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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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Haghdoust R, Singh D, Park RF, Dracatos PM. Characterizing the Genetic Architecture of Nonhost Resistance in Barley Using Pathogenically Diverse Puccinia Isolates. PHYTOPATHOLOGY 2021; 111:684-694. [PMID: 32931394 DOI: 10.1094/phyto-05-20-0193-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Barley is an intermediate or near nonhost to many cereal rust pathogens that infect grasses, making it a highly suitable model to understand the evolution and genetic basis of nonhost resistance (NHR) in plants. To characterize the genetic architecture of NHR in barley, we used the Oregon Wolfe Barley doubled haploid and Morex × SusPtrit recombinant inbred line mapping populations. To elicit a wide array of NHR responses, we tested 492 barley accessions and both mapping populations with pathogenically diverse cereal rust isolates representing distinct formae speciales adapted to Avena, Hordeum, Triticum, and Lolium spp.: P. coronata f. sp. avenae (oat crown rust pathogen) and P. coronata f. sp. lolii (ryegrass crown rust pathogen), P. graminis f. sp. avenae (oat stem rust pathogen) and P. graminis f. sp. lolii (the ryegrass stem rust pathogen), and P. striiformis f. sp. tritici (wheat stripe rust pathogen) and P. striiformis f. sp. pseudo-hordei (barley grass stripe rust pathogen). With the exception of P. coronata f. sp. lolii and P. coronata f. sp. avenae, susceptibility and segregation for NHR was observed in the barley accessions and both mapping populations. Quantitative trait loci (QTLs) for NHR were mapped on all seven chromosomes. NHR in barley to the heterologous rusts tested was attributable to a combination of QTLs with either or both overlapping and distinct specificities. Across both mapping populations, broadly effective NHR loci were also identified that likely play a role in host specialization.
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Affiliation(s)
- R Haghdoust
- Plant Breeding Institute, University of Sydney, Cobbitty, Narellan, New South Wales 2567, Australia
| | - D Singh
- Plant Breeding Institute, University of Sydney, Cobbitty, Narellan, New South Wales 2567, Australia
| | - R F Park
- Plant Breeding Institute, University of Sydney, Cobbitty, Narellan, New South Wales 2567, Australia
| | - P M Dracatos
- Plant Breeding Institute, University of Sydney, Cobbitty, Narellan, New South Wales 2567, Australia
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Siyoum GZ, Zeng Q, Zhao J, Chen X, Badebo A, Tian Y, Huang L, Kang Z, Zhan G. Inheritance of Virulence and Linkages of Virulence Genes in an Ethiopian Isolate of the Wheat Stripe Rust Pathogen ( Puccinia striiformis f. sp. tritici) Determined Through Sexual Recombination on Berberis holstii. PLANT DISEASE 2019; 103:2451-2459. [PMID: 31322491 DOI: 10.1094/pdis-02-19-0269-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Stripe rust, caused by Puccinia striiformis f. sp. tritici, is one of the most devastating wheat diseases in Ethiopia. To study virulence genetics of the pathogen, 117 progeny isolates were produced through sexual reproduction of an Ethiopian isolate of the stripe rust pathogen on Berberis holstii plants under controlled conditions. The parental and progeny isolates were characterized by phenotyping on wheat lines carrying single Yr genes for resistance and genotyped using 10 polymorphic simple sequence repeated (SSR) markers. The progeny isolates were classified into 37 virulence phenotypes and 75 multilocus genotypes. The parental isolate and progeny isolates were all avirulent to resistance genes Yr5, Yr10, Yr15, Yr24, Yr32, YrTr1, YrSP, and Yr76 but virulent to Yr1 and Yr2, indicating that the parental isolate was homozygous avirulent or homozygous virulent at these loci. The progeny isolates segregated for virulence to 12 Yr genes. Virulence phenotypes to Yr6, Yr28, Yr43, and Yr44 were controlled by a single dominant gene; those to Yr7, Yr9, Yr17, Yr27, Yr25, Yr31, and YrExp2 were each controlled by two dominant genes; and the virulence phenotype to Yr8 was controlled by two complementary dominant genes. A linkage map was constructed with seven SSR markers, and 16 virulence loci corresponding to 11 Yr resistance genes were mapped with some loci linked to each other. These results are useful in understanding host-pathogen interactions and selecting resistance genes to develop wheat cultivars with highly effective resistance to stripe rust.
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Affiliation(s)
- Gebreslasie Zeray Siyoum
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Qingdong Zeng
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of 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, People's Republic of China
| | - Xianming Chen
- Wheat Health, Genetics, and Quality Research Unit, U.S. Department of Agriculture Agricultural Research Service, Pullman, WA 99164-6430, U.S.A
| | - Ayele Badebo
- International Maize and Wheat Improvement Center (CIMMYT) Ethiopia, International Livestock Research Institute Gurd Shola Campus, Addis Ababa, Ethiopia
| | - Yuan Tian
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Lili Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Gangming Zhan
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
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Grant EL, Conroy GC, Lamont RW, Reddell PW, Wallace HM, Ogbourne SM. Short distance pollen dispersal and low genetic diversity in a subcanopy tropical rainforest tree, Fontainea picrosperma (Euphorbiaceae). Heredity (Edinb) 2019; 123:503-516. [PMID: 31076650 DOI: 10.1038/s41437-019-0231-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 03/28/2019] [Accepted: 04/24/2019] [Indexed: 11/09/2022] Open
Abstract
Gene flow via pollen movement affects genetic variation in plant populations and is an important consideration in plant domestication. Fontainea picrosperma is a subcanopy rainforest tree that is of commercial interest because it is the source of tigilanol tiglate, a natural product used for the treatment of solid tumors. We identify patterns of pollen-mediated gene flow within natural populations of F. picrosperma and estimate genetic parameters and genetic structure between adult and juvenile groups using microsatellite markers. Our results show pollination events occur over much shorter distances than reported for tropical canopy species. At least 63% of seeds are sired by male trees located within 30 m of the mother. On average, 27% of the local male population contributed to successful reproduction of F. picrosperma with most fathers siring a single seed, however, the contributions to reproduction were uneven. Larger male trees with more flowers had greater reproductive success than those with less flowers (P < 0.05). There were comparatively low levels of genetic variation across the species (HE = 0.405 for adult trees and 0.379 for juveniles) and we found no loss of genetic diversity between adult and juvenile trees. Short distance pollen flow and low genetic diversity is theoretically a prelude to genetic impoverishment, however F. picrosperma has persisted through multiple significant climatic oscillations. Nevertheless, the remaining low genetic diversity is of concern for domestication programs which require maximal genetic diversity to facilitate efficient selective breeding and genetic improvement of this commercially significant species.
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Affiliation(s)
- Elektra L Grant
- GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Gabriel C Conroy
- GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Robert W Lamont
- GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | | | - Helen M Wallace
- GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Steven M Ogbourne
- GeneCology Research Centre, University of the Sunshine Coast, Sippy Downs, QLD, Australia.
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Artificial barriers prevent genetic recovery of small isolated populations of a low-mobility freshwater fish. Heredity (Edinb) 2018; 120:515-532. [PMID: 29326479 PMCID: PMC5943333 DOI: 10.1038/s41437-017-0008-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 09/05/2017] [Accepted: 09/08/2017] [Indexed: 11/08/2022] Open
Abstract
Habitat loss and fragmentation often result in small, isolated populations vulnerable to environmental disturbance and loss of genetic diversity. Low genetic diversity can increase extinction risk of small populations by elevating inbreeding and inbreeding depression, and reducing adaptive potential. Due to their linear nature and extensive use by humans, freshwater ecosystems are especially vulnerable to habitat loss and fragmentation. Although the effects of fragmentation on genetic structure have been extensively studied in migratory fishes, they are less understood in low-mobility species. We estimated impacts of instream barriers on genetic structure and diversity of the low-mobility river blackfish (Gadopsis marmoratus) within five streams separated by weirs or dams constructed 45-120 years ago. We found evidence of small-scale (<13 km) genetic structure within reaches unimpeded by barriers, as expected for a fish with low mobility. Genetic diversity was lower above barriers in small streams only, regardless of barrier age. In particular, one isolated population showed evidence of a recent bottleneck and inbreeding. Differentiation above and below the barrier (FST = 0.13) was greatest in this stream, but in other streams did not differ from background levels. Spatially explicit simulations suggest that short-term barrier effects would not be detected with our data set unless effective population sizes were very small (<100). Our study highlights that, in structured populations, the ability to detect short-term genetic effects from barriers is reduced and requires more genetic markers compared to panmictic populations. We also demonstrate the importance of accounting for natural population genetic structure in fragmentation studies.
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Yuan C, Wang M, Skinner DZ, See DR, Xia C, Guo X, Chen X. Inheritance of Virulence, Construction of a Linkage Map, and Mapping Dominant Virulence Genes in Puccinia striiformis f. sp. tritici Through Characterization of a Sexual Population with Genotyping-by-Sequencing. PHYTOPATHOLOGY 2018; 108:133-141. [PMID: 28876207 DOI: 10.1094/phyto-04-17-0139-r] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Puccinia striiformis f. sp. tritici, the wheat stripe rust pathogen, is a dikaryotic, biotrophic, and macrocyclic fungus. Genetic study of P. striiformis f. sp. tritici virulence was not possible until the recent discovery of Berberis spp. and Mahonia spp. as alternate hosts. To determine inheritance of virulence and map virulence genes, a segregating population of 119 isolates was developed by self-fertilizing P. striiformis f. sp. tritici isolate 08-220 (race PSTv-11) on barberry leaves under controlled greenhouse conditions. The progeny isolates were phenotyped on a set of 29 wheat lines with single genes for race-specific resistance and genotyped with simple sequence repeat (SSR) markers, single nucleotide polymorphism (SNP) markers derived from secreted protein genes, and SNP markers from genotyping-by-sequencing (GBS). Using the GBS technique, 10,163 polymorphic GBS-SNP markers were identified. Clustering and principal component analysis grouped these markers into six genetic groups, and a genetic map, consisting of six linkage groups, was constructed with 805 markers. The six clusters or linkage groups resulting from these analyses indicated a haploid chromosome number of six in P. striiformis f. sp. tritici. Through virulence testing of the progeny isolates, the parental isolate was found to be homozygous for the avirulence loci corresponding to resistance genes Yr5, Yr10, Yr15, Yr24, Yr32, YrSP, YrTr1, Yr45, and Yr53 and homozygous for the virulence locus corresponding to resistance gene Yr41. Segregation was observed for virulence phenotypes in response to the remaining 19 single-gene lines. A single dominant gene or two dominant genes with different nonallelic gene interactions were identified for each of the segregating virulence phenotypes. Of 27 dominant virulence genes identified, 17 were mapped to two chromosomes. Markers tightly linked to some of the virulence loci may facilitate further studies to clone these genes. The virulence genes and their inheritance information are useful for understanding the host-pathogen interactions and for selecting effective resistance genes or gene combinations for developing stripe rust resistant wheat cultivars.
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Affiliation(s)
- Congying Yuan
- First and sixth authors: College of Biology, Hunan University, Changsha, Hunan 410082, China; first, second, fourth, fifth, and seventh authors: Department of Plant Pathology, Washington State University, Pullman 99164-6430; and third, fourth, and seventh authors: U.S. Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics, and Quality Research Unit, Pullman, WA 99164-6430
| | - Meinan Wang
- First and sixth authors: College of Biology, Hunan University, Changsha, Hunan 410082, China; first, second, fourth, fifth, and seventh authors: Department of Plant Pathology, Washington State University, Pullman 99164-6430; and third, fourth, and seventh authors: U.S. Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics, and Quality Research Unit, Pullman, WA 99164-6430
| | - Danniel Z Skinner
- First and sixth authors: College of Biology, Hunan University, Changsha, Hunan 410082, China; first, second, fourth, fifth, and seventh authors: Department of Plant Pathology, Washington State University, Pullman 99164-6430; and third, fourth, and seventh authors: U.S. Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics, and Quality Research Unit, Pullman, WA 99164-6430
| | - Deven R See
- First and sixth authors: College of Biology, Hunan University, Changsha, Hunan 410082, China; first, second, fourth, fifth, and seventh authors: Department of Plant Pathology, Washington State University, Pullman 99164-6430; and third, fourth, and seventh authors: U.S. Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics, and Quality Research Unit, Pullman, WA 99164-6430
| | - Chongjing Xia
- First and sixth authors: College of Biology, Hunan University, Changsha, Hunan 410082, China; first, second, fourth, fifth, and seventh authors: Department of Plant Pathology, Washington State University, Pullman 99164-6430; and third, fourth, and seventh authors: U.S. Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics, and Quality Research Unit, Pullman, WA 99164-6430
| | - Xinhong Guo
- First and sixth authors: College of Biology, Hunan University, Changsha, Hunan 410082, China; first, second, fourth, fifth, and seventh authors: Department of Plant Pathology, Washington State University, Pullman 99164-6430; and third, fourth, and seventh authors: U.S. Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics, and Quality Research Unit, Pullman, WA 99164-6430
| | - Xianming Chen
- First and sixth authors: College of Biology, Hunan University, Changsha, Hunan 410082, China; first, second, fourth, fifth, and seventh authors: Department of Plant Pathology, Washington State University, Pullman 99164-6430; and third, fourth, and seventh authors: U.S. Department of Agriculture, Agricultural Research Service, Wheat Health, Genetics, and Quality Research Unit, Pullman, WA 99164-6430
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Lean J, Hammer MP, Unmack PJ, Adams M, Beheregaray LB. Landscape genetics informs mesohabitat preference and conservation priorities for a surrogate indicator species in a highly fragmented river system. Heredity (Edinb) 2017; 118:374-384. [PMID: 27876805 PMCID: PMC5345605 DOI: 10.1038/hdy.2016.111] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Revised: 09/27/2016] [Accepted: 09/27/2016] [Indexed: 11/09/2022] Open
Abstract
Poor dispersal species represent conservative benchmarks for biodiversity management because they provide insights into ecological processes influenced by habitat fragmentation that are less evident in more dispersive organisms. Here we used the poorly dispersive and threatened river blackfish (Gadopsis marmoratus) as a surrogate indicator system for assessing the effects of fragmentation in highly modified river basins and for prioritizing basin-wide management strategies. We combined individual, population and landscape-based approaches to analyze genetic variation in samples spanning the distribution of the species in Australia's Murray-Darling Basin, one of the world's most degraded freshwater systems. Our results indicate that G. marmoratus displays the hallmark of severe habitat fragmentation with notably scattered, small and demographically isolated populations with very low genetic diversity-a pattern found not only between regions and catchments but also between streams within catchments. By using hierarchically nested population sampling and assessing relationships between genetic uniqueness and genetic diversity across populations, we developed a spatial management framework that includes the selection of populations in need of genetic rescue. Landscape genetics provided an environmental criterion to identify associations between landscape features and ecological processes. Our results further our understanding of the impact that habitat quality and quantity has on habitat specialists with similarly low dispersal. They should also have practical applications for prioritizing both large- and small-scale conservation management actions for organisms inhabiting highly fragmented ecosystems.
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Affiliation(s)
- J Lean
- Molecular Ecology Laboratory, School of Biological Sciences, Flinders University, Adelaide, South Australia, Australia
| | - M P Hammer
- Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, South Australia, Australia
- Curator of Fishes, Museum and Art Gallery of the Northern Territory, Darwin, Northern Territory, Australia
| | - P J Unmack
- Institute for Applied Ecology and Collaborative Research Network for Murray-Darling Basin Futures, University of Canberra, Canberra, Australian Capital Territory, Australia
| | - M Adams
- Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide, South Australia, Australia
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - L B Beheregaray
- Molecular Ecology Laboratory, School of Biological Sciences, Flinders University, Adelaide, South Australia, Australia
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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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García C, Escribano-Ávila G. An optimised protocol to isolate high-quality genomic DNA from seed tissues streamlines the workflow to obtain direct estimates of seed dispersal distances in gymnosperms. JOURNAL OF PLANT RESEARCH 2016; 129:559-563. [PMID: 26943162 DOI: 10.1007/s10265-016-0806-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 12/18/2015] [Indexed: 06/05/2023]
Abstract
Genotyping of maternally derived seed tissues from georefered seeds that moved away from their source tree yield direct estimates of seed dispersal distances when the location and the genotype of the fruiting tree are available. These estimates are instrumental in forecasting the response of plant communities to drivers of global change, such as fragmentation or the expansion of invasive species. Obtaining robust assessments of seed dispersal distances requires comparing reliable multilocus genotypes of maternally derived seed tissues and fruiting trees, as previously shown for angiosperm species. However, robust estimates of seed dispersal distances based on direct methods are rare in non-model gymnosperms due to the difficulty in isolating high quality DNA from inconspicuous maternally derived seed tissues. These tissues tend to yield low DNA quantities that increase the frequency of genotyping errors. Here, we deliver a step-by-step visual protocol used to identify and isolate different seed tissues of interest for dispersal studies: embryos (2n, bi-parentally derived), seed coats (2n, maternally derived), and megagametophytes (n, maternally derived). We also provide an optimised lab protocol used to obtain multilocus genotypes from the target seed tissue. These broadly applicable protocols proved successful both in avoiding contamination among different seed tissues and providing reliable multilocus genotypes.
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Affiliation(s)
- C García
- Plant Biology, CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal.
| | - G Escribano-Ávila
- Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, c/Tulipán s/n, 28933, Móstoles, Spain
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Lloret F, García C. Inbreeding and neighbouring vegetation drive drought‐induced die‐off within juniper populations. Funct Ecol 2016. [DOI: 10.1111/1365-2435.12655] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Francisco Lloret
- CREAF Cerdanyola del Vallés Barcelona 08193 Spain
- Unitat d'Ecologia Department of Biologia Animal, Biologia Vegetal i Ecologia Universitat Autonòma Barcelona Cerdanyola del Vallés Barcelona 08193 Spain
| | - Cristina García
- Investigação em Biodiversidade e Biología Evolutiva (CIBIO/InBIO‐UP) Campus Agrário de Vairão, Rua Padre Armando Quintas Vairão 4485‐661 Porto Portugal
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Tang XT, Ji Y, Chang YW, Shen Y, Tian ZH, Gong WR, Du YZ. Population genetic structure and migration patterns of Liriomyza sativae in China: moderate subdivision and no Bridgehead effect revealed by microsatellites. BULLETIN OF ENTOMOLOGICAL RESEARCH 2016; 106:114-123. [PMID: 26615869 DOI: 10.1017/s0007485315000905] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
While Liriomyza sativae (Diptera: Agromyzidae), an important invasive pest of ornamentals and vegetables has been found in China for the past two decades, few studies have focused on its genetics or route of invasive. In this study, we collected 288 L. sativae individuals across 12 provinces to explore its population genetic structure and migration patterns in China using seven microsatellites. We found relatively low levels of genetic diversity but moderate population genetic structure (0.05 < F ST < 0.15) in L. sativae from China. All populations deviated significantly from the Hardy-Weinberg equilibrium due to heterozygote deficiency. Molecular variance analysis revealed that more than 89% of variation was among samples within populations. A UPGMA dendrogram revealed that SH and GXNN populations formed one cluster separate from the other populations, which is in accordance with STRUCTURE and GENELAND analyses. A Mantel test indicated that genetic distance was not correlated to geographic distance (r = -0.0814, P = 0.7610), coupled with high levels of gene flow (M = 40.1-817.7), suggesting a possible anthropogenic influence on the spread of L. sativae in China and on the effect of hosts. The trend of asymmetrical gene flow was from southern to northern populations in general and did not exhibit a Bridgehead effect during the course of invasion, as can be seen by the low genetic diversity of southern populations.
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Affiliation(s)
- X-T Tang
- School of Horticulture and Plant Protection & Institute of Applied Entomology, Yangzhou University,Yangzhou 225009,China
| | - Y Ji
- School of Horticulture and Plant Protection & Institute of Applied Entomology, Yangzhou University,Yangzhou 225009,China
| | - Y-W Chang
- School of Horticulture and Plant Protection & Institute of Applied Entomology, Yangzhou University,Yangzhou 225009,China
| | - Y Shen
- Agriculture and Forestry Bureau of Binhu District,Wuxi 214071,China
| | - Z-H Tian
- Plant Protection Station of Jiangsu Province,Nanjing 21003,China
| | - W-R Gong
- Plant Protection Station of Jiangsu Province,Nanjing 21003,China
| | - Y-Z Du
- School of Horticulture and Plant Protection & Institute of Applied Entomology, Yangzhou University,Yangzhou 225009,China
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Jiménez RA, Ornelas JF. Historical and current introgression in a Mesoamerican hummingbird species complex: a biogeographic perspective. PeerJ 2016; 4:e1556. [PMID: 26788433 PMCID: PMC4715438 DOI: 10.7717/peerj.1556] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 12/11/2015] [Indexed: 11/20/2022] Open
Abstract
The influence of geologic and Pleistocene glacial cycles might result in morphological and genetic complex scenarios in the biota of the Mesoamerican region. We tested whether berylline, blue-tailed and steely-blue hummingbirds, Amazilia beryllina, Amazilia cyanura and Amazilia saucerottei, show evidence of historical or current introgression as their plumage colour variation might suggest. We also analysed the role of past and present climatic events in promoting genetic introgression and species diversification. We collected mitochondrial DNA (mtDNA) sequence data and microsatellite loci scores for populations throughout the range of the three Amazilia species, as well as morphological and ecological data. Haplotype network, Bayesian phylogenetic and divergence time inference, historical demography, palaeodistribution modelling, and niche divergence tests were used to reconstruct the evolutionary history of this Amazilia species complex. An isolation-with-migration coalescent model and Bayesian assignment analysis were assessed to determine historical introgression and current genetic admixture. mtDNA haplotypes were geographically unstructured, with haplotypes from disparate areas interdispersed on a shallow tree and an unresolved haplotype network. Assignment analysis of the nuclear genome (nuDNA) supported three genetic groups with signs of genetic admixture, corresponding to: (1) A. beryllina populations located west of the Isthmus of Tehuantepec; (2) A. cyanura populations between the Isthmus of Tehuantepec and the Nicaraguan Depression (Nuclear Central America); and (3) A. saucerottei populations southeast of the Nicaraguan Depression. Gene flow and divergence time estimates, and demographic and palaeodistribution patterns suggest an evolutionary history of introgression mediated by Quaternary climatic fluctuations. High levels of gene flow were indicated by mtDNA and asymmetrical isolation-with-migration, whereas the microsatellite analyses found evidence for three genetic clusters with distributions corresponding to isolation by the Isthmus of Tehuantepec and the Nicaraguan Depression and signs of admixture. Historical levels of migration between genetically distinct groups estimated using microsatellites were higher than contemporary levels of migration. These results support the scenario of secondary contact and range contact during the glacial periods of the Pleistocene and strongly imply that the high levels of structure currently observed are a consequence of the limited dispersal of these hummingbirds across the isthmus and depression barriers.
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Affiliation(s)
- Rosa Alicia Jiménez
- Departamento de Biología Evolutiva, Instituto de Ecología A.C. , Xalapa , Veracruz , Mexico
| | - Juan Francisco Ornelas
- Departamento de Biología Evolutiva, Instituto de Ecología A.C. , Xalapa , Veracruz , Mexico
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Li SL, Vasemägi A, Ramula S. Genetic variation facilitates seedling establishment but not population growth rate of a perennial invader. ANNALS OF BOTANY 2016; 117:187-194. [PMID: 26420202 PMCID: PMC4701146 DOI: 10.1093/aob/mcv145] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 06/22/2015] [Accepted: 08/17/2015] [Indexed: 06/05/2023]
Abstract
BACKGROUND AND AIMS Assessing the demographic consequences of genetic variation is fundamental to invasion biology. However, genetic and demographic approaches are rarely combined to explore the effects of genetic variation on invasive populations in natural environments. This study combined population genetics, demographic data and a greenhouse experiment to investigate the consequences of genetic variation for the population fitness of the perennial, invasive herb Lupinus polyphyllus. METHODS Genetic and demographic data were collected from 37 L. polyphyllus populations representing different latitudes in Finland, and genetic variation was characterized based on 13 microsatellite loci. Associations between genetic variation and population size, population density, latitude and habitat were investigated. Genetic variation was then explored in relation to four fitness components (establishment, survival, growth, fecundity) measured at the population level, and the long-term population growth rate (λ). For a subset of populations genetic variation was also examined in relation to the temporal variability of λ. A further assessment was made of the role of natural selection in the observed variation of certain fitness components among populations under greenhouse conditions. KEY RESULTS It was found that genetic variation correlated positively with population size, particularly at higher latitudes, and differed among habitat types. Average seedling establishment per population increased with genetic variation in the field, but not under greenhouse conditions. Quantitative genetic divergence (Q(ST)) based on seedling establishment in the greenhouse was smaller than allelic genetic divergence (F'(ST)), indicating that unifying selection has a prominent role in this fitness component. Genetic variation was not associated with average survival, growth or fecundity measured at the population level, λ or its variability. CONCLUSIONS The study suggests that although genetic variation may facilitate plant invasions by increasing seedling establishment, it may not necessarily affect the long-term population growth rate. Therefore, established invasions may be able to grow equally well regardless of their genetic diversity.
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Affiliation(s)
- Shou-Li Li
- Section of Ecology, Department of Biology, University of Turku, 20014 Turku, Finland, Department of Biology and Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, Pennsylvania, USA,
| | - Anti Vasemägi
- Division of Genetics and Physiology, Department of Biology, University of Turku, 20014 Turku, Finland, Department of Aquaculture, Estonian University of Life Sciences, Tartu, Estonia and
| | - Satu Ramula
- Section of Ecology, Department of Biology, University of Turku, 20014 Turku, Finland, Aronia Coastal Zone Research Team, Åbo Akademi University and Novia University of Applied Sciences, Raseborgsvägen 9, 10600 Ekenäs, Finland
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Luo H, Wang X, Zhan G, Wei G, Zhou X, Zhao J, Huang L, Kang Z. Genome-Wide Analysis of Simple Sequence Repeats and Efficient Development of Polymorphic SSR Markers Based on Whole Genome Re-Sequencing of Multiple Isolates of the Wheat Stripe Rust Fungus. PLoS One 2015. [PMID: 26448643 DOI: 10.1145/2818302] [Citation(s) in RCA: 1199] [Impact Index Per Article: 133.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023] Open
Abstract
The biotrophic parasitic fungus Puccinia striiformis f. sp. tritici (Pst) causes stripe rust, a devastating disease of wheat, endangering global food security. Because the Pst population is highly dynamic, it is difficult to develop wheat cultivars with durable and highly effective resistance. Simple sequence repeats (SSRs) are widely used as molecular markers in genetic studies to determine population structure in many organisms. However, only a small number of SSR markers have been developed for Pst. In this study, a total of 4,792 SSR loci were identified using the whole genome sequences of six isolates from different regions of the world, with a marker density of one SSR per 22.95 kb. The majority of the SSRs were di- and tri-nucleotide repeats. A database containing 1,113 SSR markers were established. Through in silico comparison, the previously reported SSR markers were found mainly in exons, whereas the SSR markers in the database were mostly in intergenic regions. Furthermore, 105 polymorphic SSR markers were confirmed in silico by their identical positions and nucleotide variations with INDELs identified among the six isolates. When 104 in silico polymorphic SSR markers were used to genotype 21 Pst isolates, 84 produced the target bands, and 82 of them were polymorphic and revealed the genetic relationships among the isolates. The results show that whole genome re-sequencing of multiple isolates provides an ideal resource for developing SSR markers, and the newly developed SSR markers are useful for genetic and population studies of the wheat stripe rust fungus.
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Affiliation(s)
- Huaiyong Luo
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, People's Republic of China; State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, Shaanxi, People's Republic of China
| | - Xiaojie Wang
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, People's Republic of China; State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, Shaanxi, People's Republic of China
| | - Gangming Zhan
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, People's Republic of China; State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, Shaanxi, People's Republic of China
| | - Guorong Wei
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, People's Republic of China; State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, Shaanxi, People's Republic of China
| | - Xinli Zhou
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, People's Republic of China; State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, Shaanxi, People's Republic of China
| | - Jing Zhao
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, People's Republic of China; State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, Shaanxi, People's Republic of China
| | - Lili Huang
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, People's Republic of China; State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, Shaanxi, People's Republic of China
| | - Zhensheng Kang
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, People's Republic of China; State Key Laboratory of Crop Stress Biology for Arid Areas, Yangling, Shaanxi, People's Republic of China
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