NDLI: Diversity and differentiation of Oryza sativa and O. rufipogon in Indonesia

Content Provider	Springer Nature Link
Author	Muhamad, Kadapi Ebana, Kaworu Fukuoka, Shuichi Oku, Kazutoshi
Copyright Year	2015
Abstract	Analysis of the genetic structure of Indonesian Oryza sativa and O. rufipogon using neighbour-joining trees based on single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers revealed that O. sativa in Indonesia is separated from O. rufipogon. Accessions of O. sativa in this study were differentiated into two major groups, indica and tropical japonica, excluding some varieties. SSR and SNP markers revealed the high value of differentiation (F ST) and genetic distance (D) between indica and tropical japonica and we discovered four loci by SNP markers and one locus by SSR markers that play a role in differentiation between indica and tropical japonica. Interestingly, genetic diversity (H) in O. rufipogon was lower than that in O. sativa, however H in O. rufipogon was the highest and H in tropical japonica was the lowest when O. sativa was divided into two groups. Inbreeding coefficient (Fst) showed evidences that gene flow (Nm) between species and within species might be one of the mechanisms related to the diversification and differentiation of Indonesian rice germplasm by asymmetric pattern between species and within O. sativa as revealed by SSR and SNP markers. In addition, we found evidences on stabilizing selection in Indonesian rice germplasm and they might be the reasons why Indonesian rice germplasm did not differentiate due to source location of landrace. However, we found a weak relation between SSR and SNP markers probably due to highly polymorphic in SSR and the different properties of both markers.
Starting Page	41
Ending Page	54
Page Count	14
File Format	PDF
ISSN	09259864
Journal	Genetic Resources and Crop Evolution
Volume Number	64
Issue Number	1
e-ISSN	15735109
Language	English
Publisher	Springer Netherlands
Publisher Date	2015-11-24
Publisher Place	Dordrecht
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Domestication Gene flow Natural selection Oryza rufipogon Oryza sativa Tropical japonica Plant Sciences Plant Systematics/Taxonomy/Biogeography Plant Genetics & Genomics Plant Physiology Agriculture
Content Type	Text
Resource Type	Article
Subject	Genetics Plant Science Ecology, Evolution, Behavior and Systematics Agronomy and Crop Science

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