Advanced search
1 file | 519.98 KB Add to list

Gene-based microsatellites for cassava (Manihot esculenta Crantz): prevalence, polymorphisms, and cross-taxa utility

Author
Organization
Abstract
Background: 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. Results: A total of 846 putative microsatellites were identified in silico from an 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 in the 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 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. Conclusion: 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.
Keywords
EST-SSRS, EXPRESSED SEQUENCE TAGS, PROPAGATED CROP, REPEAT MARKERS, LINKAGE MAP, WHEAT, DATABASE, BARLEY, TRANSFERABILITY, EUPHORBIACEAE

Downloads

  • Raji 2009 BPB 9 a118.pdf
    • full text
    • |
    • open access
    • |
    • PDF
    • |
    • 519.98 KB

Citation

Please use this url to cite or link to this publication:

MLA
Raji, Adebola AJ et al. “Gene-based Microsatellites for Cassava (Manihot Esculenta Crantz): Prevalence, Polymorphisms, and Cross-taxa Utility.” BMC PLANT BIOLOGY 9 (2009): n. pag. Print.
APA
Raji, A. A., Anderson, J. V., Kolade, O. A., Ugwu, C. D., Dixon, A. G., & Ingelbrecht, I. (2009). Gene-based microsatellites for cassava (Manihot esculenta Crantz): prevalence, polymorphisms, and cross-taxa utility. BMC PLANT BIOLOGY, 9.
Chicago author-date
Raji, Adebola AJ, James V Anderson, Olufisayo A Kolade, Chike D Ugwu, Alfred GO Dixon, and Ivan Ingelbrecht. 2009. “Gene-based Microsatellites for Cassava (Manihot Esculenta Crantz): Prevalence, Polymorphisms, and Cross-taxa Utility.” Bmc Plant Biology 9.
Chicago author-date (all authors)
Raji, Adebola AJ, James V Anderson, Olufisayo A Kolade, Chike D Ugwu, Alfred GO Dixon, and Ivan Ingelbrecht. 2009. “Gene-based Microsatellites for Cassava (Manihot Esculenta Crantz): Prevalence, Polymorphisms, and Cross-taxa Utility.” Bmc Plant Biology 9.
Vancouver
1.
Raji AA, Anderson JV, Kolade OA, Ugwu CD, Dixon AG, Ingelbrecht I. Gene-based microsatellites for cassava (Manihot esculenta Crantz): prevalence, polymorphisms, and cross-taxa utility. BMC PLANT BIOLOGY. 2009;9.
IEEE
[1]
A. A. Raji, J. V. Anderson, O. A. Kolade, C. D. Ugwu, A. G. Dixon, and I. Ingelbrecht, “Gene-based microsatellites for cassava (Manihot esculenta Crantz): prevalence, polymorphisms, and cross-taxa utility,” BMC PLANT BIOLOGY, vol. 9, 2009.
@article{1982007,
  abstract     = {Background: 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. 
Results: A total of 846 putative microsatellites were identified in silico from an 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 in the 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 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. 
Conclusion: 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.},
  articleno    = {118},
  author       = {Raji, Adebola AJ and Anderson, James V and Kolade, Olufisayo A and Ugwu, Chike D and Dixon, Alfred GO and Ingelbrecht, Ivan},
  issn         = {1471-2229},
  journal      = {BMC PLANT BIOLOGY},
  keywords     = {EST-SSRS,EXPRESSED SEQUENCE TAGS,PROPAGATED CROP,REPEAT MARKERS,LINKAGE MAP,WHEAT,DATABASE,BARLEY,TRANSFERABILITY,EUPHORBIACEAE},
  language     = {eng},
  pages        = {11},
  title        = {Gene-based microsatellites for cassava (Manihot esculenta Crantz): prevalence, polymorphisms, and cross-taxa utility},
  url          = {http://dx.doi.org/10.1186/1471-2229-9-118},
  volume       = {9},
  year         = {2009},
}

Altmetric
View in Altmetric
Web of Science
Times cited: