i am doing molecular characterization of citrus germplasm, Presently ihave started using some of the SSR markers published in Citrus sinesis genome paper. Presently i evaluating the PCR products on 4% metaphor gels. i am getting bands of different sizes and in some cases present and absent type of bands. SInce i am amateur in scoring molecular markers. i want to know is there any article published explaining how to score a SSR marker for further analysis. thank you
hi dear Prasanth Tej Kumar Jagannadham,
usually, SSRs are mainly co-dominant markers so you have to score as 1:1, 1:2, 2:3 (dependent on the number of alleles per locus)
Thank you, Dear Mostafa, but in some the cases I am getting present and absent type of pattern also
Thank You So much for providing the information in a detailed manner
While using NTSYS Pc software for divergence analysis, the SSR data scored on the basis of presence and absence as well as molecular size difference have to be arranged into binary matrix. So each allelic variant recognized on the basis of molecular size difference is considered as marker and scored for its presence and absence and then subjected to divergence analysis.
can anyone give example for SSR scoring based on band. send some example files of band and scoring matrix. please.
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