Reference "Frequency of microsatellite sequences in rice (Oryza sativa L.)"

Reference ID

3385

Title

Frequency of microsatellite sequences in rice (Oryza sativa L.)

Source

Genome ( National Research Council Canada ), 1995, vol. 38, pp. 1170-1176

Authors (3)

Panaud-O	Chen-X
McCouch-S-R

Abstract

This study was undertaken to estimate the relative frequencies of 13
microsatellite motifs in the rice genome as a basis for efficient development of
a microsatellite map. Two dinucleotide, seven trinucleotide, and four
tetranucleotide repeat motifs were end labelled and used as hybridization probes
to screen genomic and cDNA libraries of rice, cv. IR36. Optimal washing
temperatures for identification of clones containing specific microsatellite
motifs were estimated based on washing temperatures near Td (dissociation
temperature; Td = Tm - 7.6 degrees C). Sequencing of 20 putatively positive
clones corresponding to each of 4 microsatellite motifs suggested that while Td
provides a useful predictor of washing stringency for most of the repeats
studied, those with a very high GC or AT content were most prone to error. The
results from screening the rice genomic library suggest that there are an
estimated 1360 poly(GA)n and 1230 poly(GT)n microsatellites in the rice genome,
and that the relative frequency of different repeats decreased with increasing
size of the motif. The most frequently observed microsatellites in the cDNA
library were the same as for genomic library, but no poly(CGG)n, poly(ATC)n, or
tetranucleotide motifs were observed among cDNA in this study.