How to score microsatellites for analysis through NTSYS pc? Should I use some other program? which one is the best and available on line? Please guide me in details.
I think people could give you better answers if you write what kind of analysis you want to perform.
I have different genotypes of rice genotyped on the basis of SSRs.
When we genotype a set of rice germplasm with SSR, we can get varying number of alleles for each SSR based on the genetic diversity.
For scoring this kind of data we can score each allele for its presence and absence in the form of 1 and 0 (present and absent respectively).
Identify different alleles for each SSR, tag them appropriately and then score as 1 and 0.
Hello Arup Kumar Mukherjee.
Depending on the form the SSR data is in; if it's still in peak form (from the analyzer), you can use Genemarker or genemapper to score the alleles. If you have the data already scored; then you can use GenAIEx software for analysis (AMOVA, Isolation by distance (IBD), Fst, Fis, Gst, Nm). In GenAIEx, the data can be in the form of haploid(1,0) or diploid(2 alleles at a locus). If you may want to download GenAIEx, https://biology-assets.anu.edu.au/GenAlEx/Download.html.
You can then use powermarker or molkin software to calculate the diversity indices (He, PIC, H, Ho, Ne).
0 1 sheet is prefer for NTSYS. If the band is present in genotype marked as 1, if that particular band is not present in other genotype marked as 0.
Dear Shivaji Lavale
Besides 0 & 1 format, you can directly write the exact allele size (band size). You may use them for genetic diversity analysis with the available softwares. Furthermore, band size based scoring will be useful for population structure analysis, association mapping analysis, marker profiling analysis, AMOVA etc.
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