Professor Konkuk University seoul, Seoul-t'ukpyolsi, Republic of Korea
For most crops, Yield is the upmost valuable factor in crop industry. Geumgang1(Milyang307) rice is super-high yield rice developed by Rural Development Administration, National Institute of Crop Science, Republic of Korea. Geumgang1 is sorted by Tongil Variety known as high yield rice variety crossing of Oryza Sativa Japonica and Indica variety. To make a good use of molecular breeding to finding secrets of super-high yield of Geumgang1, WGS(Whole Genome Sequencing) of Geumgang1 is needed to be done precisely. So, We generated sequence read data of Geumgang1 by PacBioⓇHiFi sequencing and performed assembly. Genome assembly is performed two ways, one is reference-based assembly and the other one is de novo assembly. In Reference-based assembly, Due to Tongil variety’s crossing, 3 different varieties of Oryza Sativa L. (Japonica cv. Nipponbare, Indica cv. IR64, Indica cv. R498) are used. To assess assembly quality, Benchmarking Universal Single-Copy Orthologs (BUSCO) has been used, no differences between reference-based and de novo assembly. Moreover, N50 of all reference-based assembly shows approximately 30 - 32Mbp using QUAST. However, N50 of de novo assembly shows very short length. Gap filling steps are carried out by filling gaps with query sequence which is reference genome or aligned De novo assembly that has no gaps within. Genome synteny analysis was performed through Geumgang1 and three reference genomes to find large structural variants. Further, Gene annotation analysis, including synteny analysis, is performed for structural and functional annotation of Geumgang1 genome.