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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

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  • URLhttps://db.koreascholar.com/Article/Detail/302682
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한국육종학회 (The Korean Breeding Society)
초록

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.

저자
  • Wei Tong(Department of Plant Resources, College of Industrial Sciences, Kongju National University)
  • Qiang He(Department of Plant Resources, College of Industrial Sciences, Kongju National University)
  • Xiao-Qiang Wang(Department of Plant Resources, College of Industrial Sciences, Kongju National University)
  • Min-Young Yoon(Department of Plant Resources, College of Industrial Sciences, Kongju National University)
  • Won-Hee Ra(Department of Plant Resources, College of Industrial Sciences, Kongju National University)
  • Feng Peng Li(Department of Plant Resources, College of Industrial Sciences, Kongju National University)
  • Jie Yu(Department of Plant Resources, College of Industrial Sciences, Kongju National University)
  • Win Htet Oo(Department of Plant Resources, College of Industrial Sciences, Kongju National University)
  • Sun-Kyung Min(Department of Plant Resources, College of Industrial Sciences, Kongju National University)
  • Buung Choi(Department of Plant Resources, College of Industrial Sciences, Kongju National University)
  • Eun-Beom Heo(Department of Plant Resources, College of Industrial Sciences, Kongju National University)
  • Byoung-Kook Yun(Department of Industrial & Systems Engineering, Kongju National University)
  • Kyu-Won Kim(Department of Plant Resources, College of Industrial Sciences, Kongju National University)
  • Tae-Sung Kim(Department of Plant Resources, College of Industrial Sciences, Kongju National University)
  • Chang-Yong Lee(Department of Industrial & Systems Engineering, Kongju National University)
  • Yong-Jin Park(Department of Plant Resources, College of Industrial Sciences, Kongju National University, Legume Bio-Resource Center of Green Manure (LBRCGM), Kongju National University) Corresponding Author