Characterization and multiplexing of EST‐SSR primers in <i>Cynodon</i> (Poaceae) species<sup>1</sup>

Jewell, Margaret; Frère, Céline; Prentis, Peter J.; Lambrides, Christopher J.; Godwin, Ian D.

doi:10.3732/ajb.1000254

Cited by 23 publications

(22 citation statements)

References 12 publications

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“…In addition, one of the dyes is used as an in‐lane size standard, greatly improving the sizing precision of alleles. Multiplex PCR now forms the basis for many studies, on both diploid and polyploid species (Jewell et al. 2010; Raabova et al.…”

Section: Introductionmentioning

confidence: 99%

“…In addition, one of the dyes is used as an in-lane size standard, greatly improving the sizing precision of alleles. Multiplex PCR now forms the basis for many studies, on both diploid and polyploid species (Jewell et al 2010;Raabova et al 2010), reducing very significantly the cost and time of genetic analyses (Box 2). Important progresses have also been made in SSR data scoring, a critical and time-limiting step.…”

Section: Introductionmentioning

confidence: 99%

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Current trends in microsatellite genotyping

Guichoux

Lagache

Wagner

et al. 2011

Molecular Ecology Resources

753

740

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Microsatellites have been popular molecular markers ever since their advent in the late eighties. Despite growing competition from new genotyping and sequencing techniques, the use of these versatile and cost-effective markers continues to increase, boosted by successive technical advances. First, methods for multiplexing PCR have considerably improved over the last years, thereby decreasing genotyping costs and increasing throughput. Second, next-generation sequencing technologies allow the identification of large numbers of microsatellite loci at reduced cost in non-model species. As a consequence, more stringent selection of loci is possible, thereby further enhancing multiplex quality and efficiency. However, current practices are lagging behind. By surveying recently published population genetic studies relying on simple sequence repeats, we show that more than half of the studies lack appropriate quality controls and do not make use of multiplex PCR. To make the most of the latest technical developments, we outline the need for a well-established strategy including standardized high-throughput bench protocols and specific bioinformatic tools, from primer design to allele calling.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Current trends in microsatellite genotyping

Guichoux

Lagache

Wagner

et al. 2011

Molecular Ecology Resources

753

740

View full text Add to dashboard Cite

show abstract

“…These strategies allow to simultaneously amplify more than one locus in a single reaction using multiple primer pairs. Multiplex PCR protocols have been developed and successfully applied for different uses in many species, such as the detection of colorectal tumors in humans (Patil et al 2012), monitoring of rat strains (Bryda and Riley 2008), genetic characterization of different plant species (Jewell et al 2010;Postolache et al 2013;Drašnarová et al 2014), identification of selfed progenies in switchgrass (Liu and Wu 2012), or to facilitate systematic and rapid genetic mapping in soybean (Sayama et al 2011). Multiplex PCR design requires a priori knowledge of the range of allelic sizes for each marker in order to avoid amplicons overlapping and the optimization of PCR conditions to obtain a balanced amplification of all the targeted fragments (Butler 2005a).…”

Section: Introductionmentioning

confidence: 99%

Whole-genome genotyping of grape using a panel of microsatellite multiplex PCRs

Zarouri¹,

Vargas²,

Gaforio³

et al. 2015

Tree Genetics & Genomes

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The use of microsatellite markers in large-scale genetic studies is limited by its low throughput and high cost and labor requirements. Here, we provide a panel of 45 multiplex PCRs for fast and cost-efficient genome-wide fluorescencebased microsatellite analysis in grapevine. The developed multiplex PCRs panel (with up to 15-plex) enables the scoring of 270 loci covering all the grapevine genome (9 to 20 loci/chromosome) using only 45 PCRs and sequencer runs. The 45 multiplex PCRs were validated using a diverse grapevine collection of 207 accessions, selected to represent most of the cultivated Vitis vinifera genetic diversity. Particular attention was paid to quality control throughout the whole process (assay replication, null allele detection, ease of scoring). Genetic diversity summary statistics and features of electrophoretic profiles for each studied marker are provided, as are the genotypes of 25 common cultivars that could be used as references in other studies.

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“…Compared to the source germplasm (the germplasm present in the entire source population), the AC contains increased gene diversity (H = 0.18 versus H = 0.14), > 95% of the total number of alleles, and similar proportions of accessions representing specific climates, ploidy levels, and environment type. DNA extraction procedures and EST-SSR analyses have been reported previously (Jewell et al 2010;Kearns et al 2009;Zhou et al 2009). DNA from 59 international accessions representing global distribution was provided by the USDA-ARS in Tifton, GA (international collection; IC; Anderson et al 2009).…”

Section: Plant Materials Est-ssr Genotyping and Core Collection Devementioning

confidence: 99%

Introduction and Adaptation of Cynodon L. C. Rich Species in Australia

Jewell

Anderson

Loch

et al. 2012

Breeding Strategies for Sustainable Forage and Turf Grass Improvement

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Cynodon L. C. Rich comprises warm season grass species that are valuable as turf and forage in warm climates across the globe. Traditionally, Cynodon breeding programs have aimed to produce varieties with improved turf and forage grass quality characteristics. More recent goals, such as improved abiotic stress tolerance, aim to address challenges associated with climate change. Germplasm collections representing a fraction of the global distribution of Cynodon comprise the plant resource for these breeding programs. We compared a core collection consisting of 116 Australian genotypes with an international core collection of 59 genotypes representing Cynodon's global distribution. Our aims were to determine whether unique genetic diversity exists amongst Australian Cynodon that may enhance international breeding resources. This research will facilitate the incorporation of Australian Cynodon genetic resources, which have expanded and naturalized under harsh Australian climates, into existing germplasm collections.

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Characterization and multiplexing of EST‐SSR primers in Cynodon (Poaceae) species¹

Abstract: The 16 markers show sufficient variation for the characterization of Cynodon core collections and analysis of population genetic diversity in Cynodon grasses.

Cited by 23 publications

References 12 publications

Current trends in microsatellite genotyping

Current trends in microsatellite genotyping

Whole-genome genotyping of grape using a panel of microsatellite multiplex PCRs

Introduction and Adaptation of Cynodon L. C. Rich Species in Australia

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Characterization and multiplexing of EST‐SSR primers in Cynodon (Poaceae) species1

Abstract: The 16 markers show sufficient variation for the characterization of Cynodon core collections and analysis of population genetic diversity in Cynodon grasses.

Cited by 23 publications

References 12 publications

Current trends in microsatellite genotyping

Current trends in microsatellite genotyping

Whole-genome genotyping of grape using a panel of microsatellite multiplex PCRs

Introduction and Adaptation of Cynodon L. C. Rich Species in Australia

Contact Info

Product

Resources

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Characterization and multiplexing of EST‐SSR primers in Cynodon (Poaceae) species¹