PICcalc: An Online Program to Calculate Polymorphic Information Content for Molecular Genetic Studies

Nagy, S.; Poczai, Péter; Cernák, István; Gorji, Ahmad Mousapour; Hegedűs, Géza; Taller, János

doi:10.1007/s10528-012-9509-1

Cited by 302 publications

(211 citation statements)

References 7 publications

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“…In this respect, three DNA unique fragments were detected in the varieties, IRAT170 and one fragment in each of the genotypes Giza178, A22 and WAB56-125. PIC value:-PIC value refers to the value of a marker for detecting polymorphism within a population, depending on the number of detectable alleles and the distribution of their frequency; thus, it provides an estimate of the discriminating power of the marker (Nagy et al, 2012). As it is shown in Table (9), the PIC values for the SSR used in this study varied from 0.38 to 0.80 with an average of 0.68.…”

Section: Number Of Alleles and Allelic Diversitymentioning

confidence: 99%

Genetical and Molecular Studies on Salinity and Drought Tolerance in Rice (Oryza Sativa L.)

2016

Journal of Sustainable Agricultural Sciences

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Section: Number Of Alleles and Allelic Diversitymentioning

confidence: 99%

Genetical and Molecular Studies on Salinity and Drought Tolerance in Rice (Oryza Sativa L.)

2016

Journal of Sustainable Agricultural Sciences

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“…To estimate the marker allele variation of the selected SSR loci in the 95 barley accessions, the polymorphism information content (PIC) was calculated using PICcalc so ware (10). This index provides an estimate of the discriminating power of each co-dominant marker locus and it depends on the number of detectable marker alleles and on the distribution of their frequency.…”

Section: Marker Analysismentioning

confidence: 99%

Developing a Molecular Identification Assay of Old Landraces for the Genetic Authentication of Typical Agro-Food Products: the Case Study of the Barley ‘Agordino’

Palumbo¹,

Galla²,

Barcaccia³

2017

Food Technol. Biotechnol.

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SummaryThe orzo Agordino is a very old local variety of domesticated barley (Hordeum vulgare ssp. distichum L.) that is native to the Agordo District, Province of Belluno, and is widespread in the Veneto Region, Italy. Seeds of this landrace are widely used for the preparation of very famous dishes of the dolomitic culinary tradition such as barley soup, bakery products and local beer. Understanding the genetic diversity and identity of the Agordino barley landrace is a key step to establish conservation and valorisation strategies of this local variety and also to provide molecular traceability tools useful to ascertain the authenticity of its derivatives. The gene pool of the Agordino barley landrace was reconstructed using 60 phenotypically representative individual plants and its genotypic relationships with commercial varieties were investigated using 21 pure lines widely cultivated in the Veneto Region. For genomic DNA analysis, following an initial screening of 14 mapped microsatellite (SSR) loci, seven discriminant markers were selected on the basis of their genomic position across linkage groups and polymorphic marker alleles per locus. The genetic identity of the local barley landrace was determined by analysing all SSR markers in a single multi-locus PCR assay. Extent of genotypic variation within the Agordino barley landrace and the genotypic di erentiation between the landrace individuals and the commercial varieties was determined. Then, as few as four highly informative SSR loci were selected and used to develop a molecular traceability system exploitable to verify the genetic authenticity of food products deriving from the Agordino landrace. This genetic authentication assay was validated using both DNA pools from individual Agordino barley plants and DNA samples from Agordino barley food products. On the whole, our data support the usefulness and robustness of this DNA-based diagnostic tool for the orzo Agordino identi cation, which could be rapidly and e ciently exploited to guarantee the authenticity of local varieties and the typicality of food products.

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“…Further, an indirect estimate of the level of gene flow (N m ) between the genotypes was calculated using the formula: Nm = 0.25 (1 -/ ) using GenAlex. Polymorphic information content (PIC) was calculated using the formula: PIC =∑ 2 , where P ij is the frequency of j th allele of the i th locus (Nagy et al, 2012). The F-statistics such as genetic differentiation (F ST ), fixation index or inbreeding coefficient (F IS ) and overall fixation index (F IT ) were calculated according to Wright's original derivation (Wright, 1951).…”

Section: Genetic Diversity Analysismentioning

confidence: 99%

Assessment of the genetic diversity of dessert watermelon (Citrullus lanatus var. lanatus) landrace collections of South Africa using SSR markers

Mashilo¹,

Shimelis²,

Odindo³

et al. 2017

Aust J Crop Sci

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Dessert watermelon landraces could provide useful germplasm sources for commercial watermelon breeding and/or conservation. This study assessed the genetic diversity present among dessert watermelon landrace collections of South Africa using simple sequence repeat (SSR) markers. Thirty one diverse dessert watermelon landraces were genotyped using 10 polymorphic SSR markers. A total of 94 alleles were amplified among the sampled population. The number of alleles ranged from 2 to 19 with a mean of 9.4 per locus. The number of effective alleles ranged from 1.07 to 9.94 with a mean of 4.61. Observed heterozygosity values ranged from 0.07 to 1.00 with a mean of 0.53. Expected heterozygosity, which measures gene diversity, was 0.66; which partitioned 75, 25 and 0% of the variation within individuals, among individuals and between populations, respectively. The mean gene fixation was 0.18 suggesting high levels of heterozygosity among the collections. The mean polymorphic information content (PIC) of the SSR loci was 0.65 suggesting their value in genetic diversity analysis of watermelon. The collections were allocated into three genetic groups using cluster analysis. The results revealed the presence of genetic diversity among South African dessert watermelon collections. Genetically unique landraces such as SWM-39, SWM-01, SWM-04, SWM-27, SWM-24, SWM-10 and SWM-36 from cluster I; SWM-35, SWM-21, SWM-02, SWM-34, SWM-07 and SWM-31 from cluster II; and SWM-22 and SWM-18 from cluster III were selected based on their high dissimilarity index. These are recommended for further phenotyping using horticultural attributes for effective breeding and strategic conservation.

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PICcalc: An Online Program to Calculate Polymorphic Information Content for Molecular Genetic Studies

Cited by 302 publications

References 7 publications

Genetical and Molecular Studies on Salinity and Drought Tolerance in Rice (Oryza Sativa L.)

Genetical and Molecular Studies on Salinity and Drought Tolerance in Rice (Oryza Sativa L.)

Developing a Molecular Identification Assay of Old Landraces for the Genetic Authentication of Typical Agro-Food Products: the Case Study of the Barley ‘Agordino’

Assessment of the genetic diversity of dessert watermelon (Citrullus lanatus var. lanatus) landrace collections of South Africa using SSR markers

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