Genome Structure of Tongil: Korean Green Revolution Variety Derived from Japonica x Indica Hybrids

Tongil (IR667-98-1-2) developed in 1972 was a high yielding rice variety derived from a three-way cross between indica and japonica, and contributed to the Korean Green Revolution. In this study, we analyzed the genome structure of Tongil rice and parental varieties with reference Nipponbare using Illumina Genome Analyzer. A total of 17,339 X 10⁶ raw reads of Tongil were generated with 47X coverage depth which covered 88.8% of the Nipponbare sequence and aligned onto the Nipponbare reference genome. A total of 2,149,991 SNPs were detected between Tongil and Nipponbare, and the average SNP frequency of Tongil was 5.77 per one Kb. In comparisons with the parental genomes, Tongil genome had 1,234,336 SNPs (91.2%) against indica parent (IR8 and/or TN1) and 119,822 SNPs (8.8%) with japonica parent (Yukara). Genome analysis, based on SNP data set and determination of window size for calling indica or japonica genome, revealed that 91.8% of Tongil genome was originated from indica parents and 7.9% was from japonica parents. High copy number of SSR motif, ORF gene distribution, Gene Ontology (GO) annotation, yield related QTLs or genes locations, and polymorphic transposon insertions were analyzed between Tongil and the parents using sequence-based tool. This result indicates that each genetic factor was transferred from the parents into Tongil in proportion to whole genome composition. Collectively, analysis results on genome composition and genetic factors of Tongil rice demonstrate that Tongil genome was composed mostly of indica genome with small portion of japonica genome introgression.

Keywords: Tongil rice, Three-way cross, Next Generation Sequencing, SEG map, Indica/Japonica hybrid rice

*Corresponding author : (Tel.: +82-02-880-4541, E-mail  heejkoh@snu.ac.kr)