Accelerated Gene Discovery from Setaria to Maize: SvAUX1 and ZmAUX1 are Required for Inflorescence Branch Development and Root Agravitropism

Setaria viridis is an emerging model system for panicoid grasses due to its small size, short life cycle, good seed production, ease of crossing and transformation. To identify genes that are associated with agronomically important traits in the grasses such as panicle structure, we have developed an NMU mutagenized population consisting of ~ 20,000 M2 families. Screens of approximately 2700 families identified four mutants with sparse panicle phenotype. To fine map the gene that underlies the sparse panicle 1 (spp1) phenotype, we used bulked segregant analysis (BSA) by sequencing and mapped the gene into an interval of approximately 1Mb. Within this interval two disruptive mutations were identified in two genes. Deep resequencing of spp3 identified an independent disruptive mutation in SvAUX1, one of the two candidate genes in the ~1Mb interval, which is the only disrupted gene shared by spp1 and spp3. Complementation tests between spp1 and spp3 indicate that the mutations are allelic, thus confirming that SvAUX1 is the gene responsible for sparse panicle phenotype. Observation of early panicle development with scanning electron microscopy shows that size, shape, and position of primary branches is altered in the mutants. Synteny comparisons identified a maize ortholog of SvAUX1 and mutant characterizations confirmed a role of ZmAUX1 in inflorescence and root development. In conclusion, Setaria viridis is a tractable genetic model for rapid gene candidate identification and functional characterizations, which will accelerate functional genomics studies in maize.