Physical and Genetic structure of Maize

PLOS Genetics - 2007

Summary

1. Maize undergone 2 rounds of duplication
   1. Ancient one before maize-rice divergence
   2. Recent - after tetraploidization
2. Reconstructed the progenitors of Maize

Facts

1. 2300MB of genome
2. Clone by clone sequencing
3. Allotetraploidy
4. 2/3 of genome is with transposable element of which 95% is retro-transposons
5. Retro-transposons emerged after the speciation of maize (<1 Mil.Year old)
6. Physical Map
   1. HICF
   2. FPC
   3. genetic markers
   4. sequence based marker data (overgos, BES)

Integrated Physical and Genetic Map

1. Digest - HICF (350,253 fingerprints -> 1500 FPC contigs)
2. 25908 markers (~1900 genetic + ~24000 BES/overgos )
3. 24000 additional markers based on EST (STS/genebased markers in BES)
4. Final FPC contigs 721 covering 2100MB of the genome
   1. 421 is anchored by 1901 genetic markers
   2. Looking at the Map, it is show that EST derived markers are directly correlated with the genetic markers, suggesting that tight association of gene distribution and genetic recombination

Maize Rice synteny

synteny was computed using SyMap

1. Uneven expansion of synteny blocks were found
   1. due to loss of genetic segments
   2. due to insertion of transposable elements

Genome duplication and rearrangements in Maize

1. detection of ~3 copies of each overgo supports the idea that
   1. Present emerged from tetraploidization of several ancient duplicated genes
   2. Multiple duplication
   3. several genome rearrangements

Why Maize has more transposable elements/multiple re-arrangements

1. Ph1 gene prevents homeologous paring (otherwise called as gene diploidization) there by it
   1. maintains the integrity of the genome
   2. strictly allows homologous paring
2. Maize lacks the Ph1 gene, which results in
   1. paring of non homologous chromosomes
   2. results in ectopic paring
   3. ultimately results in huge rearrangements of chrl. segments

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