We are working with SSR and ISSR primers. The resolving power of various SSR primers to distinguish among the genotypes could be evaluated by calculating PIC, Marker index, Shanon index. We used GenAlEx software for this. But ISSR primers yield multilocus biallelic products. The data output for such types of markers, using software GenALEx, gives various values for different locus rather than for individual primer. How to calculate MI, PIC etc for ISSR markers? Has anybody used this software for this purpose? Or can anybody suggest some other software for calculation of these parameters for dominant biallelic marker system?
You can calculate the polymorphism information content (PIC) according to (Botstein et al., 1980) for each primer using PICcalc (Nagy et al., 2012).
Marker index (MI), as measured by PIC, and effective multiplex ratio may provide a convenient estimate of marker utility MI = PIC x E. E=nβ where β is the fraction of polymorphic markers, estimated after considering the polymorphic loci (np) and non-polymorphic loci (nnp) as β = np/(np+ nnp).
You can calculate the polymorphism information content (PIC) according to (Botstein et al., 1980) for each primer using PICcalc (Nagy et al., 2012).
Marker index (MI), as measured by PIC, and effective multiplex ratio may provide a convenient estimate of marker utility MI = PIC x E. E=nβ where β is the fraction of polymorphic markers, estimated after considering the polymorphic loci (np) and non-polymorphic loci (nnp) as β = np/(np+ nnp).
The following paper explains clearly how to calculate PIC, MI, RP etc. for dominant markers.
http://www.academicjournals.org/article/article1380877408_Kayis%20et%20al.pdf
I believe you can easily perform the calculations in excel.
Ok
you can use powermarker software because in that, you can have 2 allele for a marker, for example: A/B or A/A or B/B.
The following paper explains clearly how to calculate PIC, MI, RP etc. for dominant markers
http://link.springer.com/article/10.1007/s00606-013-0970-z
all the best
You can also use iMEC instead of PICcalc https://irscope.shinyapps.io/iMEC/ which calculates PIC, MI, R, D, H and EMR. You can cite it as Amiryousefi A, Hyvönen J, Poczai P (2018) iMEC: Online Marker Efficiency Calculator. Applications in Plant Science, in press
The paper will be out soon!
Following Milbourne et al. (1997), marker index (MI) can be calculated as product of PICi and effective multiplex ratio (EMR), which is defined as the product of the fraction of polymorphic loci and the number of polymorphic loci.
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