I am studying the genetic variation that exist within two colour strains of African Grasscutter (Thyrononymus swinderianus). I used RAPD marker for my study. I have scored the gel image, but I'm having serious challenge with the analysis of the scored gel image. Which software is most convenient, and which parameters will help me achieve this aim.
DNA fingerprinting analysis of different markers usually done by scoring using UVIDoc software. The presented band scored as 1 and 0 for the absent for each specific molecular size of gel agarose photo.
Based on scoring, data recorded should be converted to a binary matrix. NTSYS (Exeter Biological Software, Setauket, NY, USA) should be used to analyze the data.
The input of data should be formatted based on the manual of software.
The coefficient similarity should be calculated by Jaccard’s and used to construct the dendrogram tree by UPGMA (Unweighted Pair Group Method with Arithmetic Mean) algorithm.
POPGENE (population genetic analysis) should be used to estimate the genetic structure parameters for each marker total loci, polymorphism loci and percentage, Shannon index (I), gene diversity (H) Nei's (1973), Effective number of alleles (Ne) [Kimura and Crow (1964)] and Observed number of alleles (Na).
Unbiased Expected Heterozygosity (uHe) and Analysis of molecular variance (AMOVA) should be estimated using GenAlEx.
@Wael Alsultan. Thank you very much. I have been able to score the gel and estimated the parameters mentioned for the popgene software. But the genalex, I have installed it I my PC, but don't know how it works? I can not do anything with it. How do I go about usi g the genalex software? For the Jaccard's, please guide me more
POPGENE software can help you to to calculate the genetic distance and similarities. The most efficient tool especially for RAPD markers. Further, you can use power-marker or XLSTAT to evaluate PIC, PCA and AMOVA.
You can see check these articles
Article Evaluation of Genetic Diversity Among Exotic Sorghum (Sorghu...
Article Genetic Diversity Analysis of Brassica Species Using PCR-Bas...
If you are interested in more parameters, you can follow this article. Although I have calculated all these new parameters for Brassica species for the first time.
https://cyberleninka.ru/article/n/evaluation-of-the-measure-of-polymorphism-information-of-genetic-diversity
U better use other dominant markers like issr, scot, ipbs etc. Rapd is less reliable and good journals will hesitate to take ur study. For the analysis u can do manual scoring of the bands and analysis done in softwares like popgene, genealyx etc.
Potshangbam Nongdam Ali Raza Wael Alsultan
Can you please share the GenAlex/Popgene input data format for the RAPD/SCoT/ISSR markers, especially when multiple (>2 bands) are obtained?
Thanks
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