Improving yams with genomics

Despite their importance in West Africa, yams have little recognition worldwide and are often confused with the completely unrelated sweet potato. Termed an “orphan crop” because of this restricted recognition, research into improving the crop has so far been limited. But now, new research published in BMC Biology reports the whole genome sequence of Guinea yam, setting the stage for genomics-assisted improvement to the crop.

Human diet depends mainly on crops and a large number of species have been independently domesticated from wild relatives across the globe. In terms of quantity of the production however, a small number of crops currently dominate the world share, such as maize, wheat and rice. Accordingly the research efforts and investment for improvement have been restricted to these major crops. The crops that are regionally important but have little recognition outside the region are known as “orphan crops”.

Yam is one such orphan crop, representing perennial tuber crops belonging to the genus Dioscorea of the monocotyledons. About ten species are known in tropical and temperate regions of the world that have been independently domesticated.

In a recent study from a research consortium led by the International Institute of Tropical Agriculture (IITA), Nigeria, we reported a high quality genome of Guinea yam, with the size of 594 Mb, and 26,198 protein coding genes predicted. The whole genome sequence of Guinea yam sets the stage for its genomics-assisted improvement.

A history of humans and yam

Most of Dioscorea species are distributed in regions with seasonal rainfall. In the end of rainy season, assimilated carbohydrates are transferred to tubers, the underground storage organ, which becomes dormant during dry season.

A man carrying tubers of Guinea yam at the yam market of Ibadan, Nigeria.

Different from other plant species with underground storage organs, the majority of Dioscorea failed to evolve efficient toxic compounds to deter predators, making their tubers attractive food sources for mammals. Interactions between Dioscorea species and humans may date back to soon after humanity originated.

Guinea yam of West Africa accounts for the largest share (>90%) of world yam production. The major producers are Nigeria, Ghana, Cote d’Ivoire, Togo, Benin and Cameroon. After harvest, tuber skin is peeled, and the cut tubers are boiled in water. Boiled tubers are usually pounded by ladies in a big wooden mortar using a wooden pestle and served with other vegetables and soups. Pounded yam is regarded as the “king of food” in the region.

Guinea yam is important not only as food, but also as an integral part of West African culture as indicated by widespread “yam festivals” in the regions and various rituals associated with the yam.

Despite its importance in the region, yam has been unrecognized outside Africa; still many people mistake sweet potato (Ipomoea batatas) for yam. Research efforts have been scarce and improvement of Guinea yam has been slow.

A genomic revolution for orphan crops

Genomics Revolution ushered by the development of next generation sequencing (NGS) has started changing the research environment of genetic improvement of such orphan crops as exemplified by our paper.

Guinea yam and the entire genus of Dioscorea are characterized by dioecy, meaning that male and female flowers are born on separate plants. Knowing the sex of plants is important for cross breeding. However, we have had no measure to determine plant sex before they start flowering. To address sex determination of Guinea yam, we made use of the genome sequence.

Starting yam research 30 years ago, I never expected the whole genome sequence of Guinea yam to be possible during my lifetime.

After a cross of two plants, their progeny segregated to males and females. DNA of multiple males and females were separately pooled and compared to each other using the genome sequence. This analysis resulted in a rapid identification of a genomic region involved in sex determination.

DNA markers developed in the region should be useful for sex diagnosis of the plants at their seedling stage, which should allow breeders to save space and effort required for growing unnecessary plants before cross breeding.

We expect similar approaches based on the genome sequence will enable researchers to identify other genes controlling important traits such as yield, quality, and disease resistance required for improvement of Guinea yam and other orphan crops.

Starting yam research 30 years ago, I never expected the whole genome sequence of Guinea yam to be possible during my lifetime. The last two decades saw the research field dominated by model species, as represented by Arabidopsis and rice, to explore conserved mechanisms of plant molecular biology. Not being able to feed myself with yam research, I switched to rice research 20 years ago.

Günter Kahl (1936-2015)

The pursuit of common molecular mechanisms is of course important and will continue. However, I feel the Genomics Revolution is already starting to change the scene: it allows studying diversity and evolutionary history of hitherto neglected species and crops through elucidating genetic sequences of their whole genomes.

I personally wish to pay my tribute to the late Professor Günter Kahl, University of Frankfurt, a coauthor of this research. His group succeeded in genetic transformation of monocot species for the first time, using yam. He kept an exceptional enthusiasm on yam research while guiding many researchers to this orphan crop and also to genomics. He was a great scientist and a mentor who advocated for free and open science for the benefit of the people of the world.

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