Classification of “Kintoki ninjin” and other groups of carrot (Daucus carota) based on simple sequence repeat markers

Carrot (Daucus carota) is cultivated in temperate regions for its taproot. Eastern and Western types have been differentiated. In Japan, the former type is categorized into Kintoki, Takinogawa oonaga, and Toso, with a few local cultivars. However, their genetic relationships are unclear because of the paucity of reports. We classified the Japanese Eastern and selected Western types based on simple sequence repeat (SSR) markers. Field traits, including root weight, length, diameter, and skin color, were also examined. Our field tests showed clear differences between the Kintoki and Western-type cultivars, confirming their differentiation. A phylogram based on nine SSRs classified 24 cultivars into groups I and II. Group I included all Eastern-type carrots examined (Kintoki and Toso groups, plus two local and two foreign cultivars), with the exception of an Indian cultivar (‘Pusa rudhira red’). Among them, red carrots including Kintoki were clustered into two subgroups. Western-type, Eastern-Western hybrid, and ‘Pusa rudhira red’ were included in group II. A population structure analysis revealed the split between the Eastern and the other types. This study elucidates the genetic characteristics of the Eastern type of carrot, which will be valuable information for carrot breeding, especially when using the Eastern type as a source.