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A chloroplast variation map generated using whole genome re‐sequencing of Korean landrace rice reveals phylogenetic relationships among Oryza sativa subspecies

Tong, Wei, He, Qiang, Wang, Xiao‐Qiang, Yoon, Min‐Young, Ra, Won‐Hee, Li, Fengpeng, Yu, Jie, Oo, Win Htet, Min, Sun‐Kyung, Choi, Bu‐Woong, Heo, Eun‐Beom, Yun, Byoung‐Kook, Kim, Kyu‐Won, Kim, Tae‐Sung, Lee, Chang‐Yong, Park, Yong‐Jin
Biological journal of the Linnean Society 2015 v.115 no.4 pp. 940-952
Oryza rufipogon, Oryza sativa, chloroplast genome, chloroplasts, landraces, phylogeny, population structure, rice, single nucleotide polymorphism, strains
Although the overall structure of the chloroplast genome is generally conserved, several sequence variations have been identified that 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 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 the results to six rice chloroplast references. These data demonstrated that although nucleotide diversity is low in all strains tested, aus and indica have a higher nucleotide diversity than japonica.