In search of ‘the wild chicken’: ILRI and other geneticists unravel the past to help secure the future

Susan von Struensee, Art and Agriculture Series - poultry

ILRI and other geneticists are closing in on ‘the wild chicken’ that became the world’s favoured barnyard (all illustrations on this page on Flickr by Susan von Struensee, Art and Agriculture Series using Tagxedo).

The journal Science reports that ‘Researchers are melding genetics and archaeology to close in on the origin of the world’s most common bird—and potentially help protect a major source of animal protein.’

The article quotes Olivier Hanotte, a livestock geneticist now at the University of Nottingham who formerly spent 13 years at the Nairobi-based International Livestock Research Institute (ILRI) helping to unravel the origins of a second domestication of cattle, in Africa. And it was in Nairobi that Hanotte first got interested in chickens. (Watch the 3.5-minute ILRI Film Chickens: The world’s most numerous livestock.)

‘. . . A key thrust of research in the past decade has been to track the genetic changes that turned a remarkably shy creature into today’s meat-and-eggs dynamo, with an eye to protecting and improving breeds. But this research has also given scientists the opportunity to unravel a long-standing mystery that fascinated Charles Darwin: Where, when, and how was the chicken domesticated? . . .

‘Researchers agree that the red jungle fowl gave rise to the barnyard chicken somewhere in South Asia. But they agree on little else. . . .

‘Identifying the chicken’s wild cousins and preserving their genetic diversity may one day prove critical for improving the stock, some researchers say. Genes from wild birds may help breed birds resistant to avian influenza and other illnesses, for example.

‘The red jungle fowl—Gallus gallus—ranges from the western foothills of the Himalaya Mountains to the tip of Sumatra. . . . . Unlike modern-day chickens, all roosters sport elaborate plumage, the females lack a comb, and both genders have thin, dark legs and can fly considerable distances. The fowl is also generally half the size of a White Leghorn domesticated chicken, but it can produce fertile offspring with domestic chickens.

Susan von Struensee, Art and Agriculture Series - poultry

‘Humans carried the easily portable bird around the world. How this began remains controversial. . . .

‘“We need to reconcile all the data,” says Olivier Hanotte, a geneticist at the University of Nottingham. He favors a single origin in northern Southeast Asia, based on the enormous diversity of chicken breeds there. . . .

‘Ultimately, researchers hope to get ancient DNA from well-dated bones. But “replicable DNA has been as rare as hen’s teeth,” Zeder says, thanks to contamination issues and tropical climes that degrade DNA. One team recently claimed to have mtDNA from an ancient Polynesian chicken bone in Chile—a dramatic find that would prove Polynesians reached the Americas before Columbus—but the find has been questioned as possibly contaminated (Science, 11 June 2010, p. 1344). Techniques are improving, however. . . .

[T]he genetic information in truly wild fowl could kill two birds with one stone, unraveling the chicken’s past while potentially ensuring its future. . . .

Susan von Struensee, Art and Agriculture Series - poultry

‘On a tidy farm in the mountains of northwest Vietnam, Chinese biologist Jianlin Han expertly grabs a nervous red jungle fowl recently captured in this region’s quickly disappearing forest. The bird—which sports a long and dangerously sharp spur—is part of Han’s hands-on effort to breed better animals to benefit the rural poor, while at the same time gathering a massive data set to understand the genetic underpinnings of the domestic chicken. Han, who grew up raising chickens in rural China, is as comfortable in the lab as in the barnyard. . . .

‘The chicken, which grows quickly and is the most intensely bred of domestic animals, provides an intriguing model for understanding those issues, says Han, who works for the International Livestock Research Institute based in Nairobi but spends most of his time in his Beijing lab and in the field across South Asia. . . . The goal is to produce a domes-ticated chicken that caters to local tastes while providing more meat and eggs. Han is also investigating the unusually high number of local varieties found in surrounding villages—many more than elsewhere in South Asia—which may be a hint that the chicken was originally domesticated in this rugged area. Han has an ambitious plan to catalog the genetic makeup of today’s jungle fowl, charting its diversity in different regions and also revealing whether it includes genes from domestic chickens. . . .

‘“Jianlin’s brute-force approach definitely has its merits,” says archaeologist Greger Larson of Durham University in the United Kingdom. “I suspect we can’t possibly know what all the variation is out there unless you go and sequence a ton of stuff.” Geneticist Olivier Hanotte of the University of Nottingham in the United Kingdom agrees . . . .

‘Han is also curious about what happens when chickens go feral. Natural selection reasserts itself when humans no longer make breeding deci-sions or provide regular food and protection. “This will help us understand how the genome works, and how plastic it is,” Han says. “This is the most fundamental biological question.” The lowly chicken may one day provide humans with more than just a cheap joke or a fast meal.’

Read the whole articles in Science: In search of the wild chicken and the accompanying feature article on Han Jianlin, From farmyard to the lab (News Focus, Animal Domestication), both by Andrew Lawler, 23 November 2012: 1020–1024.

Read related earlier articles on this blog: Research paper casts doubt on claims for pre-Colombian Chilean chickens, 13 Oct 2008, and Award-winning ILRI geneticist takes up prestigious UK appointment, 17 Dec 2008.

Scientists argue the importance of Africa’s diverse livestock — and the need for genebanks to conserve them

Steve Kemp, a geneticist at the Nairobi laboratories of the International Livestock Research Institute (ILRI) for both ILRI and the University of Liverpool, argues in this short video (2:24 minutes) the new opportunities — as well as urgent need — for exploring the remarkably rich livestock diversity that evolved and still exists on the highly diverse African continent.

‘We need to study the genetics of the animals,’ he says, as well as ‘the farming systems in which they are being used and their production characteristics. And that has never been done systematically in situ across this extraordinary diversity of African livestock.’ Kemp describes fast-improving technologies in the ‘new genetics’ — technologies that are allowing scientists, for the first time, to attempt these very broad kinds of genetic analyses. And he makes a case for establishing livestock genebanks to help preserve the continent’s livestock diversity, which is rapidly being lost. ‘Unless you move relatively quickly,’ warns Kemp, ‘there’ll be nothing left to study.’ Kemp makes these points in an article published in a June 2010 issue of the international journal Science. The co-authors of the article are Tadelle Dessie, an ILRI livestock breeding specialist based at ILRI’s campus in Addis Ababa, Ethiopia, and Olivier Hanotte, a geneticist that formerly worked at ILRI and now directs a Frozen Ark initiative at the University of Nottingham, in the UK. Although genebanks are an important ‘stop-gap’ for preserving livestock diversity, says Kemp, his article makes the point that ‘at the same time that you bank, you must understand the characteristics of what you’re preserving.' 'ILRI is well positioned to catalyze this kind of research,’ Kemp says. ‘It has strong links with Africa and with African partners, who have access to the livestock. It has the mix of skills it needs to understand the function of livestock, right across the spectrum from disease resistance to their role in the marketplace. And it also has the technology — the molecular tools and the informatics tools — to allow us to begin this process.’ ‘But ILRI cannot perform any of this analysis alone,’ warns Kemp. ‘It needs to network with partners in the West and across Africa.’

Science: 'Time to tap Africa's livestock genomes', 25 Jun 2010

BBC News: 'African livestock offers untapped genetic resource', 24 Jun 2010

A frozen zoo in Nottingham ‘bio-banks’ wildlife threatened with extinction


We thought it appropriate in this United Nations ‘International Year of Biodiversity’ to highlight not only work by the International Livestock Research Institute (ILRI) and its partners (see ‘Livestock Diversity Needs Genebanks Too’, an opinion piece by ILRI Director General Carlos Seré published on the SciDevNet website on 21 May 2010) to conserve breeds and genes of native livestock that are rapidly disappearing, but also those of wild animals similarly threatened.

The Frozen Ark is such an initiative. It is led by Olivier Hanotte, an animal geneticist who spent many years at ILRI working to conserve livestock genetic resources indigenous in developing countries. These days Hanotte is running The Frozen Ark Consortium, a worldwide group of institutions coordinated from an office within a Frozen Ark Unit at the School of Biology at the University of Nottingham in the United Kingdom:

The aim of the Frozen Ark is to preserve, for hundreds if not thousands of years, critical information about the species collected. As their website explains: ‘Despite the best efforts of conservationists, thousands of extinctions have occurred before the animals could be rescued. There has not been enough knowledge or money to stem the tide. This pattern is being repeated across all animal groups and emphasises the importance of collecting the DNA and cells of endangered animals before they go extinct. The loss of a species destroys the results of millions of years of evolution. If the cells and DNA are preserved, a very great deal of information about the species is saved. . . . For animals endangered but not yet extinct, the stored DNA and cells can also provide renewable resources of variation for revitalising captive breeding populations when the loss of variation through inbreeding threatens their survival.’

What has caught the public’s imagination is the possibility—a possibility ever more credible in light of ongoing, transformative, breakthroughs in molecular biology, particularly genetics and genomics, as well as drastic falls in the cost of sequencing genomes—that in future scientists will be able to reconstruct extinct animals from such preserved material.

‘While the reconstruction of extinct species from frozen material is not yet practicable, the possibility is not remote,’ says Hanotte. ‘If we fail to preserve the DNA and cells, the information and the possibilities will be lost forever. If DNA is stored in liquid nitrogen at -196 degrees Centigrade, it should survive intact for many hundreds, and possibly thousands, of years.’

The International Union of the Conservation of Nature (IUCN) Red List distinguishes more than 16,000 animal species that are under threat. The Fozen Ark aims eventually to collect the DNA of all these species, and the viable cells (somatic cells, eggs, embryos and sperm) of as many as possible, over the next 50 years. But Hanotte is quick to point out that the Frozen Ark Project is not a substitute for conserving the world’s diverse wildlife species, but is rather ‘a practical and timely backup of their genetic material.’

For more information, visit the Frozen Ark Website.

And watch the online version of this week’s broadcast (30 Mar 2010) of the American television program ’60 Minutes’, which explores the possibility of Resurrecting the Extinct from frozen samples.

Award-winning ILRI geneticist takes up prestigious UK appointment

After 13 years with ILRI, geneticist Oliver Hanotte is taking up a new appointment at the University of Nottingham.
ILRI geneticist Olivier Hanotte starts his new position as professor of population genetics and conservation at the University of Nottingham, UK on 1st January. He will also be the director of a charity based at the university called Frozen Ark. The charity is concerned with the ex situ conservation of endangered animals, including wildlife as well as livestock.

Hanotte joined ILRI in 1995 when the Nairobi-based International Laboratory for Research on Animal Diseases (ILRAD) merged with the Addis Ababa-based International Livestock Centre for Africa (ILCA). Since then ILRI has shifted from a predominantly African focus to a global focus, with ILRI offices not only in East, West and Southern Africa but also in South Asia and South East Asia, providing new opportunities for Hanotte’s research focus.

Research highlights
In his 13 years at ILRI, animal geneticist Olivier Hanotte has worked to unravel the diversity of developing-world livestock using the latest molecular technologies of DNA sequencing and genotyping.

ILRI deputy director general – research, John McDermott, says ‘In 1995, when Hanotte began his work at ILRI, we knew that the world’s livestock diversity was shrinking fast, but no one knew exactly what was being lost and where we should target conservation efforts. Africa and Asia’s genetic diversity was largely unknown and unmapped.

‘We now have a much better picture of the livestock diversity hotspots in Africa and Asia and where the world needs to focus its conservation and genetic improvement efforts. This is due in large part to Hanotte’s scientific leadership, commitment to scientific excellence, innovative partnerships and capacity building activities across two continents’ says McDermott.

In 2003, Hanotte became leader of ILRI’s project on Improving Animal Genetic Resources Characterization. He has supervised project members working in Nairobi, Addis Ababa and, since 2005, in Beijing at a joint laboratory established with the Chinese Academy of Agricultural Science on livestock and forage genetic resources. He has established long term collaborations with several research institutes such as Trinity College at the University of Dublin (Ireland), Rural Development Agency, RDA (South Korea) and the joint FAO-IAEA division in Seibersdorf and Vienna (Austria).

Seminal work by Hanotte and his team has disclosed the origin and distribution of genetic diversity of livestock species including cattle, sheep, goat, yak and chicken in Africa and Asia. These findings are now providing a rationale for targeted conservation and utilization programs for developing-country livestock breeds at risk of extinction. This work also gives us a glimpse into the distant past of the peoples and civilizations of Africa and Asia.

Hanotte’s research has been published in leading scientific journals, including Science, PNAS, Animal Genetics and Molecular Ecology. He has produced over 80 scientific publications and received several international awards, including the CGIAR Science Award in 2003 for Outstanding Scientific Article. He has also supervised and co-supervised research projects of over 50 students and scientists.

Hanotte and colleagues at ILRI continue to break new ground. Current work includes research to better understand and characterize the adaptive traits of indigenous livestock to their local production environments, specifically the genetic and adaptive mechanisms for resistance and tolerance to infection and disease. Research includes tolerance of trypanosome infections in ruminants, resistance to gastro-intestinal worms in sheep and resistance to avian viral infection in poultry. Their work supports the new field of ‘livestock landscape genomics’, which has the long-term and ambitious aim of exploiting advances in the genomics and information revolutions to reliably match breeds to environments and sustainably increase livestock productivity.

Recognized as a leading expert in livestock diversity, Hanotte was invited to write the opening chapter, on the Origin and History of Livestock Diversity, for a major FAO-led study, ‘The State of the World’s Animal Genetic Resources for Food and Agriculture’, released at a Swiss conference in September 2007. He serves on the editorial boards of two major livestock journals (Animal Genetics and the Journal of Animal Breeding and Genetics), and as a regular scientific referee for major scientific journals. His group collaborate with ILRI’s sister CGIAR institution ICARDA in the characterization of the genetic resources of small ruminants.

Hanotte says, ‘I’m very much looking forward to my new position, but leaving ILRI is bittersweet. I have spent the greater part of professional life here in Kenya. I will greatly miss my colleagues and the rich culture of Africa. But I also know that there will be opportunities for collaborations in the future’

‘When you are studying or working in the North, you can get distorted information about Africa and Asia. And you can become removed from the realities. One of the big advantages of working with ILRI is that you’re based in a developing country. That means you’re never too far away from the people that you’re working for. ILRI is an open door to African and Asian farming societies and cultures’


Olivier Hanotte
Professor of Population and Conservation Genetics /Director of theFrozen Ark
School of Biology
University of Nottingham
NG7 2RD, United Kingdom

John McDermott
Deputy Director General – Research
International Livestock Research Institute (ILRI)
Nairobi, Kenya

Further information:
Olivier Hanotte’s recent published research on BioInfoBank:,O
Overview of ILRI research on Improving Animal Genetic Resources Characterization
The State of the World’s Animal Genetic Resources for Food and Agriculture
Frozen Ark website

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