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To save the shea tree, scientists explore predictive breeding tools

Decline threatens value chain
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Women work on shea butter production near Chiana, Kassena Nankana District in Ghana. CIFOR/Axel Fassio

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Better known outside Africa for shea butter, which is used in chocolate manufacturing, cuisine and cosmetics, the shea (Vitellaria paradoxa) is an evergreen flowering tree found across the African continent, from Senegal in the west to the foothills of the Ethiopian highlands in the east.

Its numbers are on the decline, threatening the value chain.

Scientists like Prasad Hendre from the Center for International Forestry Research and World Agroforestry (CIFOR-ICRAF) and Iago Hale from the University of New Hampshire in the United States have now settled on a solution that may save the tree that also provides millions of households with a highly nutritious cooking oil, as well as a vital source of income, with its supply chain almost entirely controlled by women.

In a recent study published in Frontiers in Plant Science, the experts explore new means to bring back the declining shea populations on farmlands and parklands by providing improved planting material bred using genomics.

“With genomic analysis, we are trying to understand how the traits we see – the phenotype – are linked to or determined by an individual tree’s DNA,” Hendre said. “There are regions in the genome called — as genes directly control these traits – for example, butter quality, butter yield, the number of nuts, and the number of fruits produced by each plant.”

He adds that genetically improved varieties are not genetically modified which would essentially involve taking a gene from one plant and putting it into another.

“This is a traditional breeding method, but using modern, faster and more efficient tools,” said Hendre.

Hale, an associate professor in agriculture, nutrition, and food systems, who led the project said the shea tree has faced environmental challenges even as local farmers prioritize other crops.

Land use change has pushed out the shea tree which is largely found in “stressful environments” where temperatures are high and long droughts are the norm, he said.

“There’s a substantial opportunity cost in letting a tree grow slowly over decades, especially when there are competing land uses that would pay off much more quickly,” Hale said. “One example is the conversion of parklands to agriculture, for crops like mangoes and cashews, which happen to be largely controlled by men. So, not only does it threaten shea tree numbers, but it also potentially undermines economic opportunities for women.”

Locals have also found shea wood to be a good material for charcoal making, so instead of waiting for 20 years for the tree to produce nuts they can harvest, they use it to make charcoal to make quick returns.

The scientists say that use of genomics tools is imperative for shea tree, which takes long time to mature unlike other annual crops.

The genomics approach involves assembling collections of diversity of shea and examining their phenotypes by genetically “fingerprinting” those trees. This can be started by making associations between important traits and the underlying DNA.

The scientists say the genome analysis provides an opportunity to predict the performance of an individual seed even before it is sown in the field. This way they can support a rational decision making on which seedlings to keep and which ones to cull based on its likelihood to produce more fruits.

Hale explains that “genetic fingerprinting” involves using DNA sequencing to “see” what versions of shea’s naturally-occurring genes any given tree possesses.

This way, the versions, or alleles, of genes that are desirable, and some are undesirable, from a production standpoint can be identified in new seedlings before they mature.

“Let’s say you’d like to visit a certain city you’ve never been to before and not spend countless hours driving random directions in hope of landing there. For this task, you need a map. Such a map, coupled with landmarks and road signs, are the tools needed to efficiently navigate and reach your destination,” Hale explained.

“In a similar way, if you want to ascertain if a certain tree carries natural versions of genes that are desirable for end users, you need a reference genome (the map) and genetic markers (the landmarks or signposts). By creating a reference genome for the species Vitellaria paradoxa, the shea tree, we have developed and made available a navigation tool for use by the whole shea improvement community.”

Technically, this is done by extracting the DNA from plant tissue — usually from young leaves — and sequencing it.

Iago further explains that while it may be premature to forecast the implications likely to be created by the availability of the shea tree genome for the farmers in the Sahel, the tool will be very helpful for national programs throughout the shea belt and institutions like CIFOR-ICRAF and other partners in the region who can use it.

According to Hendre, although the African Plant Breeding Academy exists, which will ensure a critical mass of early- and mid-career plant breeders working in African institutes who have been empowered to use these tools in their breeding programs, more still needs to be done.

“We need to be creative and think of innovative ways that have not been thought earlier,” he said. “It should involve not just the breeders and genomics; it has to happen in the farmers’ fields. That’s something that we’re working on at the moment: how can we incorporate all the facets of shea improvement and work with farmers in a participatory way?”

For shea breeders, they will be required to send a small tissue sample — for example, a hole punch from a leaf — to the central lab in Nairobi and receive the marker data for that sample within four to six weeks, a much faster way to make production decisions than wait for trees to reach reproductive maturity.

For more information on this topic, please contact Prasad Hendre at P.Hendre@cgiar.org.
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