Although the overall structure of the chloroplast genome is generally conserved, a number of sequence variations have been identified, which are valuable for plant population and evolutionary studies. Here, we constructed a chloroplast variation map of 30 landrace rice strains of Korean origin, using the Oryza rufipogon chloroplast genome (Genbank: NC_017835) as a reference. Differential distribution of single nucleotide polymorphisms (SNPs) and indels across the rice chloroplast genome is suggestive of a region-specific variation. Population structure clustering revealed the existence of two clear subgroups (indica and japonica) and an admixture group (aus). Phylogenetic analysis of the 30 landrace rice strains and six rice chloroplast references suggested and supported independent evolution of O. sativa indica and japonica. Interestingly, two “aus” type accessions, which were thought to be indica type, shared a closer relationship with the japonica type. One hypothesis is that “Korean aus” was intentionally introduced and may have obtained japonica chloroplasts during cultivation. We also calculated the nucleotide diversity of 30 accessions and compared to six rice chloroplast references, which shown a higher diversity in the indica and aus groups than in the japonica group in lower level substitution diversity.

Genetic diversity of Korean landrace rice accessions was assessed with microsatellite markers. The 214 alleles weregedfrom 3 for SSS locus to 37 for RM206 locus with an average number of 12.6 alleles per locus. Gene diversity values according tothe 17 mic

The mode of inheritance and allelic relationship of resistance genes in a Korean landrace, Guju and a Korean weedy rice, Geumleungaengmi 33 were studied using Korean isolate (HB9101, race K1) of Xanthomonas oryzae pv. oryzae. The analysis of F₁