Rice Genetics IV - IRRI books - International Rice Research Institute

are indicated with RM locus designations and primer sequences designed and testedin our laboratory, along with previously reported OSR names and links to the originalGenBank and DDBJ entries. Approximately 500 bp of sequence from all SSR-containinggenomic clones (summarized by Chen et al 1997 and Temnykh et al 2000) arealso available in GenBank. These sequences were derived from the screening of smallinsertclone libraries from IR36 and provide an immediate link to genomic sequencefrom cv. Nipponbare and an in silico view of polymorphism between indica andjaponica cultivars.Applications of SSRs to evolutionary studies, genetics, and breedingSeveral useful reviews summarize the advantages of using SSRs in plant research andin applications such as marker-based breeding, improving the efficiency of germplasmmanagement, evaluating seed purity, and as the basis of intellectual property protection(Hahn and Grifo 1996, Powell et al 1996, Mitchell et al 1997). Yang et al (1994)used SSRs to demonstrate that levels of allelic diversity in a collection of landraceswere higher than in a corresponding collection of rice cultivars. Olufowote et al (1997)demonstrated that a selected set of highly informative SSR markers could be used todifferentiate varieties, and that these markers were especially useful in identifyingallele frequencies in complex mixtures of pure lines that were characteristic of manytraditional (landrace) varieties. SSR-based fingerprinting was used to classify breedingmaterial in Korea (Ji et al 1998) and red rice accessions in the United States(Vaughan et al 2001). These markers also provide an efficient methodology for checkingvarietal purity in commercial settings, where price differentials for certain premiumrice varieties motivate unacceptable seed-mixing practices in the marketplace (Jain etal, personal communication).Of particular interest to geneticists and breeders are studies in which SSR markershave been used to make inferences about the genetics, pedigrees, evolution, and/or identity of various traits and/or germplasm accessions. Temnykh et al (2000) suggestedthat certain regions of the rice genome are associated with higher than averagelevels of SSR diversity and speculated about the reasons for their observations. Studiesby Bligh et al (1995, 1998) demonstrated that expansion/contraction of an SSRmotif occurring at the splice site in the 3’ UTR of the waxy gene was correlated withamylose content of the grain, and Ayres et al (1997) used SSRs to make predictionsabout the inheritance of waxy alleles in complex pedigrees. Further investigation byLarkin and Park (1999) demonstrated that a single nucleotide polymorphism at thissite conferred temperature sensitivity and altered transcript accumulation in developingrice endosperm.Microsatellites have proved especially useful in evaluating diversity in narrowlydefined gene pools in which other kinds of molecular markers such as amplified fragmentlength polymorphism, restriction fragment length polymorphism, or randomlyamplified polymorphic DNA are unable to detect polymorphism (Powell et al 1996).Examples in rice include O. glaberrima accessions from West Africa (Lorieux et al2000, Semon et al 2001, Talag et al 2000), basmati rice from northern India (S. Jain,Microsatellite markers in rice: . . . 127