Progress Towards an Engineering Quality Sorghum Reference Genome Sequence

Sorghum bicolor is a genetic model system for the design of C4 grass crops. Sorghum hybrids are drought resilient annual crops used for production of grain, forage, sugar and biomass. A high quality genome reference sequence is required for gene and regulatory element annotation, accurate sequence variant profiling, ENCODE analysis, and genome engineering.  In this project, the quality of the sorghum reference sequence was upgraded using advanced sequencing technology, genome sequence order and completeness was increased using a high resolution genetic map, and genome annotation improved using information from deeply sequenced RNAseq libraries. The improved sorghum V3 reference genome sequence release includes 351Mb of high quality finished sorghum gene space sequence that was generated using manual review, directed primer walk sequencing for gap closure, transposon annotation for tandem repeat resolution, and targeted whole BAC/fosmid based sequencing. Sequence order in the final assembly was improved using a high-resolution genetic map constructed from 10,789 Digital Genotyping GBS-markers ordered using breakpoints present in 400 RILs derived from a cross of BTx623 (reference) and IS3620C. Previously unassembled super contigs were integrated into the reference genome sequence guided by genetic analysis. Overall reference sequence quality was further improved by whole genome sequencing on Illumina platforms.  The genome was annotated using deep RNAseq data derived from roots, leaves, stems, and panicles collected at different stages of development. The resulting sorghum RNA Atlas is being used to identify genes expressed in stems that are involved in growth, cell wall biology, and the accumulation of non-structural carbohydrates such as sucrose.