I study mechanisms of shoot meristem function and plant reproduction, using developmental, molecular and evolutionary genetic approaches. My lab uses genomics technologies and classical genetics in maize qto isolate genes acting in the developing inflorescence or female gametophyte of maize. By elucidating the underlying molecular genetic mechanisms and examining those pathways and developmental processes in a comparative framework, I seek to identify similarities and differences between various grasses.
The ramosa1 and ramosa2 genes in maize regulate meristem activity and therefore branch length in the inflorescence. In a genetic pathway that acts after the transition to the reproductive phase, ra1 expression controls inflorescence architecture by imposing short branch identity as branch meristems are initiated. ra1 encodes a small protein with a single C2H2-type zinc finger. ra2 acts on branch length through ra1 by regulating ra1 gene expression levels. We hypothesize that the evolution of different long-branch architectures in the grasses is related to molecular evolution of genes in the ramosa pathway. In support of this hypothesis, patterns of nucleotide diversity indicate that ra1 was a domestication gene, recently targeted by positive selection during the evolution of maize.
We have analyzed developmental morphology and RNA expression dynamics associated with natural variants of ra1 including an allele that shows tight genetic linkage to a branch-number QTL in maize and the ra1 orthologs in Miscanthus sinensis and Sorghum bicolor. In each of these examples we see a correlation between timing and/or levels of ra1 expression and lateral branch meristem determinacy in the inflorescence. Recent work in my lab extends this analysis by comparative genomics and functional analysis in rice and broader sampling of the grass phylogeny. Our findings suggest a general role for the ramosa genes in regulating long-branch architecture in cereals, and implicate the ramosa pathway in the evolutionary diversification of grass inflorescence development.