“This is revolutionizing the agricultural sector”

Scientists are using genomics to fight malnutrition in Africa and more. The African Orphan Crops Consortium (AOCC), founded in 2011, promotes the production of nutritious orphan crops to African consumers through the adoption of modern breeding methods for crop improvement. The AOCC is based at the World Agroforestry Center (WAC) in Nairobi, Kenya. Its objective is to sequence, assemble and open source the genomic data of more than a hundred traditional African food crops in order to improve their nutritional content, productivity and climatic adaptability. These often overlooked crops have the potential to both boost farmers’ incomes and combat malnutrition and child stunting on the continent. “This is a very ambitious project to sequence, assemble and annotate the genomes of 101 cultures that have not been studied before,”explained WGA CEO Dr. Tony Simons.

In 2017, he joined forces with American company Illumina, which specializes in DNA sequencing and chip-based technologies. The project uses technology from Illumina, specifically the HiSeq 4000, which can sequence up to 12 genomes, 100 whole transcriptome samples, or 180 exomes in three and a half days or less.

The future of the African food system?

AOCC founder Howard-Yana Shapiro felt that this technology would greatly accelerate his plans. “I thought it would take me 17 years to complete the job,”he said. “With this machine, it might take three or four years. It’s a surprising change in abilities. The AOCC plans to train hundreds of plant breeders in Africa so that they can breed new lines of more nutritious plants. “In 10 years, these 101 crops will be the fundamental basis of the African food system”,Shapiro said.

“We got involved because it was the right thing to do,”added Associate Director of Agrigenomics, Dr. Ryan Rapp. “We recognized the impact that genetics could have on these crop species to really boost food security and nutrition across the continent. By installing this machine here in Africa, we hope to provide the region with one of the most powerful sequencing instruments on the continent to truly advance this mission.

The project focused on distinguishing between genomic sequencing (where scientists can use sequence information to, in effect, turn certain genes on or off) and genetic modification of plants, which adds a specific portion of DNA into the plant’s genome to make it look new or different. characteristics.

“Genomic sequencing is revolutionizing agriculture right now,”said Dr Ranjana Bhattacharjee, a molecular geneticist at the International Institute of Tropical Agriculture (IITA) in Ibadan, Nigeria. Dr. Bhattacharjee was recently awarded the 2022 Illumina Agricultural Greater Good Initiative grant. This is granted to proposals that will increase the sustainability and productivity of important food products and animal species.

Selection of a more resilient “crop king”

Bhattacharjee is using whole genome sequencing to breed a more resilient yam in West Africa. In many tropical countries, yams are known as the “queen of crops”. Worldwide, they are the fourth most widely used root and tuber crop – after potatoes, cassava and sweet potatoes – and they feed hundreds of millions of people.

Because yams are grown in so many different regions, they are also incredibly diverse: to the tune of around 600 species, and each of these species comes in several cultivars or varieties. The world’s largest producer is West Africa’s ‘yam belt’, which stretches from southeast Guinea to northwest Cameroon, with Nigeria contributing the highest yield.

The yam not only contributes to ensure food security and nutrition, but it is also an integral socio-cultural symbol. They often play an important role in wedding ceremonies and festivals.

But as widespread and important as yams are, they have been largely overlooked by researchers, especially compared to other root and tuber crops, Dr Bhattacharjee said.

When she joined IITA in 2009, she revealed, knowledge of yam genomics was limited due to lack of funding. However, she recognized the nutritional and economic importance of these starchy tubers and became motivated to conduct extensive genomics-assisted research on them.

As the 2022 grant recipient, Bhattacharjee will be able to perform whole genome sequencing of approximately 1,000 Guinea yam samples – one of the largest numbers of yam samples ever sequenced. This will be achieved using another Illumina sequencing system, the NovaSeq 6000.

Dr. Bhattacharjee and his colleagues look forward to using the grant to understand the genetic relationships between different species (both cultivated and wild) of yams in West Africa and to study crop-specific genes that may confer disease resistance, resilience and higher yield. . Sequencing data will be made public on IATI’s open-access platforms.

Raising the status of orphan crops

She hopes that with this sequencing project, the amount of knowledge generated will change the status of this orphan culture. Yam is a crop with “huge potential”,added Dr. Robert Asiedu, former yam farmer and Director Emeritus of IITA-West Africa. But “Modern, high-throughput tools and technologies are needed to try to transfer targeted traits from one species to another,”he explained.

For example, when supplies of domesticated yams become scarce, yam farmers and breeders often go in search of wild varieties which they then cross with farmed or cultivated varieties. But this process is laborious and has not been optimized, Dr. Asiedu explained. Although yams can grow well without fertilizers or herbicides, they should be staked, hilled and monitored regularly for weeds. Farmers and breeders have to wait about a decade to develop a new variety or hybrid.

“If children cannot have adequate nutrition, all of their cognitive abilities are compromised from the start and while they are expected to study, learn and grow. So the future of a whole generation is really at risk if you can’t ensure food security,”added Dr. Asiedu. “With the Illumina Prize, we’re going to take a big leap in the work we do on yams to benefit millions of farmers.”

Dr. Bhattacharjee hopes the partnership with Illumina will cut the time needed to develop a new cultivar in half and help identify traits that will provide more clues to improve such an important crop through comparative genomics. “Ultimately, the goal is to make a culture more resilient,”she says. “I think there is a need for the world to recognize the need for yams and start investing in this fantastic crop and making sure its value can be realized.”

Lana T. Arthur