Assembling Maize Inbred CML247: The Maize Pan-Genome Takes Off

Maize has a complex genome, exhibiting highest amounts of structural variations (SVs) among the major crop species. For example, only about half of the genome is shared between any two maize varieties. Recently studies indicated that SV plays an important role in phenotypic variation for maize. However, the single B73 reference genome is insufficient to represent all of the genomic content of maize. Hence, a pan-genome, including multiple reference genomes of representative maize varieties, is needed to capture those valuable and untapped genetic variations. Initializing the maize pan-genome construction, we recently started sequencing and assembling maize inbred line CML247 as a pilot project, to optimize maize de novo assembly approach by testing different sequencing platforms and assembly algorithms. This optimized approach can be replicated in diverse maize inbred lines to constitute the pan-genome. A set of ultrahigh density genetic markers (4.4M) is used to assess the quality of assemblies. Currently, the NRGENE approach, DISCOVAR de novo, Nanopore MinION device, and BioNano Irys System are being tested. The progress will be reported in the conference.