Analysis of Dongxiang Wild Rice to Investigate Lost or Acquired Genes during Rice Domestication
April 27, 2016| |
It is widely accepted that cultivated rice (Oryza sativa L.) was domesticated from common wild rice (Oryza rufipogon Griff.). A research team led by Fantao Zhang and Tao Xu now aim to genetically explain the phenotypic and physiological changes from wild rice to cultivated rice at the whole genome level.
Instead of comparing two assembled genomes, the team directly compared the Dongxiang wild rice (DXWR) Illumina sequencing reads with the Nipponbare (O. sativa) complete genome. Structural variations between DXWR and Nipponbare were determined to locate deleted genes which could have been acquired by Nipponbare during rice domestication. The DXWR transcriptome was also sequenced and compared with the Nipponbare transcriptome to discover the genes which could have been lost in DXWR during domestication.
A total of 1,591 Nipponbare-acquired genes and 206 DXWR-lost transcripts were further analyzed using annotations from multiple sources. The NGS data are available in the NCBI SRA database. These results help better understand the domestication from wild rice to cultivated rice at the whole genome level and provide a genomic data resource for rice genetic research or breeding.
For more information, read the article on BMC Plant Biology.
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