Optimization and characterization of novel EST-SSR markers for cassava (Manihot esculenta)

Abstract

Microsatellites, or simple sequence repeats (SSRs) are very useful molecular

markers for a number of plant species. They are commonly used in cultivar

identification, plant variety protection, as anchor markers in genetic mapping, and in

marker-assisted breeding. Their utility is due to their abundance, hyper variability,

and suitability for high-throughput analysis. Early development of SSRs was

hampered by the high cost of library screening and clone sequencing. Currently,

large public SSR datasets exist for many crop species, but the numbers of publicly

available, mapped SSRs for cassava are relatively low. A database mining approach

to identify SSR-containing expressed sequence tags (EST) in the IITA/Craig Venter

Institute database was utilized. The overall aim of this study was to optimize and

characterize in terms of polymorphism new EST-SSR primers that may be useful for

diversity assessments and genetic linkage mapping in cassava. Seventy primer pairs

were synthesized and used to amplify SSRs from diverse cassava DNA genotypes.

This study identified 33 (63%) useful SSRs markers which were polymorphic in a set

of 24 cassava genotypes from South America and Africa together with four parents

of a mapping population from drought tolerant and four parents of a cassava brown

streak disease (CBSD) mapping population. The polymorphic information content

(PIC) values ranges were from 0.0 to 0.7381 and average allele frequency of 2.5. The

high proportion of (63%) polymorphic EST-SSRs obtained in this work validates the

use of transcribed sequences as a source of markers. These markers will be useful for

genetic mapping, diversity assessments and genomic research.