Development of Genomic Tools for Germplasm Characterization and Breeding of Brachiaria ruziziensis, an Important Forage Species in the Tropics

Brachiaria ruziziensis (ruzigrass) is one of the most important forage species planted in the tropics. Genomic tools can aid in selection and support ruzigrass breeding programs. However, very little is known about the B. ruziziensis genome. The availability of genomic tools, such as molecular markers, is rather limited. We applied next-generation sequencing to develop tools for ruzigrass germplasm characterization and breeding, gaining basic knowledge about the genome of this species. A partial assembly of the B. ruziziensis genome from paired-end Illumina reads was performed. We estimate we were able to assemble approximately 33% of the ruzigrass genome, which allowed a preliminary investigation of genomic features such as retroelements, transposons, and microsatellites. We present a first validated set of SSR markers for ruzigrass, selected from de novo partial genome assembly. A total of 85,567 perfect microsatellite loci were detected in contigs with a minimum 10X coverage. We tested 269 primer pairs, 198 of which were polymorphic on 11 representative ruzigrass accessions. Descriptive statistics for these primer pairs are presented, as well as estimates of marker transferability to other relevant brachiaria species. A set of 11 multiplex panels containing the 30 most informative markers was proposed and validated for genetic analyses of ruzigrass germplasm. To our knowledge, this is the first set of microsatellite markers developed for this important species. Finally, we were able to assemble the nearly complete chloroplast genome sequence for ruzigrass, and are currently trying to develop PCR-based markers to identify different brachiaria species.