Closely-related cultivars generally used for crossing in breeding lack sufficient known DNA polymorphisms with already developed DNA markers even though they exhibit remarkable phenotype difference. However, next-generation sequencing (NGS) enables the identification of massive DNA polymorphisms such as single nucleotide polymorphisms (SNPs) and insertions-deletions (InDels) between highly homologous genomes. This study conducted a whole-genome re-sequencing of two Korean japonica rice varieties, Junam and Nampyeong. The sequencing yielded 16.6 × 10⁹ bps for Junam, and 15.1 × 10⁹ bps for Nampyeong. After quality trimming and read mapping onto the reference genome sequence of Nipponbare, 11.9 × 10⁹ bps from Junam and 10.6 × 10⁹ bps from Nampyeong were mapped onto the reference sequence. The final effective mapping depth was 31.98x for Junam and 28.41x for Nampyeong. This study found 398,123 DNA polymophisms between Junam and Nampyeong. These were classified into 352,478 SNPs (88.5%) and 45,645 InDels (11.5%) by polymorphism types, 338,485 homozygous (85%) and 59,638 (15%) heterozygous by zygosity, and 331,855 intergenic (83.4%) and 66,268 genic (16.6%) by genomic location. To see the availability of these results in DNA marker development, Cleaved Amplified Polymorphic Sequences (CAPS) markers were developed based on 22 SNPs lying in restriction enzyme sites. Among them, 17 CAPS markers showed polymorphisms between Junam and Nampyeong. It is expected that sufficient DNA markers for mapping genes/QTLs with progeny population from a cross between Junam and Nampyeong can be developed based on the results of the study.

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