Comparative Analysis of Six Maize Plastid Genomes

We sequenced and annotated six maize plastid genomes.  The A188 and B73 maize genotypes are of interest to us because they are the progenitors of Hi-II germplasm, whose robust tissue culture performance and strong agronomic properties make it ideal for transformation.  Our analysis revealed 16 SNPs and 10 indels, a subset of which was used as markers to confirm maternal chloroplast inheritance in progeny of A188 and B73 reciprocal crosses.  The B73 and B37 plastid genomes are identical.  B73 and to a lesser degree B37, are progenitors of most inbred lines used today to produce commercial hybrid seed.  Both of these lines have the NB mitochondrial cytotype. In contrast, A188 has the substantially different NA mitochondrial cytotype.  The plastid genomes of A188 and B73 are strikingly similar compared to the extensive rearrangments and 131kb size difference between their mitochondrial genomes.  We have sequenced and are currently analyzing the plastid genomes of CMS-T, CMS-S and CMS-C cytoplasmic male sterile cytotypes.