Defining the genome structure of `Tongil' rice, an important cultivar in the Korean 'Green Revolution'

다국어 초록 (Multilingual Abstract)

<P><B>Background</B></P><P>Tongil (IR667-98-1-2) rice, developed in 1972, is a high-yield rice variety derived from a three-way cross between <I>indica</I> and <I>japonica</I> varieties. Tongil contributed to the self-sufficiency of staple food production in Korea during a period known as the `Korean Green Revolution'. We analyzed the nucleotide-level genome structure of Tongil rice and compared it to those of the parental varieties.</P><P><B>Results</B></P><P>A total of 17.3 billion Illumina Hiseq reads, 47× genome coverage, were generated for Tongil rice. Three parental accessions of Tongil rice, two <I>indica</I> types and one <I>japonica</I> type, were also sequenced at approximately 30x genome coverage. A total of 2,149,991 SNPs were detected between Tongil and Nipponbare varieties. The average SNP frequency of Tongil was 5.77 per kb. Genome composition was determined based on SNP data by comparing Tongil with three parental genome sequences using the sliding window approach. Analyses revealed that 91.8% of the Tongil genome originated from the <I>indica</I> parents and 7.9% from the <I>japonica</I> parent. Copy numbers of SSR motifs, ORF gene distribution throughout the whole genome, gene ontology (GO) annotation, and some yield-related QTLs or gene locations were also comparatively analyzed between Tongil and parental varieties using sequence-based tools. Each genetic factor was transferred from the parents into Tongil rice in amounts that were in proportion to the whole genome composition.</P><P><B>Conclusions</B></P><P>Tongil was derived from a three-way cross among two <I>indica</I> and one <I>japonica</I> varieties. Defining the genome structure of Tongil rice demonstrates that the Tongil genome is derived primarily from the <I>indica</I> genome with a small proportion of <I>japonica</I> genome introgression. Comparative gene distribution, SSR, GO, and yield-related gene analysis support the finding that the Tongil genome is primarily made up of the <I>indica</I> genome.</P><P><B>Electronic supplementary material</B></P><P>The online version of this article (doi:10.1186/s12284-014-0022-5) contains supplementary material, which is available to authorized users.</P>