population genomics of maize

1. Comparative population genomics of maize domestication and improvement

2. Genome-wide genetic changes during modern breeding of maize

3. Dynamic evolution of bz orthologous regions in the Andropogoneae and other grasses
We estimate that the  average divergence times between maize and Tripsacum, Coix and Sorghum are 8.5,  12.1, and 12.4 million years ago (MYA), respectively, and that between Coix and Sorghum is 9.3 MYA.

4. data set
http://www.panzea.org/lit/data_sets.html#HapMapV2

5. annotation
ftp://ftp.jgi-psf.org/pub/JGI_data/phytozome/v8.0/Zmays/annotation/

6.  Sireviruses represent theonly TE genus whose members contain a variety of highly conserved short (20-40bp) sequencemotifs, regardless of the evolutionary distance of their hosts. 
http://bat.ina.certh.gr/research/TEs/index.html


7. repeat annotation for maize genome
http://ftp.maizesequence.org/current/repeats/
readme for all maize genomic data
http://ftp.maizesequence.org/current/README.txt

http://archive.maizesequence.org/index.html

mips Repeat Element database (mips-REdat)
http://mips.helmholtz-muenchen.de/plant/cgenomics.jsp


8. domestication of maize
http://teosinte.wisc.edu/questions.html

Earliest Evidence Of Domesticated Maize Discovered: Dates Back8,700 Years