Where did greater yams come from? A global effort to track the ‘yummy’ dispersal history of a polyploid plant

Over 600 species of yams belong to the genus Dioscorea but about 10 species are cultivated. Yams are a very important tropical crop, mainly grown in Africa, Asia, the Pacific and South America. On 8.7 million hectares, the overall yam production was 72.6 million tonnes in 2018. The greater or water yam, Dioscorea alata is the most commonly grown species.

A large international team, led by Dr Hana Chaïr at CIRAD and colleagues from France, Austria, Sweden, Vietnam, Vanuatu, Madagascar, Sri Lanka, Papua New Guinea, Nigeria and Japan sequenced 643 greater yam accessions to investigate the dispersal history of yams. The scientists found that greater yams had two independent domestication origins, Mainland Southeast Asia and the Pacific, and the Indian Peninsula gene pool led to the African gene pool which was then introduced to the Caribbean. Dr Chaïr previously showed that wild yam conservation is crucial for the future of this crop and found that African yam growing originated from the Niger River basin.

In 1886, De Candolle first suggested that yams were originated in the Indo-Malayan region and over the years and even today, the domestication of yams is still unresolved. Yams are cultivated through clonal propagation and most of the new varieties are somaclones produced by tissue culture. Identifying yam domestication centres and diverse gene pools are much needed for finding more resilient and higher-yielding varieties in the future.

In 1886, De Candolle first suggested that yams were originated in the Indo-Malayan region and over the years and even today, the domestication of yams is still unresolved. Yams are cultivated through clonal propagation and most of the new varieties are somaclones produced by tissue culture. Identifying yam domestication centres and diverse gene pools are much needed for finding more resilient and higher-yielding varieties in the future.

The scientists identified 352 diploid accessions which clustered according to geographical origin, whilst 100 triploids were mostly from Asia and 34 tetraploid accessions were close to the triploid groups. Further analysis found only 92 independent diploid genotypes from the 352 diploid accessions, suggesting high clonality within this species. There was low genetic richness and negative inbreeding coefficients within continents which are signs of strong domestication bottlenecks.

When investigating the genetic structure and ancestry of these samples, “[O]ur genetic analysis and demographic inference supported an early divergence of greater yam between Mainland Southeast Asia and Pacific, followed most probably by two independent domestication events. Then the species would have reached the Indian Peninsula, subsequently Africa and from there the Caribbean”, the scientists explain. 

“We also revealed high clonality and low nucleotide diversity, which are indicators of a strong domestication bottleneck and a diversification process achieved mainly via somaclonal accumulation”, they added. “The narrow diversity raises concerns about the scope for genetic improvement of traits of interest”.

This global research effort not only revealed the main domestication events but also produced an important dataset of yam genetic diversity. See more at https://yambase.org/.