Molecular Genetics and Genomics

, Volume 271, Issue 3, pp 298–307 | Cite as

Sources and predictors of resolvable indel polymorphism assessed using rice as a model

Original Paper


The principal sources of genetic variation that can be assayed with restriction enzymes are base substitutions and insertions/deletions (indels). The likelihood of detecting indels as restriction fragment length polymorphisms (RFLPs) is determined by the size and frequency of the indels, and the ability to resolve small indels as RFLPs is limited by the distribution of restriction fragment sizes. In this study, we use aligned sequences from the indica and japonica subspecies of rice ( Oryza sativa L.) to quantify and compare the ability of restriction enzymes to detect indels. We look specifically at two abundant transposable element-derived indel sources: miniature inverted repeat transposable elements (MITEs) and long terminal repeat (LTR) retroelements. From this analysis we conclude that indels rather than base substitutions are the prevailing source of the polymorphism detected in rice. We show that, although MITE derived indels are more abundant than LTR-retroelement derived indels, LTR-retroelements have a greater capacity to generate visible restriction fragment length polymorphism because of their larger size. We find that the variation in the detectability of indels among restriction enzymes can be explained by differences in the frequency and dispersion of their restriction sites in the genome. The parameters that describe the fragment size distributions obtained with the restriction enzymes are highly correlated across the sequenced genomes of rice, Arabidopsis and human, with the exception of some extreme deviations in frequency for particular recognition sequences corresponding to variations in the levels and modes of DNA methylation in the three disparate organisms. Thus, we can predict the relative ability of a restriction enzyme to detect indels derived from a specific source based on the distribution of restriction fragment sizes, even when this is estimated for a distantly related genome.


Transposable elements  Oryza sativa L. Rice Insertions/Deletions (Indels) Restriction Fragment Length Polymorphisms (RFLPs) 



We thank Drs. T. Brutnell, N. Jiang, and S. R. Wessler for critical reading of the manuscript. We also thank K.Y. Chang for programming assistance, and L. Swales for manuscript formatting. This material is based upon work supported by the National Science Foundation under Grant No. 0077709, and by a graduate assistantship to JD Edwards provided by the Cornell Plant Cell and Molecular Biology Program (DOE/NSF/USDA Interagency Training Grant)

Supplementary material

Supplementary Table 1 For each commercially available enzyme, the percent of the total aligned sequence in restriction fragments detecting polymorphism due to: all indels, LTR-retroelement derived indels, and MITE derived indels

supp1.pdf (22 kb)
(PDF 23 KB)

Supplementary Table 2 Parameters describing the distributions of restriction fragments

supp2.pdf (17 kb)
(PDF 18 KB)


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Copyright information

© Springer-Verlag 2004

Authors and Affiliations

  1. 1.Department of Plant BreedingCornell UniversityIthacaUSA

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