The impact and origin of copy number variations in the Oryza species.

ABSTRACT:

Background

Copy number variation (CNV), a complex genomic rearrangement, has been extensively studied in humans and other organisms. In plants, CNVs of several genes were found to be responsible for various important traits; however, the cause and consequence of CNVs remains largely unknown. Recently released next-generation sequencing (NGS) data provide an opportunity for a genome-wide study of CNVs in rice.

Results

Here, by an NGS-based approach, we generated a CNV map comprising 9,196 deletions compared to the reference genome 'Nipponbare'. Using Oryza glaberrima as the outgroup, 80% of the CNV events turned out to be insertions in Nipponbare. There were 2,806 annotated genes affected by these CNV events. We experimentally validated 28 functional CNV genes including OsMAD

SUBMITTER: Bai Z 

PROVIDER: S-EPMC4812662 | biostudies-literature | 2016 Mar

REPOSITORIES: biostudies-literature