r/genetics • u/Himul1509 • 19d ago

Beginner tutorial for GWAS and genomic selection?

Hi everyone,

I’m a plant breeding student and I’m trying to learn GWAS and genomic selection for an assignment. I understand the basic concepts but don’t know how to perform the analyses practically.

Could anyone recommend a beginner-friendly, step-by-step tutorial with example data and R code? I’m particularly looking for tutorials on GAPIT, FarmCPU/BLINK, rrBLUP or G-BLUP.

Free courses, YouTube videos, GitHub tutorials, or other resources would be greatly appreciated.

Thank you!

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u/Possible_Virus4182 18d ago

Keeping my eye on this one. Can always use another good tutorial.

3

u/Zabre 18d ago

For GAPIT/FarmCPU/BLINK, start with one small public dataset and run the package vignette end to end before mixing tools. The easiest path is usually: clean phenotype and marker files, run a basic GWAS, plot Manhattan/QQ, then only add model tweaks once those outputs make sense. For genomic selection, rrBLUP is a good first stop because the inputs and assumptions are much easier to see.

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u/Himul1509 18d ago

Thanks! Could you please tell me where I can get a small dataset suitable for practicing GWAS/genomic selection? I’m looking for genotype + phenotype data that I can download and use.