Rice Genetics IV - IRRI books - International Rice Research Institute

Microsatellite markers in rice:abundance, diversity, and applicationsS.R. McCouch, S. Temnykh, A. Lukashova, J. Coburn, G. DeClerck,S. Cartinhour, S. Harrington, M. Thomson, E. Septiningsih, M. Semon,P. Moncada, and Jiming LiA well-distributed set of 500 microsatellite markers has been geneticallymapped onto the rice genome. These markers link the genetic and physicalmaps with the genomic sequence of rice, facilitating studies that seek todetermine the relationship between the structure and function of genes andgenomes. To facilitate the development of new microsatellite markers usingpublicly available DNA sequence information, a simple sequence repeat identificationtool (SSRIT) has been developed for semiautomated identificationof nonredundant simple sequence repeat (SSR) loci and for primer design(available at http://www.gramene.org/microsat/). Using this script, a totalof 57.8 Mb of DNA sequence from rice was searched to determine the frequencyand distribution of different SSRs in the genome. Because the lengthof the SSR unit in any single genome has proven to be a reasonably goodpredictor of overall polymorphism in related genotypes, SSR loci were categorizedinto two groups (class I and class II) based on the length of therepeat motif. Microsatellites with poly(AT)n repeats represented the mostabundant and polymorphic class of SSRs but were frequently associatedwith the Micropon family of miniature inverted repeat transposable elements(MITEs) and were difficult to amplify. Estimates of total microsatellite frequenciesin rice suggested that there were approximately 28,340 Class Iand 70,530 Class II SSRs, or about 100,000 di-, tri-, and tetra-nucleotideSSR motifs in the rice genome. The distribution of SSR sequences showedthat regions of the rice genome that were richer in expressed genes alsotended to be richer in SSR sequences, underscoring their usefulness asgenetic markers. Applications of SSRs in variety protection, diversity analysis,gene and QTL identification, marker-assisted selection, physical mapping,and gene isolation will be discussed.Simple sequence repeats (SSRs), commonly referred to as microsatellites, are tandemlyrepeated mono- to hexa-nucleotide motifs that are ubiquitous in eukaryotic genomesand exhibit highly variable numbers of repeats at a locus. Their abundance andMicrosatellite markers in rice: . . . 117