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Title: Gene-based Microsatellites for Cassava (Manihot esculenta Crantz): Prevalence, Polymorphisms, and Cross-taxa Utility

Author
item RAJI, ADEBOLA - International Institute For Tropical Agriculture
item Anderson, James
item KOLADE, OLUFISAYO - International Institute For Tropical Agriculture
item UGWU, CHIKE - International Institute For Tropical Agriculture
item DIXON, ALFRED - International Institute For Tropical Agriculture
item INGELBRECHT, IVAN - International Institute For Tropical Agriculture

Submitted to: BMC Plant Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/11/2009
Publication Date: 9/11/2009
Citation: Raji, A.A., Anderson, J.V., Kolade, O.A., Ugwu, C.D., Dixon, A.G., Ingelbrecht, I.L. 2009. Gene-based Microsatellites for Cassava (Manihot esculenta Crantz): Prevalence, Polymorphisms, and Cross-taxa Utility. Biomed Central (BMC) Plant Biology. 9:118. DOI:10.1186/1471-2229-9-118.

Interpretive Summary: Cassava is a starchy root crop grown in tropical and subtropical climates and is the sixth most important crop in the world. Simple sequence repeat (SSR) markers for cassava were identified from a cassava unigene database. Candidate SSRs were screened for polymorphism among a panel of cassava cultivars from Africa, Latin America and Asia, four wild Manihot species, as well as two other important taxa of Euphorbiaceae, leafy spurge and castor bean. Of 168 markers with clean amplification products, 124 displayed polymorphisms. Of 85 EST-SSR markers screened, 80 amplified alleles from one or more wild species whereas 13 amplified alleles from castor bean and 9 amplified alleles from leafy spurge. Thus, all markers were transferable to wild relatives of M esculenta while only a fraction was transferable to the more distantly related taxa. In a subset of 20 bi-allelic EST-SSRs assessed by fluorescence-based genotyping, the number of alleles per locus ranged from 2 to 10 with an average of 4.55 per locus. These markers showed genetic relationships consistent with existing information on these genotypes. A set of 124 new, unique polymorphic EST-SSRs was developed and characterized which extends the repertoire of SSR markers for cultivated cassava and its wild relatives. These markers will be useful for cultivar identification, taxonomic studies, and genetic mapping.

Technical Abstract: Cassava (Manihot esculenta Crantz), a starchy root crop grown in tropical and subtropical climates, is the sixth most important crop in the world after wheat, rice, maize, potato and barley. The repertoire of simple sequence repeat (SSR) markers for cassava is limited and warrants a need for a larger number of polymorphic SSRs for germplasm characterization and breeding applications. A total of 846 putative microsatellites were identified in silico from a 8,577 cassava unigene set with an average density of one SSR every 7 kb. One hundred and ninety-two candidate SSRs were screened for polymorphism among a panel of cassava cultivars from Africa, Latin America and Asia, four wild Manihot species, as well as two other important taxa of Euphorbiaceae, leafy spurge (Euphorbia esula) and castor bean (Ricinus communis). Of 168 markers with clean amplification products, 124 (73.8%) displayed polymorphism based on high resolution agarose gels. Of 85 EST-SSR markers screened, 80 (94.1%) amplified alleles from one or more wild species (M epruinosa, M glaziovii, M brachyandra, M tripartita) whereas 13 (15.3%) amplified alleles from castor bean and 9 (10.6%) amplified alleles from leafy spurge; hence nearly all markers were transferable to wild relatives of M esculenta while only a fraction was transferable to the more distantly related taxa. In a subset of 20 bi-allelic EST-SSRs assessed by fluorescence-based genotyping the number of alleles per locus ranged from 2 to 10 with an average of 4.55 per locus. These markers had a polymorphism information content (PIC) from 0.19 to 0.75 with an average value of 0.55 and showed genetic relationships consistent with existing information on these genotypes. A set of 124 new, unique polymorphic EST-SSRs was developed and characterized which extends the repertoire of SSR markers for cultivated cassava and its wild relatives. The markers show high PIC values and therefore will be useful for cultivar identification, taxonomic studies, and genetic mapping. The study further shows that mining ESTs is a highly efficient strategy for polymorphism detection within the cultivated cassava gene pool.