Genomics Tools for the Characterization of Genetic Adaptation of Low Input Extensively Raised Chickens

Abstract

Evolutionary change emanating from diferential contribution of genotypes to the next generation can determine success in survival and reproduction in chickens. For extensively raised chickens reared under low-input production systems in smallholder farming areas, conditions of resources deprivation and exposure to diverse and threatening natural selection pressures are common in many countries worldwide. Numerous studies have demonstrated that village chickens and other extensively raised chicken populations represent a valuable source of biodiversity adapted to the local production conditions and selection pressures. Manipulation of their acquired adaptive genetic diversity depends on unravelling the selection footprints in the genomes of these chickens that could point towards candidate genes for traits that enable the animals to survive under the harsh production environments. This chapter summarizes the evidence for chickens adaptation to extreme environments and describes an inventory of modern tools that could be used in characterizing the production systems of chicken genetic resources. The role of natural selection in shaping the biodiversity of chicken genetic resources is discussed. The continued advancement of biotechnological tools to assess chicken populations has been beneicial to research in genetic adaptation. Genomics tools, as evidenced by assays of whole genome and transcriptome sequences, and single nucleotide polymorphism SNP) genotypes of chickens, now allow analyses of functional genomic regions that are linked to adaptation. The use of these methods to characterize and investigate signatures of selection in the chicken genomes is highlighted. This chapter looks at how information on the selection hotspots in the chicken genomes can be manipulated to improve genetic adaptation in indigenous chicken populations with the desire to transfer the beneits to other chicken breeds raised under similar production systems.

Innate Immune Genes Associated With Newcastle Disease Virus Load in Chick Embryos From Inbred and Outbred Lines

“…Newcastle disease virus (NDV) is an important poultry pathogen in low- and middle-income countries where the disease is endemic (Ashraf and Shah, 2014). In these areas, poultry is farmed extensively with little to no veterinary care, minimal biosecurity, and the constant threat of exposure to pathogens (Minga et al, 2014; Muchadeyi and Dzomba, 2017). Vaccination and biosecurity in high-income countries and intensively farmed poultry control NDV, however, in low- to middle-income countries, it is uncommon or ineffective due to lack of proper storage of the vaccines or lack of adoption by smallholder farmers (Alexander et al, 2004, 2012; Wen et al, 2017; Campbell et al, 2018).…”

“…Backyard farming heavily relies on natural selection to drive the adaptations and genetic diversity (Minga et al, 2014; Muchadeyi and Dzomba, 2017). These chickens are generally believed to be less susceptible to many poultry pathogens, however, there are few studies examining the genetic variation and disease resistance in attempt to explain their diversity and the distribution in Africa.…”

Seroprevalence of Newcastle Disease Virus in Local Chickens in Njombe and Bahi Districs in Tanzania

“…In Tanzania, like most other African countries, there is a large population of backyard poultry with over 90% of all poultry being farmed extensively (Ministry of Agruculture et al, 2016). In these conditions, the chickens are regularly exposed to inadequate feeds, poor management and housing, predation, and infectious diseases (Minga et al, 2004;Gilbert et al, 2015;Lawal et al, 2016;Muchadeyi and Dozmba, 2017). There are also risk factors in these farms that contribute to the spread and persistence of infection including the absence of preventative measures or vaccination, frequent contact with wild birds, improper disposal of carcasses and waste products, and the general practice of selling/buying birds which all have the possibility of introducing disease to healthy birds and ocks (Chaka et al, 2013).…”

Integrated environmental and genomic analysis reveals the drivers of local adaptation in African indigenous chickens

“…Despite the observational knowledge that African indigenous chickens are adapted to their harsh environmental conditions, the genetic mechanisms underlying these adaptations are still largely unknown (8). Likewise, the environmental factors that trigger adaptive response have not been dissected thoroughly (8). Conventionally, environment-genome adaptation studies have focused on the adaptation to an inferred specific environmental stressor, e.g.…”