Ancestral Rice Blocks Define Multiple Related Regions in the Maize Genome

Abstract

A simulated ancestral reference genome identifies the remnants of the complex evolution of the maize (Zea mays L.) genome. Syntenic regions were defined in Oxford grid comparisons by the analysis of diagonals from colinear arrangements of homologous sequences between chromosomes. A program called Crush and Compare was developed to manage the identification of syntenic regions, create ancestral gene arrangements, and create Oxford grids for graphical displays. Seventeen ancestral gene arrangements were created by computationally condensing the synteny within rice (Oryza sativa L.) into ancestral rice blocks (ARBs), simulating the nonduplicated state of all grass genomes. Permutation analyses found 14 of the rice syntenic regions to be significant with P < 0.05 and were used to identify the genomic duplications present in grass genomes. Synteny analysis of the ancestral gene arrangements within the ARBs revealed a new ancient duplication in the rice genome. An analysis with the maize genetic map identified 54% of its genome syntenic with the ARBs. Multiple evolutionarily related copies of the ARBs were identified in maize with an average of 3.0 related copies with a range of 1 to 6. Use of the ARBs as a reference for maize supports the theory of the maize genome once being an ancient tetraploid composed of genomes that also contained genomic duplications. Defining the genomic relationships within maize and between rice and maize can improve candidate gene discoveries.