A multi-million dollar research group co-founded by the confectionery company Mars is set to publish the genetic maps to five traditional African crops as part of an ambitious project that it says could help end malnutrition on the continent.

The project is applying modern biotechnology to African “orphan crops” – including finger millet and the “superfood” moringa – with the goal of breeding new versions that are more productive or more tolerant to drought or disease.

It is one of several new initiatives to develop improved varieties of crops that have been grown by small-scale farmers for generations but long-overlooked by international researchers and industry focused on globally traded staples like wheat and maize.

The researchers say they will publish the crops’ genome sequences online for anyone to download for free; they are also training hundreds of African plant breeders on how to use the data.

At UN food talks in Rome last month, Howard-Yana Shapiro, chief agricultural officer Mars, one of the world’s largest food companies with revenues in 2015 of $33bn (£26.5bn), said the project will “significantly improve the nutrition of an entire continent”.

Critics of the project say efforts to map the genetic data of crops are more likely to help private companies moving into new African seed markets rather than smallholder farmers.

Mariam Mayet, director of the African Centre for Biodiversity, said: “What are farmers going to do with gene sequences? … These top-down, techno-fix solutions sound good, and sound like we’re entering the 21st century, but they’re not what small farmers need.”

Patrick Mulvaney, at the UK Food Group, said that even if genetic data is freely available online, “the only ones that can really make use of it are the big companies”. He suggested corporations “want orphan crops too, to consolidate their control” of global food systems.

“It won’t be too long before you can’t grow maize in southern France, because of climate change. Sorghum, cassava, yams – these are also backups if you’re in trouble,” added Pat Mooney, at the ETC Group, who also questioned corporate motives for work on these crops.

Chikelu Mba, from the UN’s Food and Agriculture Organisation, said advanced biotechnology tools like genome sequencing could help develop “new, superior, more nutritious, drought tolerant varieties of these crops that very poor people need to survive”.

But he stressed they are not a magic bullet. Small-scale farmers also need infrastructure and access to “quality seeds and planting materials at affordable prices”, he added.

“It needs to be in people’s minds that downstream, some of the products may be restricted by intellectual property rights … which are supposed to encourage and reward innovation but can also be misused and/or abused,” Mba added.

African countries, he said, must also support public sector crop development rather than leaving it to private initiative alone. “It is a worthwhile use of taxpayer resources to encourage work on these for the simple reason that they are food security crops.”

The African Orphan Crops Consortium (AOCC), founded in 2011, has partners including Mars and Google, a Chinese research group, a Nairobi laboratory, and biotech firms. It calls itself a “public-private partnership” led by the New Partnership for Africa’s Development (NEPAD) arm of the African Union.

The UN children’s agency, Unicef, is also listed as a partner to advocate and “raise support” for the project.

Allen Van Deynze, a scientist at the University of California-Davis who is involved in the project, said it is worth about $40m-50m, but that most of this has come in-kind from the group’s partners contributing their own in-house staff time and facilities.

The project has listed 101 focus crops including some that already have more obvious commercial value like coconut, avocado and oil palm along with others including spiderplant and breadfruit.

The first major data release, expected within the next two months, will be genetic maps to finger millet, African eggplant, acacia, and moringa – a tree with leaves unusually rich in iron, protein and vitamins.

“Making nutritious crops productive – that’s the mission, and then getting them to the people who need them,” said Van Deynze. “For me, that’s the way out of poverty – feed people properly … Give everyone the resources that they need, mentally and physically.”

But the science behind using genomics to develop crops is complex and it’s not expected that small farmers will use this data themselves – seed companies are likely to be involved.

A fruit from a baobab tree – another orphan crop – hangs from a branch in Thiawe Thiawe, Senegal. Photograph: Georges Gobet/AFP/Getty Images

Most seeds in Africa are saved and traded by farmers themselves in informal systems, though several countries have adopted controversial new laws and policies to encourage commercial investment, protect intellectual property and develop regional seed markets.

Elizabeth Mpofu, general coordinator of the global peasants’ movement La Vía Campesina, said this is not what small farmers like her need. “We really need to protect our own indigenous seeds.”

Mpofu, who grows groundnut and sorghum in Zimbabwe, said she is concerned about increasing corporate interest in “crops that we farmers have grown for ages and ages … These are perfect organic crops. Why should we tamper with these?”

The AOCC is making its data free online to users who agree not to patent the genome sequences. But companies can still use this information to develop improved commercial varieties to sell.

“We’re saying our information is free. We’re not saying [that] you have to give your varieties away for free – that’s very different. If we were to say that, we would be doomed,” said Van Deynze. “There has to be a business model around everything.”

The project is itself focusing on speeding up conventional crop breeding but it also leaves the door open to more controversial techniques where genes are cut, spliced or moved between species.

“All DNA technology could be used for synthetic biology, transgenics, conventional breeding, gene editing, so it’s open,” said Van Deynze.

He said he doubts companies will develop genetically modified crops using the data because of regulatory issues and consumer opposition.

But earlier this year, the African Biodiversity Centre found field trials of GM crops were already under way in seven African countries. It said these “will undoubtedly be accompanied by intellectual property laws, seed regulations, and other products and practices amenable to agribusiness”.

“The GM industry appears to be expanding its grasp over traditional subsistence crops which had, until recently, been disregarded,” it said.

Agrochemical giant Monsanto is involved in work to genetically engineer new versions of cowpea with the African Agricultural Technology Foundation, set up in part with US and UK aid money. DuPont Pioneer is a partner in a “biofortified” sorghum project supported by the Bill and Melinda Gates Foundation.

The Syngenta Foundation is backing research on tef, a gluten-free “ancient grain” grown in Ethiopia.

An international project called DivSeek, meanwhile, aims to sequence and publish genetic data on crops with samples in the world’s seed banks.

Sean Mayes, a British geneticist involved in the separate Crops for the Future initiative, said concern over climate change, the need to feed a growing global population, and rising demand in rich countries for more varied foods are fuelling new interest in these plants.

All of these crops, he said, have “potential to increase yields, nutrition … but the work hasn’t been done, because there hasn’t been that commercial drive”.