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Background
Yam is a collective name for tuber-bearing crops belonging to the monocotyledonous Dioscorea genus in the family Dioscoreaceae of the order Dioscoreales. This genus contains approximately 450 species which are primarily distributed in tropical and subtropical regions worldwide [1]. Among the Dioscoreaceae, three minor genera are monoecious (having male and female flowers on a plant), but the entire genus Dioscorea is characterized by dioecy (the presence of separate male and female plants), a feature shared by only 5-6% of angiosperms [2]. The origin of Dioscorea is supposed to be in the Late Cretaceous (~80 Mya [3]), suggesting that the origin of dioecy dates back to this time. Approximately 10 Dioscorea species have been independently domesticated in West Africa, Southeast Asia, and the Pacific and Caribbean islands [4]. D. rotundata is the most popular species in West and Central Africa, the main region for yam production worldwide, which contributed approximately 96% of the 63 million tons of yam produced globally in 2013 (Additional file 1: Table S1 and Additional file 2: Figure S1). D. rotundata (white Guinea yam) and D. cayenensis (yellow Guinea yam) represent a major source of food and income in this region, as well as an integral part of the socio-cultural life. This geographical region is often referred to as the “civilization of the yam,” reflecting the West African societies that are tightly linked to yam cultivation [5, 6].
Despite its considerable regional importance, Guinea yam has long been regarded as an “orphan” crop, as it is not traded around the world, and it has attracted little attention from researchers and little investment. Guinea yam cultivation is constrained by several factors. Seeds are seldom used as starting materials; instead, yams are commonly propagated clonally using small whole tubers (referred to as “seed yams”) or tuber pieces. Yam is an annual climber that requires stakes for support and is highly vulnerable to a plethora of pests and diseases. Therefore, an understanding of yam genetics and a systematic improvement of yam based on crossbreeding for traits associated with tuber yield and quality, a reduced requirement for staking, and resistance/tolerance to disease and nematodes are urgently needed. Genetic analysis of Dioscorea has been constrained by the small number of available genetic markers. Furthermore, Dioscorea cultivars...