Genome-wide analysis of transposon insertion polymorphisms reveals intraspecific variation in cultivated rice

Plant Physiol. 2008 Sep;148(1):25-40. doi: 10.1104/pp.108.121491. Epub 2008 Jul 23.

Abstract

Insertions and precise eliminations of transposable elements generated numerous transposon insertion polymorphisms (TIPs) in rice (Oryza sativa). We observed that TIPs represent more than 50% of large insertions and deletions (>100 bp) in the rice genome. Using a comparative genomic approach, we identified 2,041 TIPs between the genomes of two cultivars, japonica Nipponbare and indica 93-11. We also identified 691 TIPs between Nipponbare and indica Guangluai 4 in the 23-Mb collinear regions of chromosome 4. Among them, retrotransposon-based insertion polymorphisms were used to reveal the evolutionary relationships of these three cultivars. Our conservative estimates suggest that the TIPs generated approximately 14% of the genomic DNA sequence differences between subspecies indica and japonica. It was also 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, drastically changing intron length, and affecting expression levels of adjacent genes. These analyses provide genome-wide insights into evolutionary history and genetic variation of rice.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • DNA Transposable Elements*
  • DNA, Complementary
  • Evolution, Molecular*
  • Gene Expression
  • Genome, Plant
  • Introns
  • Oryza / genetics*
  • Polymorphism, Genetic*
  • Promoter Regions, Genetic
  • Retroelements*

Substances

  • DNA Transposable Elements
  • DNA, Complementary
  • Retroelements