AGRO-932 Spring 2022 HW3 (100 points): Due Date: May. 3rd, 2022 at 9 PM
- Create a version-controlled directory system to host the homework3.
- Using the rice data (Zhao et al., 2011) as shown in class, choose a phenotype other than the plant height and then conduct GWAS using the QK model.
- Visualize the GWAS results and briefly report your discovery.
I chose to look at leaf length to see if there were any variants that were proven to be significant in GWAS. There was no indication of major QTLs that showed up in the analysis. I used the rrBLUP method and the profiling folder contains the code. The graph folder contains the output of the manhattan plot.Since there no major QTLs noted, this trait may need to contain more SNPs (maybe millions?) to identify. The marker panel was only 34k which isn't very many to begin with when conducting a GWAS.