How to identify the different varieties of same species in Plants?

Question

[Shahzad]

Dear All I want to establish a system to differentiate between the varieties of same species(specifically plants). Please let me know if anyone has done it with any protocol.

Best Regards Shahzad

[Matteo Schiavinato]

Sounds like a very good name for a phd project :D It depends on what data you have!

[Shahzad]

@Macspider Thank you for the reply. I am starting this project. So, I can opt any method. I have experience with Next Gen data and also have molecular biology skills. I just want to enlist all the options which can lead to success of this project.

Answer 1

[Matteo Schiavinato]

Since this is exactly my project as well (lol) I would suggest you to first have a look to:

• differential expression if you have RNASeq data
• variants if you have DNA Seq data
• chromosomal rearrangements if you have assemblies available
• GC content and contamination content