Genetics and Genomics Advancements to Tackle Constraints to Smallholder Poultry Production in Africa

Newcastle disease

In many low and middle-income countries, indigenous chickens are an integral part of the farming system and are an important resource for enhancing food security and livelihoods, especially in rural communities. In Africa, indigenous chicken feeding systems are based on scavenging, requiring minimal investment, thereby offering smallholder farmers security against financial risk while providing an essential source of sustenance for family needs. Local village chickens can increase the availability of high-quality protein and micro- and macronutrients in household diets which are vital for preventing cognitive deficiencies, stunting, and other growth delays in children. In Africa, village chickens are mainly under the control of women who direct the income toward the household for medical care, school fees, and food, leading to improvements in health, education, and nutritional status.

In Africa, Newcastle disease (ND) is endemic and poses a substantial threat to the poultry sector. Currently, it is the most devastating disease and a major challenge for African smallholder producers. Highly pathogenic strains of the ND virus can result in 100 percent mortality in affected flocks and can have significant economic impacts in rural communities. Although vaccination against Newcastle disease virus (NDV) can reduce mortality among village flocks, ND vaccination programs are difficult to sustain, especially in rural areas with limited extension services. Furthermore, NDV vaccines do not provide complete protection against virulent strains of the virus leading to persistent shedding and continual transmission of the virus.

Genomics to Improve Poultry Innovation Lab

Genetic selection and breeding of indigenous chickens with enhanced innate resistance to NDV offers a promising approach to complement traditional disease prevention and control measures. Over the past decade, scientists have mapped the chicken genome allowing for genetic improvement of targeted traits, including disease resistance. To this end, the Genomics to Improve Poultry Innovation Lab (GIP IL), which is led by the University of California, Davis in collaboration with Iowa State University, Sokoine University of Agriculture in Tanzania, University of Ghana, and the International Livestock Research Institute is working to enhance innate resistance to ND  in chickens adapted to the African environment, thereby increasing food security, nutrition, and livelihoods in Africa—key goals of the United States Agency of International Development Feed the Future Program.

The GIP IL is applying cutting-edge genomics and genetics approaches to develop an economical selection platform that includes genetic markers, biomarkers, and indicator traits associated with ND resistance and other economically important traits, such as egg production and growth rate. We identified the most robust genes and markers for genetic resistance through an integrated analysis of NDV challenge experiments and genomic analyses of well-characterized chicken lines under strictly controlled environmental conditions by RNA-seq and genome-wide association analysis (GWAS) using whole-genome genotyping, and of six African indigenous chicken ecotypes by GWAS. Our results confirmed the polygenic control of resistance to NDV and suggested that viral load and antibody titer following infection are important parameters for evaluating disease resistance. We estimated heritabilities for these traits in African chicken to be moderate to high, which indicates that selection to improve these ecotypes for resistance to ND is feasible. The results above have led to the development of an affordable selection platform that will be used for genetic selection of NDV resistance (i.e., reduced viral load and higher levels of natural antibodies and antibodies against NDV) in indigenous chickens in Africa. Further investigation on the associations of natural genetic variations with NDV viral shedding and survival rate of African indigenous chickens following natural exposure to highly virulent NDV will be used to refine the selection platform. Trials to evaluate biomarkers and other economically important poultry production traits for which the associations with NDV resistance are unknown, are also underway.

Following validation of ND resistance in African indigenous chicken ecotypes after initial selection and breeding using the selection platform, it will be applied for genetic selection and breeding of chickens with enhanced resistance to ND in Ghana and Tanzania. The research team is conducting a poultry value chain assessment to evaluate the factors that limit and or facilitate uptake of the genetically improved indigenous ecotypes among target producers, assess potential demand for ecotypes and the economic viability of production to meet demand, and identify and evaluate the most likely business models for distribution and marketing to producers. This analysis will consider how the improved ecotypes fit into existing value chains for poultry, identifying different market segments for initial promotion and business strategies for scaling. Key to this analysis will be an understanding of the potential role of the private sector, as well as collective actors, and their willingness and barriers to investment.

Capacity strengthening has been an integral component of the program. In addition to supporting major improvements to research and laboratory facilities at the universities in Tanzania and Ghana, the GIP IL has provided several training opportunities for students and scientists to expand their expertise in infectious diseases, genetics/genomics, and poultry science. Furthermore, community engagement through education and outreach activities targeting a range of stakeholders in the private and public sectors has enhanced knowledge on poultry husbandry and disease prevention and control strategies. These improvements to institutional and human capacity are making important contributions to building the workforce needed to sustainably improve poultry production systems in Africa. 

The GIP IL is working to support the Feed the Future Program mission through genetic improvement of indigenous chicken ecotypes. Decreasing mortality in indigenous chickens through enhanced disease resistance will result in increased agricultural productivity, which in turn will have positive impacts on livelihoods, particularly for women and children, who are most commonly the beneficiaries of poultry production in Africa.

This article was made possible by the generous support of the American people through the United States Agency for International Development (USAID). The contents are the responsibility of the University of California and do not necessarily reflect the views of USAID or the United States government.

Field Notes

The Chicago Council is pleased to launch a new blog series, "Breaking Ground," to explore how food systems innovation and agricultural research and development can empower farmers and feed the world. A special subsection of this series, "Field Notes," features voices from Feed the Future Innovation Labs and CGIAR centers.