran. SSRs revealed more polymorphisms than ISSRs, indicating they were more effective in differentiating P. triticina populations. Based on a dissimilarity matrix with a variable mutation rate for SSRs and a Dice coefficient for ISSRs, the isolates were separated into three large groups, each including isolates from diverse geographic origins and hosts. The grouping of SSR genotypes in UPGMA dendrograms was consistent with the grouping inferred from the Bayesian approach. However, isolates with a common origin clustered into separate subgroups within each group. The high proportion of heterozygous alleles suggests that in Iran clonal reproduction prevails over sexual reproduction of the pathogen. A significant correlation was found between SSR and ISSR genotypes and the virulence phenotypes of the isolates, as determined in a previous study.
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Affiliation(s)
- Zahra Nemati
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
| | - Ali Dadkhodaie
- Department of Plant Production and Genetics, School of Agriculture, Shiraz University, Shiraz 71441-65186, Iran
| | | | - Rahim Mehrabi
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan 81431-53784, Iran
| | - Santa Olga Cacciola
- Department of Agriculture, Food and Environment (Di3A), University of Catania, 95123 Catania, Italy
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Volkova G, Kudinova O, Vaganova O, Agapova V. Effectiveness of Leaf Rust Resistance Genes in the Adult and Juvenile Stages in Southern Russia in 2011–2020. PLANTS 2022; 11:plants11060793. [PMID: 35336675 PMCID: PMC8953555 DOI: 10.3390/plants11060793] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/12/2022] [Accepted: 03/14/2022] [Indexed: 11/16/2022]
Abstract
Puccinia triticina Erikss. is a causative agent of wheat leaf rust spread worldwide. Wheat rust is a major disease on wheat in southern regions of Russia, which are leaders in grain production and have favorable conditions for pathogen development. In this paper we studied the effectiveness of 52 NILs of cv. Thatcher with Lr genes in field trials and 41 NILs—in the juvenile phase in a greenhouse during 2011–2020. We conclude that the lines with Lr9, Lr42 and Lr43+24 genes remained immune in the adult phase during ten years of research. Lines with Lr genes: 19, 24, 29, 36, 37, 38, 43, 45, 47, 50 showed efficiency in field tests (1–5 R on the CIMMYT scale). No immune lines to Puccinia triticina were registered in the juvenile phase during 2011–2020. The line with the Lr9 gene remained immune up to 2020; Lr19 and Lr41—up to 2015; Lr42—up to 2018, and Lr50—up to 2019. In 2020, there was an increase of P. triticina isolates with virulence to Thatcher lines with Lr: 9, 14a, 16, 19, 21, 28, 30, 33, 40, 45, W, 50. Additionally, we registered a change in infection types towards more susceptible in isogenic Lr gene lines: 1, 2a, 12, 14b, 15, 18, 20, 23, 25, 28, 29, 32, 35, 36, 37, 38, 40, 44, 45 in the field. A sharp increase in the frequencies of virulent isolates was recorded in 2018–2020 due to unfavorable weather in the growing seasons. This indicates the ability of a dangerous pathogen to rapidly evolve in response to biotic and abiotic stresses. Therefore, annual monitoring of the reaction of isogenic lines, selected released varieties and the study of the virulence of the phytopathogen are important measures necessary to prevent and control leaf rust in grain-producing regions of the world.
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Gultyaeva EI, Shaydayuk EL, Kazartsev IA, Kosman E. Race Characterization and Molecular Genotyping of Puccinia triticina Populations from Durum Wheat in Russia. PLANT DISEASE 2021; 105:1495-1504. [PMID: 33797936 DOI: 10.1094/pdis-09-20-1927-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Variability of the Russian population of Puccinia triticina from durum wheat was studied with virulence and simple sequence repeat (SSR) markers. The pathogen was sampled during 2017 to 2019 in all regions with sizable durum wheat (Triticum durum) growing areas from winter (North Caucasus) and spring (Middle Volga, Ural, and West Siberia) wheat. A total of 474 isolates were tested on a set of 20 Lr-gene lines. Molecular genotypes for 105 selected isolates were determined at 11 SSR loci. Variable virulence/avirulence reaction was observed only on three Lr-gene lines, whereas just five SSR loci were polymorphic with two alleles at each. Seven different virulence phenotypes and 11 SSR genotypes were found among 474 and 105 isolates, respectively, indicating a very low variability of the pathogen. One virulence phenotype and three SSR genotypes occurred in all Russian regions. However, two phenotypes were specific to the European regions of Russia (North Caucasus and Middle Volga), while another two were found only in the Asian part of Russia (Ural and West Siberia). Significant differentiation between six populations of P. triticina from durum wheat in the Asian and European (mainly North Caucasus) regions was also shown with numerous metrics and approaches for data with and without clone correction. Relationships among the regional populations of P. triticina from durum wheat established with virulence phenotypes significantly associated with those for SSR genotypes and was similar to the relationships among the regional populations of the pathogen from common wheat.
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Affiliation(s)
- Elena I Gultyaeva
- All-Russian Institute of Plant Protection, St. Petersburg-Pushkin 196608, Russia
| | | | - Igor A Kazartsev
- All-Russian Institute of Plant Protection, St. Petersburg-Pushkin 196608, Russia
| | - Evsey Kosman
- Institute for Cereal Crops Improvement, School of Plant Sciences and Food Security, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
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Kosman E, Scheiner SM, Gregorius H. Severe limitations of the FEve metric of functional evenness and some alternative metrics. Ecol Evol 2021; 11:123-132. [PMID: 33437418 PMCID: PMC7790661 DOI: 10.1002/ece3.6974] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 10/13/2020] [Indexed: 12/01/2022] Open
Abstract
The metric of functional evenness FEve is an example of how approaches to conceptualizing and measuring functional variability may go astray. This index has several critical conceptual and practical drawbacks: Different values of the FEve index for the same community can be obtained if the species have unequal species abundances; this result is highly likely if most of the traits are categorical.Very minor differences in even one pairwise distance can result in very different values of FEve.FEve uses only a fraction of the information contained in the matrix of species distances. Counterintuitively, this can cause very similar FEve scores for communities with substantially different patterns of species dispersal in trait space.FEve is a valid metric only if all species have exactly the same abundances. However, the meaning of FEve in such an instance is unclear as the purpose of the metric is to measure the variability of abundances in trait space. We recommend not using the FEve metric in studies of functional variability. Given the wide usage of FEve index over the last decade, the validity of the conclusions based on those estimates is in question. Instead, we suggest three alternative metrics that combine variability in species distances in trait space with abundance in various ways. More broadly, we recommend that researchers think about which community properties (e.g., trait distances of a focus species to the nearest neighbor or all other species, variability of pairwise interactions between species) they want to measure and pick from among the appropriate metrics.
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Affiliation(s)
- Evsey Kosman
- Institute for Cereal Crops ImprovementTel Aviv UniversityTel AvivIsrael
| | - Samuel M. Scheiner
- Division of Environmental BiologyNational Science FoundationAlexandriaVAUSA
| | - Hans‐Rolf Gregorius
- Institut für Populations‐ und ökologische GenetikGöttingenGermany
- Abteilung Forstgenetik und ForstpflanzenzüchtungUniversität GöttingenGöttingenGermany
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Pchelin IM, Mochalov YV, Azarov DV, Romanyuk SA, Chilina GA, Vybornova IV, Bogdanova TV, Zlatogursky VV, Apalko SV, Vasilyeva NV, Taraskina AE. Genotyping of Russian isolates of fungal pathogen Trichophyton rubrum, based on simple sequence repeat and single nucleotide polymorphism. Mycoses 2020; 63:1244-1254. [PMID: 32785975 DOI: 10.1111/myc.13162] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/25/2020] [Accepted: 08/01/2020] [Indexed: 02/05/2023]
Abstract
BACKGROUND The Trichophyton rubrum species group consists of prevalent causative agents of human skin, nail and hair infections, including T rubrum sensu stricto and T violaceum, as well as other less well-established or debatable taxa like T soudanense, T kuryangei and T megninii. Our previous study provided limited evidence in favour of the existence of two genetic lineages in the Russian T rubrum sensu stricto population. OBJECTIVES We aimed to study the genetic structure of the Russian population of T rubrum and to identify factors shaping this structure. METHODS We analysed the polymorphism of 12 simple sequence repeat (SSR or microsatellite) markers and single nucleotide polymorphism in the TERG_02941 protein-coding gene in 70 T rubrum isolates and performed a phylogenomic reconstruction. RESULTS All three types of data provided conclusive evidence that the population consists of two genetic lineages. Clustering, performed by means of microsatellite length polymorphism analysis, was strongly dependent on the number of nucleotide repeats in the 5'-area of the fructose-1,6-bisphosphate aldolase gene. Analysis of molecular variance (AMOVA) on the basis of SSR typing data indicated that 22%-48% of the variability was among groups within T rubrum. There was no clear connection of population structure with types of infection, places of geographic origin, aldolase gene expression or urease activity. CONCLUSION Our results suggest that the Russian population of T rubrum consists of two cosmopolitan genetic lineages.
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Affiliation(s)
- Ivan M Pchelin
- Kashkin Research Institute of Medical Mycology, North-Western State Medical University named after I.I. Mechnikov, Saint Petersburg, Russia
| | - Yuri V Mochalov
- Kashkin Research Institute of Medical Mycology, North-Western State Medical University named after I.I. Mechnikov, Saint Petersburg, Russia
| | - Daniil V Azarov
- Department of Epidemiology, Parasitology and Disinfectology, North-Western State Medical University named after I.I. Mechnikov, Saint Petersburg, Russia
| | | | - Galina A Chilina
- Kashkin Research Institute of Medical Mycology, North-Western State Medical University named after I.I. Mechnikov, Saint Petersburg, Russia
| | - Irina V Vybornova
- Kashkin Research Institute of Medical Mycology, North-Western State Medical University named after I.I. Mechnikov, Saint Petersburg, Russia
| | - Tatiyana V Bogdanova
- Department of Medical Microbiology, North-Western State Medical University named after I.I. Mechnikov, Saint Petersburg, Russia
| | - Vasily V Zlatogursky
- Department of Invertebrate Zoology, Faculty of Biology, St. Petersburg State University, Saint Petersburg, Russia
| | | | - Natalia V Vasilyeva
- Kashkin Research Institute of Medical Mycology, North-Western State Medical University named after I.I. Mechnikov, Saint Petersburg, Russia
- Department of Medical Microbiology, North-Western State Medical University named after I.I. Mechnikov, Saint Petersburg, Russia
| | - Anastasia E Taraskina
- Kashkin Research Institute of Medical Mycology, North-Western State Medical University named after I.I. Mechnikov, Saint Petersburg, Russia
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Nemati Z, Mostowfizadeh-Ghalamfarsa R, Dadkhodaie A, Mehrabi R, Steffenson BJ. Virulence of Leaf Rust Physiological Races in Iran From 2010 to 2017. PLANT DISEASE 2020; 104:363-372. [PMID: 31850835 DOI: 10.1094/pdis-06-19-1340-re] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The wheat leaf rust fungus, Puccinia triticina, has widespread geographical distribution in Iran within the Fertile Crescent region of the Middle East where wheat was domesticated and P. triticina originated. Therefore, it is of great importance to identify the prevalence and distribution of P. triticina pathotypes in this area. From 2010 to 2017, 241 single-uredinium isolates of P. triticina were purified from 175 collections of P. triticina made from various hosts in 14 provinces of Iran, and they were tested on 20 Thatcher near-isogenic lines carrying single-leaf rust resistance genes. In total, 86 pathotypes were identified, of which the pathotypes FDTTQ, FDKPQ, FDKTQ, and FDTNQ were most prevalent. No virulence for Lr2a was detected, whereas virulence for Lr1 was found only on bread wheat in a few provinces in 2016. Only isolates from durum wheat and wild barley were virulent to Lr28. Although virulence for Lr9, Lr20, and Lr26 was observed in some years, the virulence frequency for these genes was lower than that of the other Lr genes. P. triticina collections from host plants with different ploidy levels or genetically dissimilar backgrounds were grouped individually according to genetic distance. Based on these results, collections from barley, durum wheat, oat, triticale, and wild barley were different from those of bread wheat.
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Affiliation(s)
- Zahra Nemati
- Department of Plant Protection, School of Agriculture, Shiraz University, Shiraz, Iran
| | | | - Ali Dadkhodaie
- Department of Crop Production and Plant Breeding, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Rahim Mehrabi
- Department of Biotechnology, College of Agricultural Engineering, Isfahan University of Technology, Isfahan, Iran
| | - Brian J Steffenson
- Department of Plant Pathology, University of Minnesota, Minneapolis, MN, U.S.A
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SLAF-seq Uncovers the Genetic Diversity and Adaptation of Chinese Elm (Ulmus parvifolia) in Eastern China. FORESTS 2020. [DOI: 10.3390/f11010080] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The Chinese elm is an important tree ecologically; however, little is known about its genetic diversity and adaptation mechanisms. In this study, a total of 107 individuals collected from seven natural populations in eastern China were investigated by specific locus amplified fragment sequencing (SLAF-seq). Based on the single nucleotide polymorphisms (SNPs) detected by SLAF-seq, genetic diversity and markers associated with climate variables were identified. All seven populations showed medium genetic diversity, with PIC values ranging from 0.2632 to 0.2761. AMOVA and Fst indicated that a low genetic differentiation existed among populations. Environmental association analyses with three climate variables (annual rainfall, annual average temperature, and altitude) resulted in, altogether, 43 and 30 putative adaptive loci by Bayenv2 and LFMM, respectively. Five adaptive genes were annotated, which were related to the functions of glycosylation, peroxisome synthesis, nucleic acid metabolism, energy metabolism, and signaling. This study was the first on the genetic diversity and local adaptation in Chinese elms, and the results will be helpful in future work on molecular breeding.
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Kosman E, Chen X, Dreiseitl A, McCallum B, Lebeda A, Ben-Yehuda P, Gultyaeva E, Manisterski J. Functional Variation of Plant-Pathogen Interactions: New Concept and Methods for Virulence Data Analyses. PHYTOPATHOLOGY 2019; 109:1324-1330. [PMID: 30958099 DOI: 10.1094/phyto-02-19-0041-le] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Classical virulence analysis is based on discovering virulence phenotypes of isolates with regard to a composition of resistance genes in a differential set of host genotypes. With such a vision, virulence phenotypes are usually treated in a genetic manner as one of two possible alleles, either virulence or avirulence in a binary locus. Therefore, population genetics metrics and methods have become prevailing tools for analyzing virulence data at multiple loci. However, a basis for resolving binary virulence phenotypes is infection type (IT) data of host-pathogen interaction that express functional traits of each specific isolate in a given situation (particular host, environmental conditions, cultivation practice, and so on). IT is determined by symptoms and signs observed (e.g., lesion type, lesion size, coverage of leaf or leaf segments by mycelium, spore production and so on), and assessed by IT scores at a generally accepted scale for each plant-pathogen system. Thus, multiple IT profiles of isolates are obtained and can be subjected to analysis of functional variation within and among operational units of a pathogen. Such an approach may allow better utilization of the information available in the raw data, and reveal a functional (e.g., environmental) component of pathogen variation in addition to the genetic one. New methods for measuring functional variation of plant-pathogen interaction with IT data were developed. The methods need an appropriate assessment scale and expert estimations of dissimilarity between IT scores for each plant-pathogen system (an example is presented). Analyses of a few data sets at different hierarchical levels demonstrated discrepancies in results obtained with IT phenotypes versus binary virulence phenotypes. The ability to measure functional IT-based variation offers promise as an effective tool in the study of epidemics caused by plant pathogens.
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Affiliation(s)
- E Kosman
- 1Institute for Cereal Crops Improvement, Tel Aviv University, Tel Aviv 69978, Israel
| | - X Chen
- 2United States Department of Agriculture-Agricultural Research Service Wheat Health, Genetics, and Quality Research Unit, and Washington State University, Pullman, WA 99164-6430, U.S.A
| | - A Dreiseitl
- 3Agrotest Fyto Ltd., Havlíčkova 2787, CZ-767 01 Kroměříž, Czech Republic
| | - B McCallum
- 4Agriculture and Agri-Food Canada, 195 Dafoe Rd, Winnipeg, Manitoba R3T 2M9, Canada
| | - A Lebeda
- 5Department of Botany, Faculty of Science, Palacky University in Olomouc, Slechtitelu 27, 783 71, Olomouc-Holice, Czech Republic
| | - P Ben-Yehuda
- 1Institute for Cereal Crops Improvement, Tel Aviv University, Tel Aviv 69978, Israel
| | - E Gultyaeva
- 6All-Russian Institute of Plant Protection, Sh. Pobelskogo, 3, 196608, Saint Petersburg-Pushkin, Russia
| | - J Manisterski
- 1Institute for Cereal Crops Improvement, Tel Aviv University, Tel Aviv 69978, Israel
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Kosman E, Jokela J. Dissimilarity of individual microsatellite profiles under different mutation models: Empirical approach. Ecol Evol 2019; 9:4038-4054. [PMID: 31015986 PMCID: PMC6467862 DOI: 10.1002/ece3.5032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 01/21/2019] [Indexed: 11/25/2022] Open
Abstract
Microsatellites (simple sequence repeats, SSRs) still remain popular molecular markers for studying neutral genetic variation. Two alternative models outline how new microsatellite alleles evolve. Infinite alleles model (IAM) assumes that all possible alleles are equally likely to result from a mutation, while stepwise mutation model (SMM) describes microsatellite evolution as stepwise adding or subtracting single repeat units. Genetic relationships between individuals can be analyzed in higher precision when assuming the SMM scenario with allele size differences as a proxy of genetic distance. If population structure is not predetermined in advance, an empirical data analysis usually includes (a) estimating proximity between individual SSR profiles with a selected dissimilarity measure and (b) determining putative genetic structure of a given set of individuals using methods of clustering and/or ordination for the obtained dissimilarity matrix. We developed new dissimilarity indices between SSR profiles of haploid, diploid, or polyploid organisms assuming different mutation models and compared the performance of these indices for determining genetic structure with population data and with simulations. More specifically, we compared SMM with a constant or variable mutation rate at different SSR loci to IAM using data from natural populations of a freshwater bryozoan Cristatella mucedo (diploid), wheat leaf rust Puccinia triticina (dikaryon), and wheat powdery mildew Blumeria graminis (monokaryon). We show that inferences about population genetic structure are sensitive to the assumed mutation model. With simulations, we found that Bruvo's distance performs generally poorly, while the new metrics are capturing the differences in the genetic structure of the populations.
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Affiliation(s)
- Evsey Kosman
- Institute for Cereal Crops ImprovementTel Aviv UniversityTel AvivIsrael
| | - Jukka Jokela
- ETH Zurich, Department of Environmental Systems ScienceInstitute of Integrative Biology (IBZ)ZurichSwitzerland
- EAWAGAquatic EcologyDübendorfSwitzerland
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Plotnikova LY, Meshkova LV, Gultyaeva EI, Mitrofanova OР, Lapochkina IF. A tendency towards leaf rust resistance decrease in common wheat introgression lines with genetic material from Aegilops speltoides Tausch. Vavilovskii Zhurnal Genet Selektsii 2018. [DOI: 10.18699/vj18.395] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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