Agricultural Grant To Help Breed More Resilient Yams in West Africa

Agriculture studies aim to increase the sustainability, productivity and nutritional density of vital crop and livestock species. Illumina’s Agricultural Greater Good Initiative Grant is an award designed to boost research in this field with the end goal of reducing malnutrition, hunger and poverty by improving crop yields and enhancing livestock welfare and productivity.

The 2022 grant winner is Dr. Ranjana Bhattacharjee, molecular geneticist at the International Institute of Tropical Agriculture (IITA) in Ibadan, Nigeria. Her research aims to tackle food insecurities in Western Africa by studying yam species (a major food source in this region) using whole-genome sequencing.

Technology Networks spoke with Bhattacharjee to find out more about how genetic analysis of yam species could improve crop yields and generate more resilient varieties of this under-researched crop.

Sarah Whelan (SW): Could you tell me about your research and the focus of the work in your lab?

Ranjana Bhattacharjee (RB): I am a plant breeder and molecular geneticist, and the focus of my research is on using molecular markers and genomics-assisted breeding. My area of expertise is in yams and cacao, as well as other crops like taro and coffee. Most of the time, it is very difficult to make any changes to crop traits of interest like yield or disease resistance using conventional methods. This is when we use genomics or genome-wide associations to understand these traits of interest and make changes based on genomics.

SW: This new project focuses on yams. Can you explain how important yams are agriculturally and as a food source?

RB: Firstly, I want to say that in places such as the US, yams are often confused with sweet potatoes. However, they are two distinct crops belonging to two different families. Sweet potatoes are Ipomoea batatas, while yams belong to the genus Dioscorea. There are 600 species of yams found all over the world covering Asia, Africa, Latin America, Oceania and the Pacific. Out of these 600 species, approximately 10 are cultivated, such as Dioscorea rotundata, Dioscorea cayenensis and Dioscoria alata.

As yams are so widespread, they are very important as a food security crop for almost 3 million people. They are the main crop for smallholder farmers that have between one to three hectares of land. Additionally, the cost of production of yams is very high, so yam farmers will often sell their yams to get the money to buy other crops – like cassava, maize or rice – which are much cheaper. Yams are also very rich in starch and are reported to have one of the lowest glycemic indexes compared to other starchy crops.

Yams are also an income-secured crop. There are reports that the market value is around $13.7 billion, giving yams the nickname “King of Crops” in West Africa. Furthermore, yams contain valuable secondary metabolites like diosgenin, saponins and shikimic acid. These are important ingredients for pharmaceutical companies. These metabolites can be produced synthetically but can also be sourced naturally from certain species of yam. Therefore, if these can be extracted, this can provide a very large source of income.

SW: What would you say are the main challenges facing yam agriculture today?

RB: Issues such as low yield and diseases are the major challenges. There are diseases that affect certain yam species, for example, Dioscorea alata can develop a fungal infection caused by Colletotrichum gloeosporioides called anthracnose disease. Another yam species, Dioscorea rotundata, can contract a viral infection which results in yam mosaic disease. Both diseases can reduce crop yield by 80% or more.

The cost of production is another major challenge. As this crop is a vine, every plant needs to be staked in the ground. The lack of mechanization in West Africa makes both planting and harvesting very labor-intensive. These crops are underground tubers that can weigh up to eight or ten kilos, and each plant can produce multiple tubers. Another challenge is the seed system itself. As yams are a clonally propagated crop, farmers must keep some as planting material for seed tubers. This becomes very difficult for the farmers because they must keep seed tubers for the next year, while also keeping some for their own consumption.

Lastly, there is the need for recognition of yams as a priority crop in West Africa. Nigeria is the highest producer of yams in the world, but policymakers and the government don't recognize yams as a priority crop. This makes it very difficult to secure funding for research to make improvements, the rate of which in terms of genetics and genomics is very slow. When we speak to policymakers about why they don't want to prioritize these crops, they say that the production in Nigeria is so high that a lot of tubers are rotting. However, this is down to a lack of storage facilities post-harvest. When these crops are not stored properly and are stacked one on top of the other, a lot of heat is generated and the tubers can rot, be attacked by insects and become vulnerable to fungal infections. This means that a lot of crops can be lost.

SW: Congratulations on your award of the 2022 Illumina Agricultural Greater Good Grant. Can you describe some of the aims of the study that you are going to carry out with the help of this grant?

RB: This award was initially supposed to do whole genome sequencing of only 100 genotypes. However, after a lot of discussion with Illumina, I am very grateful that they have now recognized the value of this crop and allowed me to submit approximately 1000 yam genotypes, including both cultivated and wild species.

One of the major issues with yams in West Africa is that two cultivated species – Dioscorea rotundata and Dioscorea cayenensis (also known as white yam and yellow yam, respectively) – are grown together with wild species. Farmers go into the forested areas and collect wild tubers, physically cultivating them into a regular, cylindrical shape which can take four or five years. These tubers are then referred to as cultivated white yams. However, there is a lot of confusion around whether these tubers are white yams, yellow yams, a wild–cultivated interspecific hybrid or a completely wild species. And if it is a wild species, which species is it? Therefore, in this project, the major aim is to do genome sequencing of many white, yellow and probable wild yams which are all grown together. With this, we can understand what the genetic relationship is between these cultivated and wild species. We will know whether these are white yams, yellow yams or interspecific hybrids.

For the second aim, we will investigate the viral DNA which is integrated within the yam genome and very difficult to separate. We will perform whole genome sequencing of 100 isolates of viruses that we have extracted from the yams themselves. This will allow us to find the regions for viral resistance in the yam genome. Interestingly, we have the draft reference genome already available for the white yam, meaning we can align the sequencing data with the available draft reference genome. This will allow us to find regions of conserved resistance genes as well as genes for other important quality traits such as dry matter content and starch quality.

SW: How might this research increase the sustainability and productivity of this crop?

RB: It may not directly and immediately impact the sustainability and the production of the crop. However, in the long run, once we understand the genes that are responsible for different traits, we can perform genomics-assisted breeding and fast-track the breeding cycle.

Currently, it can take eight to ten years to generate a new yam variety, and the varietal turnover is very low. Furthermore, when improved varieties are finally released to the farmers, the adoption rate of improved varieties is also very low. Producers rely on “landraces”, which are the farmers’ locally adapted varieties. From a metabolomic study, we found that the taste of the landraces is much better than the improved varieties. So, when we try to improve a variety, there seems to be a negative correlation between the yield and some of the quality traits like starch properties, minerals and taste. With whole genome sequencing, we will be able to find the genes responsible for these traits and perform genomics-assisted breeding to transfer these genes into some of these improved varieties.

Genome sequencing is also going to generate a large amount of data, so we need to do a lot of gene mining and understand whether these genes are functional. However, this will take much less time than for many other crops, as things are already being understood in other crop species. For example, a lot of research has gone into improving our understanding of rice, and rice and yams are both monocots. This means we can apply a lot of the same principles to understand gene functions in yams using our knowledge of rice. Taken together, this means that we might not see immediate benefits, but I believe that within the next five or six years this can have a large impact on increasing sustainability and productivity.

SW: How important do you think this grant will be to this relatively under-researched topic?

RB: I think this is the first time Illumina has given a grant towards researching a crop that is very important to West Africa. With this grant and the publicity, already people are starting to understand that yam is its own crop and is not the same as sweet potato, so there are a lot of misunderstandings that are already being cleared up. At the same time, a lot of investors will probably now be interested in these crops. We hope that the status of the crop will change from an orphan crop to a well-researched crop with this grant. Genome sequencing is revolutionizing the world of crop improvement, and now we are adding yams to the list of crops that have undergone large-scale genome sequencing.

Dr. Ranjana Bhattacharjee was speaking to Sarah Whelan, Science Writer for Technology Networks.