Permanent Genetic Resources added to Molecular Ecology Resources Database 1 February 2013–31 March 2013

Arias, Maria Cristina; Attéké, Christiane; Augusto, Solange Cristina; Bailey, James; Bazaga, Pilar; Beheregaray, Luciano B.; Benoit, Laure; Blatrix, Rumsaïs; Born, Céline; Brito, Rute Magalhães; Chen, Haikui; Covarrubias, Sara; Vega, Clara de; Djiéto‐Lordon, Champlain; Dubois, Marie‐Pierre; Francisco, Flávio de Oliveira; García, Cristina; Gonçalves, Paulo Henrique Pereira; González, Clementina; Gutiérrez‐Rodríguez, Carla; Hammer, Michael P.; Herrera, Carlos M.; Itoh, Hajime; Kamimura, Satomi; Karaoglu, Haydar; Kojima, Soichi; Li, Shou-Li; Ling, Hannah J.; Matos‐Maraví, Pável; McKey, Doyle; Mezui-M'eko, Judicaël; Ornelas, Juan Francisco; Park, Robert; Pozo, María I.; Ramula, Satu; Rigueiro, Cristina; Sandoval‐Castillo, Jonathan; Santiago, Leandro Rodrigues; Seino, Miyuki M.; Song, Chang-Bing; Takeshima, Hirohiko; Vasemägi, Anti; Wellings, C. R.; Yan, Jiye; Du, Yu‐Zhou; Zhang, Changrong; Zhang, Tian-Yun

doi:10.1111/1755-0998.12121

Cited by 47 publications

(13 citation statements)

References 5 publications

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“…The 84 previously published Pst SSR markers [20–24] were downloaded and amplified by E-PCR for comparison.…”

Section: Methodsmentioning

confidence: 99%

“…For Pst , SSR markers have been developed using microsatellites enrichment DNA library [20] and expression sequence tag (EST) libraries [21–23], as well as genomic sequences [24], and are the primary molecular markers used in genetic and population studies. For example, SSR markers were used to reveal the existence of the sexual and parasexual cycles [25–27], estimate the genetic diversity of different Pst populations [28–31] and analyze the origin, migration routes and worldwide population structures of Pst [32].…”

Section: Introductionmentioning

confidence: 99%

“…The first reported Pst genome is that of isolate PST-130 in the USA, which was obtained through next generation sequencing [33]. Bailey et al [24] reported 25 SSR markers derived from the sequences of this isolate. The genome of the CYR32, one of the most dominant Pst races in China, was assembled using a 'fosmid-to-fosmid' strategy to reduce the affect of genome heterozygosity [34].…”

Section: Introductionmentioning

confidence: 99%

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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

et al. 2015

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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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“…The 84 previously published Pst SSR markers [20–24] were downloaded and amplified by E-PCR for comparison.…”

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

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

et al. 2015

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“…To provide the appropriate detailed genetic resolution, we employed a suite of recently developed microsatellite markers (Arias et al, 2013) and a comprehensive sampling of catchments and localities across the MDB. We expect G. marmoratus populations to exhibit low genetic diversity and high levels of population structure.…”

Section: Introductionmentioning

confidence: 99%

Landscape genetics informs mesohabitat preference and conservation priorities for a surrogate indicator species in a highly fragmented river system

et al. 2016

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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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“…in Australian isolates). A recent publication reported 25 polymorphic genomederived SSRs in Australian Pst isolates (Bailey et al, 2013), and these markers were developed using genomic sequence of North American race PST130 (genome size about 64.8 Mb) published by Cantu et al (2011) and supplemented with sequence data from collaborators at the Australian National University. A total of 1889 SSR loci were identified in these datasets.…”

Section: Introductionmentioning

confidence: 99%

Screening for simple sequence repeat markers in Puccinia striiformis tritici based on genomic sequence

Zhan

Wang

Luo

et al. 2015

J. Zhejiang Univ. Sci. B

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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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Permanent Genetic Resources added to Molecular Ecology Resources Database 1 February 2013–31 March 2013

Abstract: This article documents the addition of 142 microsatellite marker loci to the Molecular Ecology Resources database. Loci were developed for the following species:

Cited by 47 publications

References 5 publications

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

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

Landscape genetics informs mesohabitat preference and conservation priorities for a surrogate indicator species in a highly fragmented river system

Screening for simple sequence repeat markers in Puccinia striiformis tritici based on genomic sequence

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