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Adaptive Traits in Chicken: Analysis of Signatures

Sigei Chepkorir Caroline
QTL: Quantitative Trait Locus
WHO: World Health Organization
KNBS: Kenya National Bureau of Statistics
GDP: Gross Domestic Product
MLD: Ministry of Livestock Development
Background Information
The indigenous chicken (Gallus domesticus) is a type of bird that is widely domesticated across the world. They are believed to have been the first birds to be domesticated and integrated into the human culture nearly 8000 years ago (Dohner 2001 and Price 2002). According to Charles Darwin, the current varieties and breeds of domestic chicken can be traced back to their wild descendants, the Red Jungle Fowl (Gallus bankiva, also known as Gallus gallus), which is still wildly distributed in the rainforests of India and parts of Southeast Asia (Crawford 1990; Miao et al. 2013). Recent genetic advances and analyses have confirmed descent of chicken from the red jungle fowl. Other evidence suggests that several other wild species such as the Grey Jungle Fowl (G. sonnerati), the Green Jungle Fowl (G. varius) and Geylon Jungle Fowl (G. lafayettei) might have also contributed to the ancestral origin of domestic chickens (Nishibori et al. 2005; Eriksson et al. 2008; Sawai et al. 2010). Today, domestic chicken is thought to be more closely related to the Grey Jungle Fowl due to the yellow colouring of its skin. Several names have been adapted to refer to indigenous chicken. These include: Native chicken, free-range chicken, local chicken, backyard chicken, scavenging chicken, rural chicken, village chicken, and traditional chicken, among others.
The native chicken population constitutes 80% of the total world chicken population. In Africa, 80% of the over 800 million chickens are local (Gueye, 1998). In terms of poultry composition (chicken, turkeys and ducks), Gueye, 2003 noted that chickens dominate at approximately 98% of the total poultry numbers that are kept in Africa. In Kenya, agriculture contributes 25-26% of gross domestic product (GDP), 4% of which is from poultry sub-sector (KNBS 2010). Local chickens constitute 70% of the 30 million domesticated birds, 75% of which are mainly reared by resource-poor families (MLD 2010). Generally, indigenous chickens in Africa are hardy and well adapted to survive in adverse environments. They are self reliant and can scavenge for a major part of their own food with the capacity to withstand harsh weather condition, poor nutrition as well as pests and disease (F.O. Ajayi, 2010). In addition, a small initial investment capital is required to rear village chickens thus making it an affordable source of livelihood in terms of food security, income and general welfare for resource-poor people, more so women and children (Olwande 2009; Wachira et al 2010). In Kenya, it is estimated that family chickens contribute 47% and 55% to the national egg and meat production, respectively (Kingori et al., 2010). Chicken meat and eggs are considered to be a complete source of proteins since they contain all essential amino acids as well as important vitamins, fats, and minerals needed for good human health. Other benefits derived from chicken include manure for gardens and feathers for stuffing pillows and craft making. They also play an important role in pest control and are sometimes used for cultural ceremonies and festivals.
Despite the economic significance associated with rearing indigenous chickens, the sector is constrained by a number of challenges which impact negatively on productivity. Although there is a general belief that domestic chicken are resistant to diseases based on the observation that village chicken can survives in a harsh environment with a host of pathogens without any veterinary intervention, large populations have occasionally been wiped out due to disease outbreaks. In addition, chickens are exposed to harsh and stressful environment, poor nutrition and unfavourable climates and weather. As a result, mortalities of over 50% have been recorded during chick-hood and up to 80% between chick-hood to adult-hood. Native chicken survival and continuity is partly due to non-encounter of pathogens, immunity following recovery from infection and most importantly, their natural adaptability and resistance. The indigenous chickens have thus been subjected to natural selection as imposed by the mentioned stresses which has resulted in a heterogeneous populations that show large variations in both qualitative and quantitative traits (Feather morphology, plumage colour, comb types, skin colour, disease-resistance, productivity and body size among others) (Msoffe et al. 2001; Dana et al.2010). The immense biodiversity has ensured their survival in diverse ecological zones by naturally being selected for survival fitness. Natural selection favours multilocus quantitative traits directly associated with the fitness of individuals in their local environment and hence preserve adaptive genetic variation (Giovambattista et al, 2001). Natural selection which was proposed by Charles Darwin seems to be the major force behind genetic variability. However, other factors like genetic drift, mutations, migration and recombination of chromosomes have also been shown to play a significant role. Rural chicken ecotypes which have evolved in and adapted to stressful environments are likely to carry a valuable pool of genes and gene combinations found in Gallus gallus domesticus that control specific behavioural, physiological and disease as well as parasite resistance traits. This is contrary to the selection imposed by man whereby few economically important traits are selected for as dictated by profits and economics as seen in commercial chicken hybrids. Unfortunately, this leads to loss of genetic variation within species and breeds, thus restricting the options available to meet unpredictable future demands or requirements (Giovambattista et al, 2001).
With the current technological advancements in sequencing, whole genomes can now be sequenced cheaply and efficiently. This has provided an excellent opportunity to study and analyze the chicken genome for phyllogenetic ad evolutionary studies as well as perform quantitative trait locus (QTL) mapping analysis and other genome wide association studies in order to better understand how genes controlling traits of economic significance in chicken have evolved and adapted the local scavenging chicken to its environment. The results generated will be of significance to breeders and other researchers in conserving the genotypes and biodiversity of indigenous chicken for future breeding purposes with a view to breed for better productivity and for disease and drought resistance.
Statement of the Problem
The current population surge in Kenya has led to land competition and depletion with subsequent depletion of natural resources. This has resulted in harsh economic times that have caused a rise in food prices, farm inputs, animal feeds and unpredictable climactic conditions which have made it even harder to farm. The end result is poor economic growth, food insecurity, poverty and malnutrition. Currently, Kenyan population is projected as 44, 611,813 (World Population Review 2014). In 2010, the total population was estimated at 40, 512, 682, 77.8 % of which were living in rural areas; approximately 38.2% (15, 475, 763.5) of the rural population were estimated to be below the poverty line.
It’s also estimated that 80% of Kenya’s total land mass is Arid and Semi-Arid with approximately 10 million inhabitants. Over 60% of these people live below poverty line and usually derive their living from subsistence agriculture and few other sources of income which may not be sufficient to feed and sustain an entire household. Years of drought in such regions have had a serious impact on the well-being of children and women, increasing malnutrition rates, morbidity and mortality. The statistics that were revealed by WHO in 2000 revealed that malnutrition plays a major role in the deaths of over five million children annually in Africa. In Ghana, 36% of children less than five years old are stunted and 54% of mortality among children below five years is caused by malnutrition (Poel et al., 2007).
Indigenous poultry farming presents a viable opportunity for the affected population to ensure food security, self employment and improved livelihoods while contributing to national economic growth. Free-range poultry farming is easy to establish, they are more prolific and unproblematic to rear on small plots of land and are more genetically diverse, well adapted, and more resistant to local pests and diseases. However, this sector is also subject to some constraints which lower the productivity of traditional chicken. Diseases like Newcastle Disease, Marek’s Disease, Gumboro, Fowl Pox and Fowl typhoid play a major role followed by drought and poor husbandry practices among others. Although, rural chicken has been shown to be more resistant and adaptive, some varieties have lesser capacity. Also the rural chicken is genetically unimproved. This proposal therefore seeks to unravel the genetic basis of adaptive evolution of the free-range scavenging chicken for better productivity in future.
Selective breeding can have a major impact in adapting the chicken to the climate changes anticipated in the 21st century as well as enhance its capacity to resist or tolerate certain diseases that are of economic importance. The subject of this proposal is to map out genes that have enabled the rural chicken to survive in spite of the harsh and stressful conditions under which it’s raised based on the fact that these adaptive traits are genetically controlled. Research has shown that genetic diversity in livestock population is crucial in terms of the complex responses they confer to epidemics, duration of infection and mortality rates (Sringbett 2003). The result is maintenance of viable livestock and preservation of biodiversity. The native poultry species represent a valuable resource for livestock development due to their extensive genetic diversity which allows for rearing of poultry under varied environmental conditions. The indigenous chicken therefore exhibit a large genetic pool from which genes of interest can be exploited to provide a basis for genetic improvement and diversification to produce breeds that are adapted to varied conditions for the benefit of farmers in developing countries (Horst, 1988; Sonaiya et al., 1999).
A lot of research has focused more on improving the genetic potential of poultry to be high yielding in terms of meat and egg production but limited research has been carried out to exploit their genetic potential for disease and drought resistance. Normally, diseases are managed using chemotherapeutic agents and implementation of vaccination protocols. However, in some cases such interventions have had negative consequences by prompting variability among microorganisms and the appearance of drug-resistant strains, which has resulted further in serious animal healthcare problems (Savić, 2007). Additionally, viral disease management through vaccinations are sometimes met with constant challenges since every new generation of vaccination protocols results in the discovery of new more virulent viral strains, as was the case with Marek’s disease in poultry ( Bishop and Mackenzie 2003). Therefore, by taking into consideration the negative impacts of widespread drug use and the related costs, current strategies should focus towards increasingly more sophisticated use of genetic methods in disease control among farm animal species Gibson and Bishop (2005). With the current sequencing technologies, it’s possible to map genes for disease resistance and heat-stress tolerance among local chicken. This information can be used for selective breeding for a chicken type that is resistant to economically important diseases and with high productivity potential under village management system. Alternatively, cross breeding can be implemented for a breed that can perform well under scavenging village conditions.
There is no relatedness in terms of phylogeny and molecular evolution of signatures for adaptive traits in chicken both within and between other avian species.
Broad Objective
To determine the phylogeny and molecular evolution of disease and drought resistant genes for adaptive evolution of indigenous chicken using computational techniques and Genome Wide Association Studies.
Specific Objectives
To determine phylogeny and molecular evolution of the Toll-like receptor genes associated with innate and adaptive immune response against specific pathogens.
To determine phylogeny and molecular evolution of Mx gene associated with antiviral activity in response to diseases like Avian Influenza and New Castle Disease.
To determine phylogeny and molecular evolution of Heat shock Protein (Hsp 70) genes associated with heat-stress tolerance in chicken.
Expected Output
It’s anticipated that key genes that have favoured the adaptive evolution of the free-range scavenging chicken will be mapped out. The knowledge generated can be used by breeders to implement strategies of improving these traits through marker-assisted selection and introgression of the resistant genes. These genetic improvements will significantly reduce morbidity and mortality due to drought and diseases and this will translate to improved productivity, economic growth and food security. This means that all people will have physical and economic access to adequate, safe and nutritious food to meet their dietary needs and food preferences for an active and healthy life at all times. Additionally, the findings will form a basis or foundation for further scientific investigations and discoveries.
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Cell Adhesion Molecules in Olfactory Connection Formation

This dissertation study investigated expression, function and the regulatory mechanism of cell adhesion molecules in the formation of olfactory connections. Identification and characterization of a novel protocadherin, Pcdh20, provided additional evidence that multiple cell adhesion molecules are involved in the development of the olfactory system. In combination with several established studies by Sakano and Yoshihara’s group, my study further supports the neural identity model and provides a regulatory mechanism involving MeCP2 in the establishment and maintenance of this combinatory cell adhesion molecule expression in the olfactory sensory neurons.
OR identity in correlation with cell adhesion molecule expression
Though many cell adhesion molecule expression patterns were described, few of them were correlated with specific ORs. On the other side of the coin, it is also unknown whether a specific OR is correlated with a specific set of cell adhesion molecules throughout development. In adult mice, Pcdh20 expression is in a subpopulation of OSNs and their axons terminate in a small number of discrete Pcdh20-positive glomeruli in the OB. Interestingly, the distribution and numbers of Pcdh20-positive glomeruli are markedly different across gender. More Pcdh20-positive glomeruli with a wider distribution pattern are observed in the male OB, whereas fewer glomeruli with more restricted clustering of Pcdh20-positive glomeruli are found in female OB. The sexually dimorphic expression of Pcdh20 suggests that there may be different ORs associated with Pcdh20 in different sexes. 103
If Pcdh20 expression is correlated with specific OR expression, identification of Pcdh20 associated ORs could reveal possible sex-specific OR expression and aid in further investigation of OR-specific ligand function. In previous studies, cDNA libraries from a single OSN were obtained. OR expression in a single OSN can be identified by PCR using degenerate primers (Dulac and Axel, 1995). In collaboration with Dr. T. Cutforth from Stanford University, I have initiated this study by isolating single OSNs by dissociation of OE and attempting to identify Pcdh20 expressing cells by PCR. Several attempts were made to confirm OR expression using degenerate primers designed by L. Buck (Buck and Axel, 1989). Though I will not be able to complete this study during my dissertation research, identification of Pcdh20 associated ORs will provide important insight into not only OR and CAM association but also understanding of differential OR gene expression in different sexes and whether or not the main OB is related to pheromone recognition.
Neuronal activity and regulation of cell adhesion molecule expression
Neuronal activity results in long term changes in neurons by regulating gene expression. OSNs constantly respond to external stimuli throughout the life of the animal. Using genetic models and surgical manipulations, it is shown that blocking odorant evoked activity alters the expression of selected cell adhesion molecules. Even though regulation of cell adhesion molecule expression is important for the formation of olfactory axonal converge into glomeruli, the regulatory mechanism of gene expression is undetermined.
I reported here that olfactory axon convergence is disrupted in MeCP2 null mice. Furthermore, I also obtained evidence that MeCP2 directly regulated Kirrel 2/3 expression. In MeCP2 KO mice, significant increases in Kirrel2/3 gene transcripts were observed in OE, suggesting that MeCP2 is a transcription suppressor for Kirrel 2/3 gene expression. In addition, my data provide evidence that MeCP2 function is regulated by neuronal activity. With the presence of odorant evoked 104
activity, MeCP2 is phosphorylated at Serine80 and also possesses enhanced binding affinity to promoters of Kirrel2 and Kirrel3 genes. Though MeCP2 increased its binding to promoters of both Kirrel2 and Kirrel3, transcript level changes are markedly different between Kirrel2 and Kirrel3 under odorant stimulation. Other transcription factors were shown to be regulated by neuronal activity. It is likely that both Kirrel2 and Kirrel3 are regulated under multiple neural activity dependent transcription factors.
We propose a model in which a balanced transcriptional regulation from both repressors (like MeCP2) and enhancers (like CREB, MEF) determines the expression levels of Kirrel2 and Kirrel3. When both repressor and enhancer are under neural activity regulation, how the balance tilts will determine whether Kirrel2/3 expression will be up- or down-regulated in OSNs.
In this study, the olfactory system serves as an excellent model system to study gene regulation of MeCP2 by neuronal activity at physiological levels. Previously, the mechanism of MeCP2 on gene expression regulation by neuronal activity was only studied in vitro. The brain is composed of heterogeneous cells and their neuronal circuits are extremely complex. In contrast, the OE is composed of a single type of neuron. This property provides an opportunity to study neuronal subtype specific MeCP2 function. In addition, the olfactory system provides an excellent system to study the effect of neuronal activity due to it accessibility. Odorant stimulation can be given to the OSNs in the nasal cavity to allow investigation of gene regulation under physiological level of stimulation. To further investigate the model we proposed, it is important to elucidate the full spectrum of MeCP2 target gene regulation. Future study should be done to screen MeCP2 target binding through ChIP-Chip analysis. MeCP2 binding sequence will provide information in the target genes they regulate in the OSNs. To further provide or block odorant evoked activity, changes in MeCP2 binding will allow us to identify target genes that are activity dependent. Furthermore, identification of odorant evoked activity dependent transcription enhancers in OSNs will allow further validation of the regulatory model we proposed here.
Understanding neural activity dependent MeCP2 function is critical in elucidating the mechanisms of Rett Syndrome. Though rapid progress has been made in the identification of MeCP2 targeting genes, we still do not understand how changes in gene expression result in neuronal structural and functional changes. Rett Syndrome is exacerbated during the early postnatal period. Neural activity plays a critical role in this process. Understanding the relationship between physiological levels of neuronal activity and MeCP2 regulation is the obvious next challenge. The olfactory system provides an excellent model for the easy manipulation of activity stimulation and examination of subtle axonal targeting defects. This study established that cell adhesion molecules are regulated by MeCP2 in an activity dependent manner. Further genomic analysis will provide a comprehensive understanding of MeCP2 regulation of gene expression and could help in the development of treatment strategies for Rett Syndrome.