I am interested to study the genetic diversity of a plant fungal pathogen. I have gathered potential genetic markers (around 30 sets) from journals to investigate their % polymorphism before selecting the suitable ones for further analysis. I have a total of 50 isolates of fungal pathogen. Do I have to screen 50 isolates at one time using one set of genetic marker?
In other words, can I just use 10 representative isolates, instead of 50 isolates, to screen for suitable genetic markers with high % of polymorphism? How many bands is needed to produce reliable genetic diversity results?
Thank you in advance.
I remembered when I did my SSR screening, my supervisor asked me to choose 5 individuals from each population, in order to test the polymorphism of a specific marker. So i guess using 10 isolates out of 50 should be enough. For SSR, I guess markers showing more than 3 genotypes in your population would be good. Hope this helps.
If you have prior information regarding relatedness among your fungal isolates, e.g., morphology, host range, reproductive characteristics etc., select smaller subset representing the most diverse isolates and screen SSRs on them to find out polymorphic SSRs for the whole sample. Hope this may help!
Dear Wong, You may select some representative isolates from the total based on different parameters such as growth, pathogenicity and/or previous studies. The number of bands depends on the type of markers and clarity of PCR. You may get some information from this article.
http://www.dbpia.co.kr/Journal/ArticleDetail/NODE07080642
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