Simple sequence repeat (SSR) markers survey of the cassava (Manihot esculenta Crantz) genome: towards an SSR-based molecular genetic map of cassava

The development of PCR-based, easily automated molecular genetic markers, s uch as SSR markers, are required for realistic cost-effective marker-assist ed selection schemes. This paper describes the development and characteriza tion of 172 new SSR markers for the cassava genome. The placement of 36 of these markers on the existing RFLP framework map of cassava is also reporte d. Two similar enrichment methods were employed. The first method yielded 3 5 SSR loci, for which primers could be designed, out of 148 putative DNA cl ones. A total of 137 primer pairs could be designed from 544 putative clone s sequenced for the second enrichment. Most of the SSRs (95%) were di-nucle otide repeats, and 21% were compound repeats. A major drawback of these met hods of SSR discovery is the redundancy - 20% duplication; in addition, pri mers could not be designed for many SSR loci that were too close to the clo ning site - 45% of the total. All 172 SSRs amplified the corresponding loci in the parents of the mapping progeny, with 66% of them revealing a unique allele in at least one of the parents, and 26% having unique alleles in bo th of the parents. Of the 36 SSRs that have been mapped, at least 1 was pla ced on 16 out of the 18 linkage groups of the framework map, indicating a b road coverage of the cassava genome. This preliminary mapping of the 36 mar kers has led to the joining of a few small groups and the creation of one n ew group. The abundance of allelic bridges as shown by these markers will l ead to the development of a consensus map of the male- and female-derived l inkage groups. In addition, the relatively higher number of these allelic b ridges, 30% as against 10% for RFLPs in cassava, underscores SSR as the mar ker of choice for cassava. The 100% primer amplification obtained for this set of primers also confirms the appropriateness of SSR markers for use in cassava genome analysis and the transferability of the technology as a low- cost approach to increasing the efficiency of cassava breeding. Current eff orts are geared towards the generation of more SSR markers to attain a goal of 200 SSR markers, or 1 SSR marker every 10 cM.