So maybe in those samples where you get no amplification there is no microsatellite, or they're mutated in a way your primers don't work. Maybe the DNA of that samples is degraded. Maybe they're related to mobile elements...

I'm sorry I'm not an expert on this...

Bests

Hi!

Is the similarity with the other species leading to a closely related genus? If so, could there be a cryptic species? Otherwise, could your samples be contaminated? (eg mold growth on samples before DNA extraction?)

Best,

Hi!

First of all PCRs are sensitive reactions you should be very careful always though it appear simple. That too you are doing multiplex. You should take enough care and very very careful (especially while adding primers by chance if you miss either F or R you will not see any amplification).

As Galo mentioned might be null allele even after repeating many times if you are not getting the amplification.

Finally try once again with utmost care and confirm or ask somebody else to set the reaction to cross check.

Good Luck!

I think you need to check the quality of the DNA you are using, the ones that are not amplifying. If the DNA is in order then may be the null allele could play in

The reason might definitely be the presence of null alleles (alleles that do not produce a detectable PCR amplification product). To a certain extent, this may not affect the reliability of your microsatellite analysis; specific software applications allow you to test whether null alleles will affect your results and the F-statistics estimation, e.g. ML-NullFreq, Microchecker, FreeNA...

Hi,

I also have a bit experience on working microsatellites. I happens sometimes that  one is getting amplification in some samples and in some other it is not amplifying. You have to be careful while doing PCR. check quantity of the all samples and try to use same concentration of the DNA in all samples. If problem still presist then check for purity that wheather sample which are not amplifing they have same purity as compared to the nonamplifying samples. If the probem still remain the check whether these are the samples of the same species or from two or more identical species. All the best

Null alleles is a likely answer, and some samples will never amplify because of that (but as Roberta suggests, this might not be a major problem with analysis). If you decide to try one more amplification, you might try spiking the PCR of the reluctant samples with magnesium chloride. We discovered this helped some samples significantly - I would try increasing by just 1 mM and see if you get results... just be sure you are not getting non-specific priming... microsatellites are nice because you know where the alleles should be - if you get peaks/bands outside of that region with extra MgCl, back down on how much you are putting in...

Good luck!

Yes as mentioned by Stephen n Arun you better check the quality of DNA. You are doing multiplex (how many sets of primers are you using per reaction) you need to take a bit more DNA compared to normal PCR. Check carefully once then you can confirm whether null allele or set up problem.

Good Luck!! 

When those markers fail in some individuals, do other markers amplify in the same samples? eg. for Individual A, marker 1 fails and marker 2 works. Is that the case? if so, i would also suggest null alleles. However if the sample fails for all markers I would say probably DNA degradation. I experience both examples in some of my samples. When they fail I always repeat 2 or 3 times to make sure nothing is amplified as it happened during the first trial.

Thank you soooo much for all of you. DNA quality was good since the failed samples works with other markers and gave good products.  (( for Individual A, marker 1 fails and marker 2 works)) Yes this is the situation in my samples.

But, as I know, the null alleles means amplifying of one allele and absence of the second allele. Here I am facing no PCR product at all in some samples even after several repeats from my other members of the research group. 

I think there could be some releation with mobile elements as suggested by Galo Adrián Goig 

I understand you managed your protocol to be uniform with all samples.  However, did you check the melting temperatures of your primers?  Some may be different than others by several degrees and as such may not amplify if they are subject to inappropriate annealing temperatures.  Use an annealing step of 5 degrees below the Tm value and add MgCl as Amy McMillan suggested.

They could be homozygous for the null allele. You may check with the software Roberta Gargiulo suggested (ML-NullFreq, Microchecker, FreeNA) whether this is a plausible hypothesis.

Null alleles usually occur due to mutations in the priming region(s) of individuals (samples) which mean that during PCR your primers don't anneal properly.Samples that are homozygous for a null allele will result in no PCR product.

As mentioned earlier you could try modifying (relaxing) PCR conditions either by adding more Magnesium to the reaction or by reducing the temperature during the annealing step of your PCR. If you are going to adjust PCR conditions it is probably best to do this using a single primer set in each reaction (that is don't multiplex). You may even find that by not multiplexing you get amplification of markers that have been causing you trouble.