Application of a double-enrichment procedure for microsatellite isolation and the use of tailed primers for high throughput genotyping

Diniz, Fábio Mendonça; Iyengar, Arati; Lima, P. S. da C.; Maclean, Norman; Bentzen, Paul

doi:10.1590/s1415-47572007000300014

Cited by 16 publications

(11 citation statements)

References 28 publications

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“…This approach was improved by Diniz et al (2007) and McPherson et al (2001), and finally our protocol followed the double-hybridization method as outlined in Winkler & Weiss (2008), including all details of adaptor and probe design.…”

Section: Genetic Markersmentioning

confidence: 99%

Genetic evaluation of the self-sustaining status of a population of the endangered Danube salmon, Hucho hucho

Weiss

Schenekar

2016

Hydrobiologia

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A new multiplex microsatellite protocol was developed for population screening of the endangered Danube salmon (or huchen) Hucho hucho. Allelic variation was screened at five newly cloned and four previously published loci in 246 samples to help evaluate the self-sustaining status of an urban population of huchen in the framework of a controversial environmental assessment in the Mur River, Austria. The loci revealed 78 alleles (mean = 8.6), and in the Mur River an average expected heterozygosity of 0.668. We inferred that the huchen population in and around the city of Graz is self-sustaining based on the following evidence, which includes both genetic and non-genetic sources of information: (1) there is little to no current stocking; (2) presence of juvenile huchen in multiple year classes; (3) sighting of spawning events; (4) documentation of 14 spawning redds; (5) no deviation from Hardy-Weinberg equilibrium; and (6) limited number of recaptures or parental matches with presumed parent fish of stocking operations. We discuss the potential application of such an analysis in evaluating threatened huchen populations throughout their native distribution.

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Section: Genetic Markersmentioning

confidence: 99%

Genetic evaluation of the self-sustaining status of a population of the endangered Danube salmon, Hucho hucho

Weiss

Schenekar

2016

Hydrobiologia

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“…This technique was first described in studies to evaluate genotypes in humans (Oetting et al, 1995). It was also used for genotyping animals (Diniz et al, 2007;Arruda et al, 2010) and several plant species, such as common beans (Oblessuc et al, 2009), rice (Goulart et al, 2011), apricot, cherry, barley, wheat (Hayden et al, 2008), Eucalyptus (Missiaggia & Grattapaglia, 2006), and soybean (Priolli et al, 2010).…”

Section: Introductionmentioning

confidence: 99%

Molecular characterization of soybean cultivars by microsatellite markers with universal tail sequence

Ribeiro

Tanure

Maciel

et al. 2013

Pesq. agropec. bras.

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-The objective of this work was to standardize a semiautomated method for genotyping soybean, based on universal tail sequence primers (UTSP), and to compare it with the conventional genotyping method that uses electrophoresis in polyacrylamide gels. Thirty soybean cultivars were genotypically characterized by both methods, using 13 microsatellite loci. For the UTSP method, the number of alleles (NA) was 50 (2-7 per marker) and the polymorphic information content (PIC) ranged from 0.40 to 0.74. For the conventional method, the NA was 38 (2-5 per marker) and the PIC varied from 0.39 to 0.67. The genetic dissimilarity matrices obtained by the two methods were highly correlated with each other (0.8026), and the formed groups were coherent with the phenotypic data used for varietal registration. The 13 markers allowed the distinction of all analyzed cultivars. The low cost of the UTSP method, associated with its high accuracy, makes it ideal for the characterization of soybean cultivars and for the determination of genetic purity.Index terms: Glycine max, cultivar protection, genetic diversity, genotyping method, random identity probability. Caracterização molecular de cultivares de soja por meio de marcadores microssatélites com sequência de cauda universalResumo -O objetivo deste trabalho foi padronizar um método semi-automatizado para genotipagem de soja, baseado na metodologia de iniciadores com sequências de cauda universal (PSCU), e compará-lo ao método de genotipagem convencional de eletroforese em gel de poliacrilamida. Trinta cultivares de soja foram caracterizadas genotipicamente por ambos os métodos, com o uso de 13 locos microssatélites. Para o método PSCU, o número de alelos (NA) foi de 50 (2-7 por marcador) e o conteúdo de informação polimórfica (PIC) variou de 0,40 a 0,74. Para o método convencional, o NA foi de 38 (2-5 por marcador) e o PIC variou de 0,39 a 0,67. As matrizes de dissimilaridade genética obtidas pelos dois métodos apresentaram alta correlação entre si (0,8026), e os grupos formados foram coerentes com dados fenotípicos utilizados para o registro varietal. Os 13 marcadores permitiram a distinção de todas as cultivares analisadas. O baixo custo do método PSCU, associado a sua alta acurácia, torna-o ideal para a caracterização de cultivares de soja e a determinação de pureza genética.Termos para indexação: Glycine max, proteção de cultivar, diversidade genética, método de genotipagem, probabilidade de identidade ao acaso.

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“…The inclusion of an extended fluorescently labeled tail in the SSR primers has been proposed to improve automation and reduce genotyping costs (Cryer et al, 2005;Arruda et al, 2010;Diniz et al, 2007;Hayden et al, 2008;Missiaggia and Grattapaglia, 2006;Ribeiro et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

Universal tail sequence-SSR applied to molecular characterization of tropical maize hybrids

Ribeiro

Pinto

Maciel

et al. 2017

Sci. agric. (Piracicaba, Braz.)

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The development of efficient and low-cost genotyping methods is essential to precise genetic characterization of cultivars. Here, we present a system based on fluorescently labeled universal tail sequence primers (UTSP) to resolve microsatellite (SSR) markers as an alternative for molecular fingerprinting of maize. A set of 20 SSRs using the UTSP presented an average polymorphic information content of 0.84, which provided a probability of random identity ranging from 10 −7 to 10 −14, and a minimum exclusion power of 99.99998 % in a group of 48 tropical maize single-cross hybrids traded in Brazil. The genetic diversity analysis based on multidimensional scaling explained approximately 28 % of the total variance for the first two coordinates, tending to group the hybrids according to their respective origin. Additionally, this genotyping system presented a high distinctiveness capacity, which is widely recommended for genetic purity and fingerprinting analyses. Thus, this marker system has a strong potential as a tool for complementary analysis of distinguishability, uniformity and stability required for cultivar registration.

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Application of a double-enrichment procedure for microsatellite isolation and the use of tailed primers for high throughput genotyping

Cited by 16 publications

References 28 publications

Genetic evaluation of the self-sustaining status of a population of the endangered Danube salmon, Hucho hucho

Genetic evaluation of the self-sustaining status of a population of the endangered Danube salmon, Hucho hucho

Molecular characterization of soybean cultivars by microsatellite markers with universal tail sequence

Universal tail sequence-SSR applied to molecular characterization of tropical maize hybrids

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