Reference "Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential"

Reference ID

7962

Title

Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential

Source

Genome research, 2001, vol. 11, pp. 1441-1452

Authors (6)

Temnykh-S	DeClerck-G
Lukashova-A	Lipovich-L
Cartinhour-S	McCouch-S

Abstract

A total of 57.8 Mb of publicly available rice (Oryza sativa L.) DNA sequence
was searched to determine the frequency and distribution of different simple
sequence repeats (SSRs) in the genome. SSR loci were categorized into two
groups based on the length of the repeat motif. Class I, or hypervariable
markers, consisted of SSRs > or =20 bp, and Class II, or potentially variable
markers, consisted of SSRs > or =12 bp <20 bp. The occurrence of Class I SSRs
in end-sequences of EcoRI- and HindIII-digested BAC clones was one SSR per 40
Kb, whereas in continuous genomic sequence (represented by 27 fully sequenced
BAC and PAC clones), the frequency was one SSR every 16 kb. Class II SSRs were
estimated to occur every 3.7 kb in BAC ends and every 1.9 kb in fully
sequenced BAC and PAC clones. GC-rich trinucleotide repeats (TNRs) were most
abundant in protein-coding portions of ESTs and in fully sequenced BACs and
PACs, whereas AT-rich TNRs showed no such preference, and di- and
tetranucleotide repeats were most frequently found in noncoding, intergenic
regions of the rice genome. Microsatellites with poly(AT)n repeats represented
the most abundant and polymorphic class of SSRs but were frequently associated
with the Micropon family of miniature inverted-repeat transposable elements
(MITEs) and were difficult to amplify. A set of 200 Class I SSR markers was
developed and integrated into the existing microsatellite map of rice,
providing immediate links between the genetic, physical, and sequence-based
maps. This contribution brings the number of microsatellite markers that have
been rigorously evaluated for amplification, map position, and allelic
diversity in Oryza spp. to a total of 500.