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

Adebola Aj Raji,Alfred Go Dixon,Olufisayo A Kolade,Chike D Ugwu,James V Anderson,Ivan L Ingelbrecht

doi:10.1186/1471-2229-9-118

Adebola Aj Raji, Alfred Go Dixon + Show 4 more

Open Access

https://doi.org/10.1186/1471-2229-9-118

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Abstract

BackgroundCassava (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.ResultsA 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.ConclusionA 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.

Highlights

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
A total of 18,177 ESTs were used in this study, which were clustered in 8,577 unigenes [20]
The number of published simple sequence repeat (SSR) markers is limited compared to other major crops

Summary

Introduction

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. Native to the Neotropics [2], cassava is cultivated in tropical and subtropical regions in Asia, Latin America and Africa. Cassava can grow under adverse climatic conditions with erratic rainfall and on marginal land under low intensity management [4]. Because of these attributes, cassava plays an essential food security role in Africa. Cassava has important industrial uses for the production of starch-based products, alcohol and animal feed [5,6]

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