Development of a high-density SSR genetic linkage map in sweet potato

Simple sequence repeat (SSR) markers have been proved to be a very powerful tool for quantitative trait locus (QTL) mapping, marker-assisted selection and comparative genomics research in many crop species. However, a high-density SSR genetic linkage map is still lacking because there are only a few SSR markers available in sweet potato. In this study, a total of 2545 simple sequence repeat (SSR) primer pairs, including 1215 genomic SSR (gSSR) primer pairs and 1330 BES-SSR (bSSR) primer pairs designed from the genome sequence and BAC-end sequence of sweet potato, respectively, were screened with sweet potato cultivars Luoxushu 8 and Zhengshu 20 and their randomly sampled two F₁ individuals and 571 of them generated polymorphic bands. The selected 571 polymorphic SSR primer pairs and 35 EST-based SSR (eSSR) primer pairs developed at our laboratory were used to genotype 240 F₁ individuals derived from a cross between Luoxushu 8 and Zhengshu 20. A double pseudo-test-cross strategy was applied for linkage analysis. The Luoxushu 8 map included 90 linkage groups with 5057 SSR markers and covered 13,299.9 cM with a marker density of 2.6 cM, and the Zhengshu 20 map contained 90 linkage groups with 3009 SSR markers and covered 11,122.9 cM with a marker density of 3.7 cM. Fifteen homologous groups were identified in both parent maps. These are the first SSR linkage maps consisting of the complete 90 linkage groups and 15 homologous groups, which are consistent with the autohexaploid nature of sweetpotato, and are also the linkage maps with the highest SSR marker density reported to date. These results provide a basis for QTL mapping, marker-assisted breeding and comparative genomics research of sweet potato.