Title: Methylation variations in Zea
Jinliang: I suggest we following this workflow for the project. Basically, you need to:
- Fork the repo
- Clone to your own server
- Do what ever you want in your forked repo, like add, commit, push without worry about the conflict issues
- Send pull request to the master repo RILAB/GBSMethylation when you want to share your progress
- If no conflict, we can just merge it. Otherwise, some body have to fix the conflicts
- Do not forget to merge from the updated RILAB master repo to your own fork
- Suggestion welcomed
The md files are located in the folder example_ideaKC/
- Bisulfite sequencing of 20 teosinte plants
- Whole genome sequencing (~20X) and WGBS (~10-15X) on each
- GBS on ~100 progenies from each plant, all 100 phenotyped for multiple traits
- should be able to impute whole genome for progeny
- plants are from Palmar Chico. For more info on this population, see e.g. our paper on fine-scale genetic stcuture
- Bisulfite sequecing of ~20 addditional maize/teosinte
- TIL1 and TIL11 (unsure about access permission)
- ~20 maize lines, including Oh43, Mo17, W22, and a diverse set of inbreds
- Bob Schmitz mentioned possibility (informally) to sequence more
- It would be interesting to see the m6A methylome in maize and teosinte.
- Identification of methylation variation in Zea
- Correlation with TE
- Is there a TE map? DB of TE annotation is here- MC Stitzer re-annotation of TEs in maize genome
- Whether selection sweeps associated with differential methylation patterns: see new Tajima's D-like statistic
- Methylation and fitness?
- Mapping the genetic control of methylation variation?
- needs methylation data in offspring, which we don't have
See also recent example of WGBS in natural pops here.