Long-term changes in temperature, humidity, rainfall patterns and extreme weather events are increasingly posing a threat to global food security. Already, climate change is challenging farming practices, crop production and the nutritional quality of food crops. Genomics, the study of DNA, may provide valuable insights into climate resilience.
Image courtesy of Unsplash
Jacqueline Smith, Senior Research Fellow at the Roslin Institute, along with colleagues from the University of Nottingham, University in Nigeria, and the International Livestock Research Institute in Ethiopia have been examining the genomes of Nigerian indigenous chickens to identify which genes are responsible for their resilience against harsh tropical environments. The team identified genes vital for thermotolerance (ability to withstand high temperatures) and immune response. These genes may improve the breeding of chickens in areas of the world where extreme heat and drought are becoming more common, and can help conserve valuable genetic resources.
The research, published in Scientific Reports, is the first-of-its-kind, large-scale whole-genome sequencing analysis of Nigerian indigenous chickens from regions with different agro-climatic conditions. The work is part of an ongoing project within the Centre for Tropical Livestock, Genetics and Health, enabled by funding from the Bill and Melinda Gates Foundation.
Poultry farming in Nigeria
In Nigeria, poultry production is an important means of income, with 45% of the country’s population involved in mostly small or medium-scale farming. Over half of Nigeria’s chickens are raised in extensive backyard farming systems, and about 80% of these chickens are considered “unimproved” local breeds, known in the study as Nigerian Indigenous Chickens (NICs). The researchers describe them as unimproved to indicate their genes have not been altered to encourage larger growth for food consumption. As such, NICs have a lower productivity, compared to commercial chickens, from a lack of interventional breeding. Yet, they are able to thrive under harsh tropical environments to forage for food, hatch on their own and brood, and tolerate endemic disease challenges. The local community also prefer NICs’ egg and meat products. These local chickens represent important genetic resources for the sustainable development of Nigeria’s poultry programme to cater future needs arising from climate challenges and consumer demands.
“We want first to try and understand the genetics of these local birds to help improve productivity for local farmers, but also identify why these birds are resilient to things like heat stress,” Smith said. “This will be knowledge we can then take back to commercial populations and use the genetic information to help produce more resilient birds. Right now, we’re seeing the effects of climate change, so birds (and other animals) are going to have to be able to withstand higher temperatures.”
Interpreting the Genome
The research group accessed DNA samples from 120 birds in Nigeria, representing 14 different populations. They conducted deep whole-genome sequencing to identify genes responsible for resilience traits, like tolerance to high temperatures. The researchers identified regions of DNA under selection for thermal regulation, stress response and immunity.
“Local birds appear to have a more highly activated immune system than intensively selected birds,” Smith explained. “This is in response to having to deal with environmental stress and exposure to pathogens and helps explain why these birds tend to be more disease resistant than their commercial counterparts. Having to be able to adapt to these environmental conditions seems to go hand-in-hand with an increase in their immune potential, which makes them sturdy with regards to disease tolerance.”
Smith described how when you compare local (unimproved) birds to those which have been selectively improved over a few generations, key differences begin to emerge. There is a trade-off when you start selecting birds for production. They may lay more eggs and grow larger for meat, but they are less resilient to disease and can’t cope with stressful environments quite so well.
“If we start introducing local genetics into commercial breeding, there is the potential for birds to get more of that resilience back.”
To ensure this gene expression for thermotolerance and immunity is not specific to only NICs, the research group is entering into phase two of the project. They will be collecting samples from chickens in other hot countries with different environmental conditions. Instead of just looking at variation in the genome, the group will incorporate transcriptomic analyses, examining the gene expression in birds from high temperature areas compared to low temperature areas. They will also look at how genes are regulated by examining their methylation patterns. The addition of methyl groups can affect how some molecules act. For example, methylation of a DNA sequence of a gene may turn that gene off.
Global food security
The findings from this study, and the work the research group continues to embark on, will continue to support poultry production. Designing breeding programs to minimise heat stress and enhance disease resistance has fundamental applications for global food security.
“We have a rapidly expanding population, so we have more and more people requiring food. At the same time, we have less land available for growing that food, so we have to come up with ways of being as efficient as a r possibly,” Smith described.
According to the Food and Agriculture Organization of the United Nations, increases in global meat production are led mainly by poultry production. Meat consumption has been shifting towards a strong demand for poultry products, which is predicted to continue to increase. It was estimated in 2018 that farmed poultry made up 70% of all birds on Earth, by mass. In lower income countries, poultry is less expensive than other meats. Similarly, higher-income countries prefer poultry for cost savings, and white meat is viewed as a more straightforward and healthier meat to cook.
Smith added, “If we can make birds as resilient as possible with regards to disease, that’s going to be hugely beneficial, with a lot less waste. The bird’s welfare is also improved. If we are able to develop birds that are more heat tolerant, we can harness breeding in regions that are currently inhospitable, thus decreasing losses, improving production and maximising land use.”
