Mapping a major QTL and development of PCR-based markers to select sweetpotato varieties for direct planting

• A major QTL, DPc11.1 , involved in suitability for direct planting in sweetpotato was identified by GWAS. • DPc11.1 decreased the weight of the mother root and direct-daughter roots and increased that of indirect-daughter roots. • PCR-based markers to detect DPc11.1 were developed. • The markers can be used for marker-assisted selection of suitability for direct planting. Suitability of sweetpotato for direct planting indicates high productivity of daughter roots and low enlargement of the mother root. Direct planting of sweetpotato is labor-saving, but as most varieties are not suited to it, breeding of new varieties is needed. In this study, we crossed a variety unsuitable for direct planting, Koganesengan, and a breeding line suitable for direct planting, Kyushu 199, and used the F 1 population for genome-wide association study. We identified a major QTL on chromosome 11, DPc11.1 , that conferred suitability for direct planting in two consecutive years. Using variants in the DPc11.1 region, we developed four PCR-based markers (DPc11_5.72, DPc11_6.18, DPc11_8.69, and DPc11_11.36) and used them to genotype the F 1 lines. A simplex allele of Kyushu 199 in DPc11.1 significantly increased the weight of indirect-daughter roots and decreased the weight of the mother root and direct-daughter roots, suggesting that DPc11.1 regulates distribution of assimilates to the mother root and daughter roots. Among the four markers, the genotype of DPc11_8.69 was particularly strongly related to the traits required for direct planting. Genotyping of various germplasms suggested that DPc11.1 in Kyushu 199 was derived from Resisto, but most major varieties in Japan have no Kyushu 199-type allele of DPc11_8.69. Thus, DPc11_8.69 will be a versatile marker to select progeny suitable for direct planting from populations produced by crossing Kyushu 199 and various Japanese varieties. Our results can accelerate selection in breeding programs for direct planting by marker-assisted selection, and contribute to the development of varieties for direct planting.