The Role of Differential Fractionation in Maize Genome Content Variation

Maize is an ancient allotetraploid produced through a hybridization event between two progenitor species. Fractionation through extensive gene loss following whole-genome duplication has led to many of the maize-sorghum syntenic orthologs being present in only one of the two underlying maize subgenomes. The differential fractionation of homeologous genes among maize inbreds is one mechanism through which the considerable genome content variation observed in maize may have arisen. In this study, we show that two elite inbred lines, B73 and PH207, share extensive similarities in syntenic block composition compared to sorghum. A detailed analysis of synteny with sorghum revealed 1,489 genes are differentially fractionated between these two genomes. Many of the genes involved in differential fractionation exhibit expression consistent with other syntenic genes not involved in differential fractionation. We also found evidence for extensive genome content variation between these inbred lines for non-syntenic genes. Expression analysis of non-syntenic genes confirmed previous observations that non-syntenic genes are on average expressed lower, more variable, and expressed in fewer tissues than syntenic genes. Thus, differential fractionation is only one of the mechanisms underlying the high levels of genome content variation observed in maize. However, given evidence that supports that variation in syntenic genes contributes to phenotypic variation, these genes likely represent an important class of genome content variants for future functional studies.