Title: Methylation variations in Zea

The md files are located in the folder ideas/:

• Kate's
• Jinliang's
• Simon's

3. 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

4. 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

5. Bob Schmitz mentioned possibility (informally) to sequence more

   • It would be interesting to see the m6A methylome in maize and teosinte.

1. Identification of methylation variation in Zea
2. Correlation with TE
   - Is there a TE map? DB of TE annotation is here
   • MC Stitzer re-annotation of TEs in maize genome
3. Whether selection sweeps associated with differential methylation patterns: see new Tajima's D-like statistic
4. Methylation and fitness?
5. 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.