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Genome-wide SNPs detection by genomic comparison between Dongxiang wild rice (Oryza rufipogon) and cultivated rice Nipponbare (Oryza sativa ssp. japonica)

Published online by Cambridge University Press:  26 July 2017

Meng Zhang
Affiliation:
College of Life Sciences, Jiangxi Normal University, Nanchang 330022, People's Republic of China
Wenyang Huang
Affiliation:
College of Life Sciences, Jiangxi Normal University, Nanchang 330022, People's Republic of China
Zijun Xia
Affiliation:
College of Life Sciences, Jiangxi Normal University, Nanchang 330022, People's Republic of China
Jiahui Liu
Affiliation:
College of Life Sciences, Jiangxi Normal University, Nanchang 330022, People's Republic of China
Jiankun Xie*
Affiliation:
College of Life Sciences, Jiangxi Normal University, Nanchang 330022, People's Republic of China
Fantao Zhang*
Affiliation:
College of Life Sciences, Jiangxi Normal University, Nanchang 330022, People's Republic of China
*
*Corresponding author. E-mail: zhang84004@163.com; xiejiankun11@163.com
*Corresponding author. E-mail: zhang84004@163.com; xiejiankun11@163.com

Abstract

Dongxiang wild rice (Oryza rufipogon, DXWR) exhibits valuable agronomic traits and represents a precious germplasm resource for rice breeding. The use of genetic markers can greatly speed up the breeding process and facilitate research on genetics and genomics. In our previous study, we identified insertion–deletion polymorphisms between DXWR and cultivated rice Nipponbare (Oryza sativa ssp. japonica), using whole-genome sequencing in DXWR. In this study, to further explore the genetic variations and enrich the available genetic markers of DXWR, we identified 1,089,478 single-nucleotide polymorphisms (SNPs) (corresponding to one SNP per 0.33 kb of the genome) by genomic comparison between DXWR and Nipponbare, using the genome sequencing data and bioinformatics approaches. Furthermore, the accuracy of the identified SNPs was also validated by polymerase chain reaction amplification and Sanger sequencing. This genome-wide SNPs identification greatly increases the number of genetic markers available for DXWR and provides new opportunities to exploit this valuable and endangered germplasm resource.

Type
Short Communication
Copyright
Copyright © NIAB 2017 

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