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Published on July 23, 2008; 10.1104/pp.108.121491

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Received April 21, 2008
Accepted July 17, 2008

Genome-wide analysis of transposon insertion polymorphisms reveals intra-specific variation in cultivated rice (Oryza sativa L.)

Xuehui Huang , Guojun Lu , Qiang Zhao , Xiaohui Liu , and Bin Han *

National Center for Gene Research & Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, China

* Corresponding author; email: bhan{at}ncgr.ac.cn.

Insertions and precise eliminations of transposable elements generated numerous transposon insertion polymorphisms (TIPs) in rice. We observed that TIPs represent >50% of large insertions and deletions (indels) (>100bp) in the rice genome. Using a comparative genomic approach, we identified 2,041 TIPs between the genomes of two cultivars, Oryza sativa japonica cv. Nipponbare and indica cv. 93-11. We also identified 691 TIPs between japonica cv. Nipponbare and indica cv. Guangluai 4 in the 23-Mb collinear regions of chromosome 4. Among them, retrotransposon-based insertion polymorphisms (RBIPs) were used to reveal the evolutionary relationship of these three cultivars. Our conservative estimates suggest that the TIPs generated ~14% of the genomic DNA sequence differences between subspecies indica and japonica. It has also been found that more than 10% of TIPs were located in expressed gene regions, representing an important source of genetic variation. Transcript evidence implies that these TIPs induced a series of genetic differences between two subspecies, including interrupting host genes, creating different expression forms, changing drastically intron length, and affecting expression levels of adjacent genes. These analyses provided genome-wide insights into evolutionary history and genetic variation of rice.




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