Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2000 Oct;156(2):847-54.
doi: 10.1093/genetics/156.2.847.

Computational and experimental characterization of physically clustered simple sequence repeats in plants

L Cardle  1 , L Ramsay, D Milbourne, M Macaulay, D Marshall, R Waugh
Affiliations

Computational and experimental characterization of physically clustered simple sequence repeats in plants

L Cardle et al. Genetics. 2000 Oct.

Abstract

The type and frequency of simple sequence repeats (SSRs) in plant genomes was investigated using the expanding quantity of DNA sequence data deposited in public databases. In Arabidopsis, 306 genomic DNA sequences longer than 10 kb and 36,199 EST sequences were searched for all possible mono- to pentanucleotide repeats. The average frequency of SSRs was one every 6.04 kb in genomic DNA, decreasing to one every 14 kb in ESTs. SSR frequency and type differed between coding, intronic, and intergenic DNA. Similar frequencies were found in other plant species. On the basis of these findings, an approach is proposed and demonstrated for the targeted isolation of single or multiple, physically clustered SSRs linked to any gene that has been mapped using low-copy DNA-based markers. The approach involves sample sequencing a small number of subclones of selected randomly sheared large insert DNA clones (e.g., BACs). It is shown to be both feasible and practicable, given the probability of fortuitously sequencing through an SSR. The approach is demonstrated in barley where sample sequencing 34 subclones of a single BAC selected by hybridization to the Big1 gene revealed three SSRs. These allowed Big1 to be located at the top of barley linkage group 6HS.

PubMed Disclaimer

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Nature. 1982 Jul 22;298(5872):396-8 - PubMed
    1. Mol Gen Genet. 1998 Jun;258(5):466-78 - PubMed
    1. Genomics. 1991 Jul;10(3):807-15 - PubMed
    1. Mol Gen Genet. 1992 Feb;231(3):353-9 - PubMed
    1. Genetics. 1992 Dec;132(4):1131-9 - PubMed

Publication types