Selection of technique is depend on facility available in our lab ,  If fragment analyzer   (ABI) available use it, ABI3730 is capable to resolve 1 nucleotide variation , If not available go with PAGE

1. Check first if microsatellite markers have been already developed and available for your species and genus. Otherwise you need to do it yourself.

2. Once they are available, then you need to optimize the amplification process for your species.

 Microsatellites are used  to check the interbreeding phemenon between species by determining some genetic factors such as FsT, FiS, Fit, coefficient of interbreeding but you need to perform PCR with primers available on the species concerned. 

Hi

first of all check for Microsatellites primers if they are available for your species then use them and perform study. Either u can perform through ABI sequence analyzer or polyacrlamide gel electrophoresis or you can check amplification using metaphore agarose and choice of using techniques is totally depend on the facility available with your laboratory.

If primers are not available then U have to develop primers for your species by constructing genomic library followed by sequencing and the designing the ssr and using for your own study. This is further depend on facility and your purpose of experimentation.

Further if  you dont have facility then these days people are using cross transferability method for designing and amplifying the microsates in which sequences of a species of same genus are used to design SSR for amplifying the DNA of other species of that genus.  Hope this will be helpful. Gud luck

Hi

If your species are within the farm animals you can use the recommended panel from ISAG/FAO for studying genetic diversity. information about primers and multiplex PCR are provided here:http://www.fao.org/docrep/014/i2413e/i2413e00.pdf

Regarding the techniques you can use LI-COR DNA analyzer.

I agree with many of the answers. The most important is to verify if your species have primers available. From there and depending on your funding you can go from agarose gels to sophisticated fragment analysis systems. You can be very successful using any of those approaches if your materials have enough diversity to be detected and enough range of diversity to move to breeding gains.

I think some researchers are moving to SNP variations, CNV (copy numbers of variation), instead of fragment size like microsatellite, RAPD. However, SNP panels are not available for all species we interested.

Ok. for my opinion, microsatellite markers are vey useful markers for breeding and population genetic studies. they give a series of comprehensive results.