I want to analysis the population genetics of a plant pathogen with SSR marker. I did this with 8 pairs primers, but only 4 marker(primers) show polymorphism. So I want to know when I analysis my data with Structure、Popgene、Poppr or some other software, whether the data of 8 markers should be used during the analysis or only the 4 markers that show polymorphism be used. Thank you!
Dear friend
As per my knowledge, it is not enough. Use more markers
H
hello , you should use only the polymorphic since the monomorphic do not show variation and are not informative for the analysis of your population. How big is your population? You should also test more SSR markers, more places in the genome will be better to conclude about the variation existing in your genotypes.ello,
Use more markers, if markers are not available, you can develop SSRs by retrieving sequence information of your organism from NCBI.
please change anealing tempreture and repeat PCR reaction. four SSR have not shown actual vatiation in your population individuals.
Hi,
Usually getting 50 polymorphic loci leads to a goof population genetic analysis.
Hi.
Ofcourse you can introduce your monomorphic primers in your paper but it is better don't share them in your analysis. If you can find 3-4 other polymorphic locus, It will be better.
Maybe I could try to write down my own answer. When I submit my paper to the journal, a reviewer gave me an advice: as my population is a clonal line, so a "genotype accumulation curve" should be calculated to test whether my four SSR marker have enough power to differentiate the genotypes. Of course, four SSR markers is indeed not enough. So I tried my best to screen more loci and identified more markers.
So if the populations we tested is a sexual population, maybe many markers will be polymorphic among isolates. But if the population we tested is a asexual line with low polymorphism, we should calculate the "genotype accumulation curve" to confirm the markers we used has enough power to differentiate the genotypes we got.
Thanks all the investigators above and welcome you to leave your answer here that maybe useful for rookie like me.
Thank you!
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