The polyploid origin of maize

Maize has exhibited a remarkable level of genetic variation leading to the assumption that continuous breeding of a rich repertoire of haplotypes facilitated its success as a major crop worldwide. Now, with genomic sequences of two close relatives, rice and sorghum, and a gene-dense physical map of maize chromosomes at hand, we can use DNA sequence alignments to further our understanding of the molecular basis of its genetic variability and the origin of its chromosomes. There are two striking features emerging from such studies, one is polyploidy, the other is recent chromosome expansion and contraction. Based on synteny, collinear arrangement of chromosomal segments, rice and sorghum match maize at a ratio of 1:2, which is typical for a whole-genome duplication event. Because meiosis offers a strong selection against polyploidy, different pathways have evolved to stabilize chromosome structure. It appears that, in case of maize, polyploidy has triggered chromosome breakage and fusion events reshaping today's maize chromosomes relative to its predecessors. Diploidization, a process to transition a genome from polyploid to diploid status, seems to have benefited from the uneven expansion of maize chromosomes by retrotransposition, thereby preventing pairing of homoeologous chromosomal segments during meiosis. In addition, loss of orthologous gene copies was followed by copy and paste of paralogous gene copies enhancing non-collinearity in syntenic regions.