HUSCAP logo Hokkaido Univ. logo

Hokkaido University Collection of Scholarly and Academic Papers >
Graduate School of Agriculture / Faculty of Agriculture >
Peer-reviewed Journal Articles, etc >

Profiling SNP and Nucleotide Diversity to Characterize Mekong Delta Rice Landraces in Southeast Asian Populations

This item is licensed under:Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International

Files in This Item:

The file(s) associated with this item can be obtained from the following URL:

Title: Profiling SNP and Nucleotide Diversity to Characterize Mekong Delta Rice Landraces in Southeast Asian Populations
Authors: Nguyen Thanh Tam Browse this author
Dwiyanti, Maria Stefanie Browse this author
Koide, Yohei Browse this author →KAKEN DB
Nagano, Atsushi J. Browse this author →KAKEN DB
Ky, Huynh Browse this author
Huynh Quang Tin Browse this author
Nguyen Loc Hien Browse this author
Le Viet Dung Browse this author
Kishima, Yuji Browse this author →KAKEN DB
Issue Date: 1-Nov-2019
Publisher: Crop Science Society of America
Journal Title: Plant genome
Volume: 12
Issue: 3
Start Page: 1
End Page: 11
Publisher DOI: 10.3835/plantgenome2019.06.0042
Abstract: Recent analyses using single nucleotide polymorphism (SNP) are a feasible mean for local collections which potentially possess useful, but not large, genetic variations. Genomic sequences of more than 3000 accessions released by the International Rice Research Institute (IRRI) can be used to characterize various local rice (Oryza sativa) populations. The aim of this study was to develop a method to facilitate genomic characterization of local rice populations. We mainly used 99 indica rice accessions (81 landraces and 18 improved varieties) from the Mekong Delta Development Research Institute (MDI). We obtained 2301 SNPs after a genomic sequencing analysis of the 99 rice accessions and subsequent filtering. Within the IRRI's dataset, the landraces fell into a cluster consisting of accessions from Southeast Asian countries (Ind3 cluster), and the MDI improved varieties were grouped in a cluster containing IRRI improved varieties (Ind1B cluster). A principal component analysis suggested that geographical location strongly affects phylogenetic relationships, and the MDI landraces were placed into a Vietnam+Cambodia group. To detect the nucleotide diversity within a population, pi-value is commonly used. We think that whole genome distribution of pi-values representing the nucleotide diversity of each population can be used to characterize local populations. Our simple profiling using low pi-value genomic regions was able to reveal regional characteristics of rice genomes and should be useful for identifying local rice populations.
Type: article
Appears in Collections:農学院・農学研究院 (Graduate School of Agriculture / Faculty of Agriculture) > 雑誌発表論文等 (Peer-reviewed Journal Articles, etc)

Export metadata:

OAI-PMH ( junii2 , jpcoar_1.0 )

MathJax is now OFF:


 - Hokkaido University