Certain common points that i could remember are:

1. We always go for SSR markers that are polymorphic for the parents of a CRIL population.

2. If you want to choose from large number of SSR markers (based on NGS cDNA sequencing data) then please check that the nearest sequenced genome has polymorphism in that particular area of the gene.

3. Some coding regions of genes can accommodate large polymorphism during the course of evolution.

4. Use trinucleotide SSR as they are more easily maintained in the nearby varieties of a species due to triplet codon.

Hopefully more experts of this area will give there suggestions.

For better result, choose trinucleotide SSR because it is going to amplify more specifically. choose SSR marker which is flanking to your locus of interest so that you can easily screen segregating population.

Good Luck.

Some people have said that the most polymorphic SSR loci have >9 repeats, trinucleotide or more, with retrotransposons nearby.

Select SSRs uniformly from each chromosome if linkage map is available for general studies 

SSRs with high polymorphic information content values always better  

if your are looking at specific loci, select shortest distance  linked SSR/ SSRs 

Dear Ravinder Kumar,

Their is different types of DNA markers. But the best DNA markers for getting polymorphic in closely related genotypes is SSR or microsatellite markers.

It has  different advantages.

For selection you must have more markers cover you crop or plant genome. I think at leats 2-4 markers per chromosome to get good results.

For polymorphism using SSR you will find if you have different closely related genotypes the best marker is ssr

with best regards

Khaled

Muhammad Khuram Razzaq

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